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Levine ZC, Sene A, Mkandawire W, Deme AB, Ndiaye T, Sy M, Gaye A, Diedhiou Y, Mbaye AM, Ndiaye IM, Gomis J, Ndiop M, Sene D, Faye Paye M, MacInnis BL, Schaffner SF, Park DJ, Badiane AS, Colubri A, Ndiaye M, Sy N, Sabeti PC, Ndiaye D, Siddle KJ. Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing. Nat Commun 2024; 15:747. [PMID: 38272885 PMCID: PMC10810818 DOI: 10.1038/s41467-024-44800-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024] Open
Abstract
The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata in a cross-sectional study of febrile patients and healthy controls in a low malaria burden area. Using 16S and untargeted sequencing, we detected viral, bacterial, or eukaryotic pathogens in 23% (38/163) of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15.5% and 3.8% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model that can distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs (F1 score: 0.823). These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.
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Affiliation(s)
- Zoë C Levine
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
- Harvard/MIT MD-PhD Program, Boston, MA, USA
| | - Aita Sene
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Winnie Mkandawire
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Awa B Deme
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Tolla Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Mouhamad Sy
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Amy Gaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Younouss Diedhiou
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Amadou M Mbaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Ibrahima M Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Jules Gomis
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Médoune Ndiop
- Programme National de lutte contre le Paludisme, Ministère de la Santé, Dakar Fann, Senegal
| | - Doudou Sene
- Programme National de lutte contre le Paludisme, Ministère de la Santé, Dakar Fann, Senegal
| | | | - Bronwyn L MacInnis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Daniel J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aida S Badiane
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Andres Colubri
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Mouhamadou Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Ngayo Sy
- Service de Lutte Anti Parasitaire, Thies, Senegal
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Daouda Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal.
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal.
| | - Katherine J Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
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Levine ZC, Sene A, Mkandawire W, Deme AB, Ndiaye T, Sy M, Gaye A, Diedhiou Y, Mbaye AM, Ndiaye I, Gomis J, Ndiop M, Sene D, Paye MF, MacInnis B, Schaffner SF, Park DJ, Badiane AS, Colubri A, Ndiaye M, Sy N, Sabeti PC, Ndiaye D, Siddle KJ. Improving diagnosis of non-malarial fevers in Senegal: Borrelia and the contribution of tick-borne bacteria. medRxiv 2023:2023.08.24.23294564. [PMID: 37662407 PMCID: PMC10473814 DOI: 10.1101/2023.08.24.23294564] [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: 09/05/2023]
Abstract
The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata from febrile patients and healthy controls in a low malaria burden area. Using 16S and unbiased sequencing, we detected viral, bacterial, or eukaryotic pathogens in 29% of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15% and 3.7% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model to distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs. These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.
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Affiliation(s)
- Zoë C Levine
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
- Harvard/MIT MD-PhD Program, Boston, MA, 02115, USA
| | - Aita Sene
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Winnie Mkandawire
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Awa B Deme
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Tolla Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Mouhamad Sy
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Amy Gaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Younouss Diedhiou
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Amadou M Mbaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ibrahima Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Jules Gomis
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Médoune Ndiop
- Programme National de Lutte contre le Paludisme (PNLP), Ministère de la Santé, Dakar Fann, Senegal
| | - Doudou Sene
- Programme National de Lutte contre le Paludisme (PNLP), Ministère de la Santé, Dakar Fann, Senegal
| | | | - Bronwyn MacInnis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Daniel J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aida S Badiane
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Andres Colubri
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Mouhamadou Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ngayo Sy
- Service de Lutte Anti Parasitaire, Thies, Senegal
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Daouda Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Katherine J Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
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3
