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Goldhaber NH, Jacobs MB, Laurent LC, Knight R, Zhu W, Pham D, Tran A, Patel SP, Hogarth M, Longhurst CA. Integrating clinical research into electronic health record workflows to support a learning health system. JAMIA Open 2024; 7:ooae023. [PMID: 38751411 PMCID: PMC11095974 DOI: 10.1093/jamiaopen/ooae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/30/2023] [Accepted: 05/09/2024] [Indexed: 05/18/2024] Open
Abstract
Objective Integrating clinical research into routine clinical care workflows within electronic health record systems (EHRs) can be challenging, expensive, and labor-intensive. This case study presents a large-scale clinical research project conducted entirely within a commercial EHR during the COVID-19 pandemic. Case Report The UCSD and UCSDH COVID-19 NeutraliZing Antibody Project (ZAP) aimed to evaluate antibody levels to SARS-CoV-2 virus in a large population at an academic medical center and examine the association between antibody levels and subsequent infection diagnosis. Results The project rapidly and successfully enrolled and consented over 2000 participants, integrating the research trial with standing COVID-19 testing operations, staff, lab, and mobile applications. EHR-integration increased enrollment, ease of scheduling, survey distribution, and return of research results at a low cost by utilizing existing resources. Conclusion The case study highlights the potential benefits of EHR-integrated clinical research, expanding their reach across multiple health systems and facilitating rapid learning during a global health crisis.
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Affiliation(s)
- Nicole H Goldhaber
- Department of Surgery, University of California San Diego Health, La Jolla, CA 92037, United States
| | - Marni B Jacobs
- Department of Obstetrics, Gynecology and Reproductive Services, University of California San Diego Health, La Jolla, CA 92037, United States
| | - Louise C Laurent
- Department of Obstetrics, Gynecology and Reproductive Services, University of California San Diego Health, La Jolla, CA 92037, United States
| | - Rob Knight
- Department of Pediatrics, University of California San Diego Health, La Jolla, CA 92037, United States
- Department of Computer Science and Engineering, Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92037, United States
- Department of Bioengineering, Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92037, United States
| | - Wenhong Zhu
- Information Services, University of California San Diego Health, La Jolla, CA 92037, United States
| | - Dean Pham
- Information Services, University of California San Diego Health, La Jolla, CA 92037, United States
| | - Allen Tran
- Information Services, University of California San Diego Health, La Jolla, CA 92037, United States
| | - Sandip P Patel
- Division of Oncology, Department of Medicine, University of San Diego Health, La Jolla, CA 92037, United States
| | - Michael Hogarth
- Division of Biomedical Informatics, Department of Medicine, University of San Diego Health, La Jolla, CA 92037, United States
| | - Christopher A Longhurst
- Department of Pediatrics, University of California San Diego Health, La Jolla, CA 92037, United States
- Division of Biomedical Informatics, Department of Medicine, University of San Diego Health, La Jolla, CA 92037, United States
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Keehner J, Abeles SR, Longhurst CA, Horton LE, Myers FE, Riggs-Rodriguez L, Ahmad M, Baxter S, Boussina A, Cantrell K, Cardenas P, De Hoff P, El-Kareh R, Holland J, Ikeda D, Kurashige K, Laurent LC, Lucas A, Pride D, Sathe S, Tran AR, Vasylyeva TI, Yeo G, Knight R, Wertheim JO, Torriani FJ. Integrated Genomic and Social Network Analyses of SARS-CoV-2 Transmission in the Healthcare Setting. Clin Infect Dis 2024; 78:1204-1213. [PMID: 38227643 PMCID: PMC11093679 DOI: 10.1093/cid/ciad738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Infection prevention (IP) measures are designed to mitigate the transmission of pathogens in healthcare. Using large-scale viral genomic and social network analyses, we determined if IP measures used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic were adequate in protecting healthcare workers (HCWs) and patients from acquiring SARS-CoV-2. METHODS We performed retrospective cross-sectional analyses of viral genomics from all available SARS-CoV-2 viral samples collected at UC San Diego Health and social network analysis using the electronic medical record to derive temporospatial overlap of infections among related viromes and supplemented with contact tracing data. The outcome measure was any instance of healthcare transmission, defined as cases with closely related viral genomes and epidemiological connection within the healthcare setting during the infection window. Between November 2020 through January 2022, 12 933 viral genomes were obtained from 35 666 patients and HCWs. RESULTS Among 5112 SARS-CoV-2 viral samples sequenced from the second and third waves of SARS-CoV-2 (pre-Omicron), 291 pairs were derived from persons with a plausible healthcare overlap. Of these, 34 pairs (12%) were phylogenetically linked: 19 attributable to household and 14 to healthcare transmission. During the Omicron wave, 2106 contact pairs among 7821 sequences resulted in 120 (6%) related pairs among 32 clusters, of which 10 were consistent with healthcare transmission. Transmission was more likely to occur in shared spaces in the older hospital compared with the newer hospital (2.54 vs 0.63 transmission events per 1000 admissions, P < .001). CONCLUSIONS IP strategies were effective at identifying and preventing healthcare SARS-CoV-2 transmission.
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Affiliation(s)
- Jocelyn Keehner
- Division of Infectious Diseases, Department of Medicine, University of California–SanFrancisco, San Francisco, California, USA
- Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA
| | - Shira R Abeles
- Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA
- Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health, San Diego, California, USA
| | - Christopher A Longhurst
- Division of Biomedical Informatics, Department of Medicine, UC San Diego Health, La Jolla, California, USA
- Department of Pediatrics, University of California–San Diego, La Jolla, California, USA
| | - Lucy E Horton
- Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA
- Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health, San Diego, California, USA
- Vaccine Research and Development Unit, Pfizer Inc, San Diego, California, USA
| | - Frank E Myers
- Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health, San Diego, California, USA
| | - Lindsay Riggs-Rodriguez
- Population Health Services Organization—Programs and Strategy, UC San Diego Health, San Diego, California, USA
| | - Mohammed Ahmad
- Information Services EMR, UC San Diego Health, San Diego, California, USA
| | - Sally Baxter
- Division of Biomedical Informatics at the University of California–San Diego, San Diego, California, USA
| | - Aaron Boussina
- Division of Biomedical Informatics, University of California–San Diego, La Jolla, California, USA
| | - Kalen Cantrell
- Department of Computer Science & Engineering, Jacobs School of Engineering, University of California, San Diego, California, USA
| | - Priscilla Cardenas
- UC San Diego Health's Contact Tracing Team, Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health, San Diego, California, USA
| | - Peter De Hoff
- Sanford Consortium of Regenerative Medicine, University of California–San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment Laboratory, Department of Pediatrics, University of California–San Diego, La Jolla, California, USA
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, UC San Diego Health, San Diego, California, USA
| | - Robert El-Kareh
- Division of Biomedical Informatics, Department of Medicine, UC San Diego Health, La Jolla, California, USA
- Division of Hospital Medicine, Department of Medicine, UC San Diego Health, La Jolla, California, USA
| | - Jennifer Holland
- Analytics and Population Health Department, UC San Diego Health, San Diego, California, USA
| | - Daryn Ikeda
- UC San Diego Health's Contact Tracing Team, Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health, San Diego, California, USA
| | - Kirk Kurashige
- Analytics and Population Health Department, UC San Diego Health, San Diego, California, USA
| | - Louise C Laurent
- Sanford Consortium of Regenerative Medicine, University of California–San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment Laboratory, Department of Pediatrics, University of California–San Diego, La Jolla, California, USA
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, UC San Diego Health, San Diego, California, USA
| | - Andrew Lucas
- Information Services EMR, UC San Diego Health, San Diego, California, USA
| | - David Pride
- Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA
- Department of Pathology, UC San Diego Health, La Jolla, California, USA
| | - Shashank Sathe
- Sanford Consortium of Regenerative Medicine, University of California–San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California–San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment Laboratory, Department of Pediatrics, University of California–San Diego, La Jolla, California, USA
| | - Allen R Tran
- Information Services EMR, UC San Diego Health, San Diego, California, USA
| | - Tetyana I Vasylyeva
- Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA
| | - Gene Yeo
- Sanford Consortium of Regenerative Medicine, University of California–San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California–San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment Laboratory, Department of Pediatrics, University of California–San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California–San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California–San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California–San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment Laboratory, Department of Pediatrics, University of California–San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California–San Diego, La Jolla, California, USA
| | - Joel O Wertheim
- Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA
| | - Francesca J Torriani
- Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA
- Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health, San Diego, California, USA
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Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, Börner K, Snyder MP. Author Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol 2024; 26:839. [PMID: 38429479 DOI: 10.1038/s41556-024-01384-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Affiliation(s)
- Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Liming Pei
- Center for Mitochondrial and Epigenomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology and the Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Michael Angelo
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - James P Carson
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Joana P Gonçalves
- Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - James S Hagood
- Department of Pediatrics (Pulmonology) and Program for Rare and Interstitial Lung Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John W Hickey
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Neil L Kelleher
- Departments of Medicine, Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Shin Lin
- Division of Cardiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Yiing Lin
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Huiping Liu
- Departments of Pharmacology, Medicine (Hematology and Oncology), Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Andrea Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Brent R Stockwell
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Ioannis S Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Katy Börner
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
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Emeruwa UN, Azad H, Ona S, Bejerano S, Alnafisee S, Emont J, Mathew S, Batlle M, Arnold D, Ukoha EP, Laurent LC, Jacobs M, Aubey JJ, Miller RS, Gyamfi-Bannerman C. Lasix for the prevention of de novo postpartum hypertension: A randomized placebo-controlled trial (LAPP Trial). Am J Obstet Gynecol 2024:S0002-9378(24)00522-2. [PMID: 38641089 DOI: 10.1016/j.ajog.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/28/2024] [Accepted: 04/09/2024] [Indexed: 04/21/2024]
Abstract
BACKGROUND Birthing people with de novo postpartum hypertensive disorders remain among the highest risk for severe maternal morbidity. Randomized controlled trials demonstrate a benefit to oral loop-diuretics in decreasing postpartum hypertensive morbidity in patients with an antenatal diagnosis of preeclampsia. It is not known whether this same therapy benefits patients at risk for new-onset postpartum hypertension OBJECTIVE: To evaluate whether oral furosemide can reduce risk for de novo postpartum hypertension (dnPPHTN) among high-risk birthing people by reducing post-delivery blood pressure. STUDY DESIGN From October 2021 to April 2022, we conducted a randomized triple-masked placebo-controlled clinical trial of individuals at high risk for dnPPHTN at a single university-based tertiary care medical center. A total of 82 postpartum patients with no antenatal diagnosis of chronic hypertension or a hypertensive disorder of pregnancy who were at high-risk for the development of dnPPHTN based on a pre-specified risk factor algorithm were enrolled after childbirth. The participants were randomly assigned in a 1:1 ratio to a five-day course of oral furosemide 20 mg daily or identical-appearing placebo starting within eight hours of delivery. Participants were followed for 6 weeks postpartum using Bluetooth-enabled remote blood pressure monitoring and electronic surveys. The primary outcome was the difference in mean arterial pressure (MAP) averaged over the 24 hours prior to discharge or the 24 hours prior to antihypertensive therapy initiation. The study was powered to detect a 5 mmHg difference in mean MAP (standard deviation 6.4 mmHg) with 90% power at an alpha of 0.05, requiring a sample size of 41 per group. Secondary outcomes included the rate of dnPPHTN, readmission data, other measures of hypertensive and maternal morbidity, breastfeeding data, and drug-related neonatal outcomes. RESULTS The primary outcome was assessed in 80 of the 82 participants. Baseline characteristics were similar between groups. There was no significant difference in mean MAP 24 hours prior to discharge (or antihypertensive initiation) in the furosemide group (88.9 ± 7.4 mmHg) compared to the placebo group (86.8 ± 7.1 mmHg; absolute difference 2.1 mmHg, 95% CI -1.2 to 5.3). Of the 79 participants for whom secondary outcomes were assessed, 10% (n=8) developed dnPPHTN and 9% (n=7) were initiated on antihypertensive therapy. Rates were not significantly different between groups. CONCLUSIONS De novo postpartum hypertension is a common phenomenon among at-risk patients, warranting close monitoring for severe hypertension and other maternal morbidity. There is insufficient evidence to suggest that furosemide reduces mean MAP in the 24 hours prior to discharge from the delivery hospitalization (or antihypertensive medication initiation) compared to placebo.
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Affiliation(s)
- Ukachi N Emeruwa
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, NewYork-Presbyterian Hospital, New York, NY; Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego School of Medicine, UC San Diego Health, La Jolla, CA.
| | - Hooman Azad
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, NewYork-Presbyterian Hospital, New York, NY
| | - Samsiya Ona
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, NewYork-Presbyterian Hospital, New York, NY; Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Science, Icahn School of Medicine, Mount Sinai Health, New York, NY
| | - Shai Bejerano
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, NewYork-Presbyterian Hospital, New York, NY
| | - Sarah Alnafisee
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, NewYork-Presbyterian Hospital, New York, NY
| | - Jordan Emont
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, NewYork-Presbyterian Hospital, New York, NY
| | - Sharon Mathew
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, NewYork-Presbyterian Hospital, New York, NY
| | - Michelle Batlle
- Columbia University, Vagelos College of Physicians and Surgeons
| | - Denice Arnold
- Columbia University, Vagelos College of Physicians and Surgeons
| | - Erinma P Ukoha
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, NewYork-Presbyterian Hospital, New York, NY
| | - Louise C Laurent
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego School of Medicine, UC San Diego Health, La Jolla, CA
| | - Marni Jacobs
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego School of Medicine, UC San Diego Health, La Jolla, CA
| | - Janice J Aubey
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, NewYork-Presbyterian Hospital, New York, NY
| | - Russell S Miller
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, NewYork-Presbyterian Hospital, New York, NY
| | - Cynthia Gyamfi-Bannerman
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego School of Medicine, UC San Diego Health, La Jolla, CA
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Chousal JN, Morey R, Srinivasan S, Lee K, Zhang W, Yeo AL, To C, Cho K, Garzo VG, Parast MM, Laurent LC, Cook-Andersen H. Molecular profiling of human blastocysts reveals primitive endoderm defects among embryos of decreased implantation potential. Cell Rep 2024; 43:113701. [PMID: 38277271 DOI: 10.1016/j.celrep.2024.113701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 12/12/2023] [Accepted: 01/05/2024] [Indexed: 01/28/2024] Open
Abstract
Human embryo implantation is remarkably inefficient, and implantation failure remains among the greatest obstacles in treating infertility. Gene expression data from human embryos have accumulated rapidly in recent years; however, identification of the subset of genes that determine successful implantation remains a challenge. We leverage clinical morphologic grading-known for decades to correlate with implantation potential-and transcriptome analyses of matched embryonic and abembryonic samples to identify factors and pathways enriched and depleted in human blastocysts of good and poor morphology. Unexpectedly, we discovered that the greatest difference was in the state of extraembryonic primitive endoderm (PrE) development, with relative deficiencies in poor morphology blastocysts. Our results suggest that implantation success is most strongly influenced by the embryonic compartment and that deficient PrE development is common among embryos with decreased implantation potential. Our study provides a valuable resource for those investigating the markers and mechanisms of human embryo implantation.
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Affiliation(s)
- Jennifer N Chousal
- Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert Morey
- Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Srimeenakshi Srinivasan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katherine Lee
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wei Zhang
- Reproductive Partners Fertility Center - San Diego, La Jolla, CA 92037, USA
| | - Ana Lisa Yeo
- Reproductive Partners Fertility Center - San Diego, La Jolla, CA 92037, USA
| | - Cuong To
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kyucheol Cho
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - V Gabriel Garzo
- Reproductive Partners Fertility Center - San Diego, La Jolla, CA 92037, USA
| | - Mana M Parast
- Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Heidi Cook-Andersen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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Lindley KJ, Perry A, Jacobs M, Petty L, Amancherla K, Zhao S, Barker C, Davila-Roman VG, Khan SS, Osmundson SS, Tanriverdi K, Freedman JE, Below J, Shah RV, Laurent LC. Differences in Cardiometabolic Proteins in Pregnancy Prioritize Relevant Targets of Preeclampsia. Arterioscler Thromb Vasc Biol 2024. [PMID: 38385288 DOI: 10.1161/atvbaha.124.320737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/05/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Preeclampsia is a hypertensive disorder of pregnancy characterized by widespread vascular inflammation. It occurs frequently in pregnancy, often without known risk factors, and has high rates of maternal and fetal morbidity and mortality. Identification of biomarkers that predict preeclampsia and its cardiovascular sequelae before clinical onset, or even before pregnancy, is a critical unmet need for the prevention of adverse pregnancy outcomes. METHODS We explored differences in cardiovascular proteomics (Olink Explore 384) in 256 diverse pregnant persons across 2 centers (26% Hispanic, 21% Black). RESULTS We identified significant differences in plasma abundance of markers associated with angiogenesis, blood pressure, cell adhesion, inflammation, and metabolism between individuals delivering with preeclampsia and controls, some of which have not been widely described previously and are not represented in the preeclampsia placental transcriptome. While we observed a broadly similar pattern in early (<34 weeks) versus late (≥34 weeks) preeclampsia, several proteins related to hemodynamic stress, hemostasis, and immune response appeared to be more highly dysregulated in early preeclampsia relative to late preeclampsia. CONCLUSIONS These results demonstrate the value of performing targeted proteomics using a panel of cardiovascular biomarkers to identify biomarkers relevant to preeclampsia pathophysiology and highlight the need for larger multiomic studies to define modifiable pathways of surveillance and intervention upstream to preeclampsia diagnosis.
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Affiliation(s)
- Kathryn J Lindley
- Vanderbilt Translational and Clinical Research Center, Cardiovascular Division, Vanderbilt University Medical Center, Nashville, TN. (K.J.L., A.P., K.A., S.Z., K.T., J.E.F., R.V.S.)
