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1
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Beyrer C, Kamarulzaman A, Isbell M, Amon J, Baral S, Bassett MT, Cepeda J, Deacon H, Dean L, Fan L, Giacaman R, Gomes C, Gruskin S, Goyal R, Mon SHH, Jabbour S, Kazatchkine M, Kasoka K, Lyons C, Maleche A, Martin N, McKee M, Paiva V, Platt L, Puras D, Schooley R, Smoger G, Stackpool-Moore L, Vickerman P, Walker JG, Rubenstein L. Under threat: the International AIDS Society-Lancet Commission on Health and Human Rights. Lancet 2024; 403:1374-1418. [PMID: 38522449 DOI: 10.1016/s0140-6736(24)00302-7] [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] [Received: 03/25/2022] [Revised: 09/26/2023] [Accepted: 02/12/2024] [Indexed: 03/26/2024]
Affiliation(s)
- Chris Beyrer
- Duke Global Health Institute, Duke University, Durham, NC, USA; Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA.
| | | | | | - Joseph Amon
- Office of Global Health, Dornsife School of Public Health, Drexel University, Philadelphia, PA, USA
| | - Stefan Baral
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Mary T Bassett
- François-Xavier Bagnoud Center for Health and Human Rights, Harvard T H Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Javier Cepeda
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Harriet Deacon
- Treatied Spaces Research Group and Centre of Excellence in Data Science, Artificial Intelligence and Modelling, University of Hull, Hull, UK
| | - Lorraine Dean
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | | | - Rita Giacaman
- Institute of Community and Public Health, Birzeit University, Birzeit, West Bank, Palestine
| | - Carolyn Gomes
- UNAIDS HIV & Human Rights Reference Group, Kingston, Jamaica
| | - Sofia Gruskin
- Institute on Inequalities in Global Health, University of Southern California, Los Angeles, CA, USA
| | - Ravi Goyal
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, San Diego, CA, USA
| | | | | | | | | | - Carrie Lyons
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Allan Maleche
- Kenya Legal & Ethical Issues Network on HIV and AIDS, Nairobi, Kenya
| | - Natasha Martin
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, San Diego, CA, USA
| | - Martin McKee
- London School of Hygiene & Tropical Medicine, London, UK
| | - Vera Paiva
- Institute of Psychology, University of Sao Paulo, Sao Paulo, Brazil
| | - Lucy Platt
- London School of Hygiene & Tropical Medicine, London, UK
| | - Dainius Puras
- Clinic of Psychiatry, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Robert Schooley
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, San Diego, CA, USA
| | | | | | | | | | - Leonard Rubenstein
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA
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2
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Lin T, Karthikeyan S, Satterlund A, Schooley R, Knight R, De Gruttola V, Martin N, Zou J. Optimizing campus-wide COVID-19 test notifications with interpretable wastewater time-series features using machine learning models. Sci Rep 2023; 13:20670. [PMID: 38001346 PMCID: PMC10673837 DOI: 10.1038/s41598-023-47859-2] [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: 04/02/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023] Open
Abstract
During the COVID-19 pandemic, wastewater surveillance of the SARS CoV-2 virus has been demonstrated to be effective for population surveillance at the county level down to the building level. At the University of California, San Diego, daily high-resolution wastewater surveillance conducted at the building level is being used to identify potential undiagnosed infections and trigger notification of residents and responsive testing, but the optimal determinants for notifications are unknown. To fill this gap, we propose a pipeline for data processing and identifying features of a series of wastewater test results that can predict the presence of COVID-19 in residences associated with the test sites. Using time series of wastewater results and individual testing results during periods of routine asymptomatic testing among UCSD students from 11/2020 to 11/2021, we develop hierarchical classification/decision tree models to select the most informative wastewater features (patterns of results) which predict individual infections. We find that the best predictor of positive individual level tests in residence buildings is whether or not the wastewater samples were positive in at least 3 of the past 7 days. We also demonstrate that the tree models outperform a wide range of other statistical and machine models in predicting the individual COVID-19 infections while preserving interpretability. Results of this study have been used to refine campus-wide guidelines and email notification systems to alert residents of potential infections.
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Affiliation(s)
- Tuo Lin
- Department of Biostatistics, University of Florida, Gainesville, FL, 32608, USA
| | - Smruthi Karthikeyan
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Alysson Satterlund
- Student Affairs, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Robert Schooley
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Computer Science and Engineering, University of California, San Diego, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, CA, USA
| | - Victor De Gruttola
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Natasha Martin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jingjing Zou
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, 92093, USA.
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3
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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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4
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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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5
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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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Greenhalgh T, Jimenez JL, Prather KA, Tufeki Z, Fisman D, Schooley R. Transmission of SARS-CoV-2: still up in the air - Authors' reply. Lancet 2022; 399:519-520. [PMID: 35123690 PMCID: PMC8813063 DOI: 10.1016/s0140-6736(21)02795-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 12/07/2021] [Indexed: 01/22/2023]
Affiliation(s)
- Trisha Greenhalgh
- Department of Primary Care Health Sciences, University of Oxford, Oxford OX2 6GG, UK.
| | - Jose L Jimenez
- Department of Chemistry and Cooperative Institute for Research in the Environmental Sciences, University of Colorado, Boulder, CO, USA
| | - Kimberly A Prather
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Zeynep Tufeki
- School of Information and Library Science, University of North Carolina, Chapel Hill, NC, USA
| | - David Fisman
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Robert Schooley
- Department of Medicine, Division of Infectious Diseases and Global Public Health, School of Medicine, University of California, San Diego, La Jolla, CA, USA
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7
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Shaffer D, Kumwenda J, Chen H, Akelo V, Angira F, Kosgei J, Tonui R, Ssali F, McKhann A, Hogg E, Stewart VA, Murphy SC, Coombs R, Schooley R. Brief Report: No Differences Between Lopinavir/Ritonavir and Nonnucleoside Reverse Transcriptase Inhibitor-Based Antiretroviral Therapy on Clearance of Plasmodium falciparum Subclinical Parasitemia in Adults Living With HIV Starting Treatment (A5297). J Acquir Immune Defic Syndr 2022; 89:178-182. [PMID: 34693933 PMCID: PMC9425486 DOI: 10.1097/qai.0000000000002839] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 09/20/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND HIV protease inhibitors anti-Plasmodium falciparum activity in adults remains uncertain. METHODS Adults with HIV CD4+ counts >200 cells/mm3 starting antiretroviral therapy (ART) with P. falciparum subclinical parasitemia (Pf SCP) were randomized 1:1 to (step 1) protease inhibitor lopinavir/ritonavir (LPV/r)-based (arm A) or nonnucleoside reverse transcriptase inhibitor (nNRTI)-based ART (arm B) for 15 days. In step 2, participants received nNRTI-based ART and trimethoprim/sulfamethoxazole prophylaxis for 15 days. P. falciparum SCP clearance was measured by polymerase chain reaction. The Fisher exact test [95% exact confidence interval (CI)] was used to compare proportions of P. falciparum SCP clearance (<10 parasites/μL on 3 occasions within 24 hours) between LPV/r and nNRTI arms at day 15. The Kaplan-Meier method and log-rank test were used to compare time-to-clearance. RESULTS Fifty-two adults from Kenya, Malawi, and Uganda with a median age = 31 (Q1, Q3: 24-39) years, 33% women, with baseline median CD4+ counts of 324 (259-404) cells/mm3, median HIV-1 RNA viremia of 5.18 log10 copies/mL (4.60-5.71), and median estimated P. falciparum density of 454 parasites/μL (83-2219) enrolled in the study. Forty-nine (94%) participants completed the study. At day 15, there was no statistically significant difference in the proportions of P. falciparum SCP clearance between the LPV/r (23.1% clearance; 6 of the 26) and nNRTI (26.9% clearance; 7 of the 26) arms [between-arm difference 3.9% (95% CI, -21.1% to 28.4%; P = 1.00)]. No significant difference in time-to-clearance was observed between the arms (P = 0.80). CONCLUSIONS In a small randomized study of adults starting ART with P. falciparum SCP, no statistically significant differences were seen between LPV/r- and nNRTI-based ART in P. falciparum SCP clearance after 15 days of treatment.