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Soni A, Herbert C, Lin H, Yan Y, Pretz C, Stamegna P, Wang B, Orwig T, Wright C, Tarrant S, Behar S, Suvarna T, Schrader S, Harman E, Nowak C, Kheterpal V, Rao LV, Cashman L, Orvek E, Ayturk D, Gibson L, Zai A, Wong S, Lazar P, Wang Z, Filippaios A, Barton B, Achenbach CJ, Murphy RL, Robinson ML, Manabe YC, Pandey S, Colubri A, O'Connor L, Lemon SC, Fahey N, Luzuriaga KL, Hafer N, Roth K, Lowe T, Stenzel T, Heetderks W, Broach J, McManus DD. Performance of Rapid Antigen Tests to Detect Symptomatic and Asymptomatic SARS-CoV-2 Infection : A Prospective Cohort Study. Ann Intern Med 2023; 176:975-982. [PMID: 37399548 PMCID: PMC10321467 DOI: 10.7326/m23-0385] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND The performance of rapid antigen tests (Ag-RDTs) for screening asymptomatic and symptomatic persons for SARS-CoV-2 is not well established. OBJECTIVE To evaluate the performance of Ag-RDTs for detection of SARS-CoV-2 among symptomatic and asymptomatic participants. DESIGN This prospective cohort study enrolled participants between October 2021 and January 2022. Participants completed Ag-RDTs and reverse transcriptase polymerase chain reaction (RT-PCR) testing for SARS-CoV-2 every 48 hours for 15 days. SETTING Participants were enrolled digitally throughout the mainland United States. They self-collected anterior nasal swabs for Ag-RDTs and RT-PCR testing. Nasal swabs for RT-PCR were shipped to a central laboratory, whereas Ag-RDTs were done at home. PARTICIPANTS Of 7361 participants in the study, 5353 who were asymptomatic and negative for SARS-CoV-2 on study day 1 were eligible. In total, 154 participants had at least 1 positive RT-PCR result. MEASUREMENTS The sensitivity of Ag-RDTs was measured on the basis of testing once (same-day), twice (after 48 hours), and thrice (after a total of 96 hours). The analysis was repeated for different days past index PCR positivity (DPIPPs) to approximate real-world scenarios where testing initiation may not always coincide with DPIPP 0. Results were stratified by symptom status. RESULTS Among 154 participants who tested positive for SARS-CoV-2, 97 were asymptomatic and 57 had symptoms at infection onset. Serial testing with Ag-RDTs twice 48 hours apart resulted in an aggregated sensitivity of 93.4% (95% CI, 90.4% to 95.9%) among symptomatic participants on DPIPPs 0 to 6. When singleton positive results were excluded, the aggregated sensitivity on DPIPPs 0 to 6 for 2-time serial testing among asymptomatic participants was lower at 62.7% (CI, 57.0% to 70.5%), but it improved to 79.0% (CI, 70.1% to 87.4%) with testing 3 times at 48-hour intervals. LIMITATION Participants tested every 48 hours; therefore, these data cannot support conclusions about serial testing intervals shorter than 48 hours. CONCLUSION The performance of Ag-RDTs was optimized when asymptomatic participants tested 3 times at 48-hour intervals and when symptomatic participants tested 2 times separated by 48 hours. PRIMARY FUNDING SOURCE National Institutes of Health RADx Tech program.
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Affiliation(s)
- Apurv Soni
- Program in Digital Medicine, Department of Medicine; Division of Health Systems Science, Department of Medicine; and Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (A.S.)
| | - Carly Herbert
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., C.P., P.S., T.O., C.W., S.T., S.B., A.F., S.P.)
| | - Honghuang Lin
- Program in Digital Medicine and Division of Health Systems Science, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (H.L., B.W.)
| | - Yi Yan
- Office of In Vitro Diagnostics, Office of Product Evaluation and Quality, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland (Y.Y., K.R., T.L.)
| | - Caitlin Pretz
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., C.P., P.S., T.O., C.W., S.T., S.B., A.F., S.P.)
| | - Pamela Stamegna
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., C.P., P.S., T.O., C.W., S.T., S.B., A.F., S.P.)
| | - Biqi Wang
- Program in Digital Medicine and Division of Health Systems Science, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (H.L., B.W.)
| | - Taylor Orwig
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., C.P., P.S., T.O., C.W., S.T., S.B., A.F., S.P.)
| | - Colton Wright
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., C.P., P.S., T.O., C.W., S.T., S.B., A.F., S.P.)
| | - Seanan Tarrant
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., C.P., P.S., T.O., C.W., S.T., S.B., A.F., S.P.)
| | - Stephanie Behar
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., C.P., P.S., T.O., C.W., S.T., S.B., A.F., S.P.)
| | - Thejas Suvarna
- CareEvolution, Ann Arbor, Michigan (T.S., S.S., E.H., C.N., V.K.)
| | - Summer Schrader
- CareEvolution, Ann Arbor, Michigan (T.S., S.S., E.H., C.N., V.K.)
| | - Emma Harman
- CareEvolution, Ann Arbor, Michigan (T.S., S.S., E.H., C.N., V.K.)
| | - Chris Nowak
- CareEvolution, Ann Arbor, Michigan (T.S., S.S., E.H., C.N., V.K.)
| | - Vik Kheterpal
- CareEvolution, Ann Arbor, Michigan (T.S., S.S., E.H., C.N., V.K.)
| | - Lokinendi V Rao
- Quest Diagnostics, Marlborough, Massachusetts (L.V.R., L.C.)
| | - Lisa Cashman
- Quest Diagnostics, Marlborough, Massachusetts (L.V.R., L.C.)
| | - Elizabeth Orvek
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (E.O., D.A., A.Z., S.W., P.L., B.B., S.C.L.)
| | - Didem Ayturk
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (E.O., D.A., A.Z., S.W., P.L., B.B., S.C.L.)
| | - Laura Gibson
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (L.G.)
| | - Adrian Zai
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (E.O., D.A., A.Z., S.W., P.L., B.B., S.C.L.)
| | - Steven Wong
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (E.O., D.A., A.Z., S.W., P.L., B.B., S.C.L.)
| | - Peter Lazar
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (E.O., D.A., A.Z., S.W., P.L., B.B., S.C.L.)
| | - Ziyue Wang
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (