1
|
Xiao S, Abade A, Boru W, Kasambara W, Mwaba J, Ongole F, Mmanywa M, Trovão NS, Chilengi R, Kwenda G, Orach CG, Chibwe I, Bwire G, Stine OC, Milstone AM, Lessler J, Azman AS, Luo W, Murt K, Sack DA, Debes AK, Wohl S. New Vibrio cholerae sequences from Eastern and Southern Africa alter our understanding of regional cholera transmission. medRxiv 2024:2024.03.28.24302717. [PMID: 38585829 PMCID: PMC10996759 DOI: 10.1101/2024.03.28.24302717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Despite ongoing containment and vaccination efforts, cholera remains prevalent in many countries in sub-Saharan Africa. Part of the difficulty in containing cholera comes from our lack of understanding of how it circulates throughout the region. To better characterize regional transmission, we generated and analyzed 118 Vibrio cholerae genomes collected between 2007-2019 from five different countries in Southern and Eastern Africa. We showed that V. cholerae sequencing can be successful from a variety of sample types and filled in spatial and temporal gaps in our understanding of circulating lineages, including providing some of the first sequences from the 2018-2019 outbreaks in Uganda, Kenya, Tanzania, Zambia, and Malawi. Our results present a complex picture of cholera transmission in the region, with multiple lineages found to be co-circulating within several countries. We also find evidence that previously identified sporadic cases may be from larger, undersampled outbreaks, highlighting the need for careful examination of sampling biases and underscoring the need for continued and expanded cholera surveillance across the African continent.
Collapse
Affiliation(s)
- Shaoming Xiao
- Division of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ahmed Abade
- Ministry of Health, Dar es Salaam, Tanzania
- Field Epidemiology and Laboratory Training Program, Nairobi, Kenya
| | - Waqo Boru
- Field Epidemiology and Laboratory Training Program, Nairobi, Kenya
| | | | - John Mwaba
- Center for Infectious Disease Research, Zambia
- Department of Pathology and Microbiology, University Teaching Hospital, Lusaka, Zambia
| | | | | | | | - Roma Chilengi
- Zambia National Public Health Institute, Lusaka, Zambia
| | | | | | | | | | - O Colin Stine
- University of Maryland School of Medicine, Baltimore, USA
| | - Aaron M Milstone
- Division of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
| | - Andrew S Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Division of Tropical and Humanitarian Medicine, Geneva University Hospitals, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Wensheng Luo
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kelsey Murt
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - David A Sack
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Amanda K Debes
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Shirlee Wohl
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Santus L, Sopena-Rios M, García-Pérez R, Lin AE, Adams GC, Barnes KG, Siddle KJ, Wohl S, Reverter F, Rinn JL, Bennett RS, Hensley LE, Sabeti PC, Melé M. Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques. Nat Commun 2023; 14:3866. [PMID: 37391481 PMCID: PMC10313701 DOI: 10.1038/s41467-023-39627-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/19/2023] [Indexed: 07/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and are pivotal mediators of the immune response, yet little is known about their properties at the single-cell level. Here, we generate a multi-tissue bulk RNAseq dataset from Ebola virus (EBOV) infected and not-infected rhesus macaques and identified 3979 novel lncRNAs. To profile lncRNA expression dynamics in immune circulating single-cells during EBOV infection, we design a metric, Upsilon, to estimate cell-type specificity. Our analysis reveals that lncRNAs are expressed in fewer cells than protein-coding genes, but they are not expressed at lower levels nor are they more cell-type specific when expressed in the same number of cells. In addition, we observe that lncRNAs exhibit similar changes in expression patterns to those of protein-coding genes during EBOV infection, and are often co-expressed with known immune regulators. A few lncRNAs change expression specifically upon EBOV entry in the cell. This study sheds light on the differential features of lncRNAs and protein-coding genes and paves the way for future single-cell lncRNA studies.
Collapse
Affiliation(s)
- Luisa Santus
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Maria Sopena-Rios
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain
| | - Raquel García-Pérez
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain
| | - Aaron E Lin
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Program in Virology, Harvard Medical School, Boston, MA, 02115, USA
| | - Gordon C Adams
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kayla G Barnes
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Katherine J Siddle
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Shirlee Wohl
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- The Scripps Research Institute, Department of Immunology and Microbiology, La Jolla, CA, USA
| | - Ferran Reverter
- Department of Genetics, Microbiology and Statistics University of Barcelona, Barcelona, Spain
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, 80303, USA
| | - Richard S Bennett
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, 21702, USA
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, 21702, USA.
| | - Pardis C Sabeti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Harvard Program in Virology, Harvard Medical School, Boston, MA, 02115, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain.
| |
Collapse
|
4
|
Wohl S, Lee EC, DiPrete BL, Lessler J. Sample size calculations for pathogen variant surveillance in the presence of biological and systematic biases. Cell Rep Med 2023; 4:101022. [PMID: 37105175 DOI: 10.1016/j.xcrm.2023.101022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/08/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023]
Abstract
Tracking the emergence and spread of pathogen variants is an important component of monitoring infectious disease outbreaks. To that end, accurately estimating the number and prevalence of pathogen variants in a population requires carefully designed surveillance programs. However, current approaches to calculating the number of pathogen samples needed for effective surveillance often do not account for the various processes that can bias which infections are detected and which samples are ultimately characterized as a specific variant. In this article, we introduce a framework that accounts for the logistical and epidemiological processes that may bias variant characterization, and we demonstrate how to use this framework (implemented in a publicly available tool) to calculate the number of sequences needed for surveillance. Our framework is designed to be easy to use while also flexible enough to be adapted to various pathogens and surveillance scenarios.
Collapse
Affiliation(s)
- Shirlee Wohl
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Elizabeth C Lee
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Bethany L DiPrete
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; The Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
5
|
Oliveira G, Vogels CBF, Zolfaghari A, Saraf S, Klitting R, Weger-Lucarelli J, P. Leon K, Ontiveros CO, Agarwal R, Tsetsarkin KA, Harris E, Ebel GD, Wohl S, Grubaugh ND, Andersen KG. Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages. PLoS Negl Trop Dis 2023; 17:e0011055. [PMID: 36753510 PMCID: PMC9907835 DOI: 10.1371/journal.pntd.0011055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 12/22/2022] [Indexed: 02/09/2023] Open
Abstract
RNA viruses have short generation times and high mutation rates, allowing them to undergo rapid molecular evolution during epidemics. However, the extent of RNA virus phenotypic evolution within epidemics and the resulting effects on fitness and virulence remain mostly unknown. Here, we screened the 2015-2016 Zika epidemic in the Americas for lineage-specific fitness differences. We engineered a library of recombinant viruses representing twelve major Zika virus lineages and used them to measure replicative fitness within disease-relevant human primary cells and live mosquitoes. We found that two of these lineages conferred significant in vitro replicative fitness changes among human primary cells, but we did not find fitness changes in Aedes aegypti mosquitoes. Additionally, we found evidence for elevated levels of positive selection among five amino acid sites that define major Zika virus lineages. While our work suggests that Zika virus may have acquired several phenotypic changes during a short time scale, these changes were relatively moderate and do not appear to have enhanced transmission during the epidemic.