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Affiliation(s)
- Douglas Shaffer
- U.S. Centers for Disease Control and Prevention, Kigali, Rwanda (at time of research)
| | | | - Huichao Chen
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Victor Akelo
- Kenya Medical Research Institute, Center for Global Health (KEMRI/CGHR)/Emory-CDC CTU, Kisumu, Kenya
| | - Francis Angira
- Kenya Medical Research Institute, Center for Global Health (KEMRI/CGHR)/Emory-CDC CTU, Kisumu, Kenya
| | - Josphat Kosgei
- Kenya Medical Research Institute/United States Army Medical Research Directorate-Africa/Kenya, Kericho, Kenya
| | - Ronald Tonui
- Moi University School of Medicine, Eldoret, Kenya
| | | | - Ashley McKhann
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Evelyn Hogg
- Social & Scientific Systems, Inc., A DLH Holdings Company, Silver Spring, MD, USA
| | - V. Ann Stewart
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Sean C. Murphy
- Department of Laboratory Medicine and Pathology, University of Washington; Department of Microbiology, University of Washington; Center for Emerging and Re-emerging Infectious Diseases, University of Washington; Seattle, WA, USA
| | - Robert Coombs
- Department of Laboratory Medicine and Pathology; Department of Medicine, University of Washington, Seattle, WA, USA
| | - Robert Schooley
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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8
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Greenhalgh T, Jimenez JL, Prather KA, Tufekci Z, Fisman D, Schooley R. Ten scientific reasons in support of airborne transmission of SARS-CoV-2. Lancet 2021; 397:1603-1605. [PMID: 33865497 PMCID: PMC8049599 DOI: 10.1016/s0140-6736(21)00869-2] [Citation(s) in RCA: 438] [Impact Index Per Article: 146.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 12/23/2022]
Affiliation(s)
- Trisha Greenhalgh
- Department of Primary Care Health Sciences, University of Oxford, Oxford OX2 6GG, UK.
| | - Jose L Jimenez
- Department of Chemistry and Cooperative Institute for Research in the Environmental Sciences, University of Colorado, Boulder, CO, USA
| | - Kimberly A Prather
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Zeynep Tufekci
- School of Information and Library Science, University of North Carolina, Chapel Hill, NC, USA
| | - David Fisman
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Robert Schooley
- Department of Medicine, Division of Infectious Diseases and Global Public Health, School of Medicine, University of California San Diego, La Jolla, CA, USA
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9
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Aslam S, Pretorius V, Adler E, Lehman S, Morales S, Gaidamaka A, Furr C, Rosas F, Bishop-Lilly K, Biswas B, Sisson B, Fackler J, Trigg M, Schooley R. Novel Bacteriophage Therapy for Treatment of Ventricular Assist Device Infections. J Heart Lung Transplant 2019. [DOI: 10.1016/j.healun.2019.01.542] [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: 11/28/2022] Open
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10
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Smith D, Huynh C, Moore AJ, Frick A, Anderson C, Porrachia M, Scott B, Stous S, Schooley R, Little S, Santos AT. Herd Immunity Likely Protected the Men Who Have Sex With Men in the Recent Hepatitis A Outbreak in San Diego, California. Clin Infect Dis 2019; 68:1228-1230. [PMID: 30052941 PMCID: PMC7182127 DOI: 10.1093/cid/ciy592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 04/12/2018] [Accepted: 07/23/2018] [Indexed: 12/28/2022] Open
Abstract
A high seroprevalence of hepatitis A virus (81%) among human immunodeficiency virus-negative high-risk men who have sex with men is likely why this community was largely spared from a recent hepatitis A virus outbreak in San Diego, California.
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Affiliation(s)
| | | | | | | | | | | | | | - Sarah Stous
- San Diego County Health and Human Services Agency, California
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11
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Zavale BL, Spencer EA, Guilundo C, Schooley R, Patel S, Noormahomed EV, Mocumbi AO. Closing the Gaps on Medical Education in Low-Income Countries Through Information & Communication Technologies: The Mozambique Experience. Biomed J Sci Tech Res 2019; 16:12159-12165. [PMID: 37448758 PMCID: PMC10343938 DOI: 10.26717/bjstr.2019.16.002875] [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] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Background Medical training in developing countries has continuously faced challenges to produce the needed number of cadres and maintain the needed quality standards. Mozambique, a low-income country in Southern Africa, has a major disparity in distribution of medical doctors in the country and only a small proportion are trained as specialists and/or retained as faculty. In this context, we thought that Information and Communication Technologies (ICT) are an attractive tool to support expansion of medical training and residency programs and designed a strategy for its use to promote changes in the learning environment of a university teaching hospital in this country. Approach Beginning in 2010-under the Medical Education Partnership Initiative between Universidad Eduardo Mondlane, Mozambique, and University of California San Diego, United States of America - we conducted extensive interviews to 21 UEM faculty and medical trainees to assess barriers to education and medical care at the major referral hospital in Mozambique. Then, changes were made to address the issues raised mainly through building an ICT infrastructure to improve connectivity, improving access to medical information, distributing communication and mobile medical devices, as well as fostering exchange between students, residents and faculty members. These changes were tracked years after to evaluate adoption. Main Findings & Discussion Internet access with large bandwidth and devices such as tablets and computers were distributed to increase access to medical information. The students: resident ratio improved from 13:1 to 5:1 at the end of the project. Additional 25 new faculty members were involved in clinical training, mainly through incentives such as faculty development courses and research training. Teleconferences and other exchanges using ICT have evolved from being used as a platform for weekly clinical rounds and case discussions, to become a day-to-day tool for implementation of quality improvement processes and research projects. New exchange programs between local and foreign institutions were fostered to create a growing network with over 20 institutions at the end of the program. Importantly, these changes persisted beyond the project, and constituted a driver for transformative education and distance learning. Conclusion Context-tailored use of ICT and mobile medical devices transformed medical education by improving the learning environment, addressing scarcity and low quality of trained doctors in a low-income setting of Africa. This strategy has the potential to reduce health disparities and contribute to achieving universal health coverage. Efforts to guaranty sustainability and health professional's retention are warranted.
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Affiliation(s)
| | | | - Carvalho Guilundo
- Mozambique Institute for Health and Research (MIHER/MEPI), Mozambique
| | | | - Sam Patel
- Hospital Maputo Central, Mozambique
- Faculty of Medicine, Universidade Eduardo Mondlane, Mozambique
| | - Emília Virgínia Noormahomed
- University California San Diego, United States
- Faculty of Medicine, Universidade Eduardo Mondlane, Mozambique
| | - Ana Olga Mocumbi
- Faculty of Medicine, Universidade Eduardo Mondlane, Mozambique
- Instituto Nacional de Saúde, Mozambique
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12
