1
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Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell 2023; 186:5690-5704.e20. [PMID: 38101407 PMCID: PMC10795731 DOI: 10.1016/j.cell.2023.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/21/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions. By integrating genomic, mobility, and epidemiological data, we find abundant transmission occurring between both adjacent and distant locations, supported by dynamic mobility patterns. We find that changing connectivity significantly influences local COVID-19 incidence. Our findings demonstrate a complex meaning of "local" when investigating connected epidemics and emphasize the importance of collaborative interventions for pandemic prevention and mitigation.
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Affiliation(s)
| | - Gabriel W Hassler
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Anelizze Castro-Martinez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Andrea Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Anthony Veder
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ariana Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Cassandra Wauer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jacqueline Holmes
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jedediah Wilson
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Shayla N Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Tsai
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA; Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | | | - Oscar E Zazueta
- Department of Epidemiology, Secretaria de Salud de Baja California, Tijuana, Baja California, Mexico
| | | | - Manuel Sanchez-Alavez
- Centro de Diagnostico COVID-19 UABC, Tijuana, Baja California, Mexico; Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | | | - Abraham García-Gil
- Clinical Laboratory Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | | | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Jeremy Corrigan
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Alana Weiss
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emily G Spencer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emory C Hufbauer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Justin J Lee
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Alison J King
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kelly N Nguyen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kieran Saucedo
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | | | - Kathleen M Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Robert T Schooley
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Agustin J Negrete
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Horacio J Reyna
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose R Chavez
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Maria L Garcia
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose M Cornejo-Bravo
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico
| | | | | | | | | | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Benjamin Henson
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Beatriz Olivares-Flores
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Gisela Barrera-Badillo
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Irma Lopez-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - José E Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Rita Flores-León
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | | | - Alison Sanders
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Sharon L Reed
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | | | | | | | | | | | | | | | - Sara H Browne
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA; Specialist in Global Health, Encinitas, CA, USA
| | - Jocelyn Olivas Flores
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico; University of HealthMx, Tijuana, Baja California, Mexico
| | - Diana G Rincon Rodríguez
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Martin Gonzalez Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Luis C Robles Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Tijuana, Baja California, Mexico
| | - Betsy J Arellano Vera
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto Mexicano del Seguro Social, Tijuana, Baja California, Mexico
| | - Jonathan Gonzalez Garcia
- University of HealthMx, Tijuana, Baja California, Mexico; SIMNSA, Tijuana, Baja California, Mexico
| | | | - Rob Knight
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Marc A Suchard
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
| | - Abraham Campos-Romero
- Innovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | - Shirlee Wohl
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
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2
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Malone JD, Thihalolipavan S, Bakhtar O, Salamanca D, Polanco SL, Taras H. COVID-19 Rapid Antigen Testing Implementation in California K-12 Schools. J Sch Health 2022; 92:1123-1127. [PMID: 35920395 PMCID: PMC9539062 DOI: 10.1111/josh.13219] [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] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 07/09/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Affiliation(s)
- John D. Malone
- Epidemiology and Immunization Services BranchHealth and Human Services AgencyCounty of San Diego, 3851 Rosecrans Street, Room Y15San DiegoCA92110
| | - Sayone Thihalolipavan
- Medical Care ServicesHealth and Human Services AgencyCounty of San Diego, 9444 Balboa AveSan DiegoCA92123
| | - Omid Bakhtar
- Sharp Outreach LaboratorySharp Healthcare Laboratory5651 Copley Drive, Suite BSan DiegoCA92111
| | | | - Sherri Lynn Polanco
- Borrego Springs Elementary School, Borrego Springs Unified School DistrictBorrego Springs Elementary School1315 Palm Canyon DriveBorrego SpringsCA92004
| | - Howard Taras
- University of California San DiegoDivision of Child and Community Health9500 Gilman DriveLa JollaCA92093‐0927
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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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6
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Maletz A, Kang G, Chinn RY, Malone JD, Bagheri H, Turner MM, Perez E, Hose M, Shah S, Zeller M, Anderson K, McDonald E, Ruegg J, Brackman S. 432. An Outbreak of Coronavirus Disease, 2019 (COVID-19) in a Skilled Nursing Facility – California, 2021: Description, Mitigation, Challenges, and Opportunities. Open Forum Infect Dis 2021. [PMCID: PMC8644286 DOI: 10.1093/ofid/ofab466.632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Skilled nursing facility (SNF) residents comprised 11% of all COVID-19 cases in the United States; however, they account for 43% of deaths with case fatality rates (CFR) of 26.0-33.7%.
Methods
We report an outbreak of COVID-19, from June 15 to July 21, 2020 in a 159-bed SNF with a staff of 172 that resulted in an infection rate of 97% in residents and 23% in HCWs (Figure 1). A retroactive review outlined mitigation efforts, discussed challenges, identified risk factors among residents and health care workers (HCW) for acquisition of COVID-19, and reviewed opportunities for improvement (Figure 2).
Figure 1. Epi Curve of COVID-19 Outbreak in a Skilled Nursing Facility
Figure 2. Timeline of COVID-19 Outbreak in a Skilled Nursing Facility
Results
Factors that contributed to the outbreak: delay in test results had an impact on cohorting; suboptimal adherence to the principles of infection prevention and control (IPC) and minimal adherence monitoring; strict criteria were used to screen for infection; the underappreciated transmissibility of COVID-19 from presymptomatic and asymptomatic persons; symptomatic HCWs who continued to work; the changing guidance on, the suboptimal use of, and an inadequate supply of personal protective equipment; poor indoor air quality due to ventilation challenges; and the important role of community/family/interfacility spread on the outbreak. Whole genome sequencing, performed in 52 samples, identified a common strain that was also found in clusters of 2 other facilities: 1 in the same geographic location, the other in a different geographic location but whose HCWs had the same zip codes as the facility (Figure 3). Certified nursing and restorative nursing assistants had the highest risk of infection with an odds ratio (OR) of 4.02 (confidence interval 1.29-12.55, p value: 0.02) when compared to registered and licensed vocational nurses. The residents’ CFR was 24%. The OR for death was increased by 10.5 (10.20-11.00) for every decade of life as was morbid obesity (BMI > 35) with an OR of 8.50. BMI as a continuous variable increased risk of mortality for every additional unit, OR 1.07 (Tables 1, 2).
Whole Genome Sequencing of Isolates from a Skilled Nursing Facility Outbreak
Univariate Analysis of Selected Variables Associated with Mortality among Residents at Facility A during COVID-19 Outbreak, June 19 - July 21, 2021
Multivariate Analysis of Factors Associated with Mortality from COVID-19 after Adjusting for Age among Residents (N =124) of Facility A, June 15 - July 21, 2020
Conclusion
While implementation of optimal IPC measures in the pre-COVID-19 vaccination era had no impact on the infections in residents who were likely already infected or exposed at the onset of the outbreak, these measures along with non-pharmacologic strategies were effective in halting the spread among HCWs.