Collapse
Affiliation(s)
- Glenn Oliveira
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Ashley Zolfaghari
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sharada Saraf
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Raphaelle Klitting
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Karla P. Leon
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Carlos O. Ontiveros
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Rimjhim Agarwal
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Konstantin A. Tsetsarkin
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Gregory D. Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- * E-mail: (NDG); (KGA)
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (NDG); (KGA)
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Fuesslin V, Krautwurst S, Srivastava A, Winter D, Liedigk B, Thye T, Herrera-León S, Wohl S, May J, Fobil JN, Eibach D, Marz M, Schuldt K. Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon. Front Microbiol 2022; 13:909692. [PMID: 35814690 PMCID: PMC9257098 DOI: 10.3389/fmicb.2022.909692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 12/01/2022] Open
Abstract
During the last decades, antimicrobial resistance (AMR) has become a global public health concern. Nowadays multi-drug resistance is commonly observed in strains of Vibrio cholerae, the etiological agent of cholera. In order to limit the spread of pathogenic drug-resistant bacteria and to maintain treatment options the analysis of clinical samples and their AMR profiles are essential. Particularly, in low-resource settings a timely analysis of AMR profiles is often impaired due to lengthy culturing procedures for antibiotic susceptibility testing or lack of laboratory capacity. In this study, we explore the applicability of whole genome sequencing for the prediction of AMR profiles of V. cholerae. We developed the pipeline CholerAegon for the in silico prediction of AMR profiles of 82 V. cholerae genomes assembled from long and short sequencing reads. By correlating the predicted profiles with results from phenotypic antibiotic susceptibility testing we show that the prediction can replace in vitro susceptibility testing for five of seven antibiotics. Because of the relatively low costs, possibility for real-time data analyses, and portability, the Oxford Nanopore Technologies MinION sequencing platform-especially in light of an upcoming less error-prone technology for the platform-appears to be well suited for pathogen genomic analyses such as the one described here. Together with CholerAegon, it can leverage pathogen genomics to improve disease surveillance and to control further spread of antimicrobial resistance.
Collapse
Affiliation(s)
- Valeria Fuesslin
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sebastian Krautwurst
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Akash Srivastava
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Doris Winter
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Britta Liedigk
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Thorsten Thye
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Silvia Herrera-León
- National Center of Microbiology, Institute of Health Carlos III, Madrid, Spain
| | - Shirlee Wohl
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Jürgen May
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Tropical Medicine II, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Julius N. Fobil
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Accra, Ghana
| | - Daniel Eibach
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Kathrin Schuldt
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Gniazdowski V, Paul Morris C, Wohl S, Mehoke T, Ramakrishnan S, Thielen P, Powell H, Smith B, Armstrong DT, Herrera M, Reifsnyder C, Sevdali M, Carroll KC, Pekosz A, Mostafa HH. Repeated Coronavirus Disease 2019 Molecular Testing: Correlation of Severe Acute Respiratory Syndrome Coronavirus 2 Culture With Molecular Assays and Cycle Thresholds. Clin Infect Dis 2021; 73:e860-e869. [PMID: 33104776 PMCID: PMC7665437 DOI: 10.1093/cid/ciaa1616] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Repeated coronavirus disease 2019 (COVID-19) molecular testing can lead to positive test results after negative results and to multiple positive results over time. The association between positive test results and infectious virus is important to quantify. METHODS A 2-month cohort of retrospective data and consecutively collected specimens from patients with COVID-19 or patients under investigation were used to understand the correlation between prolonged viral RNA positive test results, cycle threshold (Ct) values and growth of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in cell culture. Whole-genome sequencing was used to confirm virus genotype in patients with prolonged viral RNA detection. Droplet digital polymerase chain reaction was used to assess the rate of false-negative COVID-19 diagnostic test results. RESULTS In 2 months, 29 686 specimens were tested and 2194 patients underwent repeated testing. Virus recovery in cell culture was noted in specimens with a mean Ct value of 18.8 (3.4) for SARS-CoV-2 target genes. Prolonged viral RNA shedding was associated with positive virus growth in culture in specimens collected up to 21 days after the first positive result but mostly in individuals symptomatic at the time of sample collection. Whole-genome sequencing provided evidence the same virus was carried over time. Positive test results following negative results had Ct values >29.5 and were not associated with virus culture. Droplet digital polymerase chain reaction results were positive in 5.6% of negative specimens collected from patients with confirmed or clinically suspected COVID-19. CONCLUSIONS Low Ct values in SARS-CoV-2 diagnostic tests were associated with virus growth in cell culture. Symptomatic patients with prolonged viral RNA shedding can also be infectious.
Collapse
Affiliation(s)
- Victoria Gniazdowski
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - C Paul Morris
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- National Institutes of Allergy and Infectious Disease, Bethesda, Maryland, USA
| | - Shirlee Wohl
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Thomas Mehoke
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland,USA
| | | | - Peter Thielen
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland,USA
| | | | | | - Derek T Armstrong
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | - Karen C Carroll
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
11
|
Wohl S, Giles JR, Lessler J. Sample size calculation for phylogenetic case linkage. PLoS Comput Biol 2021; 17:e1009182. [PMID: 34228722 PMCID: PMC8284614 DOI: 10.1371/journal.pcbi.1009182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 07/16/2021] [Accepted: 06/14/2021] [Indexed: 12/16/2022] Open
Abstract
Sample size calculations are an essential component of the design and evaluation of scientific studies. However, there is a lack of clear guidance for determining the sample size needed for phylogenetic studies, which are becoming an essential part of studying pathogen transmission. We introduce a statistical framework for determining the number of true infector-infectee transmission pairs identified by a phylogenetic study, given the size and population coverage of that study. We then show how characteristics of the criteria used to determine linkage and aspects of the study design can influence our ability to correctly identify transmission links, in sometimes counterintuitive ways. We test the overall approach using outbreak simulations and provide guidance for calculating the sensitivity and specificity of the linkage criteria, the key inputs to our approach. The framework is freely available as the R package phylosamp, and is broadly applicable to designing and evaluating a wide array of pathogen phylogenetic studies. Sequencing the genetic material of viral and bacterial pathogens has become an important part of tracking and combating human infectious diseases. Specifically, comparing the pathogen DNA or RNA sequences collected from infected individuals can allow researchers and public health experts to determine who infected whom, or detect when a pathogen entered a specific country or geographic area. However, it is often impossible to collect samples from every single infected person, and these missing sequences can pose problems for this type of analysis, especially if there is some bias behind which samples were selected for sequencing. We have developed a mathematical framework that allows users to determine the probability their conclusions about pathogen transmission are correct given the number and proportion of samples from a pathogen outbreak they have sequenced. This framework is freely available, easy to use, and broadly generalizable to any pathogen, and we hope that it can be used to inform the design and sampling strategies behind future sequencing-based studies.
Collapse
Affiliation(s)
- Shirlee Wohl
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland, United States of America
| | - John R Giles
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland, United States of America
| | - Justin Lessler
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland, United States of America
| |
Collapse
|
12
|
Ekeng E, Tchatchouang S, Akenji B, Issaka BB, Akintayo I, Chukwu C, Dano ID, Melingui S, Ousmane S, Popoola MO, Nzouankeu A, Boum Y, Luquero F, Ahumibe A, Naidoo D, Azman A, Lessler J, Wohl S. Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa. eLife 2021; 10:e65159. [PMID: 34143732 PMCID: PMC8213408 DOI: 10.7554/elife.65159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/05/2021] [Indexed: 11/23/2022] Open
Abstract
Background Despite recent insights into cholera transmission patterns in Africa, regional and local dynamics in West Africa-where cholera outbreaks occur every few years-are still poorly understood. Coordinated genomic surveillance of Vibrio cholerae in the areas most affected may reveal transmission patterns important for cholera control. Methods During a regional sequencing workshop in Nigeria, we sequenced 46 recent V. cholerae isolates from Cameroon, Niger, and Nigeria (37 from 2018 to 2019) to better understand the relationship between the V. cholerae bacterium circulating in these three countries. Results From these isolates, we generated 44 whole Vibrio cholerae O1 sequences and analyzed them in the context of 1280 published V. cholerae O1 genomes. All sequences belonged to the T12 V. cholerae seventh pandemic lineage. Conclusions Phylogenetic analysis of newly generated and previously published V. cholerae genomes suggested that the T12 lineage has been continuously transmitted within West Africa since it was first observed in the region in 2009, despite lack of reported cholera in the intervening years. The results from this regional sequencing effort provide a model for future regionally coordinated surveillance efforts. Funding Funding for this project was provided by Bill and Melinda Gates Foundation OPP1195157.