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN. (K.J.L., S.S.O.)
| | - Andrew Perry
- Vanderbilt Translational and Clinical Research Center, Cardiovascular Division, Vanderbilt University Medical Center, Nashville, TN. (K.J.L., A.P., K.A., S.Z., K.T., J.E.F., R.V.S.)
| | - Marni Jacobs
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Maternal Fetal Medicine, University of California San Diego (M.J.)
| | - Lauren Petty
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN. (L.P., J.B.)
| | - Kaushik Amancherla
- Vanderbilt Translational and Clinical Research Center, Cardiovascular Division, Vanderbilt University Medical Center, Nashville, TN. (K.J.L., A.P., K.A., S.Z., K.T., J.E.F., R.V.S.)
| | - Shilin Zhao
- Vanderbilt Translational and Clinical Research Center, Cardiovascular Division, Vanderbilt University Medical Center, Nashville, TN. (K.J.L., A.P., K.A., S.Z., K.T., J.E.F., R.V.S.)
| | - Claire Barker
- Cardiovascular Imaging and Clinical Research Core Laboratory, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO (C.B., V.G.D.-R.)
| | - Victor G Davila-Roman
- Cardiovascular Imaging and Clinical Research Core Laboratory, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO (C.B., V.G.D.-R.)
| | - Sadiya S Khan
- Cardiovascular Division, Feinberg School of Medicine, Northwestern University, Chicago, IL (S.S.K.)
| | - Sarah S Osmundson
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN. (K.J.L., S.S.O.)
| | - Kahraman Tanriverdi
- Vanderbilt Translational and Clinical Research Center, Cardiovascular Division, Vanderbilt University Medical Center, Nashville, TN. (K.J.L., A.P., K.A., S.Z., K.T., J.E.F., R.V.S.)
| | - Jane E Freedman
- Vanderbilt Translational and Clinical Research Center, Cardiovascular Division, Vanderbilt University Medical Center, Nashville, TN. (K.J.L., A.P., K.A., S.Z., K.T., J.E.F., R.V.S.)
| | - Jennifer Below
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN. (L.P., J.B.)
| | - Ravi V Shah
- Vanderbilt Translational and Clinical Research Center, Cardiovascular Division, Vanderbilt University Medical Center, Nashville, TN. (K.J.L., A.P., K.A., S.Z., K.T., J.E.F., R.V.S.)
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Mestan KK, Sharma A, Lazar S, Pandey S, Parast MM, Laurent LC, Prince LS, Sahoo D. Macrophage Polarizations in the Placenta and Lung are Associated with Bronchopulmonary Dysplasia. bioRxiv 2024:2024.01.26.577443. [PMID: 38352616 PMCID: PMC10862768 DOI: 10.1101/2024.01.26.577443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The intricate interplay between macrophage polarization and placenta vascular dysfunction has garnered increasing attention in the context of placental inflammatory diseases. This study delves into the complex relationship between macrophage polarization within the placenta and its potential impact on the development of vascular dysfunction and inflammatory conditions. The placenta, a crucial organ in fetal development, relies on a finely tuned balance of immune responses for proper functioning. Disruptions in this delicate equilibrium can lead to pathological conditions, including inflammatory diseases affecting the fetus and newborn infant. We explored the interconnectedness between placental macrophage polarization and its relevance to lung macrophages, particularly in the context of early life lung development. Bronchopulmonary dysplasia (BPD), the most common chronic lung disease of prematurity, has been associated with abnormal immune responses, and understanding the role of macrophages in this context is pivotal. The investigation aims to shed light on how alterations in placental macrophage polarization may contribute to lung macrophage behavior and, consequently, influence the development of BPD. By unraveling the intricate mechanisms linking macrophage polarization, placental dysfunction and BPD, this research seeks to provide insights that could pave the way for targeted therapeutic interventions. The findings may offer novel perspectives on preventing and managing placental and lung-related pathologies, ultimately contributing to improved maternal and neonatal health outcomes.
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Affiliation(s)
- Karen K. Mestan
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Abhineet Sharma
- Department of Pediatrics, Divisions of Neonatology and Pediatric Pulmonology, University of Nebraska College of Medicine, Omaha, NE
| | - Sarah Lazar
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Sonalisa Pandey
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Mana M. Parast
- Department of Pathology, University of California San Diego, La Jolla, CA
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, CA
| | | | - Debashis Sahoo
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Department of Computer Science and Engineering, Jacob’s School of Engineering, University of California San Diego, La Jolla, CA
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8
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Rabin BA, Cain KL, Ayers LO, Lomeli A, Escoto A, Burola ML, Aguilar M, Calvillo ST, Reyes B, Salgin L, Tukey R, Laurent LC, Stadnick NA. Adaptation of the brainwriting premortem technique to inform the co-creation of COVID-19 testing strategies in underserved communities in South San Diego. BMC Health Serv Res 2024; 24:12. [PMID: 38172787 PMCID: PMC10765849 DOI: 10.1186/s12913-023-10341-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024] Open
Abstract
INTRODUCTION Meaningful engagement of partners in co-creating and refining health-related programs can increase the initial uptake, sustained implementation, broad reach, and effectiveness of these programs. This is especially important for underserved communities where resources are limited and need to be prioritized. Brainwriting premortem is a novel qualitative approach to partner engagement that combines the strengths of individual idea generation with the concept of premortem exercise that addresses failure points prior to the implementation of new programs. METHODS An adapted form of brainwriting premortem was used to inform iterative refinements to a COVID-19 testing program at a Federally Qualified Health Center (FQHC) in San Diego. Patients and providers from the FQHC participated in interviews at two time points (early- and mid-implementation of the program). Interview data were transcribed, translated, and analyzed using a rapid qualitative approach. Key themes and sub-themes were identified and used to inform refinements to the program. RESULTS A total of 11 patients (7 Spanish- and 4 English-speaking) and 8 providers participated in the brainwriting premortem interviews. Key themes related to possible reasons for COVID-19 testing program failure: advertising/sharing information; access to testing; handling of test results; staff and patient safety; patient beliefs and views regarding the SARS-CoV-2 virus; and COVID-19 testing options offered. Proposed solutions were offered for the key failures except for patient beliefs and views regarding the SARS-CoV-2 virus. Additional solutions offered were related to education, physical operations, and recruitment strategies. Real-time changes to the program flow and components were made in response to 7 suggestions from patients and 11 from providers. Changes related to the process of returning results were the most common, and included sending results via email with distinct workflows based on the test result. CONCLUSION The implementation of the adapted brainwriting premortem technique allowed us to incorporate the perspective of key partners in the delivery and iterative refinement of the COVID-19 testing program. This was an effective tool in the context of an FQHC and can be a promising and approach to incorporate iterative input from patients and providers to ensure successful program implementation. Future studies, particularly those requiring rapid response to public health emergencies, should consider the use of this technique.
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Affiliation(s)
- Borsika A Rabin
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA.
- UC San Diego Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, University of California San Diego, La Jolla, CA, USA.
| | - Kelli L Cain
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Lawrence O Ayers
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Angel Lomeli
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Arleth Escoto
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Maria Linda Burola
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Melanie Aguilar
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Stephenie Tinoco Calvillo
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Breanna Reyes
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Robert Tukey
- Superfund Research Center, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nicole A Stadnick
- UC San Diego Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Child and Adolescent Services Research Center, San Diego, CA, USA
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9
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Morey R, Poling L, Srinivasan S, Martinez-King C, Anyikam A, Zhang-Rutledge K, To C, Hakim A, Mochizuki M, Verma K, Mason A, Tran V, Meads M, Lamale-Smith L, Roeder H, Horii M, Ramos GA, DeHoff P, Parast MM, Pantham P, Laurent LC. Discovery and verification of extracellular microRNA biomarkers for diagnostic and prognostic assessment of preeclampsia at triage. Sci Adv 2023; 9:eadg7545. [PMID: 38117879 PMCID: PMC10732528 DOI: 10.1126/sciadv.adg7545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 11/17/2023] [Indexed: 12/22/2023]
Abstract
We report on the identification of extracellular miRNA (ex-miRNA) biomarkers for early diagnosis and prognosis of preeclampsia (PE). Small RNA sequencing of maternal serum prospectively collected from participants undergoing evaluation for suspected PE revealed distinct patterns of ex-miRNA expression among different categories of hypertensive disorders in pregnancy. Applying an iterative machine learning method identified three bivariate miRNA biomarkers (miR-522-3p/miR-4732-5p, miR-516a-5p/miR-144-3p, and miR-27b-3p/let-7b-5p) that, when applied serially, distinguished between PE cases of different severity and differentiated cases from controls with a sensitivity of 93%, specificity of 79%, positive predictive value (PPV) of 55%, and negative predictive value (NPV) of 89%. In a small independent validation cohort, these ex-miRNA biomarkers had a sensitivity of 91% and specificity of 57%. Combining these ex-miRNA biomarkers with the established sFlt1:PlGF protein biomarker ratio performed better than either set of biomarkers alone (sensitivity of 89.4%, specificity of 91.3%, PPV of 95.5%, and NPV of 80.8%).
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Affiliation(s)
- Robert Morey
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Lara Poling
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Srimeenakshi Srinivasan
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Carolina Martinez-King
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Adanna Anyikam
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kathy Zhang-Rutledge
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Cuong To
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marina Mochizuki
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kajal Verma
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Antoinette Mason
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Vy Tran
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Morgan Meads
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Leah Lamale-Smith
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hilary Roeder
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mariko Horii
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Gladys A. Ramos
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Peter DeHoff
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mana M. Parast
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Priyadarshini Pantham
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology and Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
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10
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Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell 2023; 186:5690-5704.e20. [PMID: 38101407 PMCID: PMC10795731 DOI: 10.1016/j.cell.2023.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/21/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions. By integrating genomic, mobility, and epidemiological data, we find abundant transmission occurring between both adjacent and distant locations, supported by dynamic mobility patterns. We find that changing connectivity significantly influences local COVID-19 incidence. Our findings demonstrate a complex meaning of "local" when investigating connected epidemics and emphasize the importance of collaborative interventions for pandemic prevention and mitigation.
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Affiliation(s)
| | - Gabriel W Hassler
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Anelizze Castro-Martinez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Andrea Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Anthony Veder
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ariana Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Cassandra Wauer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jacqueline Holmes
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jedediah Wilson
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Shayla N Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Tsai
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA; Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | | | - Oscar E Zazueta
- Department of Epidemiology, Secretaria de Salud de Baja California, Tijuana, Baja California, Mexico
| | | | - Manuel Sanchez-Alavez
- Centro de Diagnostico COVID-19 UABC, Tijuana, Baja California, Mexico; Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | | | - Abraham García-Gil
- Clinical Laboratory Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | | | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Jeremy Corrigan
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Alana Weiss
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emily G Spencer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emory C Hufbauer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Justin J Lee
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Alison J King
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kelly N Nguyen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kieran Saucedo
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | | | - Kathleen M Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Robert T Schooley
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Agustin J Negrete
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Horacio J Reyna
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose R Chavez
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Maria L Garcia
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose M Cornejo-Bravo
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico
| | | | | | | | | | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Benjamin Henson
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Beatriz Olivares-Flores
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Gisela Barrera-Badillo
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Irma Lopez-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - José E Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Rita Flores-León
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | | | - Alison Sanders
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Sharon L Reed
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | | | | | | | | | | | | | | | - Sara H Browne
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA; Specialist in Global Health, Encinitas, CA, USA
| | - Jocelyn Olivas Flores
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico; University of HealthMx, Tijuana, Baja California, Mexico
| | - Diana G Rincon Rodríguez
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Martin Gonzalez Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Luis C Robles Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Tijuana, Baja California, Mexico
| | - Betsy J Arellano Vera
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto Mexicano del Seguro Social, Tijuana, Baja California, Mexico
| | - Jonathan Gonzalez Garcia
- University of HealthMx, Tijuana, Baja California, Mexico; SIMNSA, Tijuana, Baja California, Mexico
| | | | - Rob Knight
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Marc A Suchard
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
| | - Abraham Campos-Romero
- Innovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | - Shirlee Wohl
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
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11
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Aisagbonhi O, Bui T, Nasamran CA, St Louis H, Pizzo D, Meads M, Mulholland M, Magallanes C, Lamale-Smith L, Laurent LC, Morey R, Jacobs MB, Fisch KM, Horii M. High placental expression of FLT1, LEP, PHYHIP and IL3RA - In persons of African ancestry with severe preeclampsia. Placenta 2023; 144:13-22. [PMID: 37949031 PMCID: PMC10843761 DOI: 10.1016/j.placenta.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
INTRODUCTION Mortality from preeclampsia (PE) and PE-associated morbidities are 3-to 5-fold higher in persons of African ancestry than in those of Asian and European ancestries. METHODS To elucidate placental contribution to worse PE outcomes in African ancestry pregnancies, we performed bulk RNA sequencing on 50 placentas from persons with severe PE (sPE) of African (n = 9), Asian (n = 18) and European (n = 23) ancestries and 73 normotensive controls of African (n = 10), Asian (n = 15) and European (n = 48) ancestries. RESULTS Previously described canonical preeclampsia genes, involved in metabolism and hypoxia/angiogenesis including: LEP, HK2, FSTL3, FLT1, ENG, TMEM45A, ARHGEF4 and HTRA1 were upregulated sPE versus normotensive placentas across ancestries. LTF, NPR3 and PHYHIP were higher in African vs. Asian ancestry sPE placentas. Allograft rejection/adaptive immune response genes were upregulated in placentas from African but not in Asian or European ancestry sPE patients; IL3RA was of particular interest because the patient with the highest placental IL3RA expression, a person of African ancestry with sPE, developed postpartum cardiomyopathy, and was the only patient out of 123, that developed this condition. Interestingly, the sPE patients with the highest IL3RA expression among persons of Asian and European ancestries developed unexplained tachycardia peripartum, necessitating echocardiography in the European ancestry patient. The association between elevated placental IL3RA levels and unexplained tachycardia or peripartum cardiomyopathy was found to be significant in the 50 sPE patients (p = .0005). DISCUSSION High placental upregulation of both canonical preeclampsia and allograft rejection/adaptive immune response genes may contribute to worse PE outcomes in African ancestry sPE patients.
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Affiliation(s)
- Omonigho Aisagbonhi
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA.
| | - Tony Bui
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Hailee St Louis
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Donald Pizzo
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Morgan Meads
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Megan Mulholland
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Celestine Magallanes
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Leah Lamale-Smith
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Robert Morey
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marni B Jacobs
- Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Mariko Horii
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
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12
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Tekkatte C, Lindsay SA, Duggan E, Castro-Martínez A, Hakim A, Saldana I, Zhang Y, Zhou J, Sebastian R, Liu Y, Pontigon DS, Meads M, Liu TN, Pizzo DP, Nolan J, Parast MM, Laurent LC. Identification of optimal conditions for human placental explant culture and extracellular vesicle release. iScience 2023; 26:108046. [PMID: 37829201 PMCID: PMC10565782 DOI: 10.1016/j.isci.2023.108046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 05/17/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023] Open
Abstract
Extracellular vesicles (EVs) can mediate intercellular communication, including signaling between the placenta and maternal tissues. Human placental explant culture is a versatile in vitro model system to investigate placental function. We performed systematic studies in different tissue culture media types and oxygen tensions to identify a defined serum-free culture condition that supports high trophoblast viability and metabolism, as well as the release of similar populations of EVs, compared to traditional undefined conditions that contain media additives potentially contaminated with exogenous EVs. We also determined the time frame in which trophoblast viability and functionality remain optimal. Multiplex vesicle flow cytometry with classical EV and placenta-specific markers revealed three separate populations of explant-derived EVs: small CD63+ EVs; large PLAP+ EVs; and CD63-/PLAP- EVs. These culture and analytical approaches will enable in vitro modeling of short-term effects of environmental perturbations associated with pregnancy complications on placental function and EV release.
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Affiliation(s)
- Chandana Tekkatte
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92037, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Scott A. Lindsay
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92037, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Erika Duggan
- Scintillon Institute, San Diego, CA 92121, USA
- Cellarcus Biosciences Inc, La Jolla, CA 92037, USA
| | - Anelizze Castro-Martínez
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92037, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Abbas Hakim
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92037, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Isabella Saldana
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92037, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Yan Zhang
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92037, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
- Department of Obstetrics, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jun Zhou
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92037, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
- Department of Obstetrics, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Rachel Sebastian
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92037, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Yukun Liu
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92037, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
- Department of Obstetrics and Gynecology, SUN Yat-sen Memorial Hospital, SUN Yat-sen University, Guangzhou, Guangdong, China
| | - Devin S. Pontigon
- Department of Pathology, University of California San Diego, La Jolla, CA 92037, USA
| | - Morgan Meads
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
- Department of Pathology, University of California San Diego, La Jolla, CA 92037, USA
| | - Tzu Ning Liu
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92037, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Donald P. Pizzo
- Department of Pathology, University of California San Diego, La Jolla, CA 92037, USA
| | - John Nolan
- Scintillon Institute, San Diego, CA 92121, USA
- Cellarcus Biosciences Inc, La Jolla, CA 92037, USA
| | - Mana M. Parast
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
- Department of Pathology, University of California San Diego, La Jolla, CA 92037, USA
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92037, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
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13
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Stadnick NA, Laurent LC, Cain KL, Seifert M, Burola ML, Salgin L, Watson P, Oswald W, Munoz FA, Velasquez SF, Smith JD, Zou J, Rabin BA. Community-engaged optimization of COVID-19 rapid evaluation and testing experiences: roll-out implementation optimization trial. Implement Sci 2023; 18:46. [PMID: 37784200 PMCID: PMC10544564 DOI: 10.1186/s13012-023-01306-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND There continues to be a need for COVID-19 testing that is pragmatic, community-centered, and sustainable. This study will refine and test implementation strategies prioritized by community partners: (1) walk-up no-cost testing, (2) community health worker (promotores)-facilitated testing and preventive care counseling, (3) vending machines that dispense no-cost, self-testing kits. METHODS A co-designed Theory of Change from an earlier study phase and the Practical, Robust Implementation and Sustainment Model (PRISM) will guide the study design, measures selection, and evaluation. The first aim is to refine and operationalize a multi-component implementation strategy bundle and outcome measures for COVID-19 testing. A Community and Scientific Advisory Board (CSAB) will be established and include community members, clinical providers/staff from the partnering Federally Qualified Health Center (FQHC), public health researchers, policymakers, and a county health department ambassador. Engagement of CSAB members will be assessed through structured ethnography and a survey about the quality and quantity of engagement practices. The second aim is to implement and evaluate the impact of the implementation strategy bundle to optimize COVID-19 testing in communities using a roll-out implementation optimization (ROIO) design. Seven thousand and five hundred community members will be enrolled across four FQHC clinics over 18 months. Participants will be invited to complete an electronic survey about their demographics, health, and COVID-19 testing results and experiences. CSAB members and clinic partners will participate in PRISM fit and determinant assessments prior to each clinic rollout and post-trial. Interviews will be conducted with 60 community participants and 12 providers/staff following a 3-month rollout period at each clinic, inquiring about their experiences with the implementation strategies. Quantitative data will be analyzed using hierarchical multilevel models to determine the impact of implementation strategies. Qualitative data will be analyzed using rapid qualitative approaches to summarize implementation experiences and identify necessary changes prior to subsequent rollouts. A matrix approach will be used to triangulate data from quantitative and qualitative sources based on PRISM domains. DISCUSSION This is one of the first pragmatic implementation trials to use a ROIO design and aims to co-create a sustainable and equitable COVID-19 testing program. Findings are likely to generalize to other public health prevention efforts. TRIAL REGISTRATION NCT05894655 March 2, 2023.
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Affiliation(s)
- Nicole A Stadnick
- University of California San Diego Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, La Jolla, CA, USA.
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Child and Adolescent Services Research Center, San Diego, USA.
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kelli L Cain
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Marva Seifert
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Maria Linda Burola
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Linda Salgin
- San Ysidro Health, San Diego, CA, USA
- Joint Doctoral Program in Public Health School, UC San Diego and San Diego State University, San Diego, CA, USA
| | - Paul Watson
- The Global Action Research Center, San Diego, CA, USA
| | | | | | | | - Justin D Smith
- Department of Population Health Sciences, Division of Health System Innovation and Research, Spencer Fox Eccles School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Jingjing Zou
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Borsika A Rabin
- University of California San Diego Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, La Jolla, CA, USA
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
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14
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Sveiven M, Gassman A, Rosenberg J, Chan M, Boniface J, O’Donoghue AJ, Laurent LC, Hall DA. A dual-binding magnetic immunoassay to predict spontaneous preterm birth. Front Bioeng Biotechnol 2023; 11:1256267. [PMID: 37790251 PMCID: PMC10542577 DOI: 10.3389/fbioe.2023.1256267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/25/2023] [Indexed: 10/05/2023] Open
Abstract
Complications posed by preterm birth (delivery before 37 weeks of pregnancy) are a leading cause of newborn morbidity and mortality. The previous discovery and validation of an algorithm that includes maternal serum protein biomarkers, sex hormone-binding globulin (SHBG), and insulin-like growth factor-binding protein 4 (IBP4), with clinical factors to predict preterm birth represents an opportunity for the development of a widely accessible point-of-care assay to guide clinical management. Toward this end, we developed SHBG and IBP4 quantification assays for maternal serum using giant magnetoresistive (GMR) sensors and a self-normalizing dual-binding magnetic immunoassay. The assays have a picomolar limit of detections (LOD) with a relatively broad dynamic range that covers the physiological level of the analytes as they change throughout gestation. Measurement of serum from pregnant donors using the GMR assays was highly concordant with those obtained using a clinical mass spectrometry (MS)-based assay for the same protein markers. The MS assay requires capitally intense equipment and highly trained operators with a few days turnaround time, whereas the GMR assays can be performed in minutes on small, inexpensive instruments with minimal personnel training and microfluidic automation. The potential for high sensitivity, accuracy, and speed of the GMR assays, along with low equipment and personnel requirements, make them good candidates for developing point-of-care tests. Rapid turnaround risk assessment for preterm birth would enable patient testing and counseling at the same clinic visit, thereby increasing the timeliness of recommended interventions.
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Affiliation(s)
- Michael Sveiven
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Andrew Gassman
- Sera Prognostics, Inc., Salt Lake City, UT, United States
| | - Joshua Rosenberg
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, United States
| | - Matthew Chan
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, United States
| | - Jay Boniface
- Sera Prognostics, Inc., Salt Lake City, UT, United States
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Drew A. Hall
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, United States
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15
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Wang E, Laurent LC, Hall DA, Lo YH. Sample preconcentration through airjet-induced liquid phase enrichment. Lab Chip 2023; 23:4033-4043. [PMID: 37603416 DOI: 10.1039/d3lc00481c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Sample preparation is essential for nucleic acid assays, affecting their sensitivity and reliability. However, this process often results in a significant loss or dilution of the analyte, which becomes a bottleneck that limits downstream assay performance, particularly for assays that accept a limited input sample volume. To overcome this challenge, we present an evaporative-based sample enrichment method that uses an airjet to concentrate analytes within a small, defined volume by reversing the coffee-ring effect. A small, concentrated sample can then be collected for analysis to increase the initial sample load. The effectiveness of the reported airjet enrichment was quantified using qPCR of λ-DNA, HeLa-S3 RNA, and heat-inactivated SARS-CoV-2 samples. Comparisons between airjet enrichment and conventional evaporative concentration methods demonstrated significant advantages of airjet enrichment, including the ability to concentrate a high percentage of analyte within a 1 μL volume. The enrichment method was then integrated and adapted for various fluid volumes commonly found in nucleic acid sample preparation procedures. Here, airjet enrichment reduced the overall Cq by an average of 9.27 cycles for each analyte, resulting in a 600-fold enrichment from the initial concentration. To perform selective enrichment and prevent salt-based interference in downstream analysis, PEG was added to reduce the co-enrichment of salt. In addition, a preliminary study was conducted to explore the integration of airjet enrichment into ELISA using rabbit IgG as a model antigen. These findings demonstrate how airjet enrichment can be easily integrated into existing laboratory protocols with minimal modification and significantly improve the performance of biosensors.
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Affiliation(s)
- Edward Wang
- Department of Aerospace and Mechanical Engineering, Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA, USA.
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Drew A Hall
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Yu-Hwa Lo
- Department of Aerospace and Mechanical Engineering, Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA, USA.
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA
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16
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Sluka KA, Wager TD, Sutherland SP, Labosky PA, Balach T, Bayman EO, Berardi G, Brummett CM, Burns J, Buvanendran A, Caffo B, Calhoun VD, Clauw D, Chang A, Coffey CS, Dailey DL, Ecklund D, Fiehn O, Fisch KM, Frey Law LA, Harris RE, Harte SE, Howard TD, Jacobs J, Jacobs JM, Jepsen K, Johnston N, Langefeld CD, Laurent LC, Lenzi R, Lindquist MA, Lokshin A, Kahn A, McCarthy RJ, Olivier M, Porter L, Qian WJ, Sankar CA, Satterlee J, Swensen AC, Vance CG, Waljee J, Wandner LD, Williams DA, Wixson RL, Zhou XJ. Predicting chronic postsurgical pain: current evidence and a novel program to develop predictive biomarker signatures. Pain 2023; 164:1912-1926. [PMID: 37326643 PMCID: PMC10436361 DOI: 10.1097/j.pain.0000000000002938] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 06/17/2023]
Abstract
ABSTRACT Chronic pain affects more than 50 million Americans. Treatments remain inadequate, in large part, because the pathophysiological mechanisms underlying the development of chronic pain remain poorly understood. Pain biomarkers could potentially identify and measure biological pathways and phenotypical expressions that are altered by pain, provide insight into biological treatment targets, and help identify at-risk patients who might benefit from early intervention. Biomarkers are used to diagnose, track, and treat other diseases, but no validated clinical biomarkers exist yet for chronic pain. To address this problem, the National Institutes of Health Common Fund launched the Acute to Chronic Pain Signatures (A2CPS) program to evaluate candidate biomarkers, develop them into biosignatures, and discover novel biomarkers for chronification of pain after surgery. This article discusses candidate biomarkers identified by A2CPS for evaluation, including genomic, proteomic, metabolomic, lipidomic, neuroimaging, psychophysical, psychological, and behavioral measures. Acute to Chronic Pain Signatures will provide the most comprehensive investigation of biomarkers for the transition to chronic postsurgical pain undertaken to date. Data and analytic resources generatedby A2CPS will be shared with the scientific community in hopes that other investigators will extract valuable insights beyond A2CPS's initial findings. This article will review the identified biomarkers and rationale for including them, the current state of the science on biomarkers of the transition from acute to chronic pain, gaps in the literature, and how A2CPS will address these gaps.
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Affiliation(s)
- Kathleen A. Sluka
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Tor D. Wager
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH
| | - Stephani P. Sutherland
- Department of Biostatistics, Johns Hopkins Bloomberg Schools of Public Health, Baltimore, MD
| | - Patricia A. Labosky
- Office of Strategic Coordination, Division of Program Coordination, Planning and Strategic Initiatives, Office of the Director, National Institutes of Health, Bethesda, MD
| | - Tessa Balach
- Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago, Chicago, IL
| | - Emine O. Bayman
- Clinical Trials and Data Management Center, Department of Biostatistics, University of Iowa, Iowa City, IA
| | - Giovanni Berardi
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Chad M. Brummett
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | - John Burns
- Division of Behavioral Sciences, Rush Medical College, Chicago, IL
| | | | - Brian Caffo
- Department of Biostatistics, Johns Hopkins Bloomberg Schools of Public Health, Baltimore, MD
| | - Vince D. Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State, Georgia Tech, and Emory University, Atlanta, GA
| | - Daniel Clauw
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | - Andrew Chang
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI
| | - Christopher S. Coffey
- Clinical Trials and Data Management Center, Department of Biostatistics, University of Iowa, Iowa City, IA
| | - Dana L. Dailey
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Dixie Ecklund
- Clinical Trials and Data Management Center, Department of Biostatistics, University of Iowa, Iowa City, IA
| | - Oliver Fiehn
- University of California, Davis, Davis, CA, United States
| | - Kathleen M. Fisch
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, San Diego, CA, United States
- Center for Computational Biology and Bioinformatics, University of California San Diego, San Diego, CA, United States
| | - Laura A. Frey Law
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Richard E. Harris
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | - Steven E. Harte
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | - Timothy D. Howard
- Department of Biochemistry, Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
- Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
| | - Joshua Jacobs
- Department of Orthopedic Surgery, Rush Medical College, CHicago, IL
| | - Jon M. Jacobs
- Environmental and Molecular Sciences Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | | | | | - Carl D. Langefeld
- Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
- Department of Biostatistics and Data Science, Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, San Diego, CA, United States
| | - Rebecca Lenzi
- Office of Strategic Coordination, Division of Program Coordination, Planning and Strategic Initiatives, Office of the Director, National Institutes of Health, Bethesda, MD
| | - Martin A. Lindquist
- Department of Biostatistics, Johns Hopkins Bloomberg Schools of Public Health, Baltimore, MD
| | | | - Ari Kahn
- Texas Advanced Computing Center, University of Texas, AUstin, TX
| | | | - Michael Olivier
- Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
- Department of Internal Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winstom-Salem, NC
| | - Linda Porter
- National Institute of Neurological Disorders and Stroke, Bethesda, MD
- Office of Pain Policy and Planning National Institutes of Health, Bethesda, MD
| | - Wei-Jun Qian
- Environmental and Molecular Sciences Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Cheryse A. Sankar
- National Institute of Neurological Disorders and Stroke, Bethesda, MD
| | | | - Adam C. Swensen
- Environmental and Molecular Sciences Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Carol G.T. Vance
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Jennifer Waljee
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI
| | - Laura D. Wandner
- National Institute of Neurological Disorders and Stroke, Bethesda, MD
| | - David A. Williams
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI
| | | | - Xiaohong Joe Zhou
- Center for MR Research and Departments of Radiology, Neurosurgery, and Bioengineering, University of Illinois College of Medicine at Chicago, Chicago, IL, United States
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17
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Fisher SA, Grijalva M, Guo R, Johnston SA, Laurent LC, Nguyen H, Renz J, Rosario JG, Rudich S, Gregory BD, Kim J, O’Neill K. Systematic Sampling of the Female Reproductive System for Molecular Characterization. Curr Protoc 2023; 3:e848. [PMID: 37584588 PMCID: PMC10575691 DOI: 10.1002/cpz1.848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
As part of the National Institutes of Health Human BioMolecular Atlas Program to develop a global platform to map the 37 trillion cells in the adult human body, we are generating a comprehensive molecular characterization of the female reproductive system. Data gathered from multiple single-cell/single-nucleus and spatial molecular assays will be used to build a 3D molecular atlas. Herein, we describe our multistep protocol, beginning with an optimized organ procurement workflow that maintains functional characteristics of the uterus, ovaries, and fallopian tubes by perfusing these organs with preservation solution. We have also developed a structured tissue sampling procedure that retains information on individual-level anatomic, physiologic, and individual diversity of the female reproductive system, toward full exploration of the function and structure of female reproductive cells. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Preparation and preservation of the female reproductive system (ovaries, fallopian tubes, and uterus) prior to procurement Basic Protocol 2: Removal of the female reproductive system en bloc Basic Protocol 3: Postsurgical dissection of ovaries Basic Protocol 4: Postsurgical dissection of fallopian tubes Basic Protocol 5: Postsurgical dissection of cervix Basic Protocol 6: Postsurgical dissection of uterine body Support Protocol 1: OCT-embedded tissue protocol Support Protocol 2: Tissue fixation protocol Support Protocol 3: Snap-frozen tissue protocol Basic Protocol 7: Tissue slice preparation for Visium analysis Support Protocol 4: Hematoxylin and eosin staining for 10X Visium imaging Basic Protocol 8: Manual tissue dissociation for Multiome analysis Basic Protocol 9: Tissue dissociation for Multiome analysis using S2 Singulator.
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Affiliation(s)
- Stephen A Fisher
- 433 S. University Ave., Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Marielena Grijalva
- 421 Curie Blvd., BRB II/III rm 1342, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Rong Guo
- 433 S. University Ave., Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Sarah A Johnston
- 421 Curie Blvd., BRB II/III rm 1342, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093 USA
| | - Hieu Nguyen
- 433 S. University Ave., Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - John Renz
- Gift of Life, 5901 Broken Sound Pkwy NW, Suite 600, Boca Raton, FL 33487 USA
| | - Jean G Rosario
- 433 S. University Ave., Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Steven Rudich
- Gift of Life, 5901 Broken Sound Pkwy NW, Suite 600, Boca Raton, FL 33487 USA
| | - Brian D Gregory
- 433 S. University Ave., Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Junhyong Kim
- 433 S. University Ave., Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Kathleen O’Neill
- 421 Curie Blvd., BRB II/III rm 1342, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
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18
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Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, Börner K, Snyder MP. Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol 2023; 25:1089-1100. [PMID: 37468756 PMCID: PMC10681365 DOI: 10.1038/s41556-023-01194-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/22/2023] [Indexed: 07/21/2023]
Abstract
The Human BioMolecular Atlas Program (HuBMAP) aims to create a multi-scale spatial atlas of the healthy human body at single-cell resolution by applying advanced technologies and disseminating resources to the community. As the HuBMAP moves past its first phase, creating ontologies, protocols and pipelines, this Perspective introduces the production phase: the generation of reference spatial maps of functional tissue units across many organs from diverse populations and the creation of mapping tools and infrastructure to advance biomedical research.
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Affiliation(s)
- Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Liming Pei
- Center for Mitochondrial and Epigenomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology and the Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Michael Angelo
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - James P Carson
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Joana P Gonçalves
- Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - James S Hagood
- Department of Pediatrics (Pulmonology) and Program for Rare and Interstitial Lung Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John W Hickey
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Neil L Kelleher
- Departments of Medicine, Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Shin Lin
- Division of Cardiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Yiing Lin
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Huiping Liu
- Departments of Pharmacology, Medicine (Hematology and Oncology), Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Andrea Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Brent R Stockwell
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Ioannis S Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Katy Börner
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
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19
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Lomeli A, Escoto AA, Reyes B, Burola MLM, Tinoco-Calvillo S, Villegas I, Cohen AS, Laurent LC, Salgin L, Stadnick NA, Rabin B, Seifert M. Factors associated with COVID-19 vaccine uptake in a US/Mexico border community: demographics, previous influenza vaccination, and trusted sources of health information. Front Public Health 2023; 11:1163617. [PMID: 37575117 PMCID: PMC10415906 DOI: 10.3389/fpubh.2023.1163617] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
Background COVID-19 vaccine uptake has been uneven, particularly across racial/ethnic and age groups. This study seeks to understand factors associated with COVID-19 vaccine uptake in a large cross-sectional sample of predominantly Latinos/Latinas individuals living near the US/Mexico border. Methods Data are extracted from a 176-item survey conducted as part of a parent study focused on the co-creation of a COVID-19 testing program for underserved communities developed through a partnership between an academic institution and a Federally Qualified Health Center. The following participant variables were examined: health history, COVID-19 symptoms, COVID-19 testing and vaccine experiences, and perceptions of sources of health information. Participant characteristics were compared using chi-square tests. Multivariate logistic regressions were used for the final statistical model. Results From 1 May 2021 to 30 April 2022, 4,964 adults, 66% of whom were identified as women, completed the survey. Approximately 80% of participants reported having received at least one COVID-19 vaccine. Female sex, older age, Hispanic/Latino(a) ethnicity, previous influenza vaccination, advanced education, and perceived elevated risk of COVID-19 were significantly (p < 0.05) associated with having received a COVID-19 vaccine. Regarding sources of health information, individuals who indicated they trust their doctor, healthcare provider, or the US government "a great deal" were more likely to have received a COVID-19 vaccine compared to individuals who indicated that they trusted these sources "not at all." In contrast, those who reported having "a great deal" of trust in their faith leader or their social media contacts were significantly less likely to have received a COVID-19 vaccine than those who reported that they trusted these sources "not at all." Conclusion Sex, education, past influenza vaccination, perceived risk of COVID-19 infection, and trust in specific sources of information were correlated with the uptake of COVID-19 vaccination. Additional research is needed to better understand why this confluence of factors, particularly the unique findings about trusted sources of information, are associated with vaccine uptake. Understanding these associations, specifically within underserved, Latino/Hispanic communities, is an important first step to inform efforts aimed at increasing and sustaining COVID-19 vaccine uptake and adoption of other public health interventions.