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Dornelas M, Antão LH, Moyes F, Bates AE, Magurran AE, Adam D, Akhmetzhanova AA, Appeltans W, Arcos JM, Arnold H, Ayyappan N, Badihi G, Baird AH, Barbosa M, Barreto TE, Bässler C, Bellgrove A, Belmaker J, Benedetti‐Cecchi L, Bett BJ, Bjorkman AD, Błażewicz M, Blowes SA, Bloch CP, Bonebrake TC, Boyd S, Bradford M, Brooks AJ, Brown JH, Bruelheide H, Budy P, Carvalho F, Castañeda‐Moya E, Chen CA, Chamblee JF, Chase TJ, Siegwart Collier L, Collinge SK, Condit R, Cooper EJ, Cornelissen JHC, Cotano U, Kyle Crow S, Damasceno G, Davies CH, Davis RA, Day FP, Degraer S, Doherty TS, Dunn TE, Durigan G, Duffy JE, Edelist D, Edgar GJ, Elahi R, Elmendorf SC, Enemar A, Ernest SKM, Escribano R, Estiarte M, Evans BS, Fan T, Turini Farah F, Loureiro Fernandes L, Farneda FZ, Fidelis A, Fitt R, Fosaa AM, Daher Correa Franco GA, Frank GE, Fraser WR, García H, Cazzolla Gatti R, Givan O, Gorgone‐Barbosa E, Gould WA, Gries C, Grossman GD, Gutierréz JR, Hale S, Harmon ME, Harte J, Haskins G, Henshaw DL, Hermanutz L, Hidalgo P, Higuchi P, Hoey A, Van Hoey G, Hofgaard A, Holeck K, Hollister RD, Holmes R, Hoogenboom M, Hsieh C, Hubbell SP, Huettmann F, Huffard CL, Hurlbert AH, Macedo Ivanauskas N, Janík D, Jandt U, Jażdżewska A, Johannessen T, Johnstone J, Jones J, Jones FAM, Kang J, Kartawijaya T, Keeley EC, Kelt DA, Kinnear R, Klanderud K, Knutsen H, Koenig CC, Kortz AR, Král K, Kuhnz LA, Kuo C, Kushner DJ, Laguionie‐Marchais C, Lancaster LT, Min Lee C, Lefcheck JS, Lévesque E, Lightfoot D, Lloret F, Lloyd JD, López‐Baucells A, Louzao M, Madin JS, Magnússon B, Malamud S, Matthews I, McFarland KP, McGill B, McKnight D, McLarney WO, Meador J, Meserve PL, Metcalfe DJ, Meyer CFJ, Michelsen A, Milchakova N, Moens T, Moland E, Moore J, Mathias Moreira C, Müller J, Murphy G, Myers‐Smith IH, Myster RW, Naumov A, Neat F, Nelson JA, Paul Nelson M, Newton SF, Norden N, Oliver JC, Olsen EM, Onipchenko VG, Pabis K, Pabst RJ, Paquette A, Pardede S, Paterson DM, Pélissier R, Peñuelas J, Pérez‐Matus A, Pizarro O, Pomati F, Post E, Prins HHT, Priscu JC, Provoost P, Prudic KL, Pulliainen E, Ramesh BR, Mendivil Ramos O, Rassweiler A, Rebelo JE, Reed DC, Reich PB, Remillard SM, Richardson AJ, Richardson JP, van Rijn I, Rocha R, Rivera‐Monroy VH, Rixen C, Robinson KP, Ribeiro Rodrigues R, de Cerqueira Rossa‐Feres D, Rudstam L, Ruhl H, Ruz CS, Sampaio EM, Rybicki N, Rypel A, Sal S, Salgado B, Santos FAM, Savassi‐Coutinho AP, Scanga S, Schmidt J, Schooley R, Setiawan F, Shao K, Shaver GR, Sherman S, Sherry TW, Siciński J, Sievers C, da Silva AC, Rodrigues da Silva F, Silveira FL, Slingsby J, Smart T, Snell SJ, Soudzilovskaia NA, Souza GBG, Maluf Souza F, Castro Souza V, Stallings CD, Stanforth R, Stanley EH, Mauro Sterza J, Stevens M, Stuart‐Smith R, Rondon Suarez Y, Supp S, Yoshio Tamashiro J, Tarigan S, Thiede GP, Thorn S, Tolvanen A, Teresa Zugliani Toniato M, Totland Ø, Twilley RR, Vaitkus G, Valdivia N, Vallejo MI, Valone TJ, Van Colen C, Vanaverbeke J, Venturoli F, Verheye HM, Vianna M, Vieira RP, Vrška T, Quang Vu C, Van Vu L, Waide RB, Waldock C, Watts D, Webb S, Wesołowski T, White EP, Widdicombe CE, Wilgers D, Williams R, Williams SB, Williamson M, Willig MR, Willis TJ, Wipf S, Woods KD, Woehler EJ, Zawada K, Zettler ML, Hickler T. BioTIME: A database of biodiversity time series for the Anthropocene. Glob Ecol Biogeogr 2018; 27:760-786. [PMID: 30147447 PMCID: PMC6099392 DOI: 10.1111/geb.12729] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 11/25/2017] [Accepted: 11/28/2017] [Indexed: 05/08/2023]
Abstract
MOTIVATION The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. MAIN TYPES OF VARIABLES INCLUDED The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. SPATIAL LOCATION AND GRAIN BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2). TIME PERIOD AND GRAIN BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. MAJOR TAXA AND LEVEL OF MEASUREMENT BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates. SOFTWARE FORMAT .csv and .SQL.
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Affiliation(s)
- Maria Dornelas
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Laura H. Antão
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
- Department of Biology and CESAMUniversidade de Aveiro, Campus Universitário de SantiagoAveiroPortugal
| | - Faye Moyes
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Amanda E. Bates
- National Oceanography Centre, University of Southampton Waterfront CampusSouthamptonUnited Kingdom
- Department of Ocean Sciences, Memorial University of NewfoundlandSt John'sNewfoundland and LabradorCanada
| | - Anne E. Magurran
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Dušan Adam
- Department of Forest Ecology, Silva Tarouca Research InstituteBrnoCzech Republic
| | | | - Ward Appeltans
- UNESCO, Intergovernmental Oceanographic Commission, IOC Project Office for IODEOostendeBelgium
| | | | - Haley Arnold
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | | | - Gal Badihi
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Andrew H. Baird
- ARC Centre of Excellence for Coral Reef Studies, James Cook UniversityTownsvilleQueenslandAustralia
| | - Miguel Barbosa
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
- Department of Biology and CESAMUniversidade de Aveiro, Campus Universitário de SantiagoAveiroPortugal
| | - Tiago Egydio Barreto
- Laboratório de Ecologia e Restauração Florestal, Fundação Espaço Eco, Piracicaba, São PauloBrazil
| | | | - Alecia Bellgrove
- School of Life and Environmental SciencesCentre for Integrative Ecology, Deakin UniversityWarrnamboolVictoriaAustralia
| | - Jonathan Belmaker
- School of Zoology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | | | - Brian J. Bett
- National Oceanography Centre, University of Southampton Waterfront CampusSouthamptonUnited Kingdom
| | - Anne D. Bjorkman
- Section for Ecoinformatics and Biodiversity, Department of BioscienceAarhus UniversityAarhusDenmark
| | - Magdalena Błażewicz
- Laboratory of Polar Biology and Oceanobiology, Faculty of Biology and Environmental ProtectionUniversity of ŁódźŁódźPoland
| | - Shane A. Blowes
- School of Zoology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Christopher P. Bloch
- Department of Biological SciencesBridgewater State UniversityBridgewaterMassachusetts
| | | | - Susan Boyd
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Matt Bradford
- CSIRO Land & WaterEcosciences Precinct, Dutton ParkQueenslandAustralia
| | - Andrew J. Brooks
- Marine Science Institute, University of CaliforniaSanta BarbaraCalifornia
| | - James H. Brown
- Department of BiologyUniversity of New MexicoAlbuquerqueNew Mexico
| | - Helge Bruelheide
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of Biology/Geobotany and Botanical Garden, Martin‐Luther‐University Halle‐WittenbergHalleGermany
| | - Phaedra Budy
- Department of Watershed Sciences and the Ecology Center, US Geological Survey, UCFWRU and Utah State UniversityLoganUtah
| | - Fernando Carvalho
- Universidade do Extremo Sul Catarinense (PPG‐CA)CriciúmaSanta CatarinaBrazil
| | - Edward Castañeda‐Moya
- Southeast Environmental Research Center (OE 148), Florida International UniversityMiamiFlorida
| | - Chaolun Allen Chen
- Coral Reef Ecology and Evolution LabBiodiversity Research Centre, Academia SinicaTaipeiTaiwan
| | | | - Tory J. Chase
- ARC Centre of Excellence for Coral Reef Studies, James Cook UniversityTownsvilleQueenslandAustralia
- Marine Biology and Aquaculture, College of Science and EngineeringJames Cook UniversityDouglasQueenslandAustralia
| | | | | | - Richard Condit
- Center for Tropical Forest ScienceWashingtonDistrict of Columbia
| | - Elisabeth J. Cooper
- Biosciences Fisheries and EconomicsUiT‐ The Arctic University of NorwayTromsøNorway
| | - J. Hans C. Cornelissen
- Systems Ecology, Department of Ecological Science, Vrije UniversiteitAmsterdamThe Netherlands
| | | | - Shannan Kyle Crow
- The National Institute of Water and Atmospheric ResearchAucklandNew Zealand
| | - Gabriella Damasceno
- Lab of Vegetation Ecology, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio ClaroBrazil
| | | | - Robert A. Davis
- School of ScienceEdith Cowan UniversityJoondalupWestern AustraliaAustralia
| | - Frank P. Day
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginia
| | - Steven Degraer
- Royal Belgian Institute of Natural Sciences, Operational Directorate Natural Environment, Marine Ecology and ManagementBrusselsBelgium
- Marine Biology Research Group, Ghent UniversityGentBelgium
| | - Tim S. Doherty
- School of ScienceEdith Cowan UniversityJoondalupWestern AustraliaAustralia
- School of Life and Environmental SciencesCentre for Integrative Ecology (Burwood Campus), Deakin UniversityGeelongVictoriaAustralia
| | | | - Giselda Durigan
- Divisão de Florestas e Estações Experimentais, Floresta Estadual de Assis, Laboratório de Ecologia e Hidrologia Florestal, Instituto FlorestalSão PauloBrazil
| | - J. Emmett Duffy
- Tennenbaum Marine Observatories Network, Smithsonian InstitutionWashington, District of Columbia
| | - Dor Edelist
- National Institute of Oceanography, Tel‐ShikmonaHaifaIsrael
| | - Graham J. Edgar
- Institute for Marine and Antarctic Studies, University of TasmaniaHobartTasmaniaAustralia
| | - Robin Elahi
- Hopkins Marine Station, Stanford University, StanfordCalifornia
| | | | - Anders Enemar
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - S. K. Morgan Ernest
- Department of Wildlife Ecology and ConservationUniversity of FloridaGainesvilleFL
| | - Rubén Escribano
- Instituto Milenio de Oceanografía, Universidad de ConcepciónConcepciónChile
| | - Marc Estiarte