Collapse
Affiliation(s)
- Eme Ekeng
- Nigeria Centre for Disease ControlAbujaNigeria
| | | | | | | | - Ifeoluwa Akintayo
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | | | | | - Sani Ousmane
- Centre de Recherche Médicale et SanitaireNiameyNiger
| | | | | | | | | | | | | | - Andrew Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Shirlee Wohl
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| |
Collapse
|
13
|
Thielen PM, Wohl S, Mehoke T, Ramakrishnan S, Kirsche M, Falade-Nwulia O, Trovão NS, Ernlund A, Howser C, Sadowski N, Morris CP, Hopkins M, Schwartz M, Fan Y, Gniazdowski V, Lessler J, Sauer L, Schatz MC, Evans JD, Ray SC, Timp W, Mostafa HH. Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area. JCI Insight 2021; 6:144350. [PMID: 33749660 PMCID: PMC8026189 DOI: 10.1172/jci.insight.144350] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/10/2021] [Indexed: 01/19/2023] Open
Abstract
The early COVID-19 pandemic was characterized by rapid global spread. In Maryland and Washington, DC, United States, more than 2500 cases were reported within 3 weeks of the first COVID-19 detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2 — the virus that causes COVID-19 — in the region. We analyzed 620 samples collected from the Johns Hopkins Health System during March 11–31, 2020, comprising 28.6% of the total cases in Maryland and Washington, DC. From these samples, we generated 114 complete viral genomes. Analysis of these genomes alongside a subsampling of over 1000 previously published sequences showed that the diversity in this region rivaled global SARS-CoV-2 genetic diversity at that time and that the sequences belong to all of the major globally circulating lineages, suggesting multiple introductions into the region. We also analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and found that clinically severe cases had viral genomes belonging to all major viral lineages. We conclude that efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and the interconnectedness of the region as a whole.
Collapse
Affiliation(s)
- Peter M Thielen
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Shirlee Wohl
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Thomas Mehoke
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | | | - Melanie Kirsche
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA
| | - Oluwaseun Falade-Nwulia
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nídia S Trovão
- NIH, Fogarty International Center, Bethesda, Maryland, USA
| | - Amanda Ernlund
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Craig Howser
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Norah Sadowski
- Department of Emergency Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - C Paul Morris
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark Hopkins
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthew Schwartz
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yunfan Fan
- Departments of Biomedical Engineering and Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Victoria Gniazdowski
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Justin Lessler
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Lauren Sauer
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Emergency Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jared D Evans
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Stuart C Ray
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Winston Timp
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Departments of Biomedical Engineering and Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
14
|
Jones FK, Wamala JF, Rumunu J, Mawien PN, Kol MT, Wohl S, Deng L, Pezzoli L, Omar LH, Lessler J, Quilici ML, Luquero FJ, Azman AS. Successive epidemic waves of cholera in South Sudan between 2014 and 2017: a descriptive epidemiological study. Lancet Planet Health 2020; 4:e577-e587. [PMID: 33278375 PMCID: PMC7750463 DOI: 10.1016/s2542-5196(20)30255-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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] [Received: 03/02/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Between 2014 and 2017, successive cholera epidemics occurred in South Sudan within the context of civil war, population displacement, flooding, and drought. We aim to describe the spatiotemporal and molecular features of the three distinct epidemic waves and explore the role of vaccination campaigns, precipitation, and population movement in shaping cholera spread in this complex setting. METHODS In this descriptive epidemiological study, we analysed cholera linelist data to describe the spatiotemporal progression of the epidemics. We placed whole-genome sequence data from pandemic Vibrio cholerae collected throughout these epidemics into the global phylogenetic context. Using whole-genome sequence data in combination with other molecular attributes, we characterise the relatedness of strains circulating in each wave and the region. We investigated the association of rainfall and the instantaneous basic reproduction number using distributed lag non-linear models, compared county-level attack rates between those with early and late reactive vaccination campaigns, and explored the consistency of the spatial patterns of displacement and suspected cholera case reports. FINDINGS The 2014 (6389 cases) and 2015 (1818 cases) cholera epidemics in South Sudan remained spatially limited whereas the 2016-17 epidemic (20 438 cases) spread among settlements along the Nile river. Initial cases of each epidemic were reported in or around Juba soon after the start of the rainy season, but we found no evidence that rainfall modulated transmission during each epidemic. All isolates analysed had similar genotypic and phenotypic characteristics, closely related to sequences from Uganda and Democratic Republic of the Congo. Large-scale population movements between counties of South Sudan with cholera outbreaks were consistent with the spatial distribution of cases. 21 of 26 vaccination campaigns occurred during or after the county-level epidemic peak. Counties vaccinated on or after the peak incidence week had 2·2 times (95% CI 2·1-2·3) higher attack rates than those where vaccination occurred before the peak. INTERPRETATION Pandemic V cholerae of the same clonal origin was isolated throughout the study period despite interepidemic periods of no reported cases. Although the complex emergency in South Sudan probably shaped some of the observed spatial and temporal patterns of cases, the full scope of transmission determinants remains unclear. Timely and well targeted use of vaccines can reduce the burden of cholera; however, rapid vaccine deployment in complex emergencies remains challenging. FUNDING The Bill & Melinda Gates Foundation.
Collapse
Affiliation(s)
- Forrest K Jones
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - John Rumunu
- Republic of South Sudan Ministry of Health, Juba, South Sudan
| | | | - Mathew Tut Kol
- Republic of South Sudan Ministry of Health, Juba, South Sudan
| | - Shirlee Wohl
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lul Deng
- Republic of South Sudan Ministry of Health, Juba, South Sudan
| | | | - Linda Haj Omar
- World Health Organization, Brazzaville, Republic of Congo
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | | | - Andrew S Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Médecins Sans Frontières, Geneva, Switzerland.
| |
Collapse
|
15
|
Thielen PM, Wohl S, Mehoke T, Ramakrishnan S, Kirsche M, Falade-Nwulia O, Trovão NS, Ernlund A, Howser C, Sadowski N, Morris P, Hopkins M, Schwartz M, Fan Y, Gniazdowski V, Lessler J, Sauer L, Schatz MC, Evans JD, Ray SC, Timp W, Mostafa HH. Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region. medRxiv 2020:2020.08.13.20174136. [PMID: 32817965 PMCID: PMC7430609 DOI: 10.1101/2020.08.13.20174136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND The early COVID-19 pandemic has been characterized by rapid global spread. In the United States National Capital Region, over 2,000 cases were reported within three weeks of its first detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2, the virus that causes COVID-19, in the region. By correlating genetic information to disease phenotype, we also aimed to gain insight into any correlation between viral genotype and case severity or transmissibility. METHODS We performed whole genome sequencing of clinical SARS-CoV-2 samples collected in March 2020 by the Johns Hopkins Health System. We analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and the global phylogeny to understand early establishment of the virus within the region. RESULTS We analyzed 620 samples from the Johns Hopkins Health System collected between March 11-31, 2020, comprising 37.3% of the total cases in Maryland during this period. We selected 143 of these samples for sequencing, generating 114 complete viral genomes. These genomes belong to all five major Nextstrain-defined clades, suggesting multiple introductions into the region and underscoring the diversity of the regional epidemic. We also found that clinically severe cases had genomes belonging to all of these clades. CONCLUSIONS We established a pipeline for SARS-CoV-2 sequencing within the Johns Hopkins Health system, which enabled us to capture the significant viral diversity present in the region as early as March 2020. Efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and interconnectedness of the region as a whole.
Collapse
Affiliation(s)
- Peter M. Thielen
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Shirlee Wohl
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Thomas Mehoke
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | | | - Melanie Kirsche
- Johns Hopkins University Department of Computer Science, Baltimore, Maryland 21218
| | - Oluwaseun Falade-Nwulia
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease, Baltimore, Maryland 21205
| | - Nídia S. Trovão
- National Institutes of Health, Fogarty International Center, Bethesda, Maryland 20892
| | - Amanda Ernlund
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Craig Howser
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Norah Sadowski
- Johns Hopkins University Department of Emergency Medicine, Baltimore, Maryland 21205
| | - Paul Morris
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
| | - Mark Hopkins
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
| | - Matthew Schwartz
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
| | - Yunfan Fan
- Johns Hopkins University Departments of Biomedical Engineering and Molecular Biology and Genetics, Baltimore, Maryland 21205
| | - Victoria Gniazdowski
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
| | - Justin Lessler
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Lauren Sauer
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease, Baltimore, Maryland 21205
- Johns Hopkins University Department of Emergency Medicine, Baltimore, Maryland 21205
| | - Michael C. Schatz
- Johns Hopkins University Department of Computer Science, Baltimore, Maryland 21218
| | - Jared D. Evans
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Stuart C. Ray
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease, Baltimore, Maryland 21205
| | - Winston Timp
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease, Baltimore, Maryland 21205
- Johns Hopkins University Departments of Biomedical Engineering and Molecular Biology and Genetics, Baltimore, Maryland 21205
| | - Heba H. Mostafa
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
| |
Collapse
|
16
|
Wohl S, Metsky HC, Schaffner SF, Piantadosi A, Burns M, Lewnard JA, Chak B, Krasilnikova LA, Siddle KJ, Matranga CB, Bankamp B, Hennigan S, Sabina B, Byrne EH, McNall RJ, Shah RR, Qu J, Park DJ, Gharib S, Fitzgerald S, Barreira P, Fleming S, Lett S, Rota PA, Madoff LC, Yozwiak NL, MacInnis BL, Smole S, Grad YH, Sabeti PC. Combining genomics and epidemiology to track mumps virus transmission in the United States. PLoS Biol 2020; 18:e3000611. [PMID: 32045407 PMCID: PMC7012397 DOI: 10.1371/journal.pbio.3000611] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/03/2020] [Indexed: 01/24/2023] Open
Abstract
Unusually large outbreaks of mumps across the United States in 2016 and 2017 raised questions about the extent of mumps circulation and the relationship between these and prior outbreaks. We paired epidemiological data from public health investigations with analysis of mumps virus whole genome sequences from 201 infected individuals, focusing on Massachusetts university communities. Our analysis suggests continuous, undetected circulation of mumps locally and nationally, including multiple independent introductions into Massachusetts and into individual communities. Despite the presence of these multiple mumps virus lineages, the genomic data show that one lineage has dominated in the US since at least 2006. Widespread transmission was surprising given high vaccination rates, but we found no genetic evidence that variants arising during this outbreak contributed to vaccine escape. Viral genomic data allowed us to reconstruct mumps transmission links not evident from epidemiological data or standard single-gene surveillance efforts and also revealed connections between apparently unrelated mumps outbreaks.
Collapse
Affiliation(s)
- Shirlee Wohl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Hayden C. Metsky
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Stephen F. Schaffner
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Anne Piantadosi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Meagan Burns
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Joseph A. Lewnard
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Bridget Chak
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Lydia A. Krasilnikova
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Katherine J. Siddle
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Christian B. Matranga
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Bettina Bankamp
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Scott Hennigan
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Brandon Sabina
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Elizabeth H. Byrne
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Rebecca J. McNall
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rickey R. Shah
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - James Qu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Daniel J. Park
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Soheyla Gharib
- Harvard University Health Services, Harvard University, Cambridge, Massachusetts, United States of America
| | - Susan Fitzgerald
- Harvard University Health Services, Harvard University, Cambridge, Massachusetts, United States of America
| | - Paul Barreira
- Harvard University Health Services, Harvard University, Cambridge, Massachusetts, United States of America
| | - Stephen Fleming
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Susan Lett
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Paul A. Rota
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Lawrence C. Madoff
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Nathan L. Yozwiak
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Bronwyn L. MacInnis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sandra Smole
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, United States of America
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- Center for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| |
Collapse
|
17
|
Metsky HC, Siddle KJ, Gladden-Young A, Qu J, Yang DK, Brehio P, Goldfarb A, Piantadosi A, Wohl S, Carter A, Lin AE, Barnes KG, Tully DC, Corleis B, Hennigan S, Barbosa-Lima G, Vieira YR, Paul LM, Tan AL, Garcia KF, Parham LA, Odia I, Eromon P, Folarin OA, Goba A, Simon-Lorière E, Hensley L, Balmaseda A, Harris E, Kwon DS, Allen TM, Runstadler JA, Smole S, Bozza FA, Souza TML, Isern S, Michael SF, Lorenzana I, Gehrke L, Bosch I, Ebel G, Grant DS, Happi CT, Park DJ, Gnirke A, Sabeti PC, Matranga CB. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nat Biotechnol 2019; 37:160-168. [PMID: 30718881 PMCID: PMC6587591 DOI: 10.1038/s41587-018-0006-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 12/18/2018] [Indexed: 01/24/2023]
Abstract
Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe sets, with a specified number of oligonucleotides, that achieve full coverage of, and scale well with, known sequence diversity. We focus on applying CATCH to capture viral genomes in complex metagenomic samples. We design, synthesize, and validate multiple probe sets, including one that targets the whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriches unique viral content on average 18-fold, allowing us to assemble genomes that could not be recovered without enrichment, and accurately preserves within-sample diversity. We also use these probe sets to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of uncharacterized viral infections in human and mosquito samples. The results demonstrate that CATCH enables more sensitive and cost-effective metagenomic sequencing.