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Affiliation(s)
- Angel Lomeli
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
- Herbert Wertheim School of Public Health and Longevity Science, University of California, San Diego, La Jolla, CA, United States
| | - Arleth A. Escoto
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Breanna Reyes
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Maria Linda M. Burola
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Stephenie Tinoco-Calvillo
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Isabel Villegas
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Ariel S. Cohen
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Linda Salgin
- Department of Research and Health Promotion, San Ysidro Health Center, San Ysidro, CA, United States
- Joint Doctoral Program in Public Health, San Diego State University/University of California, San Diego, San Diego, CA, United States
| | - Nicole A. Stadnick
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
- Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, University of California San Diego, La Jolla, CA, United States
- Child and Adolescent Services Research Center, San Diego, CA, United States
| | - Borsika Rabin
- Herbert Wertheim School of Public Health and Longevity Science, University of California, San Diego, La Jolla, CA, United States
- Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, University of California San Diego, La Jolla, CA, United States
| | - Marva Seifert
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
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20
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Rabin BA, Cain KL, Watson P, Oswald W, Laurent LC, Meadows AR, Seifert M, Munoz FA, Salgin L, Aldous J, Diaz EA, Villodas M, Vijaykumar S, O'Leary ST, Stadnick NA. Scaling and sustaining COVID-19 vaccination through meaningful community engagement and care coordination for underserved communities: hybrid type 3 effectiveness-implementation sequential multiple assignment randomized trial. Implement Sci 2023; 18:28. [PMID: 37443044 DOI: 10.1186/s13012-023-01283-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/18/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND COVID-19 inequities are abundant in low-income communities of color. Addressing COVID-19 vaccine hesitancy to promote equitable and sustained vaccination for underserved communities requires a multi-level, scalable, and sustainable approach. It is also essential that efforts acknowledge the broader healthcare needs of these communities including engagement in preventive services. METHODS This is a hybrid type 3 effectiveness-implementation study that will include a multi-level, longitudinal, mixed-methods data collection approach designed to assess the sustained impact of a co-created multicomponent strategy relying on bidirectional learning, shared decision-making, and expertise by all team members. The study capitalizes on a combination of implementation strategies including mHealth outreach with culturally appropriate messaging, care coordination to increase engagement in high priority preventive services, and the co-design of these strategies using community advisory boards led by Community Weavers. Community Weavers are individuals with lived experience as members of an underserved community serving as cultural brokers between communities, public health systems, and researchers to co-create community-driven, culturally sensitive public health solutions. The study will use an adaptive implementation approach operationalized in a sequential multiple assignment randomized trial design of 300 participants from three sites in a Federally Qualified Health Center in Southern California. This design will allow examining the impact of various implementation strategy components and deliver more intensive support to those who benefit from it most. The primary effectiveness outcomes are COVID-19 vaccine completion, engagement in preventive services, and vaccine confidence. The primary implementation outcomes are reach, adoption, implementation, and maintenance of the multicomponent strategy over a 12-month follow-up period. Mixed-effects logistic regression models will be used to examine program impacts and will be triangulated with qualitative data from participants and implementers. DISCUSSION This study capitalizes on community engagement, implementation science, health equity and communication, infectious disease, and public health perspectives to co-create a multicomponent strategy to promote the uptake of COVID-19 vaccination and preventive services for underserved communities in San Diego. The study design emphasizes broad engagement of our community and clinic partners leading to culturally sensitive and acceptable strategies to produce lasting and sustainable increases in vaccine equity and preventive services engagement. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT05841810 May 3, 2023.
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Affiliation(s)
- Borsika A Rabin
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA.
- Dissemination and Implementation Science Center, University of California San Diego Altman Clinical and Translational Research Institute, La Jolla, CA, USA.
| | - Kelli L Cain
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Paul Watson
- The Global Action Research Center, San Diego, CA, USA
| | | | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Audra R Meadows
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Marva Seifert
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | | | | | | | - Miguel Villodas
- Department of Psychology, San Diego State University, CA, San Diego, USA
- Child and Adolescent Services Research Center, San Diego, CA, USA
| | - Santosh Vijaykumar
- Department of Psychology, Northumbria University, Newcastle Upon Tyne, UK
| | - Sean T O'Leary
- Department of Pediatrics-Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Nicole A Stadnick
- Dissemination and Implementation Science Center, University of California San Diego Altman Clinical and Translational Research Institute, La Jolla, CA, USA
- Child and Adolescent Services Research Center, San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
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21
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Salgin L, Ayers LO, Burola ML, Engler AM, Osuna A, Gay L, Cain K, Stadnick N, Rabin B, Zaslavsky I, Laurent LC, Tukey R, Seifert M. Perceived COVID-19 risk and testing experiences in the San Ysidro U.S./Mexico border region. Transl Behav Med 2023; 13:432-441. [PMID: 36999822 PMCID: PMC10314726 DOI: 10.1093/tbm/ibac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023] Open
Abstract
Racial and ethnic disparities in COVID-19 incidence are pronounced in underserved U.S./Mexico border communities. Working and living environments in these communities can lead to increased risk of COVID-19 infection and transmission, and this increased risk is exacerbated by lack of access to testing. As part of designing a community and culturally tailored COVID-19 testing program, we surveyed community members in the San Ysidro border region. The purpose of our study was to characterize knowledge, attitudes, and beliefs of prenatal patients, prenatal caregivers, and pediatric caregivers at a Federally Qualified Health Center (FHQC) in the San Ysidro region regarding perceived risk of COVID-19 infection and access to testing. A cross-sectional survey was used to collect information on experiences accessing COVID-19 testing and perceived risk of COVID-19 infection within San Ysidro between December 29, 2020 and April 2, 2021. A total of 179 surveys were analyzed. Most participants identified as female (85%) and as Mexican/Mexican American (75%). Over half (56%) were between the age of 25 and 34 years old. Perceived Risk: 37% reported moderate to high risk of COVID-19 infection, whereas 50% reported their risk low to none. Testing Experience: Approximately 68% reported previously being tested for COVID-19. Among those tested, 97% reported having very easy or easy access to testing. Reasons for not testing included limited appointment availability, cost, not feeling sick, and concern about risk of infection while at a testing facility. This study is an important first step to understand the COVID-19 risk perceptions and testing access among patients and community members living near the U.S./Mexico border in San Ysidro, California.
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Affiliation(s)
- Linda Salgin
- San Ysidro Health, San Diego, CA, USA
- San Diego State University/University of California San Diego Joint Doctoral Program in Public Health, San Diego, CA, USA
| | - Lawrence O Ayers
- University of California, San Diego Department of Obstetrics, Gynecology, and Reproductive Sciences, San Diego, CA, USA
| | - Maria-Linda Burola
- University of California, San Diego Department of Obstetrics, Gynecology, and Reproductive Sciences, San Diego, CA, USA
| | - Anne-Marie Engler
- University of California, San Diego Department of Obstetrics, Gynecology, and Reproductive Sciences, San Diego, CA, USA
| | | | - Luis Gay
- San Ysidro Health, San Diego, CA, USA
| | - Kelli Cain
- University of California, San Diego, Herbert Wertheim School of Public Health and Human Longevity Science, San Diego, CA, USA
| | - Nicole Stadnick
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA
- University of California, San Diego Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, San Diego, CA, USA
- Child and Adolescent Services Research Center, San Diego, CA, USA
| | - Borsika Rabin
- University of California, San Diego, Herbert Wertheim School of Public Health and Human Longevity Science, San Diego, CA, USA
- University of California, San Diego Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, San Diego, CA, USA
| | - Ilya Zaslavsky
- University of California San Diego, Spatial Information Systems Lab, San Diego Supercomputer Center, San Diego, CA, USA
| | - Louise C Laurent
- University of California, San Diego Department of Obstetrics, Gynecology, and Reproductive Sciences, San Diego, CA, USA
| | - Robert Tukey
- University of California San Diego, Department of Chemistry and Biochemistry, San Diego, CA, USA
| | - Marva Seifert
- University of California San Diego, Division of Pulmonary and Critical Care Medicine, San Diego, CA, USA
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22
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LaPlante EL, Stürchler A, Fullem R, Chen D, Starner AC, Esquivel E, Alsop E, Jackson AR, Ghiran I, Pereira G, Rozowsky J, Chang J, Gerstein MB, Alexander RP, Roth ME, Franklin JL, Coffey RJ, Raffai RL, Mansuy IM, Stavrakis S, deMello AJ, Laurent LC, Wang YT, Tsai CF, Liu T, Jones J, Van Keuren-Jensen K, Van Nostrand E, Mateescu B, Milosavljevic A. exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers. Cell Genom 2023; 3:100303. [PMID: 37228754 PMCID: PMC10203258 DOI: 10.1016/j.xgen.2023.100303] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 01/01/2023] [Accepted: 03/24/2023] [Indexed: 05/27/2023]
Abstract
Although the role of RNA binding proteins (RBPs) in extracellular RNA (exRNA) biology is well established, their exRNA cargo and distribution across biofluids are largely unknown. To address this gap, we extend the exRNA Atlas resource by mapping exRNAs carried by extracellular RBPs (exRBPs). This map was developed through an integrative analysis of ENCODE enhanced crosslinking and immunoprecipitation (eCLIP) data (150 RBPs) and human exRNA profiles (6,930 samples). Computational analysis and experimental validation identified exRBPs in plasma, serum, saliva, urine, cerebrospinal fluid, and cell-culture-conditioned medium. exRBPs carry exRNA transcripts from small non-coding RNA biotypes, including microRNA (miRNA), piRNA, tRNA, small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), Y RNA, and lncRNA, as well as protein-coding mRNA fragments. Computational deconvolution of exRBP RNA cargo reveals associations of exRBPs with extracellular vesicles, lipoproteins, and ribonucleoproteins across human biofluids. Overall, we mapped the distribution of exRBPs across human biofluids, presenting a resource for the community.
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Affiliation(s)
- Emily L. LaPlante
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alessandra Stürchler
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
- Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland
| | - Robert Fullem
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne C. Starner
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 76706, USA
| | - Emmanuel Esquivel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Alsop
- Neurogenomics Division, TGen, Phoenix, AZ 85004, USA
| | - Andrew R. Jackson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ionita Ghiran
- Department of Anesthesia, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Getulio Pereira
- Department of Anesthesia, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Joel Rozowsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Justin Chang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Mark B. Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Matthew E. Roth
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey L. Franklin
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Robert J. Coffey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Robert L. Raffai
- Department of Veterans Affairs, Surgical Service (112G), San Francisco VA Medical Center, San Francisco, CA 94121, USA
- Division of Endovascular and Vascular Surgery, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Isabelle M. Mansuy
- Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Andrew J. deMello
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jennifer Jones
- Laboratory of Pathology Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Eric Van Nostrand
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 76706, USA
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bogdan Mateescu
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
- Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland
| | - Aleksandar Milosavljevic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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23
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Danesh Yazdi M, Nassan FL, Kosheleva A, Wang C, Xu Z, Di Q, Requia WJ, Comfort NT, Wu H, Laurent LC, DeHoff P, Vokonas P, Baccarelli AA, Schwartz JD. Intermediate and long-term exposure to air pollution and temperature and the extracellular microRNA profile of participants in the normative aging study (NAS). Environ Res 2023; 229:115949. [PMID: 37084943 DOI: 10.1016/j.envres.2023.115949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/27/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND The molecular effects of intermediate and long-term exposure to air pollution and temperature, such as those on extracellular microRNA (ex-miRNA) are not well understood but may have clinical consequences. OBJECTIVES To assess the association between exposure to ambient air pollution and temperature and ex-miRNA profiles. METHODS Our study population consisted of 734 participants in the Normative Aging Study (NAS) between 1999 and 2015. We used high-resolution models to estimate four-week, eight-week, twelve-week, six-month, and one-year moving averages of PM2.5, O3, NO2, and ambient temperature based on geo-coded residential addresses. The outcome of interest was the extracellular microRNA (ex-miRNA) profile of each participant over time. We used a longitudinal quantile regression approach to estimate the association between the exposures and each ex-miRNA. Results were corrected for multiple comparisons and ex-miRNAs that were still significantly associated with the exposures were further analyzed using KEGG pathway analysis and Ingenuity Pathway Analysis. RESULTS We found 151 significant associations between levels of PM2.5, O3, NO2, and ambient temperature and 82 unique ex-miRNAs across multiple quantiles. Most of the significant results were associations with intermediate-term exposure to O3, long-term exposure to PM2.5, and both intermediate and long-term exposure to ambient temperature. The exposures were most often associated with the 75th and 90th percentile of the outcomes. Pathway analyses of significant ex-miRNAs revealed their involvement in biological pathways involving cell function and communication as well as clinical diseases such as cardiovascular disease, respiratory disease, and neurological disease. CONCLUSION Our results show that intermediate and long-term exposure to all our exposures of interest were associated with changes in the ex-miRNA profile of study participants. Further studies on environmental risk factors and ex-miRNAs are warranted.
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Affiliation(s)
- Mahdieh Danesh Yazdi
- Program in Public Health, Department of Family, Population, and Preventive Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY, USA; Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA.
| | - Feiby L Nassan
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA; Biogen Inc, Cambridge, MA, USA
| | - Anna Kosheleva
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Cuicui Wang
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Zongli Xu
- Laboratory of Molecular Carcinogenesis and Biostatistics Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Qian Di
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Weeberb J Requia
- School of Public Policy and Government, Fundação Getúlio Vargas, Brasília, Distrito Federal, Brazil
| | - Nicole T Comfort
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| | - Haotian Wu
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Peter DeHoff
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Pantel Vokonas
- Department of Veterans Affairs, Boston, MA, USA; Department of Medicine, Boston University Chobanian and Avidisian School of Medicine, Boston, MA, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| | - Joel D Schwartz
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA; Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
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24
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Morey R, Farah O, Kallol S, Requena DF, Meads M, Moretto-Zita M, Soncin F, Laurent LC, Parast MM. Corrigendum: Transcriptomic drivers of differentiation, maturation, and polyploidy in human extravillous trophoblast. Front Cell Dev Biol 2023; 11:1189745. [PMID: 37057000 PMCID: PMC10086438 DOI: 10.3389/fcell.2023.1189745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fcell.2021.702046.].
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Affiliation(s)
- Robert Morey
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Maternal-Fetal Medicine, University of California, San Diego, La Jolla, CA, United States
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Omar Farah
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Sampada Kallol
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Daniela F. Requena
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Morgan Meads
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Matteo Moretto-Zita
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Francesca Soncin
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Maternal-Fetal Medicine, University of California, San Diego, La Jolla, CA, United States
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Mana M. Parast
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
- *Correspondence: Mana M. Parast,
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25
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Fielding-Miller R, Karthikeyan S, Gaines T, Garfein RS, Salido RA, Cantu VJ, Kohn L, Martin NK, Wynn A, Wijaya C, Flores M, Omaleki V, Majnoonian A, Gonzalez-Zuniga P, Nguyen M, Vo AV, Le T, Duong D, Hassani A, Tweeten S, Jepsen K, Henson B, Hakim A, Birmingham A, De Hoff P, Mark AM, Nasamran CA, Rosenthal SB, Moshiri N, Fisch KM, Humphrey G, Farmer S, Tubb HM, Valles T, Morris J, Kang J, Khaleghi B, Young C, Akel AD, Eilert S, Eno J, Curewitz K, Laurent LC, Rosing T, Knight R. Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools. Lancet Reg Health Am 2023; 19:100449. [PMID: 36844610 PMCID: PMC9939935 DOI: 10.1016/j.lana.2023.100449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Background Schools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect SARS-CoV-2 infections in controlled residential settings with high levels of accuracy. However, its effective accuracy, cost, and feasibility in non-residential community settings is unknown. Methods The objective of this study was to determine the effectiveness and accuracy of community-based passive wastewater and surface (environmental) surveillance to detect SARS-CoV-2 infection in neighborhood schools compared to weekly diagnostic (PCR) testing. We implemented an environmental surveillance system in nine elementary schools with 1700 regularly present staff and students in southern California. The system was validated from November 2020 to March 2021. Findings In 447 data collection days across the nine sites 89 individuals tested positive for COVID-19, and SARS-CoV-2 was detected in 374 surface samples and 133 wastewater samples. Ninety-three percent of identified cases were associated with an environmental sample (95% CI: 88%-98%); 67% were associated with a positive wastewater sample (95% CI: 57%-77%), and 40% were associated with a positive surface sample (95% CI: 29%-52%). The techniques we utilized allowed for near-complete genomic sequencing of wastewater and surface samples. Interpretation Passive environmental surveillance can detect the presence of COVID-19 cases in non-residential community school settings with a high degree of accuracy. Funding County of San Diego, Health and Human Services Agency, National Institutes of Health, National Science Foundation, Centers for Disease Control.
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Affiliation(s)
- Rebecca Fielding-Miller
- Division of Infectious Disease and Global Public Health, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Richard S. Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Rodolfo A. Salido
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Victor J. Cantu
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Laura Kohn
- Kohn Education Consulting, San Diego, CA, USA
| | - Natasha K. Martin
- Division of Infectious Disease and Global Public Health, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Adriane Wynn
- Division of Infectious Disease and Global Public Health, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Carrissa Wijaya
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Marlene Flores
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Vinton Omaleki
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Araz Majnoonian
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- University of California San Diego and San Diego State University Joint Doctoral Program in Public Health, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Patricia Gonzalez-Zuniga
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Megan Nguyen
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Johns Hopkins University Bloomberg School of Public Health, International Health Social and Behavioral Interventions, 615 N Wolfe St, Baltimore, MD 21205, USA
| | - Anh V. Vo
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Johns Hopkins University Bloomberg School of Public Health, International Health Social and Behavioral Interventions, 615 N Wolfe St, Baltimore, MD 21205, USA
| | - Tina Le
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Dawn Duong
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ashkan Hassani
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Samantha Tweeten
- County of San Diego, Health and Human Services Agency, 1600 Pacific Highway, San Diego, CA, 92101, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Abbas Hakim
- Department of Obstetrics Gynecology and Reproductive Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Amanda Birmingham
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Peter De Hoff
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Adam M. Mark
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Chanond A. Nasamran
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Niema Moshiri
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Kathleen M. Fisch
- Department of Obstetrics Gynecology and Reproductive Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Center for Computational Biology & Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Helena M. Tubb
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Justin Morris
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Electrical and Computer Engineering, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Jaeyoung Kang
- Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Behnam Khaleghi
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Colin Young
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ameen D. Akel
- Micron Technology, Inc., 7220 Trade Street, San Diego, CA 92121, USA
| | - Sean Eilert
- Micron Technology, Inc., 7220 Trade Street, San Diego, CA 92121, USA
| | - Justin Eno
- Micron Technology, Inc., 7220 Trade Street, San Diego, CA 92121, USA
| | - Ken Curewitz
- Micron Technology, Inc., 7220 Trade Street, San Diego, CA 92121, USA
| | - Louise C. Laurent
- University of California San Diego and San Diego State University Joint Doctoral Program in Public Health, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Tajana Rosing
- Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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26
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Jacobs MB, Valentine HD, Adkins S, Magallanes C, Morgan SC, Pereira LM, Tekkatte C, Hakim A, De Hoff P, Laurent LC, Pantham P. Humoral immune response to SARS-CoV-2 in pregnant and non-pregnant women following infection. AJOG Global Reports 2023; 3:100192. [PMID: 37113617 PMCID: PMC10010833 DOI: 10.1016/j.xagr.2023.100192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
Abstract
BACKGROUND Immune changes that occur during pregnancy may place pregnant women at an increased risk for severe disease following viral infections like SARS-CoV-2. Whether these immunologic changes modify the immune response to SARS-CoV-2 infection during pregnancy is not well understood. OBJECTIVE This study aimed to compare the humoral immune response to SARS-CoV-2 infection in pregnant and nonpregnant women. The immune response following vaccination for SARS-CoV-2 was also explored. STUDY DESIGN In this cohort study, 24 serum samples from 20 patients infected with SARS-CoV-2 during pregnancy were matched by number of days after a positive test with 46 samples from 40 nonpregnant women of reproductive age. Samples from 9 patients who were vaccinated during pregnancy were also examined. Immunoglobulin G and immunoglobulin M levels were measured. Trends in the log antibody levels over time and mean antibody levels were assessed using generalized estimating equations. RESULTS The median number of days from first positive test to sampling was 6.5 in the pregnant group (range, 3-97) and 6.0 among nonpregnant participants (range, 2-97). No significant differences in demographic or sampling characteristics were noted between the groups. No differences in immunoglobulin G or immunoglobulin M levels over time or mean antibody levels were noted among pregnant and nonpregnant participants following SARS-CoV-2 infection for any of the SARS-CoV-2 antigen targets examined (spike, spike receptor-binding domain, spike N-terminal domain, and nucleocapsid). Participants who were vaccinated during pregnancy had higher immunoglobulin G levels than pregnant patients who tested positive for all SARS-CoV-2 targets except nucleocapsid antibodies (all P<.001) and had lower immunoglobulin M spike (P<.05) and receptor-binding domain (P<.01) antibody levels. CONCLUSION This study suggests that the humoral response following SARS-CoV-2 infection does not seem to differ between pregnant women and their nonpregnant counterparts. These findings should reassure patients and healthcare providers that pregnant patients seem to mount a nondifferential immune response to SARS-CoV-2.
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Affiliation(s)
- Marni B. Jacobs
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, San Diego, CA (Dr Jacobs, Mses Valentine, Adkins, and Magallanes, Dr Morgan, Mses Pereira and Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
- Corresponding author: Marni B. Jacobs, PhD.
| | - Holly D. Valentine
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, San Diego, CA (Dr Jacobs, Mses Valentine, Adkins, and Magallanes, Dr Morgan, Mses Pereira and Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
| | - Sierra Adkins
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, San Diego, CA (Dr Jacobs, Mses Valentine, Adkins, and Magallanes, Dr Morgan, Mses Pereira and Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
| | - Celestine Magallanes
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, San Diego, CA (Dr Jacobs, Mses Valentine, Adkins, and Magallanes, Dr Morgan, Mses Pereira and Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
| | - Sydney C. Morgan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, San Diego, CA (Dr Jacobs, Mses Valentine, Adkins, and Magallanes, Dr Morgan, Mses Pereira and Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
| | - Lissa M. Pereira
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, San Diego, CA (Dr Jacobs, Mses Valentine, Adkins, and Magallanes, Dr Morgan, Mses Pereira and Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
| | - Chandana Tekkatte
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, San Diego, CA (Dr Jacobs, Mses Valentine, Adkins, and Magallanes, Dr Morgan, Mses Pereira and Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
- Sanford Consortium for Regenerative Medicine, San Diego, CA (Ms Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
| | - Abbas Hakim
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, San Diego, CA (Dr Jacobs, Mses Valentine, Adkins, and Magallanes, Dr Morgan, Mses Pereira and Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
- Sanford Consortium for Regenerative Medicine, San Diego, CA (Ms Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
| | - Peter De Hoff
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, San Diego, CA (Dr Jacobs, Mses Valentine, Adkins, and Magallanes, Dr Morgan, Mses Pereira and Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
- Sanford Consortium for Regenerative Medicine, San Diego, CA (Ms Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, San Diego, CA (Dr Jacobs, Mses Valentine, Adkins, and Magallanes, Dr Morgan, Mses Pereira and Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
- Sanford Consortium for Regenerative Medicine, San Diego, CA (Ms Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
| | - Priyadarshini Pantham
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, San Diego, CA (Dr Jacobs, Mses Valentine, Adkins, and Magallanes, Dr Morgan, Mses Pereira and Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
- Sanford Consortium for Regenerative Medicine, San Diego, CA (Ms Tekkatte, Mr Hakim, and Drs Dehoff, Laurent, and Pantham)
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27
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Rabin BA, Cain KL, Salgin L, Watson PL, Oswald W, Kaiser BN, Ayers L, Yi C, Alegre A, Ni J, Reyes A, Yu KE, Broyles SL, Tukey R, Laurent LC, Stadnick NA. Using ethnographic approaches to document, evaluate, and facilitate virtual community-engaged implementation research. BMC Public Health 2023; 23:409. [PMID: 36855118 PMCID: PMC9974043 DOI: 10.1186/s12889-023-15299-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Community Advisory Boards (CABs) have been frequently used to engage diverse partners to inform research projects. Yet, evaluating the quality of engagement has not been routine. We describe a multi-method ethnographic approach documenting and assessing partner engagement in two "virtual" CABs, for which we conducted all meetings remotely. METHODS Two research projects for increasing equitable COVID-19 testing, vaccination, and clinical trial participation for underserved communities involved remote CAB meetings. Thirty-three partners representing 17 community groups participated in 15 sessions across the two CABs facilitated by a social change organization. We developed ethnographic documentation forms to assess multiple aspects of CAB member engagement (e.g., time spent speaking, modality used, types of interactions). Documenters were trained to observe CAB sub-groups via virtual sessions. Debriefing with the documentation team after CAB meetings supported quality assurance and process refinement. CAB members completed a brief validated survey after each meeting to assess the quality and frequency of engagement. Content and rapid thematic analysis were used to analyze documentation data. Quantitative data were summarized as frequencies and means. Qualitative and quantitative findings were triangulated. RESULTS A total of 4,540 interactions were identified across 15 meetings. The most frequent interaction was providing information (44%), followed by responding (37-38%). The quality and frequency of stakeholder engagement were rated favorably (average 4.7 of 5). Most CAB members (96%) reported good/excellent engagement. Specific comments included appreciation for the diversity of perspectives represented by the CAB members and suggestions for improved live interpretation. Debriefing sessions led to several methodological refinements for the documentation process and forms. CONCLUSION We highlight key strategies for documenting and assessing community engagement. Our methods allowed for rich ethnographic data collection that refined our work with community partners. We recommend ongoing trainings, including debriefing sessions and routinely reviewed assessment of data to strengthen meaningful community engagement.
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Affiliation(s)
- Borsika A Rabin
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, San Diego, CA, United States of America.
- UC San Diego Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, University of California San Diego, La Jolla, San Diego, CA, United States of America.
| | - Kelli L Cain
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, San Diego, CA, United States of America
| | - Linda Salgin
- San Ysidro Health, San Diego, CA, United States of America
- Joint Doctoral Program in Public Health, San Diego State University, University of California San Diego, San Diego, United States of America
| | - Paul L Watson
- The Global Action Research Center, San Diego, CA, United States of America
| | - William Oswald
- The Global Action Research Center, San Diego, CA, United States of America
| | - Bonnie N Kaiser
- UC San Diego Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, University of California San Diego, La Jolla, San Diego, CA, United States of America
- Department of Anthropology and Global Health Program, University of California San Diego, La Jolla, San Diego, CA, United States of America
| | - Lawrence Ayers
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, San Diego, CA, United States of America
| | - Crystal Yi
- Department of Urban Studies and Planning, University of California San Diego, La Jolla, San Diego, CA, United States of America
| | - Alexander Alegre
- Department of Urban Studies and Planning, University of California San Diego, La Jolla, San Diego, CA, United States of America
| | - Jessica Ni
- UC San Diego Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, University of California San Diego, La Jolla, San Diego, CA, United States of America
| | - Allyn Reyes
- Department of Urban Studies and Planning, University of California San Diego, La Jolla, San Diego, CA, United States of America
| | - Kasey E Yu
- UC San Diego Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, University of California San Diego, La Jolla, San Diego, CA, United States of America
| | - Shelia L Broyles
- Department of Pediatrics, University of California San Diego, La Jolla, San Diego, CA, United States of America
- UC San Diego Altman Clinical and Translational Research Institute Community Research Partnerships, University of California San Diego, La Jolla, San Diego, CA, United States of America
| | - Robert Tukey
- Laboratory of Environmental Toxicology, Department of Pharmacology, University of California San Diego, La Jolla, San Diego, CA, United States of America
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, San Diego, CA, United States of America
| | - Nicole A Stadnick
- UC San Diego Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, University of California San Diego, La Jolla, San Diego, CA, United States of America
- Department of Psychiatry, University of California San Diego, La Jolla, San Diego, CA, United States of America
- Child and Adolescent Services Research Center, San Diego, CA, United States of America
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Emeruwa UN, Gyamfi-Bannerman C, Laurent LC. Biomarkers and the Risk of Preeclampsia. JAMA 2023; 329:539-541. [PMID: 36809333 DOI: 10.1001/jama.2022.24906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- Ukachi N Emeruwa
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla
| | - Cynthia Gyamfi-Bannerman
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla
| | - Louise C Laurent
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla
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Fielding-Miller R, Karthikeyan S, Gaines T, Garfein RS, Salido RA, Cantu VJ, Kohn L, Martin NK, Wynn A, Wijaya C, Flores M, Omaleki V, Majnoonian A, Gonzalez-Zuniga P, Nguyen M, Vo AV, Le T, Duong D, Hassani A, Tweeten S, Jepsen K, Henson B, Hakim A, Birmingham A, De Hoff P, Mark AM, Nasamran CA, Rosenthal SB, Moshiri N, Fisch KM, Humphrey G, Farmer S, Tubb HM, Valles T, Morris J, Kang J, Khaleghi B, Young C, Akel AD, Eilert S, Eno J, Curewitz K, Laurent LC, Rosing T, Knight R. Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project. medRxiv 2023:2021.10.19.21265226. [PMID: 34704096 PMCID: PMC8547528 DOI: 10.1101/2021.10.19.21265226] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background Schools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect SARS-CoV-2 infections in controlled residential settings with high levels of accuracy. However, its effective accuracy, cost, and feasibility in non-residential community settings is unknown. Methods The objective of this study was to determine the effectiveness and accuracy of community-based passive wastewater and surface (environmental) surveillance to detect SARS-CoV-2 infection in neighborhood schools compared to weekly diagnostic (PCR) testing. We implemented an environmental surveillance system in nine elementary schools with 1700 regularly present staff and students in southern California. The system was validated from November 2020 - March 2021. Findings In 447 data collection days across the nine sites 89 individuals tested positive for COVID-19, and SARS-CoV-2 was detected in 374 surface samples and 133 wastewater samples. Ninety-three percent of identified cases were associated with an environmental sample (95% CI: 88% - 98%); 67% were associated with a positive wastewater sample (95% CI: 57% - 77%), and 40% were associated with a positive surface sample (95% CI: 29% - 52%). The techniques we utilized allowed for near-complete genomic sequencing of wastewater and surface samples. Interpretation Passive environmental surveillance can detect the presence of COVID-19 cases in non-residential community school settings with a high degree of accuracy. Funding County of San Diego, Health and Human Services Agency, National Institutes of Health, National Science Foundation, Centers for Disease Control.
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Affiliation(s)
- Rebecca Fielding-Miller
- University of California San Diego, School of Medicine, Division of Infectious Disease and Global Public Health
| | | | - Tommi Gaines
- University of California San Diego, School of Medicine, Division of Infectious Disease and Global Public Health
| | - Richard S. Garfein
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | | | - Victor J. Cantu
- University of California San Diego, Department of Bioengineering
| | | | - Natasha K Martin
- University of California San Diego, School of Medicine, Division of Infectious Disease and Global Public Health
| | - Adriane Wynn
- University of California San Diego, School of Medicine, Division of Infectious Disease and Global Public Health
| | - Carrissa Wijaya
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Marlene Flores
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Vinton Omaleki
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Araz Majnoonian
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
- University of California San Diego and San Diego State University Joint Doctoral Program in Public Health
| | - Patricia Gonzalez-Zuniga
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Megan Nguyen
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
- Johns Hopkins University Bloomberg School of Public Health, International Health Social and Behavioral Interventions
| | - Anh V Vo
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
- Johns Hopkins University Bloomberg School of Public Health, International Health Social and Behavioral Interventions
| | - Tina Le
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Dawn Duong
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | - Ashkan Hassani
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science
| | | | - Kristen Jepsen
- University of California San Diego, Institute for Genomic Medicine
| | - Benjamin Henson
- University of California San Diego, Institute for Genomic Medicine
| | - Abbas Hakim
- University of California San Diego, Department of Obstetrics Gynecology and Reproductive Sciences
| | - Amanda Birmingham
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Peter De Hoff
- University of California San Diego, Department of Pediatrics
| | - Adam M. Mark
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Chanond A Nasamran
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Sara Brin Rosenthal
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Niema Moshiri
- University of California San Diego, Department of Computer Science & Engineering
| | - Kathleen M. Fisch
- University of California San Diego, Department of Obstetrics Gynecology and Reproductive Sciences
- University of California San Diego, Center for Computational Biology & Bioinformatics
| | - Greg Humphrey
- University of California San Diego, Department of Pediatrics
| | - Sawyer Farmer
- University of California San Diego, Department of Pediatrics
| | - Helena M. Tubb
- University of California San Diego, Department of Pediatrics
| | - Tommy Valles
- University of California San Diego, Department of Pediatrics
| | - Justin Morris
- University of California San Diego, Department of Computer Science & Engineering
- San Diego State University, Department of Electrical and Computer Engineering
| | - Jaeyoung Kang
- University of California San Diego, Department of Electrical and Computer Engineering
| | - Behnam Khaleghi
- University of California San Diego, Department of Computer Science & Engineering
| | - Colin Young
- University of California San Diego, Department of Computer Science & Engineering
| | | | | | | | | | - Louise C Laurent
- University of California San Diego and San Diego State University Joint Doctoral Program in Public Health
| | - Tajana Rosing
- University of California San Diego, Department of Computer Science & Engineering
| | - Rob Knight
- University of California San Diego, Department of Pediatrics
- University of California San Diego, Department of Bioengineering
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Danesh Yazdi M, Nassan FL, Kosheleva A, Wang C, Xu Z, Di Q, Requia WJ, Comfort NT, Wu H, Laurent LC, DeHoff P, Vokonas P, Baccarelli AA, Schwartz JD. Short-term air pollution and temperature exposure and changes in the extracellular microRNA profile of Normative Aging Study (NAS) participants. Environ Int 2023; 171:107735. [PMID: 36640488 PMCID: PMC10159015 DOI: 10.1016/j.envint.2023.107735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND While the health effects of air pollution and temperature are widely studied, the molecular effects are poorly understood. Extracellular microRNAs (ex-miRNAs) have the potential to serve as diagnostic or prognostic biomarkers and/or to act as intercellular signaling molecules that mediate the effects of environmental exposures on health outcomes. METHODS We examined the relationship between short-term exposure to air pollution and ambient temperature and the ex-miRNA profiles of participants in the Normative Aging Study (NAS) from 1999 to 2015. Our exposures were defined as same-day, two-day, three-day, one-week, two-week, and three-week moving averages of PM2.5, NO2, O3, and temperature which were derived from high-resolution spatio-temporal models. The ex-miRNA profiles of the subjects were obtained during follow-up visits. We analyzed the data using a longitudinal quantile regression model adjusted for individual covariates, batch effects, and time trends. We adjusted for multiple comparisons using a false discovery rate (FDR) correction. Ex-miRNAs that were significantly associated with exposures were further investigated using pathway analyses. RESULTS We found that all the examined exposures were associated with changes in ex-miRNA profiles in our study, particularly PM2.5 which was responsible for most of the statistically significant results. We found 110 statistically significant exposure-outcome relationships that revealed associations with the levels of 52 unique ex-miRNAs. Pathway analyses showed these ex-miRNAs have been linked to target mRNAs, genes, and biological mechanisms that could affect virtually every organ system, and as such may be linked to multiple clinical disease presentations such as cardiovascular disease, respiratory disease, and neurological disease. CONCLUSIONS Air pollution and temperature exposures were significantly associated with alterations in the ex-miRNA profiles of NAS subjects with possible biological consequences.
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Affiliation(s)
- Mahdieh Danesh Yazdi
- Program in Public Health, Department of Family, Population, and Preventive Medicine, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY, USA; Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA.
| | - Feiby L Nassan
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA; Biogen Inc, Cambridge, MA, USA
| | - Anna Kosheleva
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Cuicui Wang
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Zongli Xu
- Laboratory of Molecular Carcinogenesis and Biostatistics Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Qian Di
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Weeberb J Requia
- School of Public Policy and Government, Fundação Getúlio Vargas, Brasília, Distrito Federal, Brazil
| | - Nicole T Comfort
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| | - Haotian Wu
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Peter DeHoff
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Pantel Vokonas
- Department of Veterans Affairs, Boston, MA, USA; Department of Medicine, Boston University Chobanian and Avidisian School of Medicine, Boston, MA, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| | - Joel D Schwartz
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA; Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
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Eckhardt CM, Gambazza S, Bloomquist TR, De Hoff P, Vuppala A, Vokonas PS, Litonjua AA, Sparrow D, Parvez F, Laurent LC, Schwartz J, Baccarelli AA, Wu H. Extracellular Vesicle-Encapsulated microRNAs as Novel Biomarkers of Lung Health. Am J Respir Crit Care Med 2023; 207:50-59. [PMID: 35943330 PMCID: PMC9952856 DOI: 10.1164/rccm.202109-2208oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 08/08/2022] [Indexed: 02/03/2023] Open
Abstract
Rationale: Early detection of respiratory diseases is critical to facilitate delivery of disease-modifying interventions. Extracellular vesicle-enriched microRNAs (EV-miRNAs) may represent reliable markers of early lung injury. Objectives: Evaluate associations of plasma EV-miRNAs with lung function. Methods: The prospective NAS (Normative Aging Study) collected plasma EV-miRNA measurements from 1996-2015 and spirometry every 3-5 years through 2019. Associations of EV-miRNAs with baseline lung function were modeled using linear regression. To complement the individual miRNA approach, unsupervised machine learning was used to identify clusters of participants with distinct EV-miRNA profiles. Associations of EV-miRNA profiles with multivariate latent longitudinal lung function trajectories were modeled using log binomial regression. Biological functions of significant EV-miRNAs were explored using pathway analyses. Results were replicated in an independent sample of NAS participants and in the HEALS (Health Effects of Arsenic Longitudinal Study). Measurements and Main Results: In the main cohort of 656 participants, 51 plasma EV-miRNAs were associated with baseline lung function (false discovery rate-adjusted P value < 0.05), 28 of which were replicated in the independent NAS sample and/or in the HEALS cohort. A subset of participants with distinct EV-miRNA expression patterns had increased risk of declining lung function over time, which was replicated in the independent NAS sample. Significant EV-miRNAs were shown in pathway analyses to target biological pathways that regulate respiratory cellular immunity, the lung inflammatory response, and airway structural integrity. Conclusions: Plasma EV-miRNAs may represent a robust biomarker of subclinical lung injury and may facilitate early identification and treatment of patients at risk of developing overt lung disease.