Disclosures
All Authors: No reported disclosures
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Affiliation(s)
| | - Grace Kang
- County of San Diego, Epidemiology & Immunization Services Branch, San Diego, California
| | - Raymond Y Chinn
- County of San Diego, Health and Human Services Agency, San Diego, California
| | - John D Malone
- County of San Diego, Health and Human Services Agency, San Diego, California
| | - Hosniyeh Bagheri
- California Department of Public Health (CDPH), Rancho Santa Margarita, CA
| | | | - Elizar Perez
- County of San Diego, Epidemiology & Immunization Services Branch, San Diego, California
| | - Michelle Hose
- California Department of Public Health, Center for Healthcare Quality, San Diego, California
| | - Seema Shah
- County of San Diego, Health and Human Services Agency, San Diego, California
| | - Mark Zeller
- The Scripps Research Institute, San Diago, California
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7
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Chinn RY, Thihalolipavan S, Wheeler J, Kang G, Malone JD, McDonald E. 1207. Coronavirus Disease, 2019 (COVID-19) in Long-Term Care Facilities (LTCF): One Large County’s Response, California 2020-2021. Open Forum Infect Dis 2021. [PMCID: PMC8644961 DOI: 10.1093/ofid/ofab466.1399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
The coronavirus-19 disease (COVID-19) outbreak has had a particularly devasting effect on skilled nursing facility (SNF) residents and healthcare workers (HCWs). While representing only 11% of COVID-19 cases, the residents accounted for 43% of deaths in the United States.
Methods
We report a retrospective review of the support provided by our local health department (LHD) to long-term care facilities in response to the COVID-19 pandemic. This group comprised of staff from healthcare-associated infections (HAI); the Medical Operations Center (MOC); Testing, Tracing, and Treatment (T3); and the Healthcare Provider Status Taskforce (Table 1 outlines their functions). The HAI team with the State Public Health Department provided infection prevention and control (IPC) outbreak investigation, education, recommendations, and ongoing access to technical assistance. The T3 team focused on rapid response testing and tracing; the HPSTF team collected data and issued questionnaires; the MOC responded to staffing and PPE requests; and the Long-Term Care Facility sector presented routine telebriefings to update the facilities on public health guidance, share resources, and answer questions during and in between briefings.
Table 1. Sectors and Function of Response Teams to COVID-19
Results
From March 2020 through May 2021, there were 504 outbreaks in LTCFs; the HAI team performed 281 outbreak investigations (Figure 1). In the same period, 308,264 molecular tests were performed using various platforms; laboratory services were outsourced during peak testing requests (Figure 2); “strike teams were deployed to facilitate testing on 404 occasions. Self-reported fully vaccination rate for SNF staff was 73% (March 2021) and 76% for residents (April 2021). There were 568 staff requested; total orders for PPE were 4,839 and 16,892,823 PPE items were fulfilled (Figure 3). In addition to knowledge gaps in IPC, other challenges included shifting IPC guidance, PPE shortages, timeliness of test results that impacted cohorting, community acquisition of disease with transmission to residents, interfacility spread among staff, staffing shortages, and vaccine hesitancy issues.
Figure 1. Number of Outbreaks and Number of Outbreak Investigations
Figure 2. Number of Tests Performed by the Public Health Laboratory and the Number of Visits by “Strike Teams”
Figure 3. Personal Protective Equipment Fulfillment during COVID-19 Pandemic
Conclusion
The management of the recent COVID-19 outbreaks required a multi-pronged approach. Lessons learned are applicable to other highly transmissible infectious diseases.
Disclosures
All Authors: No reported disclosures
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Affiliation(s)
- Raymond Y Chinn
- County of San Diego, Health and Human Services Agency, San Diego, California
| | | | | | - Grace Kang
- County of San Diego, Epidemiology & Immunization Services Branch, San Diego, California
| | - John D Malone
- County of San Diego, Health and Human Services Agency, San Diego, California
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8
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Affiliation(s)
- John D Malone
- Epidemiology and Immunization Services Branch, Health and Human Services Agency, County of San Diego, San Diego, California
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9
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Hoang TN, LaPorta AJ, Malone JD, Champagne R, Lavell K, De La Rosa GM, Gaul L, Dukovich M. Hyper-realistic and immersive surgical simulation training environment will improve team performance. Trauma Surg Acute Care Open 2020; 5:e000393. [PMID: 32201735 PMCID: PMC7066601 DOI: 10.1136/tsaco-2019-000393] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 10/06/2019] [Revised: 11/14/2019] [Accepted: 12/18/2019] [Indexed: 11/22/2022] Open
Abstract
Background Surgical trauma care requires excellent multidisciplinary team skills and communication to ensure the highest patient survival rate. This study investigated the effects of Hyper-realistic immersive surgical team training to improve individual and team performance. A Hyper-realistic surgical training environment is defined as having a high degree of fidelity in the replication of battlefield conditions in a training environment, so participants willingly suspend disbelief that they become totally immersed and eventually stress inoculated in a way that can be measured physiologically. Methods Six multispecialty member US Navy Fleet Surgical/US Army Forward Surgical Teams (total n=99 evaluations) underwent a 6-day surgical training simulation using movie industry special effects and role players wearing the Human Worn Surgical Simulator (Cut Suit). The teams were immersed in trauma care scenarios requiring multiple complex interventions and decision making in a realistic, fast-paced, intensive combat trauma environment. Results Hyper-realistic immersive simulation training enhanced performance between multidisciplinary healthcare team members. Key efficacy quantitative measurements for the same simulation presented on day 1 compared with day 6 showed a reduction in resuscitation time from 24 minutes to 14 minutes and critical error decrease from 5 to 1. Written test scores improved an average of 21% (Medical Doctors 11%, Registered Nurses 25%, and Corpsman/Medics 26%). Longitudinal psychometric survey results showed statistically significant increases in unit readiness (17%), combat readiness (12%), leadership quality (7%), vertical cohesion (7%), unit cohesion (5%), and team communication (3%). An analysis of salivary cortisol and amylase physiologic biomarkers indicated an adaptive response to the realistic environment and a reduction in overall team stress during performance evaluations. Conclusions Hyper-realistic immersive simulation training scenarios can be a basis for improved military and civilian trauma training. Level of evidence Level III.
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Affiliation(s)
- Tuan N Hoang
- Naval Surface Forces, US Pacific Fleet, San Diego, California, USA
| | - Anthony J LaPorta
- Rocky Vista University College of Osteopathic Medicine, Parker, Colorado, USA
| | - John D Malone
- Medicine, Uniformed Services University, Bethesda, Maryland, USA
| | | | - Kit Lavell
- Strategic Operations, Inc, San Diego, California, USA
| | - Gabriel M De La Rosa
- Naval Center for Combat and Operational Stress Control, San Diego, California, USA
| | - Lawrence Gaul
- Chinle Comprehensive Health Care Facility, Chinle, Arizona, USA
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10
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Malone JD, Brigantic R, Muller GA, Gadgil A, Delp W, McMahon BH, Lee R, Kulesz J, Mihelic FM. U.S. airport entry screening in response to pandemic influenza: modeling and analysis. Travel Med Infect Dis 2009; 7:181-91. [PMID: 19717097 PMCID: PMC7185379 DOI: 10.1016/j.tmaid.2009.02.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [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: 02/05/2009] [Accepted: 02/09/2009] [Indexed: 11/02/2022]
Abstract
BACKGROUND A stochastic discrete event simulation model was developed to assess the effectiveness of passenger screening for Pandemic Influenza (PI) at U.S. airport foreign entry. METHODS International passengers arriving at 18 U.S. airports from Asia, Europe, South America, and Canada were assigned to one of three states: not infected, infected with PI, infected with other respiratory illness. Passengers passed through layered screening then exited the model. 80% screening effectiveness was assumed for symptomatic passengers; 6% asymptomatic passengers. RESULTS In the first 100 days of a global pandemic, U.S. airport screening would evaluate over 17 M passengers with 800 K secondary screenings. 11,570 PI infected passengers (majority asymptomatic) would enter the U.S. undetected from all 18 airports. Foreign airport departure screening significantly decreased the false negative (infected/undetected) passengers. U.S. attack rates: no screening (26.9%-30.9%); screening (26.4%-30.6%); however airport screening results in 800 K-1.8 M less U.S. PI cases; 16 K-35 K less deaths (2% fatality rate). Antiviral medications for travel contact prophylaxis (10 contacts/PI passenger) were high - 8.8M. False positives from all 18 airports: 100-200/day. CONCLUSIONS Foreign shore exit screening greatly reduces numbers of PI infected passengers. U.S. airport screening identifies 50% infected individuals; efficacy is limited by the asymptomatic PI infected. Screening will not significantly delay arrival of PI via international air transport, but will reduce the rate of new US cases and subsequent deaths.
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Affiliation(s)
- John D Malone
- Center for Disaster and Humanitarian Assistance Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4799, USA.
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11
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Malone JD. Pre-event smallpox vaccination for healthcare workers revisited--the need for a carefully screened multidisciplinary cadre. Int J Infect Dis 2007; 11:93-7. [PMID: 17306582 PMCID: PMC7110476 DOI: 10.1016/j.ijid.2006.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 11/02/2006] [Accepted: 11/08/2006] [Indexed: 01/13/2023] Open
Abstract
As healthcare institutions are a focus of smallpox transmission early in an epidemic, several mathematical models support pre-event smallpox vaccination of healthcare workers (HCWs). The deciding factor for HCW voluntary vaccination is the risk of disease exposure versus the risk of vaccine adverse events. In a United States military population, with careful screening to exclude atopic dermatitis/eczema and immunosuppression, over 1 million vaccinia (smallpox) vaccinations were delivered with one fatality attributed to vaccination. Among 37901 United States civilian volunteer HCWs vaccinated, 100 serious adverse events were reported including 10 ischemic cardiac episodes and six myocardial infarctions - two were fatal. This older population had a higher rate of adverse events due to age-related coronary artery disease. T-cell mediated inflammatory processes induced by live vaccinia vaccination may have a role in the observed acute coronary artery events. With exclusion of individuals at risk for coronary artery disease, atopic dermatitis/eczema, and immunosuppression, HCWs can be smallpox vaccinated with minimal risk. A carefully screened multidisciplinary cadre (physician, nurse, infection control practitioner, technician), pre-event vaccinated for smallpox, will supply the necessary leadership to alleviate fear and uncertainty while limiting spread and initial mortality of smallpox.
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Affiliation(s)
- John D Malone
- Center for Biological Monitoring and Modeling, Pacific Northwest National Laboratory, MSIN:P7-51, 902 Battelle Boulevard, PO Box 999, Richland, WA 99352, USA.
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12
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Affiliation(s)
- J D Malone
- Naval Medical Center San Diego, San Diego, California 92134-5000, USA.
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13
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Wild MA, Xin H, Maruyama T, Nolan MJ, Calveley PM, Malone JD, Wallace MR, Bowdish KS. Human antibodies from immunized donors are protective against anthrax toxin in vivo. Nat Biotechnol 2003; 21:1305-6. [PMID: 14555959 DOI: 10.1038/nbt891] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2003] [Accepted: 07/21/2003] [Indexed: 11/09/2022]
Abstract
A panel of Fabs that neutralize anthrax toxin in vitro was selected from libraries generated from human donors vaccinated against anthrax. At least two of these antibodies protect rats from anthrax intoxication in vivo. Fabs 83K7C and 63L1D bind with subnanomolar affinity to protective antigen (PA) 63, and Fab 63L1D neutralizes toxin substoichiometrically, inhibits lethal factor (LF) interaction with PA63 and binds to a conformational epitope formed by PA63.
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Affiliation(s)
- Martha A Wild
- Alexion Antibody Technologies, Inc., 3985 Sorrento Valley Blvd., San Diego, California 92121, USA
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14
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Amundson DE, Malone JD. Link Between Anthrax Immunization and Hypersensitivity Pneumonitis? Chest 2003. [DOI: 10.1016/s0012-3692(15)33736-3] [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: 11/16/2022] Open
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15
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Abstract
A case of hypersensitivity pneumonitis (HP) following anthrax vaccination is described. The patient is a 39-year-old, previously healthy man on active duty in the US Marine Corps, in whom a urticaral skin rash and progressive dyspnea on exertion developed following subcutaneous anthrax vaccination. A diagnosis of bronchiolitis obliterans with organizing pneumonia was made from transbronchial lung biopsy samples after evaluation excluded multiple infectious and collagen vascular etiologies. This appears to be the first recorded case of HP following an anthrax vaccination; however, a case report of pulmonary and cutaneous vasculitis following hepatitis B vaccination has been reported in the literature and is reviewed.
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Affiliation(s)
- Suzanne J Timmer
- Pulmonary Division, Department of Internal Medicine, Naval Hospital Pensacola, Pensacola, FL, USA
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16
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Brown AE, Dolan MJ, Michael NL, Zhou S, Perfetto SP, Hawkes C, Robb M, Lane J, Mayers D, McNeil JG, Malone JD, Garner R, Birx DL, Aronson N, Artenstein A, Davis C, Johnson S, Kelly W, Kim J, Lennox J, Mascola J, Oster C, Pascal L, Redfield R, Ruiz N, Sitz K, Sun W. Clinical Prognosis of Patients with Early-Stage Human Immunodeficiency Virus (HIV) Disease: Contribution of HIV-1 RNA and T Lymphocyte Subset Quantitation. Mil Med 2001. [DOI: 10.1093/milmed/166.7.571] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | | | - Susan Zhou
- Henry M. Jackson Foundation, Rockville, MD
| | - Stephen P. Perfetto
- Walter Reed Army Institute of Research, Washington, DC
- Henry M. Jackson Foundation, Rockville, MD
| | | | - Merlin Robb
- Walter Reed Army Institute of Research, Washington, DC
| | | | - Douglas Mayers
- Walter Reed Army Institute of Research, Washington, DC
- National Naval Medical Center, Bethesda, MD
| | | | | | - Robin Garner
- Walter Reed Army Institute of Research, Washington, DC
- Henry M. Jackson Foundation, Rockville, MD
| | | | - Naomi Aronson
- Wilford Hall Medical Center, Lackland Air Force Base, TX
| | | | - Charles Davis
- Wilford Hall Medical Center, Lackland Air Force Base, TX
| | | | - William Kelly
- Wilford Hall Medical Center, Lackland Air Force Base, TX
| | - Jerome Kim
- Walter Reed Army Institute of Research, Washington, DC
| | | | | | | | | | | | - Nancy Ruiz
- National Naval Medical Center, Bethesda, MD
| | - Karl Sitz
- Walter Reed Army Institute of Research, Washington, DC
| | - Wellington Sun
- Wilford Hall Medical Center, Lackland Air Force Base, TX
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17
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Brown AE, Dolan MJ, Michael NL, Zhou S, Perfetto SP, Hawkes C, Robb M, Lane J, Mayers D, McNeil JG, Malone JD, Garner R, Birx DL. Clinical prognosis of patients with early-stage human immunodeficiency virus (HIV) disease: contribution of HIV-1 RNA and T lymphocyte subset quantitation. Mil Med 2001; 166:571-6. [PMID: 11469026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023] Open
Abstract
Systems for the staging of individuals with human immunodeficiency virus type 1 (HIV-1) infection were developed 15 years ago. Subsequently, assays for quantitating HIV-1 RNA and immunophenotyping of lymphocyte subsets have been developed and validated. The utility of these assays for improved staging in early disease was evaluated in 256 HIV-infected adults (52% minority) with CD4 counts > or = 400 cells/microL followed in U.S. military medical centers before the highly active anti-retroviral therapy era. HIV viral load (RNA) was quantitated; the frequencies of select CD4+ immunophenotypes were determined in 112 subjects. The results were analyzed in relation to three outcome measures: death, first acquired immunodeficiency syndrome-defining opportunistic infection, and CD4 count < or = 200 cells/microL. Serum RNA level and CD4 count were each found to be predictive of all three outcomes. In addition, increases in the T-cell subsets CD28-CD4+ and CD29+CD26-CD4+ were found to be independently predictive of more rapid progression. The classification of early-stage HIV patients is improved by the quantitation of both viral RNA and T-lymphocyte subsets.
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Affiliation(s)
- A E Brown
- Walter Reed Army Institute of Research, Washington, DC, USA.
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18
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Malone JD, Sheffield J, Tribble D, Lowe-Bey F, Cannon M, Slaughter-Allen M, Brown AE, Kanki PJ. Evaluation of Three Rapid/Simple Tests for Detection of HIV-2 Antibodies*. J Acquir Immune Defic Syndr 2000. [DOI: 10.1097/00042560-200003010-00014] [Citation(s) in RCA: 2] [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: 11/25/2022]
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19
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Malone JD, Sheffield J, Tribble D, Lowe-Bey F, Cannon M, Slaughter-Allen M, Brown AE, Kanki PJ. Evaluation of three rapid/simple tests for detection of HIV-2 antibodies. J Acquir Immune Defic Syndr 2000; 23:281-3. [PMID: 10839666 DOI: 10.1097/00126334-200003010-00014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Abstract
Previous studies have revealed that the expression of CD38 on CD8+ T cells is a strong predictor of disease progression in human immunodeficiency virus (HIV)-infected individuals. Those studies were performed using fresh patient samples over an extended trial period. After demonstrating the validity of assay results on cryopreserved cells, we performed a retrospective study using frozen cell samples to determine the predictive value of CD38 expression in patients with CD4 counts above 400 cells/microl. The CD38 expression as measured by antibody binding capacity and the CD38 median channel were shown to be associated with time to new opportunistic infection or death (both P < 0.001). These results suggest that CD38 expression on CD8+ T cells, whether fresh or frozen, provides a useful predictor of HIV disease progression.
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Affiliation(s)
- S P Perfetto
- Henry M. Jackson Foundation, Rockville, Maryland, USA
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21
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Means-Markwell M, Hawkins R, Reichow K, Gaglione M, Holmboe E, Malone JD, Hyams KC. A Survey of Women's Health Care Needs on U.S. Navy Ships. Mil Med 1998. [DOI: 10.1093/milmed/163.7.439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Means-Markwell M, Hawkins R, Reichow K, Gaglione M, Holmboe E, Malone JD, Hyams KC. A survey of women's health care needs on U.S. Navy ships. Mil Med 1998; 163:439-43. [PMID: 9695606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A total of 628 female and 526 male U.S. military personnel completed a health survey questionnaire at the completion of four shipboard deployments lasting 10 to 180 days (mean, 57 days). During deployment, women visited clinic (sick call) at significantly higher rates than men: 189 versus 117 visits per week per 1,000 personnel. Except for generally minor gynecological conditions, women and men had similar medical problems. Upper respiratory complaints and requests for contraceptive pills were the most common reasons for clinic visits among women. The majority of sailors felt that they had received appropriate medical care, although fewer women (66%) than men (78%) were satisfied. Levels of cigarette and alcohol use and sexual activity were comparable among women and men and corresponded to those of the general U.S. population of young adults. Because of high levels of health, most medical needs of women sailors can be managed readily by providing routine gynecological care and by minor additions to the shipboard pharmacy.
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Affiliation(s)
- M Means-Markwell
- Pulmonary Division, National Naval Medical Center, Bethesda, MD 20889-5600, USA
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23
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Abstract
Anthrax is a zoonotic illness recognized since antiquity. Today, human anthrax has been all but eradicated from the industrialized world, with the vast majority of practitioners in the United States unlikely to have seen a case. Unfortunately, the disease remains endemic in many areas of the world, and anthrax poses a threat as a mass casualty-producing weapon if used in a biological warfare capacity.
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Affiliation(s)
- J C Pile
- Infectious Diseases Division, National Naval Medical Center, Bethesda, Md 20889-5600, USA
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24
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Buford WL, Ivey FM, Malone JD, Patterson RM, Peare GL, Nguyen DK, Stewart AA. Muscle balance at the knee--moment arms for the normal knee and the ACL-minus knee. IEEE Trans Rehabil Eng 1997; 5:367-79. [PMID: 9422462 DOI: 10.1109/86.650292] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Forces, moments and stresses at the knee are dependent upon external and internal loading factors including muscle forces, segmental position and velocity, load carried, and the moment arms (mechanical advantage) of the muscle-tendon units. Requisite to prediction of forces and moments is a detailed understanding of effective moment arms throughout the knee range-of-motion (ROM). Existing muscle models for the knee are based upon limited static studies of only a few preserved specimens. The objectives of this report are to develop a comprehensive description of muscle-tendon moment arms for the normal knee and the anterior cruciate ligament (ACL)-minus knee during flexion-extension motion. Recent research results describe two nonorthogonal, nonintersecting axes of motion for the knee--one describing flexion-extension (FE) and the other longitudinal rotation (LR, equivalent to internal-external rotation). The effective flexion-extension moment arms of the muscles crossing the knee were developed with respect to the FE axis in 15 fresh, hemi-pelvis cadaver specimens. The normal moment arms for each of 13 muscles plus the patellar tendon exhibited variable, yet repeatable and recognizable patterns throughout the ROM. For most muscles there was no significant difference between the normal and ACL-minus moment arms. The results provide a basis for more accurate predictions of joint reaction forces and moments as well as useful knowledge for practitioners and therapists to assist in the assessment of muscle balance at the knee following injury, repair, and throughout rehabilitation.