- CSIC, Global Ecology Unit CREAF‐CSIC‐UABBellaterraCataloniaSpain
- CREAF, Universitat Autònoma de BarcelonaCerdanyola del VallèsCataloniaSpain
| | - Brian S. Evans
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological ParkWashingtonDistrict of Columbia
| | - Tung‐Yung Fan
- National Museum of Marine Biology and AquariumPingtung CountyTaiwan
| | - Fabiano Turini Farah
- Laboratório de Ecologia e Restauração Florestal, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São PauloSão PauloBrazil
| | - Luiz Loureiro Fernandes
- Departamento de Oceanografia e Ecologia, Universidade Federal do Espírito Santo, Vitória, Espírito SantoBrazil
| | - Fábio Z. Farneda
- Centre for Ecology, Evolution and Environmental Changes – cE3c, Faculty of SciencesUniversity of LisbonLisbonPortugal
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research InstituteManausBrazil
- Department of Ecology/PPGEFederal University of Rio de JaneiroRio de JaneiroBrazil
| | - Alessandra Fidelis
- Lab of Vegetation Ecology, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio ClaroBrazil
| | - Robert Fitt
- School of Biological SciencesUniversity of AberdeenAberdeenUnited Kingdom
| | - Anna Maria Fosaa
- Botanical Department, Faroese Museum of Natural HistoryTorshavnFaroe Islands
| | | | - Grace E. Frank
- Marine Biology and Aquaculture, College of Science and EngineeringJames Cook UniversityDouglasQueenslandAustralia
| | | | - Hernando García
- Alexander von Humboldt Biological Resources Research InstituteBogotá DCColombia
| | | | - Or Givan
- School of Zoology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Elizabeth Gorgone‐Barbosa
- Lab of Vegetation Ecology, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio ClaroBrazil
| | - William A. Gould
- USDA Forest Service, 65 USDA Forest Service, International Institute of Tropical ForestrySan JuanPuerto Rico
| | - Corinna Gries
- Center for Limnology, University of WisconsinMadisonWisconsin
| | - Gary D. Grossman
- The Warnell School of Forestry and Natural ResourcesUniversity of GeorgiaAthensGeorgia
| | - Julio R. Gutierréz
- Departamento de Biología, Facultad de Ciencias, Universidad de La SerenaLa SerenaChile
- Centro de Estudios Avanzados en Zonas Aridas (CEAZA)La SerenaChile
- Institute of Ecology and Biodiversity (IEB)SantiagoChile
| | - Stephen Hale
- U.S. Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology DivisionNarragansettRhode Island
| | - Mark E. Harmon
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregon
| | - John Harte
- The Energy and Resources Group and The Department of Environmental Science, Policy and ManagementUniversity of CaliforniaBerkeleyCalifornia
| | - Gary Haskins
- Cetacean Research & Rescue UnitBanffUnited Kingdom
| | - Donald L. Henshaw
- U.S. Forest Service Pacific Northwest Research LaboratoryCorvallisOregon
| | - Luise Hermanutz
- Memorial University, St John'sNewfoundland and LabradorCanada
| | - Pamela Hidalgo
- Instituto Milenio de Oceanografía, Universidad de ConcepciónConcepciónChile
| | - Pedro Higuchi
- Laboratório de Dendrologia e Fitossociologia, Universidade do Estado de Santa CatarinaFlorianópolisSanta CatarinaBrazil
| | - Andrew Hoey
- ARC Centre of Excellence for Coral Reef Studies, James Cook UniversityTownsvilleQueenslandAustralia
| | - Gert Van Hoey
- Department of Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and FoodOostendeBelgium
| | | | - Kristen Holeck
- Department of Natural Resources and Cornell Biological Field StationCornell UniversityIthacaNew York
| | | | | | - Mia Hoogenboom
- ARC Centre of Excellence for Coral Reef Studies, James Cook UniversityTownsvilleQueenslandAustralia
- Marine Biology and Aquaculture, College of Science and EngineeringJames Cook UniversityDouglasQueenslandAustralia
| | - Chih‐hao Hsieh
- Institute of Oceanography, National Taiwan UniversityTaipeiTaiwan
| | | | - Falk Huettmann
- EWHALE lab‐ Biology and Wildlife DepartmentInstitute of Arctic Biology, University of AlaskaFairbanksAlaska
| | | | - Allen H. Hurlbert
- Department of BiologyUniversity of North CarolinaChapel HillNorth Carolina
| | | | - David Janík
- Department of Forest Ecology, Silva Tarouca Research InstituteBrnoCzech Republic
| | - Ute Jandt
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of Biology/Geobotany and Botanical Garden, Martin‐Luther‐University Halle‐WittenbergHalleGermany
| | - Anna Jażdżewska
- Laboratory of Polar Biology and Oceanobiology, Faculty of Biology and Environmental ProtectionUniversity of ŁódźŁódźPoland
| | | | - Jill Johnstone
- Department of BiologyUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | - Julia Jones
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State UniversityCorvallisOregon
| | - Faith A. M. Jones
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Jungwon Kang
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | | | | | - Douglas A. Kelt
- Department of WildlifeFish, and Conservation Biology, University of California, DavisDavisCalifornia
| | - Rebecca Kinnear
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
- Shetland Oil Terminal Environmental Advisory Group (SOTEAG)St AndrewsUnited Kingdom
| | - Kari Klanderud
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
| | - Halvor Knutsen
- Institute of Marine ResearchHisNorway
- Department of Natural Sciences, Faculty of Engineering and Science, Centre for Coastal Research, University of AgderKristiansandNorway
| | | | - Alessandra R. Kortz
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Kamil Král
- Department of Forest Ecology, Silva Tarouca Research InstituteBrnoCzech Republic
| | - Linda A. Kuhnz
- Monterey Bay Aquarium Research InstituteMoss LandingCalifornia
| | - Chao‐Yang Kuo
- ARC Centre of Excellence for Coral Reef Studies, James Cook UniversityTownsvilleQueenslandAustralia
| | - David J. Kushner
- Channel Islands National Park, U. S. National Park ServiceCalifornia, VenturaCalifornia
| | | | | | - Cheol Min Lee
- Forest and Climate Change Adaptation LaboratoryCenter for Forest and Climate Change, National Institute of Forest ScienceSeoulRepublic of Korea
| | - Jonathan S. Lefcheck
- Department of Biological SciencesVirginia Institute of Marine Science, The College of William & Mary, Gloucester PointVirginia
| | - Esther Lévesque
- Département des sciences de l'environnementUniversité du Québec à Trois‐Rivières and Centre d’études nordiquesQuébecCanada
| | - David Lightfoot
- Department of BiologyMuseum of Southwestern Biology, University of New MexicoAlbuquerqueNew Mexico
| | - Francisco Lloret
- CREAF, Universitat Autònoma de BarcelonaCerdanyola del VallèsCataloniaSpain
| | | | - Adrià López‐Baucells
- Centre for Ecology, Evolution and Environmental Changes – cE3c, Faculty of SciencesUniversity of LisbonLisbonPortugal
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research InstituteManausBrazil
- Museu de Ciències Naturals de GranollersCatalunyaSpain
| | | | - Joshua S. Madin
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, KaneoheHawai‘iUSA
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | | | - Shahar Malamud
- School of Zoology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Iain Matthews
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | | | - Brian McGill
- School of Biology and EcologySustainability Solutions Initiative, University of MaineOronoMaine
| | | | - William O. McLarney
- Stream Biomonitoring Program, Mainspring Conservation TrustFranklinNorth Carolina
| | - Jason Meador
- Stream Biomonitoring Program, Mainspring Conservation TrustFranklinNorth Carolina
| | | | | | - Christoph F. J. Meyer
- Centre for Ecology, Evolution and Environmental Changes – cE3c, Faculty of SciencesUniversity of LisbonLisbonPortugal
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research InstituteManausBrazil
- Ecosystems and Environment Research Centre (EERC), School of Environment and Life Sciences, University of SalfordSalfordUnited Kingdom
| | - Anders Michelsen
- Terrestrial Ecology Section, Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Nataliya Milchakova
- Laboratory of Phytoresources, Kovalevsky Institute of Marine Biological Research of RAS (IMBR)SevastopolRussia
| | - Tom Moens
- Marine Biology Research Group, Ghent UniversityGentBelgium
| | - Even Moland
- Institute of Marine ResearchHisNorway
- Department of Natural Sciences, Faculty of Engineering and Science, Centre for Coastal Research, University of AgderKristiansandNorway
| | - Jon Moore
- Shetland Oil Terminal Environmental Advisory Group (SOTEAG)St AndrewsUnited Kingdom
- Aquatic Survey & Monitoring Ltd. ASMLDurhamUnited Kingdom
| | | | - Jörg Müller
- Bavarian Forest National ParkGrafenauGermany
- Field Station Fabrikschleichach, University of WürzburgRauhenebrachGermany
| | - Grace Murphy
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | | | | | - Andrew Naumov
- Zoological Institute, Russian Academy SciencesSt PetersburgRussia
| | - Francis Neat
- Marine Scotland, Marine LaboratoryScottish GovernmentEdinburghUnited Kingdom
| | - James A. Nelson
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisiana
| | - Michael Paul Nelson
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregon
| | | | - Natalia Norden
- Alexander von Humboldt Biological Resources Research InstituteBogotá DCColombia
| | - Jeffrey C. Oliver
- University of Arizona Health Sciences Library, University of ArizonaTucsonArizona
| | - Esben M. Olsen
- Institute of Marine ResearchHisNorway
- Department of Natural Sciences, Faculty of Engineering and Science, Centre for Coastal Research, University of AgderKristiansandNorway
| | | | - Krzysztof Pabis
- Laboratory of Polar Biology and Oceanobiology, Faculty of Biology and Environmental ProtectionUniversity of ŁódźŁódźPoland
| | - Robert J. Pabst
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregon
| | - Alain Paquette
- Center for Forest Research, Université du Québec à Montréal (UQAM)MontrealQuebecCanada
| | - Sinta Pardede
- Wildlife Conservation Society Indonesia ProgramBogorIndonesia
| | - David M. Paterson
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
- Shetland Oil Terminal Environmental Advisory Group (SOTEAG)St AndrewsUnited Kingdom
| | - Raphaël Pélissier
- UMR AMAP, IRD, CIRAD, CNRS, INRA, Montpellier UniversityMontpellierFrance
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF‐CSIC‐UABBellaterraCataloniaSpain
- CREAF, Universitat Autònoma de BarcelonaCerdanyola del VallèsCataloniaSpain
| | - Alejandro Pérez‐Matus
- Subtidal Ecology Laboratory & Center for Marine Conservation, Estación Costera de Investigaciones MarinasFacultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiagoCasillaChile
| | - Oscar Pizarro
- Australian Centre of Field Robotics, University of SydneySydneyNew South WalesAustralia
| | - Francesco Pomati
- Department of Aquatic EcologyEawag: Swiss Federal Institute of Aquatic Science and TechnologySwitzerland
| | - Eric Post
- Department of WildlifeFish, and Conservation Biology, University of California, DavisDavisCalifornia
| | | | - John C. Priscu
- Department of Land Resources and Environmental SciencesMontana State UniversityBozemanMontana
| | - Pieter Provoost
- UNESCO, Intergovernmental Oceanographic Commission, IOC Project Office for IODEOostendeBelgium
| | | | | | - B. R. Ramesh
- Department of EcologyFrench Institute of PondicherryPuducherryIndia
| | | | - Andrew Rassweiler
- Channel Islands National Park, U. S. National Park ServiceCalifornia, VenturaCalifornia
| | - Jose Eduardo Rebelo
- Ichthyology Laboratory, Fisheries and AquacultureUniversity of AveiroAveiroPortugal
| | - Daniel C. Reed
- Marine Science Institute, University of CaliforniaSanta BarbaraCalifornia
| | - Peter B. Reich
- Department of Forest Resources, University of MinnesotaSt PaulMinnesota
- Hawkesbury Institute for the Environment, Western Sydney UniversityPenrithNew South WalesAustralia
| | - Suzanne M. Remillard
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregon
| | - Anthony J. Richardson
- CSIRO Oceans and AtmosphereQueensland, BioSciences Precinct (QBP)St Lucia, BrisbaneQldAustralia
- Centre for Applications in Natural Resource Mathematics, The University of QueenslandSt LuciaQueenslandAustralia
| | | | - Itai van Rijn
- School of Zoology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Ricardo Rocha
- Centre for Ecology, Evolution and Environmental Changes – cE3c, Faculty of SciencesUniversity of LisbonLisbonPortugal
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research InstituteManausBrazil
- Metapopulation Research Centre, Faculty of Biosciences, University of HelsinkiHelsinkiFinland
| | - Victor H. Rivera‐Monroy
- Department of Oceanography and Coastal Sciences, College of the Coast and EnvironmentLouisiana State UniversityBaton RougeLouisiana
| | - Christian Rixen
- Swiss Federal Institute for Forest, Snow and Landscape ResearchDavos DorfSwitzerland
| | | | - Ricardo Ribeiro Rodrigues
- Laboratório de Ecologia e Restauração Florestal, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São PauloSão PauloBrazil
| | - Denise de Cerqueira Rossa‐Feres
- Departamento de Zoologia e Botânica, Universidade Estadual Paulista – UNESPCâmpus São José do Rio Preto, São José do Rio PretoBrazil
| | - Lars Rudstam
- Department of Natural Resources and Cornell Biological Field StationCornell UniversityIthacaNew York
| | - Henry Ruhl
- National Oceanography Centre, University of Southampton Waterfront CampusSouthamptonUnited Kingdom
| | - Catalina S. Ruz
- Subtidal Ecology Laboratory & Center for Marine Conservation, Estación Costera de Investigaciones MarinasFacultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiagoCasillaChile
| | - Erica M. Sampaio
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research InstituteManausBrazil
- Department of Animal Physiology, Eberhard Karls University TübingenTübingenGermany
| | - Nancy Rybicki
- National Research Program, U.S. Geological SurveyRestonVirginia
| | - Andrew Rypel
- Wisconsin Department of Natural Resources and Center for LimnologyUniversity of Wisconsin‐MadisonMadisonWisconsin
| | - Sofia Sal
- Department of Life SciencesImperial College LondonAscotBerkshireUnited Kingdom
| | - Beatriz Salgado
- Alexander von Humboldt Biological Resources Research InstituteBogotá DCColombia
| | | | - Ana Paula Savassi‐Coutinho
- Departamento de Ciências Biológicas, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São PauloSão PauloBrazil
| | - Sara Scanga
- Department of BiologyUtica CollegeUticaNew York
| | - Jochen Schmidt
- The National Institute of Water and Atmospheric ResearchAucklandNew Zealand
| | - Robert Schooley
- Wildlife Ecology and Conservation, Department of Natural Resources and Environmental SciencesUniversity of IllinoisChampaignIllinois
| | | | - Kwang‐Tsao Shao
- Biodiversity Research Center, Academia SinicaNankang, TaipeiTaiwan
| | | | | | | | - Jacek Siciński
- Laboratory of Polar Biology and Oceanobiology, Faculty of Biology and Environmental ProtectionUniversity of ŁódźŁódźPoland
| | - Caya Sievers
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Ana Carolina da Silva
- Laboratório de Dendrologia e Fitossociologia, Universidade do Estado de Santa CatarinaFlorianópolisSanta CatarinaBrazil
| | | | | | - Jasper Slingsby
- Department of Biological Sciences, Centre for Statistics in Ecology, Environment and ConservationUniversity of CapeTownRondeboschSouth Africa
- Fynbos Node, South African Environmental Observation NetworkClaremontSouth Africa
| | - Tracey Smart
- Coastal Finfish Section, South Carolina Department of Natural Resources, Marine Resources Research InstituteCharlestonSouth Carolina
| | - Sara J. Snell
- Department of BiologyUniversity of North CarolinaChapel HillNorth Carolina
| | - Nadejda A. Soudzilovskaia
- Conservation Biology DepartmentInstitute of Environmental Studies, CML, Leiden UniversityLeidenThe Netherlands
| | - Gabriel B. G. Souza
- Laboratório de Biologia e Tecnologia Pesqueira, Universidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | | | - Vinícius Castro Souza
- Laboratório de Ecologia e Restauração Florestal, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São PauloSão PauloBrazil
| | | | - Rowan Stanforth
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | | | | | - Maarten Stevens
- INBO, Research Institute for Nature and ForestBrusselsBelgium
| | - Rick Stuart‐Smith
- Institute for Marine and Antarctic Studies, University of TasmaniaHobartTasmaniaAustralia
| | - Yzel Rondon Suarez
- Centro de Estudos em Recursos Naturais, Universidade Estadual de Mato Grosso do SulDouradosMato Grosso do SulBrazil
| | - Sarah Supp
- School of Biology and EcologyUniversity of MaineOronoMaine
| | | | | | - Gary P. Thiede
- Department of Watershed Sciences and the Ecology Center, US Geological Survey, UCFWRU and Utah State UniversityLoganUtah
| | - Simon Thorn
- Field Station Fabrikschleichach, University of WürzburgRauhenebrachGermany
| | - Anne Tolvanen
- Natural Resources Institute Finland, University of OuluOuluFinland
| | | | - Ørjan Totland
- Department of BiologyUniversity of BergenBergenNorway
| | - Robert R. Twilley
- Department of Oceanography and Coastal Sciences, College of the Coast and EnvironmentLouisiana State UniversityBaton RougeLouisiana
| | | | - Nelson Valdivia
- Universidad Austral de Chile and Centro FONDAP en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL)ValdiviaChile
| | | | | | - Carl Van Colen
- Marine Biology Research Group, Ghent UniversityGentBelgium
| | - Jan Vanaverbeke
- Royal Belgian Institute of Natural Sciences, Operational Directorate Natural Environment, Marine Ecology and ManagementBrusselsBelgium
| | - Fabio Venturoli
- Escola de Agronomia, Universidade Federal de GoiásGoiâniaBrazil
| | - Hans M. Verheye
- Department of Environmental AffairsOceans and Coastal ResearchCape TownSouth Africa
- Department of Biological SciencesMarine Research InstituteUniversity of Cape TownCape TownSouth Africa
| | - Marcelo Vianna
- Laboratório de Biologia e Tecnologia Pesqueira, Universidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Rui P. Vieira
- National Oceanography Centre, University of Southampton Waterfront CampusSouthamptonUnited Kingdom
| | - Tomáš Vrška
- Department of Forest Ecology, Silva Tarouca Research InstituteBrnoCzech Republic
| | - Con Quang Vu
- Institute of Ecology and Biological Resources, VASTHanoiVietnam
| | - Lien Van Vu
- Vietnam National Museum of NatureHanoiVietnam
- Graduate University of Science and Technology, VASTHanoiVietnam
| | - Robert B. Waide
- Department of BiologyUniversity of New MexicoAlbuquerqueNew Mexico
| | - Conor Waldock
- National Oceanography Centre, University of Southampton Waterfront CampusSouthamptonUnited Kingdom
| | - Dave Watts
- CSIRO Oceans and Atmosphere FlagshipHobartTasmaniaAustralia
| | - Sara Webb
- Biology Department, Drew UniversityMadisonNew Jersey
- Environmental Studies Department, Drew UniversityMadisonNew Jersey
| | | | - Ethan P. White
- Department of Wildlife Ecology & ConservationUniversity of FloridaGainesvilleFlorida
- Informatics Institute, University of FloridaGainesvilleFlorida
| | | | - Dustin Wilgers
- Department of Natural SciencesMcPherson CollegeMcPhersonKansas
| | - Richard Williams
- Australian Antarctic Division, Channel HighwayKingstonTasmaniaAustralia
| | - Stefan B. Williams
- Australian Centre of Field Robotics, University of SydneySydneyNew South WalesAustralia
| | | | - Michael R. Willig
- Department of Ecology & Evolutionary Biology, Center for Environmental Sciences & EngineeringUniversity of ConnecticutMansfieldConnecticut
| | - Trevor J. Willis
- Institute of Marine Sciences, School of Biological Sciences, University of PortsmouthPortsmouthUnited Kingdom
| | - Sonja Wipf
- Research Team Mountain Ecosystems, WSL Institute for Snow and Avalanche Research SLFDavosSwitzerland
| | | | - Eric J. Woehler
- Institute for Marine and Antarctic Studies, University of TasmaniaHobartTasmaniaAustralia
| | - Kyle Zawada
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Michael L. Zettler
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestr. 15, D‐18119 RostockGermany
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Aslam S, Yung G, Dan J, Reed S, LeFebvre M, Logan C, Taplitz R, Law N, Golts E, Afshar K, Lehman S, Morales S, Furr C, Rosas F, Gaidamaka A, Bilinsky I, Grint P, Biswas B, Duplessis C, Hamilton T, Schooley R. Bacteriophage Treatment in a Lung Transplant Recipient. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Mocumbi A, Majid N, Manafe N, Carlin A, Zimba I, Schooley R, Benson C. PT247 Anemia is a Predictor of Cardiac Abnormalities and Systolic Function Worsening in a African Population With Access to Antiretroviral Therapy. Glob Heart 2016. [DOI: 10.1016/j.gheart.2016.03.586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Cachay E, Wyles D, Hill L, Ballard C, Torriani F, Colwell B, Kuo A, Schooley R, Mathews WC. The Impact of Direct Acting Antivirals in the Cure of HCV in HIV-Infected Patients With Ongoing Barriers to Care. Open Forum Infect Dis 2015. [DOI: 10.1093/ofid/ofv133.1225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Cachay ER, Wyles D, Hill L, Ballard C, Torriani F, Colwell B, Kuo A, Schooley R, Mathews CW. The Impact of Direct-Acting Antivirals in the Hepatitis C-Sustained Viral Response in Human Immunodeficiency Virus-Infected Patients With Ongoing Barriers to Care. Open Forum Infect Dis 2015; 2:ofv168. [PMID: 26697509 PMCID: PMC4683297 DOI: 10.1093/ofid/ofv168] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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: 07/27/2015] [Accepted: 11/03/2015] [Indexed: 12/13/2022] Open
Abstract
Using an inclusive HCV treatment protocol that encourages prospective engagement in care, HIV-infected patients with and without ongoing barriers to care had similar chances of HCV sustained viral response irrespective of which HCV treatment regimen was used. Background. Access to hepatitis C virus (HCV) medications for human immunodeficiency virus (HIV)-infected patients with ongoing barriers to care is restricted by healthcare payers in the absence of HCV treatment outcomes data in the era of direct-acting antivirals (DAA). Methods. Retrospective analysis of HCV treatment outcomes using interferon (IFN)-free DAA regimens and an inclusive treatment protocol in an urban HIV clinic where ongoing barriers to care (drug or alcohol use, psychiatric disease, and/or unstable housing) are common. Then, using logistic regression analysis, we compared the proportion of HIV-infected patients who achieved HCV sustained viral response (SVR) in the pegylated-IFN plus ribavirin (PEG-IFN/RBV, 2008–2011), pegylated-IFN plus ribavirin and telaprevir (PEG-IFN/RBV/PI, 2011–2013), and IFN-free DAA therapy eras (2014). Results are displayed using forest plots. Results. The proportion of patients who achieved HCV SVR in the PEG-IFN/RBV, PEG-IFN/RBV/PI, and IFN-free DAA therapy eras increased from 38.4% (95% confidence interval [CI], 23.2–53.7) and 48% (95% CI, 28.4–67.6) to 83.3% (95% CI, 70.0–96.7), respectively. Similar proportions of patients with ongoing barriers to care were treated during the PEG-IFN/RBV (25 of 39 [64%]), PEG-IFN/RBV/PI (14 of 25 [56%]), and IFN-free DAA (16 of 30 [53%]) eras. Hepatitis C virus SVR among patients with ongoing barriers to care improved from 40% (95% CI, 21–59) to 76.5% (95% CI, 56–97) in the PEG-IFN/RBV and IFN-free DAA eras, respectively. After stratification for factors associated with HCV SVR such as HCV genotype and cirrhosis, HCV SVR were similar in patients regardless of the presence of ongoing barriers to care. Conclusions. Using IFN-free DAA and an inclusive HCV treatment protocol, 76.5% of HIV/HCV-treated patients with ongoing barriers to care achieved HCV SVR.
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Affiliation(s)
- Edward R Cachay
- Department of Medicine , Owen Clinic ; Department of Medicine, Division of Infectious Diseases
| | - David Wyles
- Department of Medicine , Owen Clinic ; Department of Medicine, Division of Infectious Diseases
| | - Lucas Hill
- Skaggs School of Pharmacy and Pharmaceutical Sciences
| | - Craig Ballard
- Department of Medicine , Owen Clinic ; Skaggs School of Pharmacy and Pharmaceutical Sciences
| | - Francesca Torriani
- Department of Medicine , Owen Clinic ; Department of Medicine, Division of Infectious Diseases
| | - Bradford Colwell
- Department of Medicine , Owen Clinic ; Skaggs School of Pharmacy and Pharmaceutical Sciences
| | - Alexander Kuo
- Department of Medicine, Division of Gastroenterology and Hepatology , University of California San Diego
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Gois L, Badaró R, Schooley R, Grassi MFR. Immune response to Leishmania antigens in an AIDS patient with mucocutaneous leishmaniasis as a manifestation of immune reconstitution inflammatory syndrome (IRIS): a case report. BMC Infect Dis 2015; 15:38. [PMID: 25645330 PMCID: PMC4323250 DOI: 10.1186/s12879-015-0774-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 09/18/2014] [Accepted: 01/20/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND After the onset of HAART, some HIV-infected individuals under treatment present a exacerbated inflammation in response to a latent or a previously treated opportunistic pathogen termed immune reconstitution inflammatory syndrome (IRIS). Few reports of tegumentary leishmaniasis have been described in association with IRIS. Moreover, the immunopathogenesis of IRIS in association with Leishmania is unclear. CASE PRESENTATION The present study reports on a 29-year-old HIV-infected individual who developed mucocutaneous leishmaniasis associated with immune reconstitution inflammatory syndrome (IRIS) five months following highly active antiretroviral therapy (HAART). Severe lesions resulted in the partial destruction of the nasal septum, with improvement observed 15 days after treatment with Amphotericin B and corticosteroids. The immune response of this patient was evaluated before and after the lesions healed. IRIS was diagnosed in association with high levels of TNF-α and IL-6. Decreased production of IFN-γ and a low IFN-γ/IL-10 ratio were also observed in response to Leishmania antigens. After receiving anti-leishmanial treatment, the individual's specific Th1 immune response was restored. CONCLUSION The results suggest that the production of inflammatory cytokines by unstimulated T-lymphocytes could contribute to occurrence of leishmaniasis associated with IRIS.