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Affiliation(s)
- Christina M. Eckhardt
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Irving Medical Center, New York, New York
| | - Simone Gambazza
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Healthcare Professions Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico, Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Tessa R. Bloomquist
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Peter De Hoff
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California
| | - Aishwarya Vuppala
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California
| | - Pantel S. Vokonas
- Veterans Affairs Normative Aging Study, Veterans Affairs Boston Healthcare System, Boston, Massachusetts
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Augusto A. Litonjua
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York; and
| | - David Sparrow
- Veterans Affairs Normative Aging Study, Veterans Affairs Boston Healthcare System, Boston, Massachusetts
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Faruque Parvez
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California
| | - Joel Schwartz
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Haotian Wu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
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Gabby LC, Jacobs MB, Zhang-Rutledge K, Meads M, Pham D, Liu TN, Bucknum A, Smith LL, Parast MM, Laurent LC, Ramos GA. Frequency of preeclampsia spectrum disorders by diabetes subgroup. Am J Obstet Gynecol 2023. [DOI: 10.1016/j.ajog.2022.11.887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Sesillo FB, Rajesh V, Wong M, Duran P, Rudell JB, Rundio CP, Baynes BB, Laurent LC, Sacco A, Christman KL, Alperin M. Muscle stem cells and fibro-adipogenic progenitors in female pelvic floor muscle regeneration following birth injury. NPJ Regen Med 2022; 7:72. [PMID: 36526635 PMCID: PMC9758192 DOI: 10.1038/s41536-022-00264-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Pelvic floor muscle (PFM) injury during childbirth is a key risk factor for pelvic floor disorders that affect millions of women worldwide. Muscle stem cells (MuSCs), supported by the fibro-adipogenic progenitors (FAPs) and immune cells, are indispensable for the regeneration of injured appendicular skeletal muscles. However, almost nothing is known about their role in PFM regeneration following birth injury. To elucidate the role of MuSCs, FAPs, and immune infiltrate in this context, we used radiation to perturb cell function and followed PFM recovery in a validated simulated birth injury (SBI) rat model. Non-irradiated and irradiated rats were euthanized at 3,7,10, and 28 days post-SBI (dpi). Twenty-eight dpi, PFM fiber cross-sectional area (CSA) was significantly lower and the extracellular space occupied by immune infiltrate was larger in irradiated relative to nonirradiated injured animals. Following SBI in non-irradiated animals, MuSCs and FAPs expanded significantly at 7 and 3 dpi, respectively; this expansion did not occur in irradiated animals at the same time points. At 7 and 10 dpi, we observed persistent immune response in PFMs subjected to irradiation compared to non-irradiated injured PFMs. CSA of newly regenerated fibers was also significantly smaller following SBI in irradiated compared to non-irradiated injured PFMs. Our results demonstrate that the loss of function and decreased expansion of MuSCs and FAPs after birth injury lead to impaired PFM recovery. These findings form the basis for further studies focused on the identification of novel therapeutic targets to counteract postpartum PFM dysfunction and the associated pelvic floor disorders.
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Affiliation(s)
- Francesca Boscolo Sesillo
- grid.266100.30000 0001 2107 4242Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, San Diego, San Diego, CA 92037 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 USA
| | - Varsha Rajesh
- grid.266100.30000 0001 2107 4242Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92161 USA
| | - Michelle Wong
- grid.266100.30000 0001 2107 4242Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, San Diego, San Diego, CA 92037 USA
| | - Pamela Duran
- grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 USA ,grid.266100.30000 0001 2107 4242Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093 USA
| | - John B. Rudell
- grid.266100.30000 0001 2107 4242Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, San Diego, San Diego, CA 92037 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 USA
| | - Courtney P. Rundio
- grid.266100.30000 0001 2107 4242Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, San Diego, San Diego, CA 92037 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 USA
| | - Brittni B. Baynes
- grid.266100.30000 0001 2107 4242Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, San Diego, San Diego, CA 92037 USA
| | - Louise C. Laurent
- grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 USA ,grid.267102.00000000104485736Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Maternal-Fetal Medicine, University of San Diego, La Jolla, CA 92037 USA
| | - Alessandra Sacco
- grid.479509.60000 0001 0163 8573Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Karen L. Christman
- grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 USA ,grid.266100.30000 0001 2107 4242Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093 USA
| | - Marianna Alperin
- grid.266100.30000 0001 2107 4242Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, San Diego, San Diego, CA 92037 USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 USA
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Waks AB, Martinez-King LC, Santiago G, Laurent LC, Jacobs MB. Developing a risk profile for spontaneous preterm birth and short interval to delivery among patients with threatened preterm labor. Am J Obstet Gynecol MFM 2022; 4:100727. [PMID: 35995363 DOI: 10.1016/j.ajogmf.2022.100727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/29/2022] [Accepted: 08/15/2022] [Indexed: 10/31/2022]
Abstract
BACKGROUND Threatened preterm birth is the most common reason for antepartum hospitalization in the United States, accounting for approximately 50% of these admissions. However, fewer than 10% of patients with inpatient evaluation for signs or symptoms of preterm labor ultimately deliver before term. OBJECTIVE This study aimed to generate predictive models to assess the risk of preterm delivery and time to delivery based on clinical signs and symptoms of patients evaluated in our institution for preterm labor concerns. STUDY DESIGN This was a retrospective cohort study of singleton pregnancies evaluated for signs and/or symptoms of preterm labor, including contractions, abdominal pain, vaginal bleeding, and short cervix, between 22 0/7 and 33 6/7 weeks of gestation. Inpatient evaluations were classified by patient presentation: (1) symptomatic with cervical findings (transvaginal cervical length of <2.5 cm or cervical dilation of ≥2.0 cm), (2) asymptomatic with cervical findings, and (3) symptomatic without cervical findings. The primary outcomes included incidence of spontaneous preterm birth and interval from presentation to delivery, compared between groups. The risk of preterm delivery was evaluated using log-binomial regression, and presentation to delivery timing was assessed by survival analysis and Cox proportional hazards modeling. RESULTS Of 631 patients with preterm labor concerns, 96 (16%) were symptomatic with cervical findings on evaluation, 51 (8%) were asymptomatic with cervical findings, and 466 (76%) were symptomatic without cervical findings. The occurrence of preterm birth was significantly higher among symptomatic patients with cervical findings (49%) than among those with cervical findings alone (31%) or symptoms alone (11%) (P<.0001). In addition, symptomatic patients with cervical findings were significantly more likely to deliver within 48 hours (20%), 1 week (30%), 2 weeks (33%), and 1 month (43%) of presentation than patients with cervical findings alone (2%, 2%, 6%, and 10%, respectively) or symptoms alone (0.4%, 1%, 1.5%, and 5%, respectively) (P value for trend<.0001). Adjusted for gestational age at presentation and previous preterm birth, the overall risk of preterm delivery was significantly higher among patients with symptoms and cervical findings than among patients with cervical findings alone (relative risk, 2.81; 95% confidence interval, 1.74-4.54) or symptoms alone (relative risk, 4.39; 95% confidence interval, 3.16-6.09). Adjusted for the same variables, symptomatic patients with cervical findings were also at higher risk of delivery over time after assessment than patients with cervical findings alone (hazard ratio, 2.06; 95% confidence interval, 1.47-2.90) or symptoms alone (hazard ratio, 2.16; 95% confidence interval, 1.74-2.70). The negative predictive value of these models suggested that only 1% of patients with isolated symptoms or cervical findings are at risk of preterm delivery within 1 week of initial presentation. CONCLUSION Symptomatic patients with cervical findings suggestive of preterm labor were at the greatest risk of preterm birth and a shorter interval from presentation to delivery. The study findings supported a risk profile that may facilitate the selection of patients most appropriate for admission and targeted management. Nonetheless, as nearly 50% of patients meeting this risk profile subsequently deliver at term, future research is needed to identify which of these patients will require intervention.
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Affiliation(s)
- Ashten B Waks
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego; San Diego, CA (Dr Waks, Ms Santiago, and Drs Laurent and Jacobs).
| | - L Carolina Martinez-King
- Department of Obstetrics and Gynecology, The University of Texas Rio Grande Valley; Edinburg, TX (Dr Martinez-King)
| | - Gisselle Santiago
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego; San Diego, CA (Dr Waks, Ms Santiago, and Drs Laurent and Jacobs)
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego; San Diego, CA (Dr Waks, Ms Santiago, and Drs Laurent and Jacobs)
| | - Marni B Jacobs
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego; San Diego, CA (Dr Waks, Ms Santiago, and Drs Laurent and Jacobs)
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Comfort N, Wu H, De Hoff P, Vuppala A, Vokonas PS, Spiro A, Weisskopf M, Coull BA, Laurent LC, Baccarelli AA, Schwartz J. Extracellular microRNA and cognitive function in a prospective cohort of older men: The Veterans Affairs Normative Aging Study. Aging (Albany NY) 2022; 14:6859-6886. [PMID: 36069796 PMCID: PMC9512498 DOI: 10.18632/aging.204268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Aging-related cognitive decline is an early symptom of Alzheimer's disease and other dementias, and on its own can have substantial consequences on an individual's ability to perform important everyday functions. Despite increasing interest in the potential roles of extracellular microRNAs (miRNAs) in central nervous system (CNS) pathologies, there has been little research on extracellular miRNAs in early stages of cognitive decline. We leverage the longitudinal Normative Aging Study (NAS) cohort to investigate associations between plasma miRNAs and cognitive function among cognitively normal men. METHODS This study includes data from up to 530 NAS participants (median age: 71.0 years) collected from 1996 to 2013, with a total of 1,331 person-visits (equal to 2,471 years of follow up). Global cognitive function was assessed using the Mini-Mental State Examination (MMSE). Plasma miRNAs were profiled using small RNA sequencing. Associations of expression of 381 miRNAs with current cognitive function and rate of change in cognitive function were assessed using linear regression (N = 457) and linear mixed models (N = 530), respectively. RESULTS In adjusted models, levels of 2 plasma miRNAs were associated with higher MMSE scores (p < 0.05). Expression of 33 plasma miRNAs was associated with rate of change in MMSE scores over time (p < 0.05). Enriched KEGG pathways for miRNAs associated with concurrent MMSE and MMSE trajectory included Hippo signaling and extracellular matrix-receptor interactions. Gene targets of miRNAs associated with MMSE trajectory were additionally associated with prion diseases and fatty acid biosynthesis. CONCLUSIONS Circulating miRNAs were associated with both cross-sectional cognitive function and rate of change in cognitive function among cognitively normal men. Further research is needed to elucidate the potential functions of these miRNAs in the CNS and investigate relationships with other neurological outcomes.
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Affiliation(s)
- Nicole Comfort
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Haotian Wu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Peter De Hoff
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Aishwarya Vuppala
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Pantel S. Vokonas
- VA Normative Aging Study, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Avron Spiro
- Massachusetts Veterans Epidemiology and Research Information Center, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Marc Weisskopf
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Brent A. Coull
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Joel Schwartz
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
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Cantú VJ, Belda-Ferre P, Salido RA, Tsai R, Austin B, Jordan W, Asudani M, Walster A, Magallanes CG, Valentine H, Manjoonian A, Wijaya C, Omaleki V, Sanders K, Aigner S, Baer NA, Betty M, Castro-Martínez A, Cheung W, Crescini ES, De Hoff P, Eisner E, Hakim A, Kapadia B, Lastrella AL, Lawrence ES, Ngo TT, Ostrander T, Sathe S, Seaver P, Smoot EW, Carlin AF, Yeo GW, Laurent LC, Manlutac AL, Fielding-Miller R, Knight R. Implementation of Practical Surface SARS-CoV-2 Surveillance in School Settings. mSystems 2022; 7:e0010322. [PMID: 35703437 PMCID: PMC9426517 DOI: 10.1128/msystems.00103-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/02/2022] [Indexed: 11/20/2022] Open
Abstract
Surface sampling for SARS-CoV-2 RNA detection has shown considerable promise to detect exposure of built environments to infected individuals shedding virus who would not otherwise be detected. Here, we compare two popular sampling media (VTM and SDS) and two popular workflows (Thermo and PerkinElmer) for implementation of a surface sampling program suitable for environmental monitoring in public schools. We find that the SDS/Thermo pipeline shows superior sensitivity and specificity, but that the VTM/PerkinElmer pipeline is still sufficient to support surface surveillance in any indoor setting with stable cohorts of occupants (e.g., schools, prisons, group homes, etc.) and may be used to leverage existing investments in infrastructure. IMPORTANCE The ongoing COVID-19 pandemic has claimed the lives of over 5 million people worldwide. Due to high density occupancy of indoor spaces for prolonged periods of time, schools are often of concern for transmission, leading to widespread school closings to combat pandemic spread when cases rise. Since pediatric clinical testing is expensive and difficult from a consent perspective, we have deployed surface sampling in SASEA (Safer at School Early Alert), which allows for detection of SARS-CoV-2 from surfaces within a classroom. In this previous work, we developed a high-throughput method which requires robotic automation and specific reagents that are often not available for public health laboratories such as the San Diego County Public Health Laboratory (SDPHL). Therefore, we benchmarked our method (Thermo pipeline) against SDPHL's (PerkinElmer) more widely used method for the detection and prediction of SARS-CoV-2 exposure. While our method shows superior sensitivity (false-negative rate of 9% versus 27% for SDPHL), the SDPHL pipeline is sufficient to support surface surveillance in indoor settings. These findings are important since they show that existing investments in infrastructure can be leveraged to slow the spread of SARS-CoV-2 not in just the classroom but also in prisons, nursing homes, and other high-risk, indoor settings.
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Affiliation(s)
- Victor J. Cantú
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Rodolfo A. Salido
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Brett Austin
- San Diego County Public Health Lab, San Diego, California, USA
| | - William Jordan
- San Diego County Public Health Lab, San Diego, California, USA
| | - Menka Asudani
- San Diego County Public Health Lab, San Diego, California, USA
| | - Amanda Walster
- San Diego County Public Health Lab, San Diego, California, USA
| | - Celestine G. Magallanes
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | - Holly Valentine
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | - Araz Manjoonian
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
- San Diego State University, San Diego, California, USA
| | - Carrissa Wijaya
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
| | - Vinton Omaleki
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Nathan A. Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Maryann Betty
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Rady Children's Hospital, San Diego, California, USA
| | - Anelizze Castro-Martínez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- San Diego State University, San Diego, California, USA
| | - Evelyn S. Crescini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | - Emily Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Bhavika Kapadia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Alma L. Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Elijah S. Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Toan T. Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Elizabeth W. Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Aaron F. Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Gene W. Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | | | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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37
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Cantú VJ, Sanders K, Belda-Ferre P, Salido RA, Tsai R, Austin B, Jordan W, Asudani M, Walster A, Magallanes CG, Valentine H, Manjoonian A, Wijaya C, Omaleki V, Aigner S, Baer NA, Betty M, Castro-Martínez A, Cheung W, De Hoff P, Eisner E, Hakim A, Lastrella AL, Lawrence ES, Ngo TT, Ostrander T, Plascencia A, Sathe S, Smoot EW, Carlin AF, Yeo GW, Laurent LC, Manlutac AL, Fielding-Miller R, Knight R. Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School Settings. mSystems 2022; 7:e0010922. [PMID: 35703436 PMCID: PMC9426498 DOI: 10.1128/msystems.00109-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/20/2022] [Indexed: 11/28/2022] Open
Abstract
A promising approach to help students safely return to in person learning is through the application of sentinel cards for accurate high resolution environmental monitoring of SARS-CoV-2 traces indoors. Because SARS-CoV-2 RNA can persist for up to a week on several indoor surface materials, there is a need for increased temporal resolution to determine whether consecutive surface positives arise from new infection events or continue to report past events. Cleaning sentinel cards after sampling would provide the needed resolution but might interfere with assay performance. We tested the effect of three cleaning solutions (BZK wipes, Wet Wipes, RNase Away) at three different viral loads: "high" (4 × 104 GE/mL), "medium" (1 × 104 GE/mL), and "low" (2.5 × 103 GE/mL). RNase Away, chosen as a positive control, was the most effective cleaning solution on all three viral loads. Wet Wipes were found to be more effective than BZK wipes in the medium viral load condition. The low viral load condition was easily reset with all three cleaning solutions. These findings will enable temporal SARS-CoV-2 monitoring in indoor environments where transmission risk of the virus is high and the need to avoid individual-level sampling for privacy or compliance reasons exists. IMPORTANCE Because SARS-CoV-2, the virus that causes COVID-19, persists on surfaces, testing swabs taken from surfaces is useful as a monitoring tool. This approach is especially valuable in school settings, where there are cost and privacy concerns that are eliminated by taking a single sample from a classroom. However, the virus persists for days to weeks on surface samples, so it is impossible to tell whether positive detection events on consecutive days are a persistent signal or new infectious cases and therefore whether the positive individuals have been successfully removed from the classroom. We compare several methods for cleaning "sentinel cards" to show that this approach can be used to identify new SARS-CoV-2 signals day to day. The results are important for determining how to monitor classrooms and other indoor environments for SARS-CoV-2 virus.
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Affiliation(s)
- Victor J. Cantú
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Rodolfo A. Salido
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Brett Austin
- San Diego County Public Health Lab, San Diego, California, USA
| | - William Jordan
- San Diego County Public Health Lab, San Diego, California, USA
| | - Menka Asudani
- San Diego County Public Health Lab, San Diego, California, USA
| | - Amanda Walster
- San Diego County Public Health Lab, San Diego, California, USA
| | - Celestine G. Magallanes
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | - Holly Valentine
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | - Araz Manjoonian
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
- San Diego State University, San Diego, California, USA
| | - Carrissa Wijaya
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
| | - Vinton Omaleki
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Nathan A. Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Maryann Betty
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Rady Children's Hospital, San Diego, California, USA
| | - Anelizze Castro-Martínez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- San Diego State University, San Diego, California, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | - Emily Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Alma L. Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Elijah S. Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Toan T. Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Elizabeth W. Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Aaron F. Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, USA
| | - Gene W. Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
| | | | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
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Mateescu B, Jones JC, Alexander RP, Alsop E, An JY, Asghari M, Boomgarden A, Bouchareychas L, Cayota A, Chang HC, Charest A, Chiu DT, Coffey RJ, Das S, De Hoff P, deMello A, D’Souza-Schorey C, Elashoff D, Eliato KR, Franklin JL, Galas DJ, Gerstein MB, Ghiran IH, Go DB, Gould S, Grogan TR, Higginbotham JN, Hladik F, Huang TJ, Huo X, Hutchins E, Jeppesen DK, Jovanovic-Talisman T, Kim BY, Kim S, Kim KM, Kim Y, Kitchen RR, Knouse V, LaPlante EL, Lebrilla CB, Lee LJ, Lennon KM, Li G, Li F, Li T, Liu T, Liu Z, Maddox AL, McCarthy K, Meechoovet B, Maniya N, Meng Y, Milosavljevic A, Min BH, Morey A, Ng M, Nolan J, De Oliveira Junior GP, Paulaitis ME, Phu TA, Raffai RL, Reátegui E, Roth ME, Routenberg DA, Rozowsky J, Rufo J, Senapati S, Shachar S, Sharma H, Sood AK, Stavrakis S, Stürchler A, Tewari M, Tosar JP, Tucker-Schwartz AK, Turchinovich A, Valkov N, Van Keuren-Jensen K, Vickers KC, Vojtech L, Vreeland WN, Wang C, Wang K, Wang Z, Welsh JA, Witwer KW, Wong DT, Xia J, Xie YH, Yang K, Zaborowski MP, Zhang C, Zhang Q, Zivkovic AM, Laurent LC. Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research. iScience 2022; 25:104653. [PMID: 35958027 PMCID: PMC9358052 DOI: 10.1016/j.isci.2022.104653] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The extracellular RNA communication consortium (ERCC) is an NIH-funded program aiming to promote the development of new technologies, resources, and knowledge about exRNAs and their carriers. After Phase 1 (2013-2018), Phase 2 of the program (ERCC2, 2019-2023) aims to fill critical gaps in knowledge and technology to enable rigorous and reproducible methods for separation and characterization of both bulk populations of exRNA carriers and single EVs. ERCC2 investigators are also developing new bioinformatic pipelines to promote data integration through the exRNA atlas database. ERCC2 has established several Working Groups (Resource Sharing, Reagent Development, Data Analysis and Coordination, Technology Development, nomenclature, and Scientific Outreach) to promote collaboration between ERCC2 members and the broader scientific community. We expect that ERCC2's current and future achievements will significantly improve our understanding of exRNA biology and the development of accurate and efficient exRNA-based diagnostic, prognostic, and theranostic biomarker assays.
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Affiliation(s)
- Bogdan Mateescu
- Brain Research Institute, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Jennifer C. Jones
- Laboratory of Pathology Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Eric Alsop
- Neurogenomics Division, TGen, Phoenix, AZ 85004, USA
| | - Ji Yeong An
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Mohammad Asghari
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Alex Boomgarden
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Laura Bouchareychas
- Department of Surgery, Division of Vascular and Endovascular Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- Northern California Institute for Research and Education, San Francisco, CA 94121, USA
| | - Alfonso Cayota
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
- University Hospital, Universidad de la República, Montevideo 11600, Uruguay
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Al Charest
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Daniel T. Chiu
- Department of Chemistry and Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Robert J. Coffey
- Department of Medicine/Gastroenterology and Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Saumya Das
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Peter De Hoff
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, La Jolla, San Diego, CA 92093, USA
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | | | - David Elashoff
- Statistics Core, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Kiarash R. Eliato
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Jeffrey L. Franklin
- Department of Medicine/Gastroenterology and Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - David J. Galas
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Mark B. Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Ionita H. Ghiran
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - David B. Go
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Stephen Gould
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Tristan R. Grogan
- Department of Medicine Statistics Core, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, USA
| | - James N. Higginbotham
- Department of Medicine/Gastroenterology and Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Florian Hladik
- Departments of Obstetrics and Gynecology, and Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tony Jun Huang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Xiaoye Huo
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Dennis K. Jeppesen
- Department of Medicine/Gastroenterology and Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Tijana Jovanovic-Talisman
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Betty Y.S. Kim
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sung Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Kyoung-Mee Kim
- Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Yong Kim
- Department of Oral Biology and Medicine, UCLA School of Dentistry, Los Angeles, CA 90095, USA
| | - Robert R. Kitchen
- Corrigan Minehan Heart Center and Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vaughan Knouse
- Laboratory of Pathology Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Emily L. LaPlante
- Bioinformatics Research Laboratory, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - L. James Lee
- Department of Chemical and Biomolecular Engineering and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Kathleen M. Lennon
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Guoping Li
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Feng Li
- Department of Oral Biology and Medicine, UCLA School of Dentistry, Los Angeles, CA 90095, USA
| | - Tieyi Li
- Department of Materials Science & Engineering, University of California Los Angeles, Los Angeles, CA 90095-1595, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Zirui Liu
- Department of Materials Science & Engineering, University of California Los Angeles, Los Angeles, CA 90095-1595, USA
| | - Adam L. Maddox
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Kyle McCarthy
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Nalin Maniya
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Yingchao Meng
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Aleksandar Milosavljevic
- Bioinformatics Research Laboratory, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Quantitative and Computational Biosciences Baylor College of Medicine, Houston, TX 77030, USA
| | - Byoung-Hoon Min
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University, School of Medicine, Seoul, South Korea
| | - Amber Morey
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, La Jolla, San Diego, CA 92093, USA
| | - Martin Ng
- Northern California Institute for Research and Education, San Francisco, CA 94121, USA
| | - John Nolan
- Scintillon Institute, San Diego, CA, USA
| | | | - Michael E. Paulaitis
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tuan Anh Phu
- Northern California Institute for Research and Education, San Francisco, CA 94121, USA
| | - Robert L. Raffai
- Department of Surgery, Division of Vascular and Endovascular Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- Northern California Institute for Research and Education, San Francisco, CA 94121, USA
- Department of Veterans Affairs, Surgical Service (112G), San Francisco VA Medical Center, San Francisco, CA 94121, USA
| | - Eduardo Reátegui
- Department of Chemical and Biomolecular Engineering and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Matthew E. Roth
- Bioinformatics Research Laboratory, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Joel Rozowsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Joseph Rufo
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Satyajyoti Senapati
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Sigal Shachar
- Meso Scale Diagnostics, LLC, Rockville, MD 20850, USA
| | - Himani Sharma
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Anil K. Sood
- Department of Gynecologic Oncology & Reproductive Medicine, University of Texas MD Aderson Cancer Center, Houston, TX 77030, USA
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Alessandra Stürchler
- Brain Research Institute, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Muneesh Tewari
- Department of Internal Medicine, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Juan P. Tosar
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
- Analytical Biochemistry Unit, School of Science, Universidad de la República, Montevideo 11400, Uruguay
| | | | - Andrey Turchinovich
- Cancer Genome Research (B063), German Cancer Research Center DKFZ, Heidelberg 69120, Germany
- Heidelberg Biolabs GmbH, Heidelberg 69120, Germany
| | - Nedyalka Valkov
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kasey C. Vickers
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lucia Vojtech
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
| | - Wyatt N. Vreeland
- Bioprocess Measurement Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Ceming Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - ZeYu Wang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Joshua A. Welsh
- Laboratory of Pathology Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Kenneth W. Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David T.W. Wong
- Department of Oral Biology and Medicine, UCLA School of Dentistry, Los Angeles, CA 90095, USA
| | - Jianping Xia
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Ya-Hong Xie
- Department of Materials Science & Engineering, University of California Los Angeles, Los Angeles, CA 90095-1595, USA
| | - Kaichun Yang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA
| | - Mikołaj P. Zaborowski
- Department of Gynecology, Obstetrics and Gynecologic Oncology, Division of Gynecologic Oncology, Poznan University of Medical Sciences, 60-535 Poznań, Poland
| | - Chenguang Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Qin Zhang
- Department of Medicine/Gastroenterology and Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, La Jolla, San Diego, CA 92093, USA
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39
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature 2022; 609:101-108. [PMID: 35798029 PMCID: PMC9433318 DOI: 10.1038/s41586-022-05049-6] [Citation(s) in RCA: 140] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/29/2022] [Indexed: 11/23/2022]
Abstract
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases1–3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission. Emerging SARS-CoV-2 variants of concern were detected early and multiple cases of virus spread not captured by clinical genomic surveillance were identified using high-resolution wastewater and clinical sequencing.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Evelyn S Cresini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA.,Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Angela L Scioscia
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA
| | | | | | - Dismas B Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA.,Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | | | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA.,Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Christopher Longhurst
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA
| | - Patty Maysent
- Office of the UC San Diego Health CEO, University of California, San Diego, USA
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Pradeep K Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. .,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. .,Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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40
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Cantú VJ, Salido RA, Huang S, Rahman G, Tsai R, Valentine H, Magallanes CG, Aigner S, Baer NA, Barber T, Belda-Ferre P, Betty M, Bryant M, Casas Maya M, Castro-Martínez A, Chacón M, Cheung W, Crescini ES, De Hoff P, Eisner E, Farmer S, Hakim A, Kohn L, Lastrella AL, Lawrence ES, Morgan SC, Ngo TT, Nouri A, Plascencia A, Ruiz CA, Sathe S, Seaver P, Shwartz T, Smoot EW, Ostrander RT, Valles T, Yeo GW, Laurent LC, Fielding-Miller R, Knight R. SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp. mSystems 2022; 7:e0141121. [PMID: 35575492 PMCID: PMC9239251 DOI: 10.1128/msystems.01411-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions and to test whether our past observations linking SARS-CoV-2 abundance to Rothia sp. in hospitals also hold in a residential setting, we performed a detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences (to assess the bacterial community at each location), and to the Cq value of the contemporaneous clinical test. Our results showed that the highest SARS-CoV-2 load in this setting is on touched surfaces, such as light switches and faucets, but a detectable signal was present in many untouched surfaces (e.g., floors) that may be more relevant in settings, such as schools where mask-wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association. IMPORTANCE Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g., touching a light switch) or indirectly (e.g., by droplets or aerosols settling). We found the highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g., in schools, where students did not touch the light switches and also wore masks such that they had no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.
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Affiliation(s)
- Victor J Cantú
- Department of Bioengineering, University of California San Diegogrid.266100.3, La Jolla, CA, USA
| | - Rodolfo A Salido
- Department of Bioengineering, University of California San Diegogrid.266100.3, La Jolla, CA, USA
| | - Shi Huang
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gibraan Rahman
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Holly Valentine
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Celestine G Magallanes
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Maryann Betty
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Rady Children's Hospital, San Diego, CA, USA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Martín Casas Maya
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Anelizze Castro-Martínez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- San Diego State University, San Diego, CA, USA
| | - Evelyn S Crescini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Peter De Hoff
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emily Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Laura Kohn
- Herbert Wertheim School of Public Health, University of California San Diegogrid.266100.3, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Sydney C Morgan
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alhakam Nouri
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Christopher A Ruiz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tara Shwartz
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - R Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Thomas Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health, University of California San Diegogrid.266100.3, La Jolla, CA, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diegogrid.266100.3, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
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Li G, Manning AC, Bagi A, Yang X, Gokulnath P, Spanos M, Howard J, Chan PP, Sweeney T, Kitchen R, Li H, Laurent BD, Aranki SF, Kontaridis MI, Laurent LC, Van Keuren‐Jensen K, Muehlschlegel J, Lowe TM, Das S. Distinct Stress-Dependent Signatures of Cellular and Extracellular tRNA-Derived Small RNAs. Adv Sci (Weinh) 2022; 9:e2200829. [PMID: 35373532 PMCID: PMC9189662 DOI: 10.1002/advs.202200829] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Indexed: 05/11/2023]
Abstract
The cellular response to stress is an important determinant of disease pathogenesis. Uncovering the molecular fingerprints of distinct stress responses may identify novel biomarkers and key signaling pathways for different diseases. Emerging evidence shows that transfer RNA-derived small RNAs (tDRs) play pivotal roles in stress responses. However, RNA modifications present on tDRs are barriers to accurately quantifying tDRs using traditional small RNA sequencing. Here, AlkB-facilitated methylation sequencing is used to generate a comprehensive landscape of cellular and extracellular tDR abundances in various cell types during different stress responses. Extracellular tDRs are found to have distinct fragmentation signatures from intracellular tDRs and these tDR signatures are better indicators of different stress responses than miRNAs. These distinct extracellular tDR fragmentation patterns and signatures are also observed in plasma from patients on cardiopulmonary bypass. It is additionally demonstrated that angiogenin and RNASE1 are themselves regulated by stressors and contribute to the stress-modulated abundance of sub-populations of cellular and extracellular tDRs. Finally, a sub-population of extracellular tDRs is identified for which AGO2 appears to be required for their expression. Together, these findings provide a detailed profile of stress-responsive tDRs and provide insight about tDR biogenesis and stability in response to cellular stressors.
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Affiliation(s)
- Guoping Li
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Aidan C. Manning
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Alex Bagi
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Xinyu Yang
- Fangshan Hospital of BeijingUniversity of Traditional Chinese MedicineBeijing102499China
| | - Priyanka Gokulnath
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Michail Spanos
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Jonathan Howard
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Patricia P. Chan
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Thadryan Sweeney
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Robert Kitchen
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Haobo Li
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Brice D. Laurent
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Sary F. Aranki
- Division of Cardiac SurgeryDepartment of SurgeryBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Maria I. Kontaridis
- Department of Biomedical Research and Translational MedicineMasonic Medical Research InstituteUticaNY13501USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMA02115USA
- Department of MedicineDivision of CardiologyBeth Israel Deaconess Medical CenterHarvard Medical SchoolBostonMA02215USA
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of CaliforniaSan DiegoLa JollaCA92093USA
| | | | - Jochen Muehlschlegel
- Department of Anesthesiology, Perioperative and Pain MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02115USA
| | - Todd M. Lowe
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Saumya Das
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
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42
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Berardi G, Frey-Law L, Sluka KA, Bayman EO, Coffey CS, Ecklund D, Vance CGT, Dailey DL, Burns J, Buvanendran A, McCarthy RJ, Jacobs J, Zhou XJ, Wixson R, Balach T, Brummett CM, Clauw D, Colquhoun D, Harte SE, Harris RE, Williams DA, Chang AC, Waljee J, Fisch KM, Jepsen K, Laurent LC, Olivier M, Langefeld CD, Howard TD, Fiehn O, Jacobs JM, Dakup P, Qian WJ, Swensen AC, Lokshin A, Lindquist M, Caffo BS, Crainiceanu C, Zeger S, Kahn A, Wager T, Taub M, Ford J, Sutherland SP, Wandner LD. Multi-Site Observational Study to Assess Biomarkers for Susceptibility or Resilience to Chronic Pain: The Acute to Chronic Pain Signatures (A2CPS) Study Protocol. Front Med (Lausanne) 2022; 9:849214. [PMID: 35547202 PMCID: PMC9082267 DOI: 10.3389/fmed.2022.849214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic pain has become a global health problem contributing to years lived with disability and reduced quality of life. Advances in the clinical management of chronic pain have been limited due to incomplete understanding of the multiple risk factors and molecular mechanisms that contribute to the development of chronic pain. The Acute to Chronic Pain Signatures (A2CPS) Program aims to characterize the predictive nature of biomarkers (brain imaging, high-throughput molecular screening techniques, or "omics," quantitative sensory testing, patient-reported outcome assessments and functional assessments) to identify individuals who will develop chronic pain following surgical intervention. The A2CPS is a multisite observational study investigating biomarkers and collective biosignatures (a combination of several individual biomarkers) that predict susceptibility or resilience to the development of chronic pain following knee arthroplasty and thoracic surgery. This manuscript provides an overview of data collection methods and procedures designed to standardize data collection across multiple clinical sites and institutions. Pain-related biomarkers are evaluated before surgery and up to 3 months after surgery for use as predictors of patient reported outcomes 6 months after surgery. The dataset from this prospective observational study will be available for researchers internal and external to the A2CPS Consortium to advance understanding of the transition from acute to chronic postsurgical pain.
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Affiliation(s)
- Giovanni Berardi
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Laura Frey-Law
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Kathleen A. Sluka
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Emine O. Bayman
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Christopher S. Coffey
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Dixie Ecklund
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Carol G. T. Vance
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Dana L. Dailey
- Department of Physical Therapy, St. Ambrose University, Davenport, IA, United States
| | - John Burns
- Department of Psychiatry, Rush University Medical Center, Chicago, IL, United States
| | - Asokumar Buvanendran
- Department of Anesthesiology, Rush University Medical Center, Chicago, IL, United States
| | - Robert J. McCarthy
- Department of Anesthesiology, Rush University Medical Center, Chicago, IL, United States
| | - Joshua Jacobs
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, United States
| | - Xiaohong Joe Zhou
- Departments of Radiology, Neurosurgery, and Bioengineering, University of Illinois College of Medicine at Chicago, Chicago, IL, United States
| | - Richard Wixson
- NorthShore Orthopaedic and Spine Institute, NorthShore University HealthSystem, Skokie, IL, United States
| | - Tessa Balach
- Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago, Chicago, IL, United States
| | - Chad M. Brummett
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
| | - Daniel Clauw
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, United States
| | - Douglas Colquhoun
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
| | - Steven E. Harte
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
| | - Richard E. Harris
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
| | - David A. Williams
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, United States
- Department of Psychology, University of Michigan, Ann Arbor, MI, United States
| | - Andrew C. Chang
- Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI, United States
| | - Jennifer Waljee
- Section of Plastic and Reconstructive Surgery, University of Michigan, Ann Arbor, MI, United States
| | - Kathleen M. Fisch
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Kristen Jepsen
- Institute of Genomic Medicine Genomics Center, University of California, San Diego, La Jolla, CA, United States
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Michael Olivier
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Timothy D. Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, United States
| | - Jon M. Jacobs
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Panshak Dakup
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wei-Jun Qian
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Adam C. Swensen
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Anna Lokshin
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Martin Lindquist
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Brian S. Caffo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Ciprian Crainiceanu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Scott Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Ari Kahn
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, United States
| | - Tor Wager
- Presidential Cluster in Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, United States
| | - Margaret Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - James Ford
- Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Stephani P. Sutherland
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Laura D. Wandner
- National Institute of Neurological Disorders and Stroke, The National Institutes of Health, Bethesda, MD, United States
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43
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv 2022:2021.12.21.21268143. [PMID: 35411350 PMCID: PMC8996633 DOI: 10.1101/2021.12.21.21268143] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M. Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M. Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Evelyn S Cresini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Angela L Scioscia
- Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | | | | | - Dismas B. Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C. Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L. Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Nicholson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian H Mchardy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - David P Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Richard S. Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K. Martin
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R. MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T. Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Christopher Longhurst
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA
| | - Patty Maysent
- Office of the UC San Diego Health CEO, University of California, San Diego
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA
| | - Pradeep K. Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C. Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
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44
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv 2022. [PMID: 35411350 DOI: 10.1101/2022.01.27.22269965] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Evelyn S Cresini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Angela L Scioscia
- Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | | | | | - Dismas B Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Nicholson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian H Mchardy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Christopher Longhurst
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA
| | - Patty Maysent
- Office of the UC San Diego Health CEO, University of California, San Diego
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA
| | - Pradeep K Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
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45
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Stadnick NA, Cain KL, Watson P, Oswald W, Ibarra M, Lagoc R, Pezzoli K, Laurent LC, Tukey R, Rabin AB. Engaging Underserved Communities in COVID-19 Health Equity Implementation Research: An Analysis of Community Engagement Resource Needs and Costs. Front Health Serv 2022; 2. [PMID: 36258685 PMCID: PMC9574473 DOI: 10.3389/frhs.2022.850427] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Background: Meaningful community engagement is instrumental to effective implementation and sustainment of equitable public health interventions. Significant resources are necessary to ensure that community engagement takes place in culturally sensitive, trusted ways that optimize positive public health outcomes. However, the types and costs of resources best suited to enable meaningful community engagement in implementation research are not well-documented. This study’s objectives are (1) to describe a pragmatic method for systematically tracking and documenting resources utilized for community engagement activities, (2) report resources across phases of implementation research, and (3) provide recommendations for planning and budgeting for community engagement in health equity implementation research. Methods: Community engagement partners completed a tracking log of their person-hours for community engagement activities across three phases of community engagement (startup, early, maintenance) in two implementation research projects to promote equity in COVID-19 testing and vaccination for underserved communities. Both projects completed a six-session Theory of Change (i.e., a facilitated group discussion about current and desired conditions that culminated with a set of priorities for strategic change making) over 4 months with respective Community Advisory Boards (CAB) that included community organizers, promotores, federally qualified health center providers and administrators, and public health researchers. The reported person-hours that facilitated community member engagement were documented and summarized within and across project phases. Results: For both projects, the startup phase required the highest number of person-hours (M = 60), followed by the maintenance (M = 53) and early phase (M = 47). Within the startup phase, a total of 5 community engagement activities occurred with identifying and inviting CAB members incurring the greatest number of person-hours (M = 19). Within the early phase, a total of 11 community engagement activities occurred with coordinating and leading live interpretation (Spanish) during CAB sessions incurring the greatest number of person-hours (M = 10). The maintenance phase included 11 community engagement activities with time dedicated to written translation of CAB materials into Spanish incurring the greatest number of person-hours (M = 10). Conclusions: Study findings indicate that the most significant investment of resources is required in the startup period. Needed resources decreased, albeit with a greater diversity of activities, in later phases of community engagement with Spanish language translation requiring most in the later stage of the study. This study contributes to the community engagement and implementation science literature by providing a pragmatic tracking and measurement approach and recommendations for planning for and assessing costs to facilitate meaningful community engagement in public health implementation research.
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Affiliation(s)
- Nicole A. Stadnick
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
- University of California San Diego Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, La Jolla, CA, United States
- Child and Adolescent Services Research Center, San Diego, CA, United States
- *Correspondence: Nicole A. Stadnick
| | - Kelli L. Cain
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, United States
| | - Paul Watson
- The Global Action Research Center, San Diego, CA, United States
| | - William Oswald
- The Global Action Research Center, San Diego, CA, United States
| | - Marina Ibarra
- The Global Action Research Center, San Diego, CA, United States
| | - Raphael Lagoc
- The Global Action Research Center, San Diego, CA, United States
| | - Keith Pezzoli
- Department of Urban Studies and Planning, University of California, San Diego, La Jolla, CA, United States
- Bioregional Center for Sustainability Science, Planning and Design, University of California, San Diego, La Jolla, CA, United States
- Superfund Research Center, University of California, San Diego, La Jolla, CA, United States
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, San Diego, CA, United States
| | - Robert Tukey
- Superfund Research Center, University of California, San Diego, La Jolla, CA, United States
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Adrienn Borsika Rabin
- University of California San Diego Altman Clinical and Translational Research Institute Dissemination and Implementation Science Center, La Jolla, CA, United States
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, United States
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Stadnick NA, Cain KL, Oswald W, Watson P, Ibarra M, Lagoc R, Ayers LO, Salgin L, Broyles SL, Laurent LC, Pezzoli K, Rabin B. Co-creating a Theory of Change to advance COVID-19 testing and vaccine uptake in underserved communities. Health Serv Res 2022; 57 Suppl 1:149-157. [PMID: 35243622 PMCID: PMC9108217 DOI: 10.1111/1475-6773.13910] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES To describe the use of a Theory of Change to meaningfully engage community members from or support underserved communities in two National Institutes of Health-funded implementation science projects aimed at promoting equitable access to COVID-19 testing and vaccination for underserved communities. STUDY SETTING Both projects focused on Latino, Black, and immigrant and refugee communities in South/Central San Diego and/or individuals accessing care at a federally qualified health center near the US/Mexico border during December 2020-April 2021. STUDY DESIGN By using a participatory action research design, Community Advisory Boards (CABs) were established for each project with 11 and 22 members. CAB members included community organizers, promotores de salud (community health workers), clinic providers and administrators, and public health researchers. The CABs were guided through a seven-session Theory of Change process, focused on identifying necessary conditions that must exist to eliminate COVID-19 disparities along with specified actions to create those conditions and a blueprint for assessing the impact of those actions. DATA COLLECTION Each session lasted 2 h hosted virtually and was augmented by interactive web-based activities. There was a live interpreter who facilitated the participation of Spanish-speaking CAB members. A Theory of Change for each project was completed in approximately 4 months. PRINCIPAL FINDINGS Nine necessary conditions were identified related to (1) accessible and available services; (2) culturally and linguistically competent programming; (3) investment in trusted community and faith leaders; (4) social safety nets to provide ancillary services. Corresponding actions to create these conditions and measures to indicate success in creating these conditions were operationalized by the CAB. CONCLUSIONS While resource-intensive, a CAB-led Theory of Change process yielded a rich opportunity to engage diverse groups that typically are not invited to inform these processes.
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Affiliation(s)
- Nicole A Stadnick
- Department of Psychiatry, University of California San Diego, La Jolla, California, USA.,Dissemination and Implementation Science Center, UC San Diego Altman Clinical and Translational Research Institute, La Jolla, California, USA.,Child and Adolescent Services Research Center, San Diego, California, USA
| | - Kelli L Cain
- The Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, California, USA
| | - William Oswald
- The Global Action Research Center, San Diego, California, USA
| | - Paul Watson
- The Global Action Research Center, San Diego, California, USA
| | - Marina Ibarra
- The Global Action Research Center, San Diego, California, USA
| | - Raphael Lagoc
- The Global Action Research Center, San Diego, California, USA
| | - Lawrence O Ayers
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
| | - Linda Salgin
- San Ysidro Health, San Diego, California, USA.,San Diego State University/University of California San Diego Joint Doctoral Program in Public Health, San Diego, California, USA
| | - Shelia L Broyles
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Community Engagement Unit, UC San Diego Altman Clinical and Translational Research Institute, La Jolla, California, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
| | - Keith Pezzoli
- Department of Urban Studies and Planning, University of California San Diego, La Jolla, California, USA.,Bioregional Center for Sustainability Science, Planning and Design, University of California San Diego, La Jolla, California, USA.,Superfund Research Center, Community Engagement and Research Translation Cores, University of California, San Diego, La Jolla, California, USA
| | - Borsika Rabin
- Dissemination and Implementation Science Center, UC San Diego Altman Clinical and Translational Research Institute, La Jolla, California, USA.,The Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, California, USA
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47
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Melber DJ, Pantham P, Adami RR, Fratto V, De Hoff P, Vuppala A, Srinivasan S, Afshar Y, Makhoul JA, Westermann M, Cassidy AG, Meads M, Liu TN, Magallanes CG, Martinez-King C, Fernando AN, Tran VH, To C, Jacobs MB, Murphy AM, Chung JH, Norton ME, Parast MM, Laurent LC. Maternal Serum miRNAs as Biomarkers for Abnormal Placentation. Am J Obstet Gynecol 2022. [DOI: 10.1016/j.ajog.2021.11.744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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48
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Burchard J, Markenson GR, Saade GR, Laurent LC, Heyborne KD, Coonrod DV, Schoen CN, Baxter JK, Haas DM, Longo SA, Sullivan SA, Wheeler SM, Pereira LM, Boggess KA, Hawk AF, Crockett AH, Treacy R, Fox AC, Polpitiya AD, Fleischer TC, Garite TJ, Jay Boniface J, Zupancic JAF, Critchfield GC, Kearney PE. Clinical and economic evaluation of a proteomic biomarker preterm birth risk predictor: cost-effectiveness modeling of prenatal interventions applied to predicted higher-risk pregnancies within a large and diverse cohort. J Med Econ 2022; 25:1255-1266. [PMID: 36377363 DOI: 10.1080/13696998.2022.2147771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVES Preterm birth occurs in more than 10% of U.S. births and is the leading cause of U.S. neonatal deaths, with estimated annual costs exceeding $25 billion USD. Using real-world data, we modeled the potential clinical and economic utility of a prematurity-reduction program comprising screening in a racially and ethnically diverse population with a validated proteomic biomarker risk predictor, followed by case management with or without pharmacological treatment. METHODS The ACCORDANT microsimulation model used individual patient data from a prespecified, randomly selected sub-cohort (N = 847) of a multicenter, observational study of U.S. subjects receiving standard obstetric care with masked risk predictor assessment (TREETOP; NCT02787213). All subjects were included in three arms across 500 simulated trials: standard of care (SoC, control); risk predictor/case management comprising increased outreach, education and specialist care (RP-CM, active); and multimodal management (risk predictor/case management with pharmacological treatment) (RP-MM, active). In the active arms, only subjects stratified as higher risk by the predictor were modeled as receiving the intervention, whereas lower-risk subjects received standard care. Higher-risk subjects' gestational ages at birth were shifted based on published efficacies, and dependent outcomes, calibrated using national datasets, were changed accordingly. Subjects otherwise retained their original TREETOP outcomes. Arms were compared using survival analysis for neonatal and maternal hospital length of stay, bootstrap intervals for neonatal cost, and Fisher's exact test for neonatal morbidity/mortality (significance, p < .05). RESULTS The model predicted improvements for all outcomes. RP-CM decreased neonatal and maternal hospital stay by 19% (p = .029) and 8.5% (p = .001), respectively; neonatal costs' point estimate by 16% (p = .098); and moderate-to-severe neonatal morbidity/mortality by 29% (p = .025). RP-MM strengthened observed reductions and significance. Point estimates of benefit did not differ by race/ethnicity. CONCLUSIONS Modeled evaluation of a biomarker-based test-and-treat strategy in a diverse population predicts clinically and economically meaningful improvements in neonatal and maternal outcomes.
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Affiliation(s)
| | - Glenn R Markenson
- Department of Obstetrics and Gynecology, Boston University School of Medicine, Boston, MA, USA
| | - George R Saade
- Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, CA, USA
| | - Kent D Heyborne
- Department of Obstetrics and Gynecology, Denver Health and Hospital Authority, Denver, CO, and Department of Obstetrics and Gynecology, University of Colorado Denver, Aurora, CO, USA
| | - Dean V Coonrod
- Department of Obstetrics and Gynecology, Valleywise Health, and Department of Obstetrics and Gynecology, University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Corina N Schoen
- Department of Obstetrics and Gynecology, University of Massachusetts-Baystate, Springfield, MA, USA
| | - Jason K Baxter
- Department of Obstetrics and Gynecology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - David M Haas
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sherri A Longo
- Department of Obstetrics and Gynecology, Ochsner Health, New Orleans, LA, USA
| | - Scott A Sullivan
- Department of Obstetrics and Gynecology, Medical University of South Carolina, Charleston, SC, USA
| | - Sarahn M Wheeler
- Department of Obstetrics and Gynecology, Duke University School of Medicine, Durham, NC, USA
| | - Leonardo M Pereira
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, USA
| | - Kim A Boggess
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Angela F Hawk
- Regional Obstetrical Consultants, Chattanooga, TN, USA
| | - Amy H Crockett
- Department of Obstetrics and Gynecology, University of South Carolina School of Medicine Greenville and Prisma Health-Upstate, Greenville, SC, USA
| | - Ryan Treacy
- Sera Prognostics, Inc, Salt Lake City, UT, USA
| | | | | | | | | | | | - John A F Zupancic
- Department of Pediatrics, Harvard Medical School, and Department of Neonatology, Beth Israel Deaconess Medical Center, Boston, MA, USA
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49
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Cantú VJ, Salido RA, Huang S, Rahman G, Tsai R, Valentine H, Magallanes CG, Aigner S, Baer NA, Barber T, Belda-Ferre P, Betty M, Bryant M, Maya MC, Castro-Martínez A, Chacón M, Cheung W, Crescini ES, De Hoff P, Eisner E, Farmer S, Hakim A, Kohn L, Lastrella AL, Lawrence ES, Morgan SC, Ngo TT, Nouri A, Ostrander RT, Plascencia A, Ruiz CA, Sathe S, Seaver P, Shwartz T, Smoot EW, Valles T, Yeo GW, Laurent LC, Fielding-Miller R, Knight R. SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp. medRxiv 2021. [PMID: 34909793 DOI: 10.1101/2021.03.16.21253743v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
UNLABELLED Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work has demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces such as Halloween candy, and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions, and to test whether our past observations linking SARS-CoV-2 abundance to Rothia spp. in hospitals also hold in a residential setting, we performed detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences to assess the bacterial community at each location and to the Cq value of the contemporaneous clinical test. Our results show that the highest SARS-CoV-2 load in this setting is on touched surfaces such as light switches and faucets, but detectable signal is present in many non-touched surfaces that may be more relevant in settings such as schools where mask wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association. IMPORTANCE Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g. touching a light switch) or indirectly (e.g. by droplets or aerosols settling). We found highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g. in schools, where students do not touch the light switches and also wear masks so they have no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.
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Affiliation(s)
- Victor J Cantú
- These authors contributed equally.,Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rodolfo A Salido
- These authors contributed equally.,Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shi Huang
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Gibraan Rahman
- Department of Pediatrics, University of California San Diego, La Jolla, CA.,Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA
| | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Holly Valentine
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA.,Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Celestine G Magallanes
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA.,Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Stefan Aigner
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA.,Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA.,Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Maryann Betty
- Department of Pediatrics, University of California San Diego, La Jolla, CA.,Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA.,Rady Children's Hospital, San Diego, CA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Martin Casas Maya
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Anelizze Castro-Martínez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Willi Cheung
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA.,Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA.,San Diego State University, San Diego, CA
| | - Evelyn S Crescini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Peter De Hoff
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA.,Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
| | - Emily Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Laura Kohn
- Herbert Wertheim School of Public Health, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Sydney C Morgan
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Alhakam Nouri
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - R Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Ashley Plascencia
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA.,Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA.,Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Christopher A Ruiz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Shashank Sathe
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA.,Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA.,Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Tara Shwartz
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Thomas Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Gene W Yeo
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA.,Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Louise C Laurent
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
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50
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Cantú VJ, Salido RA, Huang S, Rahman G, Tsai R, Valentine H, Magallanes CG, Aigner S, Baer NA, Barber T, Belda-Ferre P, Betty M, Bryant M, Maya MC, Castro-Martínez A, Chacón M, Cheung W, Crescini ES, De Hoff P, Eisner E, Farmer S, Hakim A, Kohn L, Lastrella AL, Lawrence ES, Morgan SC, Ngo TT, Nouri A, Ostrander RT, Plascencia A, Ruiz CA, Sathe S, Seaver P, Shwartz T, Smoot EW, Valles T, Yeo GW, Laurent LC, Fielding-Miller R, Knight R. SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp. medRxiv 2021:2021.12.06.21267101. [PMID: 34909793 PMCID: PMC8669860 DOI: 10.1101/2021.12.06.21267101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work has demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces such as Halloween candy, and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions, and to test whether our past observations linking SARS-CoV-2 abundance to Rothia spp. in hospitals also hold in a residential setting, we performed detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences to assess the bacterial community at each location and to the Cq value of the contemporaneous clinical test. Our results show that the highest SARS-CoV-2 load in this setting is on touched surfaces such as light switches and faucets, but detectable signal is present in many non-touched surfaces that may be more relevant in settings such as schools where mask wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association. IMPORTANCE Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g. touching a light switch) or indirectly (e.g. by droplets or aerosols settling). We found highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g. in schools, where students do not touch the light switches and also wear masks so they have no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.
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Affiliation(s)
- Victor J Cantú
- These authors contributed equally
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rodolfo A Salido
- These authors contributed equally
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shi Huang
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Gibraan Rahman
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA
| | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Holly Valentine
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Celestine G Magallanes
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Stefan Aigner
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Maryann Betty
- Department of Pediatrics, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Rady Children's Hospital, San Diego, CA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Martin Casas Maya
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Anelizze Castro-Martínez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Willi Cheung
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- San Diego State University, San Diego, CA
| | - Evelyn S Crescini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Peter De Hoff
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
| | - Emily Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Laura Kohn
- Herbert Wertheim School of Public Health, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Sydney C Morgan
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Alhakam Nouri
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - R Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Ashley Plascencia
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Christopher A Ruiz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Shashank Sathe
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
- Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Tara Shwartz
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Thomas Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA
| | - Gene W Yeo
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Dept of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Louise C Laurent
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
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