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Affiliation(s)
- W L Buford
- Biomechanics Laboratory, Orthopaedic Surgery and Rehabilitation, University of Texas Medical Branch, Galveston 77555, USA
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25
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Brown AE, Malone JD, Zhou SY, Lane JR, Hawkes CA. Human immunodeficiency virus RNA levels in US adults: a comparison based upon race and ethnicity. J Infect Dis 1997; 176:794-7. [PMID: 9291336 DOI: 10.1086/517304] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [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: 02/05/2023] Open
Abstract
Volunteers in a natural history study of human immunodeficiency virus type 1 (HIV-1) at two military medical centers were studied to determine whether plasma HIV-1 RNA levels differ among racial and ethnic groups of US adults infected with HIV-1. Cross-sectional analyses of plasma HIV-1 RNA and CD4 cell counts were done using demographic and clinical data collected during study visits. Age, gender, CD4 cell count, seroconversion status, and use of antiretroviral therapy were studied in 545 military members (46% white, 49% black, and 6% Hispanic). No association was found between HIV-1 RNA levels and race or ethnicity among infected adults for whom access to care and socioeconomic status were not confounding factors.
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Affiliation(s)
- A E Brown
- Combined Military Diagnostic Retrovirology Service, Walter Reed Army Institute of Research, Henry M. Jackson Foundation, and SRA Technologies, Rockville, Maryland, USA
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26
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Malone JD, Paige-Dobson B, Ohl C, DiGiovanni C, Cunnion S, Roy MJ. Possibilities for unexplained chronic illnesses among reserve units deployed in Operation Desert Shield/Desert Storm. South Med J 1996; 89:1147-55. [PMID: 8969346 DOI: 10.1097/00007611-199612000-00003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [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: 02/03/2023]
Abstract
Because Armed Forces Reserve members, especially combat support units, were rapidly mobilized during Operation Desert Shield/Desert Storm, they were at higher risk for anxiety and stress-related disorders. Personnel in reserve units in the military force structure are at greater risk for psychologic stress due to rapid mobilization and demobilization, which allows minimal time to process adverse experiences or fears. The unexpected disruption of families and careers and resulting financial pressures are magnified in older age groups who have increased personal and family commitments. Personnel in combat support units are at greatest risk when they lack necessary training, cohesion, and leadership. Prevention efforts in reserve units should involve education regarding the potential for activation and associated disruption of family and career plans. Support networks for reserve families should be encouraged. Additional training in an appropriate context regarding risks of biologic and chemical exposure, with the goal of developing confidence in training and equipment, should be stressed. Finally, group processing before demobilization and recall within 90 days of return to emphasize unit cohesion and readjustment to civilian life may be of benefit.
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Affiliation(s)
- J D Malone
- Infectious Disease Division, National Naval Medical Center, Bethesda, Md 20889-5600, USA
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27
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Abstract
Pre- and postdeployment serum samples obtained from U.S. marines in Operations Desert Shield and Desert Storm were tested for antibodies to Shigella sonnei. High predeployment levels of immunoglobulin A (IgA) and/or IgG antibodies to S. sonnei lipopolysaccharide antigen in serum and seroconversions were accompanied by higher IgA and/or IgG antibody response to Shigella invasion plasmids (Ipa). The results suggest exposure to S. sonnei in predeployment troops and frequent exposure to this bacterial agent during deployment.
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Affiliation(s)
- M M Mikhail
- U.S. Naval Medical Research Unit No. 3, Cairo, Egypt
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28
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Abstract
Falciparum malaria was a major problem among displaced Haitians in temporary camps at the US Naval Base, Guantanamo Bay, Cuba. From December 1991 to March 1992, 235 cases of unmixed falciparum malaria were diagnosed in the laboratory, giving a cumulative attack rate of 160 per 10 000 camp residents. All cases were successfully treated with oral chloroquine. Children under 16 years of age, and especially females, were at substantially higher risk of infection (attack rate 481/10 000 versus 278/ 10 000 for males in the same age range). Malaria attack rates by place of birth in Haiti were calculated per 10 000 people as Cayemite, 530; Baraderes, 375; Pestel, 285; Port Au Prince, 247; and La Gonave, 36. The time to onset of clinical malaria after embarking at the Naval Base ranged from one to 58 d. No malaria transmission was demonstrated in the migrant camp. A non-systematic survey showed a 1.7% prevalence (95% confidence interval +/- 1.9%) of falciparum malaria among asymptomatic residents. Health practitioners in areas that may receive Haitian migrants should plan to care for malaria and preventive medicine measures are indicated, as imported malaria could be transmitted in areas where competent vectors are indigenous.
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Affiliation(s)
- M P Bawden
- Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
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29
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Hyams KC, Malone JD, Bourgeois AL, Hawkins R, Hale TL, Murphy JR. Serum antibody to lipopolysaccharide antigens of Shigella species among U.S. military personnel deployed to Saudi Arabia and Kuwait during Operations Desert Shield and Desert Storm. Clin Diagn Lab Immunol 1995; 2:700-3. [PMID: 8574833 PMCID: PMC170224 DOI: 10.1128/cdli.2.6.700-703.1995] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
During Operations Desert Shield and Desert Storm, U.S. troops were at high risk of diarrheal disease due to Shigella spp., particularly Shigella sonnei. In order to better understand the serologic response to Shigella infection, 830 male U.S. combat troops were evaluated before and after the deployment to Saudi Arabia and Kuwait for immunoglobulin A (IgA) and IgG anti-Shigella lipopolysaccharide (LPS) (antibody to S. sonnei form I and Shigella flexneri serotypes 1a, 2a, and 3a) in serum. Just before deployment, 10.3% of the subjects were seropositive for IgA and 18.3% were positive for IgG anti-Shigella LPS. IgA and IgG anti-LPS antibody levels in serum prior to deployment were significantly associated with nonwhite race and ethnicity, birth outside the United States, and antibody to hepatitis A virus and Helicobacter pylori. During the deployment, which lasted for a mean of 131 days, 60% of the subjects reported at least one episode of diarrhea and 15% reported an episode of diarrhea with feverishness; also, 5.5% of the subjects exhibited IgA seroconversion to Shigella LPS and 14.0% exhibited IgG seroconversion. A significant association between the development of diarrheal symptoms and either positive predeployment anti-LPS antibody or seroconversion was not found. These data indicate that in this population of U.S. Desert Storm troops who were at high risk of Shigella infection, there was no apparent relation between IgA or IgG anti-Shigella LPS in serum and diarrheal disease.
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Affiliation(s)
- K C Hyams
- Infectious Diseases Department, U.S. Naval Medical Research Institute, Rockville, Maryland 20852, USA
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Hyams KC, Taylor DN, Gray GC, Knowles JB, Hawkins R, Malone JD. The risk of Helicobacter pylori infection among U.S. military personnel deployed outside the United States. Am J Trop Med Hyg 1995; 52:109-12. [PMID: 7856819 DOI: 10.4269/ajtmh.1995.52.109] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [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: 01/27/2023] Open
Abstract
To determine whether military personnel deployed outside the United States are at increased risk of Helicobacter pylori infection, 1,000 male U.S. Navy and Marine Corps personnel (mean age 22 years) were evaluated. Study subjects included 200 recruits, 500 shipboard personnel deployed for six months to South America, West Africa, and the Mediterranean, and 300 ground troops deployed for five months to Saudi Arabia. Among all 1,000 subjects, 247 (25%) were seropositive for H. pylori IgG antibody by an enzyme-linked immunosorbent assay; 24% of new recruits and 25% of troops who had been on active duty for a mean of four years. The prevalence of H. pylori antibody was higher among subjects who were older, nonwhite, foreign-born, and seropositive for antibody to hepatitis A virus. Among the 601 initially seronegative subjects evaluated before and after a 5-6 month deployment outside the United States, five seroconverted, for a rate of infection of 1.9% per person-year of exposure. As found in other populations in developed countries, these data indicate that among U.S. military personnel a large proportion of H. pylori infections occur before adulthood and infection is related to demographic factors. These preliminary findings also suggest that deployed U.S. military personnel may be at increased risk of H. pylori infection compared with adult populations in developed countries either from exposure in developing countries or from crowding.
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Affiliation(s)
- K C Hyams
- Infectious Diseases Threat Assessment Division, U.S. Naval Medical Research Institute, Bethesda, Maryland
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Malone JL, Paparello SF, Malone JD, Hill HE, Conrad KA, Myers JW, Lillibridge SR, Weiss PJ. Drug susceptibility of Mycobacterium tuberculosis isolates from recent Haitian migrants: correlation with clinical response. Clin Infect Dis 1994; 19:938-40. [PMID: 7893883 DOI: 10.1093/clinids/19.5.938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [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: 01/27/2023] Open
Abstract
Between November 1991 and June 1993, approximately 11,000 Haitian migrants were screened for active tuberculosis and human immunodeficiency virus type 1 (HIV-1) infection at the U.S. Naval Base in Guantánamo Bay, Cuba. Cultures of specimens from 37 of these patients yielded Mycobacterium tuberculosis; eight (22%) of these isolates were resistant to standard medications, including isoniazid (22%), rifampin (0), ethambutol (3%), and streptomycin (3%). Two isolates (5.4%) were resistant to two drugs simultaneously. All but one of 340 patients who were treated for presumptive active tuberculosis and who were followed up for about 1 month had a favorable initial clinical response to a standard four-drug regimen. Among 259 HIV-1-infected patients who had normal findings on screening chest radiographs and who received prophylaxis with isoniazid, there were 1.8 incident cases of active tuberculosis per 100 person-years; this rate was 76% lower than that (reported by others) among HIV-1-infected Haitian patients who were not treated with isoniazid. No serious toxic effects due to standard four-drug regimens or to prophylaxis with isoniazid were observed. These data suggest that standard empirical therapeutic interventions for tuberculosis are adequate and well tolerated in Haitian migrants.
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Affiliation(s)
- J L Malone
- Infectious Diseases Division, National Naval Medical Center, Bethesda, Maryland 20889-5600
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Sharp TW, Yip R, Malone JD. US military forces and emergency international humanitarian assistance. Observations and recommendations from three recent missions. JAMA 1994; 272:386-90. [PMID: 8028171] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- T W Sharp
- Naval Medical Research Institute, Bethesda, Md
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Ohl CA, Hyams KC, Malone JD, Oldfield E. Leishmaniasis among Desert Storm veterans: a diagnostic and therapeutic dilemma. Mil Med 1993; 158:726-9. [PMID: 8284061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Troops stationed in the Middle East during Operations Desert Shield/Storm were potentially exposed to leishmaniasis, a parasitic infection transmitted by sandflies. In this region, infection primarily causes cutaneous and, less often, visceral disease. Visceral leishmaniasis, which typically has an incubation period of several months, can be a difficult diagnosis as it presents with a wide range of symptoms and there are no non-invasive, reliable diagnostic tests. Cutaneous leishmaniasis is more easily diagnosed using culture and stained smears of biopsy and aspirate samples from skin lesions. Pentavalent antimonials are most often used to treat leishmaniasis; however, treatment is potentially toxic and not recommended except in cases of documented disease.
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Affiliation(s)
- C A Ohl
- Infectious Diseases Division, National Naval Medical Center, Bethesda, MD 20889-5600
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Affiliation(s)
- Christopher A. Ohl
- Infectious Diseases Division, National Naval Medical Center, Bethesda, MD
| | - Kenneth C. Hyams
- Epidemiology Division, Naval Medical Research Institute, Bethesda, MD
| | - John D. Malone
- Infectious Diseases Division, National Naval Medical Center, Bethesda, MD
| | - Edward Oldfield
- Infectious Diseases Division, San Diego Naval Hospital, San Diego, CA
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Richards AL, Malone JD, Sheris S, Weddle JR, Rossi CA, Ksiazek TG, LeDuc JW, Dasch GA, Hyams KC. Arbovirus and rickettsial infections among combat troops during Operation Desert Shield/Desert Storm. J Infect Dis 1993; 168:1080-1. [PMID: 8376827 DOI: 10.1093/infdis/168.4.1080] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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36
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Malone JL, Paparello SF, Malone JD, Hill HE, Myers JW, Weiss P. Tuberculosis and HIV infection. Lancet 1993; 342:677. [PMID: 8103159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Abstract
BACKGROUND AND OBJECTIVES Information regarding risk factors for STD transmission is needed to assist in designing and evaluating prevention and control programs for US military populations. GOAL OF THIS STUDY To obtain STD risk factor data among deployed U.S. military personnel. STUDY DESIGN A questionnaire survey was administered to military personnel deployed aboard ship for six months to South America, West Africa, and the Mediterranean during 1989-1991. RESULTS Among 1,744 male subjects (mean age, 23 years; 71% white; 96% enlisted), 49% reported prior sexual contact with a prostitute and 22% reported a history of a STD before deployment. During the subsequent six-month deployment, 42% reported sexual contact with a prostitute, 10% reported inconsistent use of condoms, and 10% acquired a new STD. By logistic regression analysis, sexual contact with a prostitute during deployment was independently associated with young age, nonwhite race/ethnicity, and being unmarried or divorced; inconsistent use of condoms was associated with Hispanic race/ethnicity. CONCLUSION These data indicate that deployed U.S. military personnel frequently engage in high-risk sexual behavior and that there is a continued need for comprehensive and culturally-sensitive STD prevention programs.
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Affiliation(s)
- J D Malone
- Infectious Disease Division, National Naval Medical Center, Bethesda, Maryland 50014-5000
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Hyams KC, Malone JD, Kapikian AZ, Estes MK, Xi J, Bourgeois AL, Paparello S, Hawkins RE, Green KY. Norwalk virus infection among Desert Storm troops. J Infect Dis 1993; 167:986-7. [PMID: 8383727 DOI: 10.1093/infdis/167.4.986] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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Malone JD, Smith ES, Sheffield J, Bigelow D, Hyams KC, Beardsley SG, Lewis RS, Roberts CR. Comparative evaluation of six rapid serological tests for HIV-1 antibody. J Acquir Immune Defic Syndr (1988) 1993; 6:115-9. [PMID: 8433277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Six commercial rapid test kits for HIV-1 antibody were evaluated. Four laboratory technologists tested sera from four groups of U.S. military personnel or dependents: 202 subjects positive for HIV-1 antibody by Western blot, 200 seronegative voluntary blood donors, 199 seronegative obstetrics/gynecology patients, and 99 subjects with sera reactive by ELISA but negative by recombinant protein EIA and indeterminate by Western blot. The three tests using solid-phase immunoassay technology demonstrated the highest mean sensitivity (> 99%) and specificity (> 91%) for all groups tested, including sera indeterminate by Western blot. Two dot-immunoblot assays were less specific, possibly due to indistinct reaction end points, and a latex agglutination assay was also less specific because of difficulty distinguishing reactive results from the granular background. In an "ease-of-use" assessment, solid-phase capture immunoassays required less time and equipment and were easier to interpret than other testing methods. Solid-phase capture immunoassays for HIV-1 antibody may be suitable for use in emergency situations and in developing countries because they are highly sensitive and specific and are rapidly performed with minimal laboratory equipment.
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Affiliation(s)
- J D Malone
- Infectious Disease Division, National Naval Medical Center, Bethesda, MD 50014-5000
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Ramphal R, Bolger M, Oblon DJ, Sherertz RJ, Malone JD, Rand KH, Gilliom M, Shands JW, Kramer BS. Vancomycin is not an essential component of the initial empiric treatment regimen for febrile neutropenic patients receiving ceftazidime: a randomized prospective study. Antimicrob Agents Chemother 1992; 36:1062-7. [PMID: 1510394 PMCID: PMC188836 DOI: 10.1128/aac.36.5.1062] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.1] [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: 12/27/2022] Open
Abstract
The use of vancomycin as part of the initial antibiotic therapy of febrile neutropenic patients has become a controversial issue. Some studies support its incorporation in the initial regimen, and others suggest that vancomycin can be added later. We examined this issue in a prospective, randomized trial. We randomized 127 febrile neutropenic patients to receive either ceftazidime alone or ceftazidime plus vancomycin as the initial empiric antibiotic treatment. We added vancomycin to the ceftazidime arm of the study when fever persisted after 96 h of monotherapy, when new fever occurred after this time, or when a moderately ceftazidime-resistant gram-positive bacterium was isolated. Each of these regimens had similar initial response rates, similar durations of initial fever, similar frequencies of new fever during therapy, similar microbiological cure rates, similar superinfection rates, and similar survival rates. We observed more renal and cutaneous toxicities in patients receiving vancomycin and ceftazidime as initial therapy. We conclude that ceftazidime is appropriate as initial therapy for febrile neutropenic patients and that the addition of vancomycin is appropriate when fever persists after 4 days of monotherapy or when fever recurs following an initial response.
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Affiliation(s)
- R Ramphal
- Department of Medicine, University of Florida, Gainesville 32610-0277
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Hawkins RE, Malone JD, Cloninger LA, Rozmajzl PJ, Lewis D, Butler J, Cross E, Gray S, Hyams KC. Risk of viral hepatitis among military personnel assigned to US Navy ships. J Infect Dis 1992; 165:716-9. [PMID: 1552201 DOI: 10.1093/infdis/165.4.716] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [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: 12/27/2022] Open
Abstract
A prevalence study of 2072 male US shipboard military personnel scheduled for deployment to South America/West Africa and the Mediterranean was conducted to determine whether serologic evidence of prior hepatitis A, B, or C infection is associated with exposure in foreign countries. There were 210 subjects (10.1%) who had antibodies to hepatitis A virus (anti-HAV), 76 (3.7%) to hepatitis B core antigen (anti-HBc), and 9 (0.4%) to hepatitis C virus (anti-HCV). By multivariate analysis, anti-HAV seropositivity was independently associated with age, non-white racial/ethnic groups, birth outside of the United States, and prior Caribbean deployment for less than 1 year. Anti-HBc seropositivity was independently associated with black and Filipino race/ethnicity, foreign birth, a history of a sexually transmitted disease, South Pacific/Indian Ocean deployment (less than 12 months), and South Pacific or Mediterranean duty for (greater than 1 year). No geographic risk factors were associated with anti-HCV positivity. These data indicate that military personnel deployed outside the United States are at increased risk of viral hepatitis infection and should be considered for vaccination.
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Affiliation(s)
- R E Hawkins
- Department of Internal Medicine, Uniformed Services University of the Health Sciences, Bethesda Naval Hospital, Maryland
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Abstract
Type I collagen is highly susceptible to proteolytic cleavage by neutral mammalian collagenase. Following an initial site specific cleavage of the substrate, two characteristic products are generated, TCA and TCB. These two products then spontaneously denature and are degraded into multiple smaller molecular weight peptides. We prepared TCA and TCB from native type I collagen by the action of rat uterine fibroblast neutral collagenase. In addition we prepared denatured type I alpha chains and exposed them to the action of collagenase under controlled conditions in order to generate small molecular weight peptides. We then examined intact type I collagen, TCA and TCB and type I gelatin peptides for chemotactic activity in a Boyden chamber assay using both human peripheral monocytes and polymorphonuclear leucocytes as target cells. Intact type I collagen, while chemotactic for neutrophils, failed to elicit any chemotactic response in mononuclear cells. In addition, the results demonstrate an absence of any detectable chemotactic activity for either TCA or TCB when human peripheral monocytes were used as the target cells. However, type I collagen peptides demonstrated chemotactic activity for peripheral monocytes. Maximum cell migration was found with digests which had been exposed to neutral mammalian collagenase for three to four hours. No chemotactic activity was found using the same peptides, when neutrophils were used as the target cells. The data strongly suggest that chemotactic activity for mononuclear cells, normally suppressed in intact type I collagen, is revealed and/or activated by neutral collagenase digestion. Conversely, chemotactic activity for neutrophils is lost when intact type I collagen is digested into smaller molecular weight fragments.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J D Malone
- Department of Medicine, St. Louis University, MO
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Tanaka H, Hruska KA, Seino Y, Malone JD, Nishii Y, Teitelbaum SL. Disassociation of the macrophage-maturational effects of vitamin D from respiratory burst priming. J Biol Chem 1991; 266:10888-92. [PMID: 1645714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
During the process of enhancing monocytic differentiation of the human leukemia line HL-60, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) also "primes" the cell for respiratory burst by increasing the uptake of Ca2+ across the plasma membrane (Hruska, K.A., Bar-Shavit, Z., Malone, J.D., and Teitelbaum, S.L. (1988) J. Biol. Chem. 263, 16039-16044). The present study asked if the maturational effect of vitamin D is dependent upon this "priming" phenomenon. To this end, we exposed HL-60 to either 1,25(OH)2D3 or its synthetic analogue (1 alpha, 3 beta, 5Z, 7E)-9-10-Secocholesta-5,7,10(19)-triene-1, 3, 25-triol (22-oxa). We found that 22-oxa induced HL-60 maturation as effectively as does the natural steroid. As expected, 48 h of 1,25(OH)2D3 exposure more than doubles (p less than 0.005) HL-60 basal cytosolic Ca2+ and increases inositol triphosphate-sensitive Ca2+ stores approximately 4-fold (p less than 0.01). 22-oxa in contrast alters neither Ca(2+)- nor inositol triphosphate-mobilizable deposits. Moreover, 1,25(OH)2D3 treatment prompts a transient Ca2+ "spike" in response to formyl-methionyl-leucyl-phenylalanine (fMLP) and a marked increase in superoxide (O-2) generation when exposed to the chemotactic peptide (p less than 0.01) or phorbol ester (p less than 0.02). Treatment with 22-oxa does not enable HL-60 to respond to fMLP with a Ca2+ spike or prime the cell for respiratory burst unless it is co-incubated with the Ca2+ ionophore, ionomycin. Similarly, phorbol ester impacts more profoundly on O-2 generation by 1,25(OH)2D3 than 22-oxa preincubated cells (p less than 0.02), unless the latter is added with ionomycin. Our findings indicate that the maturational effects of vitamin D sterols are independent of their capacity to prime cells for respiratory burst and that the Ca2+ ionophoretic effects of 1,25(OH)2D3 play a major role in such priming.