Collapse
Affiliation(s)
- Hayden C. Metsky
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0001 2341 2786grid.116068.8Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Katherine J. Siddle
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | | | - James Qu
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - David K. Yang
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Patrick Brehio
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Andrew Goldfarb
- 000000041936754Xgrid.38142.3cFaculty of Arts and Sciences, Harvard University, Cambridge, MA USA
| | - Anne Piantadosi
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0004 0386 9924grid.32224.35Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA USA
| | - Shirlee Wohl
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Amber Carter
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Aaron E. Lin
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Kayla G. Barnes
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA
| | - Damien C. Tully
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Bjӧrn Corleis
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Scott Hennigan
- 0000 0004 0378 6934grid.416511.6Massachusetts Department of Public Health, Boston, MA USA
| | - Giselle Barbosa-Lima
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yasmine R. Vieira
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lauren M. Paul
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Amanda L. Tan
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Kimberly F. Garcia
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Leda A. Parham
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Ikponmwosa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Philomena Eromon
- grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria
| | - Onikepe A. Folarin
- grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria ,grid.442553.1Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Nigeria
| | - Augustine Goba
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
| | | | - Etienne Simon-Lorière
- 0000 0001 2353 6535grid.428999.7Evolutionary Genomics of RNA Viruses, Virology Department, Institut Pasteur, Paris, France
| | - Lisa Hensley
- 0000 0001 2164 9667grid.419681.3Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Frederick, MD USA
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Eva Harris
- 0000 0001 2181 7878grid.47840.3fDivision of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA USA
| | - Douglas S. Kwon
- 0000 0004 0386 9924grid.32224.35Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA USA ,0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Todd M. Allen
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Jonathan A. Runstadler
- 0000 0004 1936 7531grid.429997.8Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA USA
| | - Sandra Smole
- 0000 0004 0378 6934grid.416511.6Massachusetts Department of Public Health, Boston, MA USA
| | - Fernando A. Bozza
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thiago M. L. Souza
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sharon Isern
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Scott F. Michael
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Ivette Lorenzana
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Lee Gehrke
- 0000 0001 2341 2786grid.116068.8Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Microbiology and Immunobiology, Harvard Medical School, Boston, MA USA
| | - Irene Bosch
- 0000 0001 2341 2786grid.116068.8Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Gregory Ebel
- 0000 0004 1936 8083grid.47894.36Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO USA
| | - Donald S. Grant
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone ,0000 0001 2290 9707grid.442296.fCollege of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Christian T. Happi
- 000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA ,Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria ,grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria ,grid.442553.1Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Nigeria
| | - Daniel J. Park
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Andreas Gnirke
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Pardis C. Sabeti
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA ,0000 0001 2167 1581grid.413575.1Howard Hughes Medical Institute, Chevy Chase, MD USA
| | | |
Collapse
|
18
|
Siddle KJ, Eromon P, Barnes KG, Mehta S, Oguzie JU, Odia I, Schaffner SF, Winnicki SM, Shah RR, Qu J, Wohl S, Brehio P, Iruolagbe C, Aiyepada J, Uyigue E, Akhilomen P, Okonofua G, Ye S, Kayode T, Ajogbasile F, Uwanibe J, Gaye A, Momoh M, Chak B, Kotliar D, Carter A, Gladden-Young A, Freije CA, Omoregie O, Osiemi B, Muoebonam EB, Airende M, Enigbe R, Ebo B, Nosamiefan I, Oluniyi P, Nekoui M, Ogbaini-Emovon E, Garry RF, Andersen KG, Park DJ, Yozwiak NL, Akpede G, Ihekweazu C, Tomori O, Okogbenin S, Folarin OA, Okokhere PO, MacInnis BL, Sabeti PC, Happi CT. Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018. N Engl J Med 2018; 379:1745-1753. [PMID: 30332564 PMCID: PMC6181183 DOI: 10.1056/nejmoa1804498] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
During 2018, an unusual increase in Lassa fever cases occurred in Nigeria, raising concern among national and international public health agencies. We analyzed 220 Lassa virus genomes from infected patients, including 129 from the 2017-2018 transmission season, to understand the viral populations underpinning the increase. A total of 14 initial genomes from 2018 samples were generated at Redeemer's University in Nigeria, and the findings were shared with the Nigerian Center for Disease Control in real time. We found that the increase in cases was not attributable to a particular Lassa virus strain or sustained by human-to-human transmission. Instead, the data were consistent with ongoing cross-species transmission from local rodent populations. Phylogenetic analysis also revealed extensive viral diversity that was structured according to geography, with major rivers appearing to act as barriers to migration of the rodent reservoir.
Collapse
Affiliation(s)
- Katherine J Siddle
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Philomena Eromon
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Kayla G Barnes
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Samar Mehta
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Judith U Oguzie
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Ikponmwosa Odia
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Stephen F Schaffner
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Sarah M Winnicki
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Rickey R Shah
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - James Qu
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Shirlee Wohl
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Patrick Brehio
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Christopher Iruolagbe
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - John Aiyepada
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Eghosa Uyigue
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Patience Akhilomen
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Grace Okonofua
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Simon Ye
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Tolulope Kayode
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Fehintola Ajogbasile
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Jessica Uwanibe
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Amy Gaye
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Mambu Momoh
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Bridget Chak
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Dylan Kotliar
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Amber Carter
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Adrianne Gladden-Young
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Catherine A Freije
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Omigie Omoregie
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Blessing Osiemi
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Ekene B Muoebonam
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Michael Airende
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Rachael Enigbe
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Benevolence Ebo
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Iguosadolo Nosamiefan
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Paul Oluniyi
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Mahan Nekoui
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Ephraim Ogbaini-Emovon
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Robert F Garry
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Kristian G Andersen
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Daniel J Park
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Nathan L Yozwiak
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - George Akpede
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Chikwe Ihekweazu
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Oyewale Tomori
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Sylvanus Okogbenin
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Onikepe A Folarin
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Peter O Okokhere
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Bronwyn L MacInnis
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Pardis C Sabeti
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| | - Christian T Happi
- From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.)
| |
Collapse
|
19
|
Barnes KG, Kindrachuk J, Lin AE, Wohl S, Qu J, Tostenson SD, Dorman WR, Busby M, Siddle KJ, Luo CY, Matranga CB, Davey RT, Sabeti PC, Chertow DS. Evidence of Ebola Virus Replication and High Concentration in Semen of a Patient During Recovery. Clin Infect Dis 2017; 65:1400-1403. [PMID: 28582513 PMCID: PMC5850519 DOI: 10.1093/cid/cix518] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 03/28/2017] [Accepted: 06/01/2017] [Indexed: 11/13/2022] Open
Abstract
In one patient over time, we found that concentration of Ebola virus RNA in semen during recovery is remarkably higher than blood at peak illness. Virus in semen is replication-competent with no change in viral genome over time. Presence of sense RNA suggests replication in cells present in semen.
Collapse
Affiliation(s)
- Kayla G Barnes
- Center for Systems Biology, Harvard University, and
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jason Kindrachuk
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda
| | - Aaron E Lin
- Center for Systems Biology, Harvard University, and
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Shirlee Wohl
- Center for Systems Biology, Harvard University, and
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - James Qu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Samantha D Tostenson
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Frederick, and
| | - William R Dorman
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Frederick, and
| | - Michele Busby
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Katherine J Siddle
- Center for Systems Biology, Harvard University, and
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Cynthia Y Luo
- Center for Systems Biology, Harvard University, and
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Christian B Matranga
- Center for Systems Biology, Harvard University, and
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Richard T Davey
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Pardis C Sabeti
- Center for Systems Biology, Harvard University, and
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Daniel S Chertow
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
20
|
Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A, Lin AE, Tomkins-Tinch CH, Ye SH, Park DJ, Luo CY, Barnes KG, Shah RR, Chak B, Barbosa-Lima G, Delatorre E, Vieira YR, Paul LM, Tan AL, Barcellona CM, Porcelli MC, Vasquez C, Cannons AC, Cone MR, Hogan KN, Kopp EW, Anzinger JJ, Garcia KF, Parham LA, Ramírez RMG, Montoya MCM, Rojas DP, Brown CM, Hennigan S, Sabina B, Scotland S, Gangavarapu K, Grubaugh ND, Oliveira G, Robles-Sikisaka R, Rambaut A, Gehrke L, Smole S, Halloran ME, Villar L, Mattar S, Lorenzana I, Cerbino-Neto J, Valim C, Degrave W, Bozza PT, Gnirke A, Andersen KG, Isern S, Michael SF, Bozza FA, Souza TML, Bosch I, Yozwiak NL, MacInnis BL, Sabeti PC. Zika virus evolution and spread in the Americas. Nature 2017; 546:411-415. [PMID: 28538734 PMCID: PMC5563848 DOI: 10.1038/nature22402] [Citation(s) in RCA: 260] [Impact Index Per Article: 37.1] [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] [Received: 03/01/2017] [Accepted: 05/02/2017] [Indexed: 12/22/2022]
Abstract
Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analysed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental United States. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of surveillance of viral infections. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those that might be relevant to the effectiveness of diagnostic tests.