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Affiliation(s)
- Luana Gois
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil.
| | - Roberto Badaró
- Hospital Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia, Brazil.
| | - Robert Schooley
- Department of Medicine, University of California, San Diego, USA.
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Meditz AL, MaWhinney S, Allshouse A, Feser W, Markowitz M, Little S, Hecht R, Daar ES, Collier AC, Margolick J, Kilby JM, Routy JP, Conway B, Kaldor J, Levy J, Schooley R, Cooper DA, Altfeld M, Richman D, Connick E. Sex, race, and geographic region influence clinical outcomes following primary HIV-1 infection. J Infect Dis 2011; 203:442-51. [PMID: 21245157 DOI: 10.1093/infdis/jiq085] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND It is unknown whether sex and race influence clinical outcomes following primary human immunodeficiency virus type 1 (HIV-1) infection. METHODS Data were evaluated from an observational, multicenter, primarily North American cohort of HIV-1 seroconverters. RESULTS Of 2277 seroconverters, 5.4% were women. At enrollment, women averaged .40 log₁₀ fewer copies/mL of HIV-1 RNA (P < .001) and 66 more CD4(+) T cells/μL (P = .006) than men, controlling for age and race. Antiretroviral therapy (ART) was less likely to be initiated at any time point by nonwhite women and men compared to white men (P < .005), and by individuals from the southern United States compared to others (P = .047). Sex and race did not affect responses to ART after 6 months (P > .73). Women were 2.17-fold more likely than men to experience >1 HIV/AIDS-related event (P < .001). Nonwhite women were most likely to experience an HIV/AIDS-related event compared to all others (P = .035), after adjusting for intravenous drug use and ART. Eight years after diagnosis, >1 HIV/AIDS-related event had occurred in 78% of nonwhites and 37% of whites from the southern United States, and 24% of whites and 17% of nonwhites from other regions (P < .001). CONCLUSIONS Despite more favorable clinical parameters initially, female HIV-1-seroconverters had worse outcomes than did male seroconverters. Elevated morbidity was associated with being nonwhite and residing in the southern United States.
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Affiliation(s)
- Amie L Meditz
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA.
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Kumarasamy N, Madhavan V, Venkatesh K, Saravanan S, Kantor R, Balakrishnan P, Devaleenal B, Poongulali S, Yepthomi T, Solomon S, Mayer K, Benson C, Schooley R. High Frequency of Clinically Significant Mutations after First‐Line Generic Highly Active Antiretroviral Therapy Failure: Implications for Second‐Line Options in Resource‐Limited Settings. Clin Infect Dis 2009; 49:306-9. [DOI: 10.1086/600044] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Fahey JL, Aziz N, Spritzler J, Plaeger S, Nishanian P, Lathey JL, Seigel J, Landay AL, Kilarui R, Schmitz JL, White C, Wara DW, Akridge R, Cutili J, Douglas SD, Reuben J, Shearer WT, Nokta M, Polland R, Schooley R, Asthana D, Mizrachi Y, Waxdal M. Need for an external proficiency testing program for cytokines, chemokines, and plasma markers of immune activation. Clin Diagn Lab Immunol 2000; 7:540-8. [PMID: 10882648 PMCID: PMC95910 DOI: 10.1128/cdli.7.4.540-548.2000] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An external evaluation program for measuring the performance of laboratories testing for cytokines and immune activation markers in biological fluids was developed. Cytokines, chemokines, soluble cytokine receptors, and other soluble markers of immune activation (CSM) were measured in plasma from a healthy human immunodeficiency virus (HIV)-seronegative reference population and from HIV-seropositive individuals as well as in supernatant fluids from in vitro-stimulated human immune cells. The 14 components measured were tumor necrosis factor (TNF) alpha, gamma interferon, interleukin-1 (IL-1), IL-2, IL-4, IL-6, IL-10, Rantes, MIP-Ia, MIP-Ibeta, soluble TNF receptor II, soluble IL-2 receptor alpha, beta(2)-microglobulin, and neopterin. Twelve laboratories associated with the Adult and Pediatric AIDS Clinical Trial Groups participated in the study. The performance features that were evaluated included intralaboratory variability, interlaboratory variability, comparison of reagent sources, and ability to detect CSM in the plasma of normal subjects as well as the changes occurring in disease. The principal findings were as follows: (i) on initial testing, i.e., before participating in the program, laboratories frequently differed markedly in their analytic results; (ii) the quality of testing of a CSM in individual participating laboratories could be assessed; (iii) most commercial kits allowed distinction between normal and abnormal plasma CSM levels and between supernatants of stimulated and unstimulated cells; (iv) different sources of reagents and reference standards frequently provided different absolute values; (v) inexperienced laboratories can benefit from participating in the program; (vi) laboratory performance improved during active participation in the program; and (vii) comparability between analyses conducted at different sites can be ensured by an external proficiency testing program.
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Affiliation(s)
- J L Fahey
- University of California, Los Angeles, USA.
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22
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Haubrich R, Thompson M, Schooley R, Lang W, Stein A, Sereni D, van der Ende ME, Antunes F, Richman D, Pagano G, Kahl L, Fetter A, Brown DJ, Clumeck N. A phase II safety and efficacy study of amprenavir in combination with zidovudine and lamivudine in HIV-infected patients with limited antiretroviral experience. Amprenavir PROAB2002 Study Team. AIDS 1999; 13:2411-20. [PMID: 10597783 DOI: 10.1097/00002030-199912030-00013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To determine the safety and efficacy of amprenavir (APV) in combination with lamivudine (3TC) and zidovudine (ZDV). DESIGN Multicenter, randomized, partially blinded trial. SETTING Nine study sites in the United States and Europe. PATIENTS A group of 84 HIV-infected subjects with no prior 3TC or protease inhibitor therapy experience, CD4 cell count > or = 150 x 10(6) cells/l, and plasma HIV RNA > 10000 copies/ml. INTERVENTIONS 3TC/ZDV with one of three doses of APV (900, 1050, or 1200 mg) versus 3TC/ZDV with 1050 mg placebo. All medications were dosed twice daily. The 1050 mg placebo and the APV 1050 mg dose were administered blinded. After 12 weeks, APV 1050 mg was substituted for 1050 mg placebo in the control group and the blind was maintained. MAIN OUTCOME MEASURES Reduction in plasma HIV RNA from baseline; proportion of subjects with plasma HIV RNA < 400 copies/ml; and an increase in CD4 cell count from baseline. RESULTS During the initial 12-week study period, APV/3TC/ZDV-treated subjects had greater viral suppression than the group receiving two nucleosides. By 48 weeks, 89% of subjects in the group taking the highest APV dose (1200 mg) had plasma HIV RNA < 400 copies/ml while 42% of the 900 mg group and 60% of the 3TC/ZDV group (1050 mg APV added at week 12) had plasma HIV RNA < 400 copies/ml using an as-treated analysis. By 60 weeks, 86% of subjects in the APV 1200 mg group had plasma HIV RNA < 400 copies/ml in the as-treated analysis, while 25% (900 mg), 43% (1050 mg), and 20% (1200 mg) of subjects had viral load <400 copies/ml in a strict intent-to-treat analysis owing to treatment discontinuations. Median CD4 cell count increases at week 60 were highest for the three treatment groups who received APV throughout the study, by intent-to-treat and as-treated analyses. The most common adverse events considered to be possibly drug related were nausea, rash, oral paresthesia, diarrhea, and fatigue. CONCLUSIONS Treatment with APV, dosed at 1200 mg twice daily in combination with 3TC/ZDV, resulted in sustained viral suppression. This combination represents a potent alternative initial antiretroviral regimen for protease inhibitor-naive individuals.
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Cotton D, Bartlett J, Schooley R, Gulick R. Therapeutic decision making in 1997. Roundtable discussion of five cases. AIDS Clin Care 1997; 9:11-5, 18. [PMID: 12212541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
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25
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Abstract
As our understanding of HIV disease pathogenesis progresses, approaches to immune-based therapy are evolving. Initial therapies aiming to alter immune function in patients with HIV infection have had mixed results. Clinical benefit in the trials so far has not been dramatic, although the studies are still at an early stage, and the correct protocols for the various agents or combinations of agents have yet to be established. As might be expected, where apparent benefit has occurred, it has been more obvious in those patients whose immune system was still intact.