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Affiliation(s)
- H Tanaka
- Department of Pathology, Jewish Hospital, Washington University Medical Center, St. Louis, Missouri 63110
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Hawkins RE, Malone JD, Ebbeling WL. Common variable hypogammaglobulinemia presenting as nontypable Haemophilus influenzae septic arthritis in an adult. J Rheumatol 1991; 18:775-6. [PMID: 1865431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Haemophilus influenzae is a rare cause of septic arthritis in adults. We describe a case of septic arthritis with nontypable Haemophilus influenzae presenting as the first invasive infection leading to a diagnosis of common variable hypogammaglobulinemia. Although nontypable strains have been shown to cause serious infections in adults, they are a rare cause of septic arthritis. Underlying immune deficiency should be considered in an adult who presents with invasive infection with Haemophilus influenzae, regardless of serotype.
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Affiliation(s)
- R E Hawkins
- Department of Internal Medicine, National Naval Medical Center, Bethesda, MD 20889-5000
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Pacifici R, Carano A, Santoro SA, Rifas L, Jeffrey JJ, Malone JD, McCracken R, Avioli LV. Bone matrix constituents stimulate interleukin-1 release from human blood mononuclear cells. J Clin Invest 1991; 87:221-8. [PMID: 1845868 PMCID: PMC295032 DOI: 10.1172/jci114975] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To test the hypothesis that mononuclear cells are stimulated to release interleukin 1 (IL-1) by bone fragments released in the bone microenvironment during the remodeling cycle, we have investigated the effects of bone matrix and some of its constituents on IL-1 secretin from peripheral blood mononuclear cells (PBMC). Increases in IL-1 activity were observed when either PBMC or adherent monocytes, but not lymphocytes depleted of monocytes, were co-cultured with either human or rat bone particles but not with latex particles of similar size. Co-culture of PBMC with bone particles in a transwell system where the cells were physically separated from the bone particles, or with osteoblast- or osteoclast-covered bone particles, did not stimulate IL-1 release, indicating that a physical contact between PBMC and the bone surface is required for eliciting IL-1 release. This was confirmed by the finding of a lower stimulatory effect of bone particles pretreated with etidronate, a bisphosphonate which decreases the bone binding capacity of PBMC. Constituents of bone matrix, such as collagen fragments, hydroxyproline, and, to a lesser extent, transforming growth factor-beta, but not osteocalcin, alpha 2HS glycoprotein, fragments of either bone sialoprotein or osteopontin, and fibronectin, stimulated PBMC IL-1 release in a dose-dependent fashion. Collagen-stimulated IL-1 release was partially and specifically inhibited by a monoclonal antibody directed against the alpha 2 beta 1-integrin cell surface collagen receptor. These data demonstrate that products of bone resorption, known to be chemotactic for mononuclear cells, stimulate PBMC IL-1 activity. These findings may help explain previous documentation of increased IL-1 secretion by circulating monocytes obtained from patients with high turnover osteoporosis.
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Affiliation(s)
- R Pacifici
- Division of Bone and Mineral Metabolism, Washington University School of Medicine and Medical Center, St. Louis, Missouri
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Hruska KA, Bar-Shavit Z, Malone JD, Teitelbaum S. Ca2+ priming during vitamin D-induced monocytic differentiation of a human leukemia cell line. J Biol Chem 1988; 263:16039-44. [PMID: 3182781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
1,25-Dihydroxyvitamin D3 (1,25-(OH)2D3) induces monocytic differentiation of the human promyelocytic leukemia line, HL-60, and enhances Ca2+ transport in target cells of the mineral metabolism system. Hence, we determined whether the steroid's maturational effect on HL-60 involves alterations of intracellular calcium [( Ca2+]i). We found that, as detected by indo-1 fluorescence, [Ca2+]i increases in a slow tonic manner from 99 +/- 11 nM in virgin HL-60 to 182 +/- 19 nM (p less than 0.001) in those treated with 1,25-(OH)2D3 for 24 h. The first apparent rise in [Ca2+]i occurs at between 6 and 12 h and parallels expression of alpha-thrombin and N-formyl-methionyl-leucyl-phenylalanine (fMLP) receptors. This increase in [Ca2+]i is derived from extracellular calcium as its reduction abolishes the effect. The increase in [Ca2+]i is associated with an increase in inositol trisphosphate-stimulated Ca2+ flux from intracellular stores. Interestingly, 1,25-(OH)2D3-mediated HL-60 differentiation as manifest by expression of the macrophage-specific antigen, 63D3, is not blocked by low extracellular calcium. In contrast, the fMLP-induced superoxide ion generation is diminished if the increase in [Ca2+]i is prevented. Furthermore, fMLP-stimulated signal transduction is also reduced by limiting the stimulation of [Ca2+]i during 1,25-(OH)2D3 treatment. Thus, although differentiation of HL-60 to the monocytic phenotype by 1,25-(OH)2D3 is Ca2+-independent, expression of response to regulatory stimuli requires priming of cellular Ca2+ stores. The latter appears to be induced by 1,25-(OH)2D3 via stimulated Ca2+ entry through the plasma membrane.
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Affiliation(s)
- K A Hruska
- Department of Medicine, Jewish Hospital, Washington University Medical Center, St. Louis, Missouri 63110
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Hruska KA, Bar-Shavit Z, Malone JD, Teitelbaum S. Ca2+ priming during vitamin D-induced monocytic differentiation of a human leukemia cell line. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37553-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Malone JD, Lebar RD, Hilder R. Procaine-induced seizures after intramuscular procaine penicillin G. Mil Med 1988; 153:191-2. [PMID: 3133585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Affiliation(s)
- John D. Malone
- Naval Medical Clinic, Internal Medicine Department, Pearl Harbor, Hawaii 96860
| | - Randi D. Lebar
- Naval Medical Clinic, Internal Medicine Department, Pearl Harbor, Hawaii 96860
| | - Richard Hilder
- Naval Medical Clinic, Internal Medicine Department, Pearl Harbor, Hawaii 96860
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