Collapse
Affiliation(s)
- Hayden C Metsky
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Shirlee Wohl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Stephen F Schaffner
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Catherine A Freije
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Sarah M Winnicki
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kendra West
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - James Qu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | - Aaron E Lin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | | | - Simon H Ye
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Cynthia Y Luo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Kayla G Barnes
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Rickey R Shah
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard University Extension School, Cambridge, Massachusetts, USA
| | - Bridget Chak
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Giselle Barbosa-Lima
- National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Edson Delatorre
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yasmine R Vieira
- National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lauren M Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Amanda L Tan
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Carolyn M Barcellona
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | | | | | - Andrew C Cannons
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, USA
| | - Marshall R Cone
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, USA
| | - Kelly N Hogan
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, USA
| | - Edgar W Kopp
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, USA
| | - Joshua J Anzinger
- Department of Microbiology, The University of the West Indies, Mona, Kingston, Jamaica
| | - Kimberly F Garcia
- Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Leda A Parham
- Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Rosa M Gélvez Ramírez
- Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
| | | | - Diana P Rojas
- Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
| | - Catherine M Brown
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Scott Hennigan
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Brandon Sabina
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Sarah Scotland
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
| | - Nathan D Grubaugh
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
| | - Glenn Oliveira
- Scripps Translational Science Institute, La Jolla, California, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lee Gehrke
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sandra Smole
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts, USA
| | - M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Luis Villar
- Grupo de Epidemiología Clínica, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Salim Mattar
- Institute for Tropical Biology Research, Universidad de Córdoba, Montería, Córdoba, Colombia
| | - Ivette Lorenzana
- Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Jose Cerbino-Neto
- National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Clarissa Valim
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, Michegan, USA
| | - Wim Degrave
- FIOCRUZ, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia T Bozza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kristian G Andersen
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
- Scripps Translational Science Institute, La Jolla, California, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Sharon Isern
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Scott F Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Fernando A Bozza
- National Institute of Infectious Diseases Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
- D'Or Institute for Research and Education, Rio de Janeiro, Brazil
| | - Thiago M L Souza
- National Institute for Science and Technology on Innovation on Neglected Diseases, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
- Center for Technological Development in Health, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Irene Bosch
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Nathan L Yozwiak
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Bronwyn L MacInnis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| |
Collapse
|
21
|
Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Luo C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC, Lichtenberger PN, Ricciardi MJ, Bailey VK, Watkins DI, Cone MR, Kopp EW, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG. Genomic epidemiology reveals multiple introductions of Zika virus into the United States. Nature 2017; 546:401-405. [PMID: 28538723 PMCID: PMC5536180 DOI: 10.1038/nature22400] [Citation(s) in RCA: 232] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/28/2017] [Indexed: 12/23/2022]
Abstract
Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016-several months before its initial detection. By analysing surveillance and genetic data, we show that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions were linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. Our study provides an understanding of how ZIKV initiates transmission in new regions.
Collapse
Affiliation(s)
- Nathan D Grubaugh
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jason T Ladner
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
- Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Gytis Dudas
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Amanda L Tan
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Michael R Wiley
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Stephen White
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, Florida 33125, USA
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Diogo M Magnani
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Karla Prieto
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Daniel Reyes
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Andrea M Bingham
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida 32399, USA
| | - Lauren M Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Glenn Oliveira
- Scripps Translational Science Institute, La Jolla, California 92037, USA
| | - Darryl Pronty
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, Florida 33125, USA
| | - Carolyn M Barcellona
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Hayden C Metsky
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Mary Lynn Baniecki
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kayla G Barnes
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Bridget Chak
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Catherine A Freije
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Andreas Gnirke
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Cynthia Luo
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Bronwyn MacInnis
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Daniel J Park
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - James Qu
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | | | - Kendra L West
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Sarah M Winnicki
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Shirlee Wohl
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Nathan L Yozwiak
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Joshua Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Joseph R Fauver
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Shannon E Brent
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Ontario M5B 1T8, Canada
| | - Robert C Reiner
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington 98121, USA
| | - Paola N Lichtenberger
- Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Michael J Ricciardi
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Varian K Bailey
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - David I Watkins
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Marshall R Cone
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida 33612, USA
| | - Edgar W Kopp
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida 33612, USA
| | - Kelly N Hogan
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida 33612, USA
| | - Andrew C Cannons
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida 33612, USA
| | - Reynald Jean
- Florida Department of Health in Miami-Dade County, Miami, Florida 33125, USA
| | - Andrew J Monaghan
- National Center for Atmospheric Research, Boulder, Colorado 80307, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana 70112, USA
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | | | | | - Elyse R Nagle
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Derek A T Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Danielle Stanek
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida 32399, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Pardis C Sabeti
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Leah D Gillis
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, Florida 33125, USA
| | - Scott F Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Sharon Isern
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA
| | - Gustavo Palacios
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA
| | - Kristian G Andersen
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
- Scripps Translational Science Institute, La Jolla, California 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| |
Collapse
|
22
|
Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D’Ambrozio J, Dellicour S, Di Caro A, Diclaro J, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kargbo B, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll M, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature 2017; 544:309-315. [PMID: 28405027 PMCID: PMC5712493 DOI: 10.1038/nature22040] [Citation(s) in RCA: 242] [Impact Index Per Article: 34.6] [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] [Received: 08/31/2016] [Accepted: 03/02/2017] [Indexed: 01/03/2023]
Abstract
The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.
Collapse
Affiliation(s)
- Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Luiz Max Carvalho
- Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew J. Tatem
- WorldPop, Department of Geography and Environment, University of Southampton, Highfield, Southampton SO17 1BJ, UK
- Flowminder Foundation, Stockholm, Sweden
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Nuno R. Faria
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Daniel J. Park
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jason T. Ladner
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Armando Arias
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
- National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark
| | - Danny Asogun
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
| | - Filip Bielejec
- Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Sarah L. Caddy
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
| | - Matthew Cotten
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Jonathan D’Ambrozio
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Simon Dellicour
- Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Antonino Di Caro
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- National Institute for Infectious Diseases ”L. Spallanzani” – IRCCS, Via Portuense 292, 00149 Rome, Italy
| | - JosephW. Diclaro
- Naval Medical Research Unit 3, 3A Imtidad Ramses Street, Cairo, 11517, Egypt
| | - Sophie Duraffour
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Michael J. Elmore
- National Infections Service, Public Health England, Porton Down, Salisbury, Wilts SP4 0JG, UK
| | | | - Ousmane Faye
- Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, 36 Avenue Pasteur, BP 220, Dakar, Sénégal
| | - Merle L. Gilbert
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | | | - Stephen Gire
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Andreas Gnirke
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Bart L. Haagmans
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Julian A. Hiscox
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 2BE, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, UK
| | - Umaru Jah
- University of Makeni, Makeni, Sierra Leone
| | - Brima Kargbo
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Jeffrey R. Kugelman
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Di Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jia Lu
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
| | | | - Suzanne Mate
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | | | | | - Luke W. Meredith
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
- University of Makeni, Makeni, Sierra Leone
| | - James Qu
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Joshua Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Suzan D. Pas
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - My VT Phan
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Georgios Pollakis
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 2BE, UK
| | - Chantal B. Reusken
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- University of Nebraska Medical Center, Omaha, NE, USA
| | | | - John S. Schieffelin
- Department of Pediatrics, Section of Infectious Diseases, New Orleans, LA 70112, USA
| | - Rachel S. Sealfon
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Etienne Simon-Loriere
- Institut Pasteur, Functional Genetics of Infectious Diseases Unit, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Génétique Fonctionelle des Maladies Infectieuses, CNRS URA3012, Paris 75015, France
| | - Saskia L. Smits
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Kilian Stoecker
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany
| | - Lucy Thorne
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
| | - Ekaete Alice Tobin
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
| | - Mohamed A. Vandi
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Simon J. Watson
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Kendra West
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Shannon Whitmer
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia, USA
| | - Michael R. Wiley
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- University of Nebraska Medical Center, Omaha, NE, USA
| | - Sarah M. Winnicki
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Shirlee Wohl
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Roman Wölfel
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany
| | - Nathan L. Yozwiak
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kristian G. Andersen
- The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, CA 92037, USA
- Scripps Translational Science Institute, La Jolla, CA 92037, USA
| | - Sylvia O. Blyden
- Ministry of Social Welfare, Gender and Children’s Affairs, New Englandville, Freetown, Sierra Leone
| | - Fatorma Bolay
- Liberian Institute for Biomedical Research, Charlesville, Liberia
| | - MilesW. Carroll
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- National Infections Service, Public Health England, Porton Down, Salisbury, Wilts SP4 0JG, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, UK
- University of Southampton, South General Hospital, Southampton SO16 6YD, UK
| | | | | | | | - Christophe Fraser
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - George F. Gao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China
| | - Robert F. Garry
- Department of Microbiology and Immunology, New Orleans, LA 70112, USA
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
- University of Makeni, Makeni, Sierra Leone
| | - Stephan Günther
- The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Christian T. Happi
- Department of Biological Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, the University of Sydney, Sydney, NSW 2006, Australia
| | - Brima Kargbo
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | | | - Paul Kellam
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, UK
- Division of Infectious Diseases, Imperial College Faculty of Medicine, London W2 1PG, UK
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus University Medical Centre, P.O. Box 2040, 300 CA Rotterdam, the Netherlands
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - N’Faly Magassouba
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | | | - Stuart T. Nichol
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia, USA
| | | | - Gustavo Palacios
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Pardis C. Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amadou Sall
- Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, 36 Avenue Pasteur, BP 220, Dakar, Sénégal
| | - Ute Ströher
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia, USA
| | - Isatta Wurie
- University of Sierra Leone, Freetown, Sierra Leone
| | - Marc A. Suchard
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Department of Biomathematics David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
- Centre for Immunology, Infection and Evolution, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
23
|
Abstract
Genomic analysis is a powerful tool for understanding viral disease outbreaks. Sequencing of viral samples is now easier and cheaper than ever before and can supplement epidemiological methods by providing nucleotide-level resolution of outbreak-causing pathogens. In this review, we describe methods used to answer crucial questions about outbreaks, such as how they began and how a disease is transmitted. More specifically, we explain current techniques for viral sequencing, phylogenetic analysis, transmission reconstruction, and evolutionary investigation of viral pathogens. By detailing the ways in which genomic data can help us understand viral disease outbreaks, we aim to provide a resource that will facilitate the response to future outbreaks.
Collapse
Affiliation(s)
- Shirlee Wohl
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138.,Broad Institute, Cambridge, Massachusetts 02142; ,
| | - Stephen F Schaffner
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138.,Broad Institute, Cambridge, Massachusetts 02142; , .,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Pardis C Sabeti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138.,Broad Institute, Cambridge, Massachusetts 02142; , .,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115
| |
Collapse
|
24
|
Folarin OA, Ehichioya D, Schaffner SF, Winnicki SM, Wohl S, Eromon P, West KL, Gladden-Young A, Oyejide NE, Matranga CB, Deme AB, James A, Tomkins-Tinch C, Onyewurunwa K, Ladner JT, Palacios G, Nosamiefan I, Andersen KG, Omilabu S, Park DJ, Yozwiak NL, Nasidi A, Garry RF, Tomori O, Sabeti PC, Happi CT. Ebola Virus Epidemiology and Evolution in Nigeria. J Infect Dis 2016; 214:S102-S109. [PMID: 27377746 PMCID: PMC5050462 DOI: 10.1093/infdis/jiw190] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Containment limited the 2014 Nigerian Ebola virus (EBOV) disease outbreak to 20 reported cases and 8 fatalities. We present here clinical data and contact information for at least 19 case patients, and full-length EBOV genome sequences for 12 of the 20. The detailed contact data permits nearly complete reconstruction of the transmission tree for the outbreak. The EBOV genomic data are consistent with that tree. It confirms that there was a single source for the Nigerian infections, shows that the Nigerian EBOV lineage nests within a lineage previously seen in Liberia but is genetically distinct from it, and supports the conclusion that transmission from Nigeria to elsewhere did not occur.
Collapse
Affiliation(s)
- Onikepe A Folarin
- Department of Biological Sciences African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State
| | - Deborah Ehichioya
- Department of Biological Sciences African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State
| | - Stephen F Schaffner
- Department of Broad Institute of Harvard and MIT Department of FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge
| | - Sarah M Winnicki
- Department of Broad Institute of Harvard and MIT Department of FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge
| | - Shirlee Wohl
- Department of Broad Institute of Harvard and MIT Department of FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge
| | - Philomena Eromon
- Department of Biological Sciences African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State
| | | | | | | | | | - Awa Bineta Deme
- Department de Parasitologie et Mycologie, Université Cheikh Anta Diop de Dakar, Fann, Dakar, Senegal
| | | | | | - Kenneth Onyewurunwa
- Department of Biological Sciences African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State
| | - Jason T Ladner
- Department of Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, Massachusetts
| | - Gustavo Palacios
- Department of Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, Massachusetts
| | | | - Kristian G Andersen
- Department of The Scripps Research Institute, Scripps Translational Science Institute, La Jolla, California
| | - Sunday Omilabu
- Department of Medical Microbiology and Parasitology, College of Medicine, University of Lagos
| | - Daniel J Park
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State Department of Broad Institute of Harvard and MIT
| | - Nathan L Yozwiak
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State Department of Broad Institute of Harvard and MIT Department of FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge
| | | | - Robert F Garry
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana
| | - Oyewale Tomori
- Department of Biological Sciences Department of Nigerian Academy of Science, Akoka-Yaba, Lagos
| | - Pardis C Sabeti
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State Department of Broad Institute of Harvard and MIT Department of FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge Department of Howard Hughes Medical Institute, Chevy Chase
| | - Christian T Happi
- Department of Biological Sciences African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State
| |
Collapse
|
25
|
Park DJ, Dudas G, Wohl S, Goba A, Whitmer SLM, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR, Matranga CB, Winnicki SM, Qu J, Gire SK, Gladden-Young A, Jalloh S, Nosamiefan D, Yozwiak NL, Moses LM, Jiang PP, Lin AE, Schaffner SF, Bird B, Towner J, Mamoh M, Gbakie M, Kanneh L, Kargbo D, Massally JLB, Kamara FK, Konuwa E, Sellu J, Jalloh AA, Mustapha I, Foday M, Yillah M, Erickson BR, Sealy T, Blau D, Paddock C, Brault A, Amman B, Basile J, Bearden S, Belser J, Bergeron E, Campbell S, Chakrabarti A, Dodd K, Flint M, Gibbons A, Goodman C, Klena J, McMullan L, Morgan L, Russell B, Salzer J, Sanchez A, Wang D, Jungreis I, Tomkins-Tinch C, Kislyuk A, Lin MF, Chapman S, MacInnis B, Matthews A, Bochicchio J, Hensley LE, Kuhn JH, Nusbaum C, Schieffelin JS, Birren BW, Forget M, Nichol ST, Palacios GF, Ndiaye D, Happi C, Gevao SM, Vandi MA, Kargbo B, Holmes EC, Bedford T, Gnirke A, Ströher U, Rambaut A, Garry RF, Sabeti PC. Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone. Cell 2015; 161:1516-26. [PMID: 26091036 PMCID: PMC4503805 DOI: 10.1016/j.cell.2015.06.007] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 05/26/2015] [Accepted: 06/01/2015] [Indexed: 11/29/2022]
Abstract
The 2013–2015 Ebola virus disease (EVD) epidemic is caused by the Makona variant of Ebola virus (EBOV). Early in the epidemic, genome sequencing provided insights into virus evolution and transmission and offered important information for outbreak response. Here, we analyze sequences from 232 patients sampled over 7 months in Sierra Leone, along with 86 previously released genomes from earlier in the epidemic. We confirm sustained human-to-human transmission within Sierra Leone and find no evidence for import or export of EBOV across national borders after its initial introduction. Using high-depth replicate sequencing, we observe both host-to-host transmission and recurrent emergence of intrahost genetic variants. We trace the increasing impact of purifying selection in suppressing the accumulation of nonsynonymous mutations over time. Finally, we note changes in the mucin-like domain of EBOV glycoprotein that merit further investigation. These findings clarify the movement of EBOV within the region and describe viral evolution during prolonged human-to-human transmission. In Sierra Leone, transmission has primarily been within-country, not between-country Infectious doses are large enough for intrahost variants to transmit between hosts A prolonged epidemic removes deleterious mutations from the viral population There is preliminary evidence for human RNA editing effects on the Ebola genome
Collapse
Affiliation(s)
- Daniel J Park
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
| | - Gytis Dudas
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Shirlee Wohl
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | | | - Shannon L M Whitmer
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Kristian G Andersen
- Scripps Translational Science Institute, The Scripps Research Institute, 3344 N Torrey Pines Court, La Jolla, CA 92037, USA
| | - Rachel S Sealfon
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jason T Ladner
- US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Jeffrey R Kugelman
- US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | | | - Sarah M Winnicki
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - James Qu
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Stephen K Gire
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | | | | | - Dolo Nosamiefan
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Nathan L Yozwiak
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Lina M Moses
- Tulane University, 1430 Tulane Avenue, SL-38, New Orleans, LA 70112, USA
| | - Pan-Pan Jiang
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Aaron E Lin
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Brian Bird
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Jonathan Towner
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Mambu Mamoh
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | | | - David Kargbo
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | | | - Edwin Konuwa
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | | | | | - Momoh Foday
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | - Bobbie R Erickson
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Tara Sealy
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Dianna Blau
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Christopher Paddock
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Aaron Brault
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Brian Amman
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Jane Basile
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Scott Bearden
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Jessica Belser
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Eric Bergeron
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Shelley Campbell
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Ayan Chakrabarti
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Kimberly Dodd
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Mike Flint
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Aridth Gibbons
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Christin Goodman
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - John Klena
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Laura McMullan
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Laura Morgan
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Brandy Russell
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Johanna Salzer
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Angela Sanchez
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - David Wang
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Irwin Jungreis
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | | | - Andrey Kislyuk
- DNAnexus, 1975 West El Camino Real, Suite 101, Mountain View, CA 94040, USA
| | - Michael F Lin
- DNAnexus, 1975 West El Camino Real, Suite 101, Mountain View, CA 94040, USA
| | - Sinead Chapman
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Bronwyn MacInnis
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Ashley Matthews
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - James Bochicchio
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Lisa E Hensley
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Chad Nusbaum
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - John S Schieffelin
- Tulane University, 1430 Tulane Avenue, SL-38, New Orleans, LA 70112, USA
| | - Bruce W Birren
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Marc Forget
- Médecins Sans Frontières, Rue de l'Arbre Bénit 46, 1050 Bruxelles, Belgium
| | - Stuart T Nichol
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Gustavo F Palacios
- US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Daouda Ndiaye
- Université Cheikh Anta Diop, BP 5005, Dakar, Sénégal
| | - Christian Happi
- Redeemers University Nigeria, KM 46 Lagos-Ibadan Expressway, Redemption City, Ogun State, Nigeria
| | - Sahr M Gevao
- University of Sierra Leone, A.J. Momoh St, Tower Hill, Freetown, Sierra Leone
| | - Mohamed A Vandi
- Sierra Leone Ministry of Health and Sanitation, Youyi Building, Freetown, Sierra Leone
| | - Brima Kargbo
- Sierra Leone Ministry of Health and Sanitation, Youyi Building, Freetown, Sierra Leone
| | - Edward C Holmes
- University of Sydney, Johns Hopkins Drive, Camperdown NSW 2050, Australia
| | - Trevor Bedford
- Fred Hutchinson Cancer Research Center, 110 Fairview Avenue North, Seattle, WA 98109, USA
| | - Andreas Gnirke
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Ute Ströher
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH9 3FL, UK; Centre for Immunology, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3FL, UK; Fogarty International Center, National Institutes of Health, 31 Center Drive, MSC 2220 Bethesda, MD 20892, USA.
| | - Robert F Garry
- Tulane University, 1430 Tulane Avenue, SL-38, New Orleans, LA 70112, USA
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
| |
Collapse
|
26
|
Gire SK, Goba A, Andersen KG, Sealfon RSG, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JLB, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 2014; 345:1369-72. [PMID: 25214632 PMCID: PMC4431643 DOI: 10.1126/science.1259657] [Citation(s) in RCA: 822] [Impact Index Per Article: 82.2] [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: 11/02/2022]
Abstract
In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2000× coverage. We observed a rapid accumulation of interhost and intrahost genetic variation, allowing us to characterize patterns of viral transmission over the initial weeks of the epidemic. This West African variant likely diverged from central African lineages around 2004, crossed from Guinea to Sierra Leone in May 2014, and has exhibited sustained human-to-human transmission subsequently, with no evidence of additional zoonotic sources. Because many of the mutations alter protein sequences and other biologically meaningful targets, they should be monitored for impact on diagnostics, vaccines, and therapies critical to outbreak response.
Collapse
Affiliation(s)
- Stephen K Gire
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Kristian G Andersen
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Rachel S G Sealfon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Mambu Momoh
- Kenema Government Hospital, Kenema, Sierra Leone. Eastern Polytechnic College, Kenema, Sierra Leone
| | - Mohamed Fullah
- Kenema Government Hospital, Kenema, Sierra Leone. Eastern Polytechnic College, Kenema, Sierra Leone
| | - Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Shirlee Wohl
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lina M Moses
- Tulane University Medical Center, New Orleans, LA 70112, USA
| | - Nathan L Yozwiak
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Winnicki
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - James Qu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Stephen F Schaffner
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xiao Yang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Pan-Pan Jiang
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mahan Nekoui
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andres Colubri
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Mbalu Fonnie
- Kenema Government Hospital, Kenema, Sierra Leone
| | - Alex Moigboi
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | | | | | - Edwin Konuwa
- Kenema Government Hospital, Kenema, Sierra Leone
| | - Sidiki Saffa
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | | | - Alice Kovoma
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | | | | | - Momoh Foday
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | | | | | | | | | | | - Cheryl Murphy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chad Nusbaum
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Young
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bruce W Birren
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Systems Biology, Harvard Medical School, Boston, MA 02115, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Sahr M Gevao
- University of Sierra Leone, Freetown, Sierra Leone
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK. Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA. Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Robert F Garry
- Tulane University Medical Center, New Orleans, LA 70112, USA
| | | | - Pardis C Sabeti
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
27
|
Wohl S. Physicians vs. hospitals: who controls the patient pool? Health Manage Q 1986:3-6. [PMID: 10300882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
|