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Affiliation(s)
- J L Fahey
- Center for Interdisciplinary Research and Disease, UCLA School of Medicine 90024-1747
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26
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Turner S, Tizard R, DeMarinis J, Pepinsky RB, Zullo J, Schooley R, Fisher R. Resistance of primary isolates of human immunodeficiency virus type 1 to neutralization by soluble CD4 is not due to lower affinity with the viral envelope glycoprotein gp120. Proc Natl Acad Sci U S A 1992; 89:1335-9. [PMID: 1741386 PMCID: PMC48444 DOI: 10.1073/pnas.89.4.1335] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Recombinant soluble CD4 (rsCD4) has potent antiviral activity against cell line-adapted isolates of the human immunodeficiency virus type 1 (HIV-1) but low activity toward HIV-1 primary isolates from patients. A simple hypothesis proposed to explain this discrepancy, which questions the therapeutic utility of soluble CD4-based approaches, is that the major envelope glycoprotein, gp120, of patient virus has lower affinity for CD4 than does gp120 from laboratory viruses. To test this hypothesis, we have produced pairs of low- and high-passage HIV-1 isolates which, depending on culture passage history, display dramatically different sensitivities to neutralization by rsCD4. Here, we present evidence that the HIV-1 major envelope glycoprotein cDNAs cloned from one such isolate pair show only minor differences in their deduced gp120 primary structures, and these occur outside regions previously shown to be involved in CD4 interactions. In addition, recombinant gp120 from a low-passage rsCD4-resistant patient virus binds rsCD4 with high affinity, equal to that previously measured for recombinant gp120 from high-passage cell line-adapted virus isolates. These data indicate that differences in CD4-gp120 affinity do not account for rsCD4 resistance in HIV-1 recently isolated from patients.
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Affiliation(s)
- S Turner
- Department of Molecular Biology, Cambridge, MA 02142
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27
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Merigan TC, Skowron G, Bozzette SA, Richman D, Uttamchandani R, Fischl M, Schooley R, Hirsch M, Soo W, Pettinelli C. Circulating p24 antigen levels and responses to dideoxycytidine in human immunodeficiency virus (HIV) infections. A phase I and II study. Ann Intern Med 1989; 110:189-94. [PMID: 2536257 DOI: 10.7326/0003-4819-110-3-189] [Citation(s) in RCA: 163] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
STUDY OBJECTIVE To determine the safety and efficacy of dideoxycytidine in patients with the acquired immunodeficiency syndrome (AIDS) or advanced AIDS-related complex. DESIGN A partially randomized phase I and II outpatient, dose-ranging study. SETTING Four university medical centers involving government-supported referral AIDS Clinical Trial Units. PATIENTS Sixty-one patients with AIDS or advanced AIDS-related complex and 100 pg/mL or more serum p24 antigen titers. INTERVENTIONS Dideoxycytidine was administered orally at 0.06, 0.03, 0.01, or 0.005 mg/kg body weight every 4 hours for 3 to 6 months depending on tolerance and benefit. MEASUREMENTS AND MAIN RESULTS In patients receiving 0.06 and 0.03 mg/kg, diffuse erythematous rash, fever, and aphthous stomatitis occurred in the first weeks of therapy, but resolved later. Hematopoietic suppression was rare. Peripheral sensory neuropathy occurred in patients receiving 0.06 mg/kg and 0.03 mg/kg and improved after discontinuation of therapy. Serum p24 antigen fell significantly (P less than 0.01) from baseline entry values in most of these patients. The CD4 lymphocytes rose transiently at the 0.03 mg/kg dosage. At the 0.005 mg/kg dosage, skin rash, fever, and aphthous stomatitis were mild or absent. Peripheral neuropathy, which occurred in all patients receiving 0.01 mg/kg was less severe than at higher dosages. At the 0.005 mg/kg dosage, peripheral neuropathy was occasionally seen. Significant suppression of serum p24 antigen was seen in most patients with AIDS-related complex receiving 0.01 mg/kg and less frequently in patients receiving 0.005 mg/kg. CONCLUSIONS Less toxic regimens of dideoxycytidine merit clinical assessment for advanced anti-human immunodeficiency virus-1 (HIV) infection. Several studies alternating dideoxycytidine and zidovudine are in progress.
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Affiliation(s)
- T C Merigan
- Stanford University School of Medicine, California
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Abstract
A patient with hemophilia A and transfusion-associated end-stage chronic liver disease underwent orthotopic liver transplantation. He had no requirement for exogenous factor VIII replacement during the 27 mo he survived. Although his hemophilia was cured, he had antibodies to the human immunodeficiency virus; ultimately he died of complications arising from acquired immunodeficiency syndrome. Liver transplantation for cirrhotic hemophiliacs can free them of the need for antihemophilic-factor therapy; however, application of this approach may be limited by the high prevalence of human immunodeficiency virus infection in multitransfused hemophiliacs.
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Affiliation(s)
- A Gibas
- Gastrointestinal Unit, Massachusetts General Hospital, Boston
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Whitley RJ, Soong SJ, Alford CA, Hirsch MS, Schooley R, Oxman MN, Connor JD, Betts R, Dolin R, Reichman RC. Design of therapeutic studies in herpes simplex encephalitis. Lancet 1985; 1:284-5. [PMID: 2857352 DOI: 10.1016/s0140-6736(85)91063-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Blazar BA, Strome M, Schooley R. Interferon and natural killing of human lymphoma cell lines after induction of the Epstein Barr viral cycle by superinfection. The Journal of Immunology 1984. [DOI: 10.4049/jimmunol.132.2.816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Interferon (IFN) production during natural killer (NK) cell assays with Raji, an EBV-carrying human lymphoma-derived cell line, was studied to determine whether IFN generated by effectors in vitro acted in target cell lysis. In 4-hr tests, Raji is insensitive to NK but becomes susceptible after superinfection with the P3HR-1 strain of EBV. IFN was not detectable by bioassay in supernatants from 4-hr assays, and the addition of antibody to IFN did not prevent the lysis of the superinfected Raji cells. In 18-hr tests the NK sensitivity of the superinfected Raji cells was markedly elevated, and a percent of the normal Raji cells was also killed. IFN alpha was found in supernatants from 18-hr tests. Antibody to IFN alpha markedly reduced the killing of superinfected Raji and slightly reduced cytotoxicity against control Raji in 18-hr tests. Taken together these results indicate that what is referred to as natural killing has IFN-related and IFN-nonrelated components.
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Blazar BA, Strome M, Schooley R. Interferon and natural killing of human lymphoma cell lines after induction of the Epstein Barr viral cycle by superinfection. J Immunol 1984; 132:816-20. [PMID: 6197476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Interferon (IFN) production during natural killer (NK) cell assays with Raji, an EBV-carrying human lymphoma-derived cell line, was studied to determine whether IFN generated by effectors in vitro acted in target cell lysis. In 4-hr tests, Raji is insensitive to NK but becomes susceptible after superinfection with the P3HR-1 strain of EBV. IFN was not detectable by bioassay in supernatants from 4-hr assays, and the addition of antibody to IFN did not prevent the lysis of the superinfected Raji cells. In 18-hr tests the NK sensitivity of the superinfected Raji cells was markedly elevated, and a percent of the normal Raji cells was also killed. IFN alpha was found in supernatants from 18-hr tests. Antibody to IFN alpha markedly reduced the killing of superinfected Raji and slightly reduced cytotoxicity against control Raji in 18-hr tests. Taken together these results indicate that what is referred to as natural killing has IFN-related and IFN-nonrelated components.
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Quinnan GV, Schooley R, Dolin R, Ennis FA, Gross P, Gwaltney JM. Serologic responses and systemic reactions in adults after vaccination with monovalent A/USSR/77 and trivalent A/USSR/77, A/Texas/77, B/Hong Kong/72 influenza vaccines. Rev Infect Dis 1983; 5:748-57. [PMID: 6622889 DOI: 10.1093/clinids/5.4.748] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Four hundred twenty-six volunteers aged 16 to 83 years were given experimental doses of inactivated monovalent [A/USSR/77 (H1N1)] and trivalent [A/USSR/77 (H1N1), A/Texas/77 (H3N2), B/Hong Kong/72] influenza vaccines as part of a double-blinded, placebo-controlled, national collaborative study. Local reactions at inoculation sites occurred in less than 6.6% of volunteers. Systemic reactions, generally consisting of low-grade fever, myalgia, or headache, lasting less than 24 hr, did not occur more frequently in vaccinees than in placebo recipients. Vaccines containing lower doses of the A/Texas/77 (H3N2) hemagglutinin (8-10 micrograms) and B/Hong Kong/72 hemagglutinin (6-9 micrograms) produced hemagglutinin-inhibiting (HAI) antibody responses equivalent to those produced by higher doses (15-28 and 19-28 micrograms, respectively) in all age groups. Single injections of vaccines containing lower doses of A/USSR/77 (H1N1) hemagglutinin (4-7 micrograms) induced titers of HAI antibody of greater than 1:40 in 93% of volunteers greater than or equal to 26 years of age but in only 58% of volunteers less than 26 years of age. In this latter group, two injections containing higher doses (10-19 micrograms) induced better antibody responses. Vaccines containing approximately 6-15 micrograms of hemagglutinin of each antigen can be expected to be well tolerated and to induce good HAI antibody responses in a one- or two-dose regimen, depending on the age group.
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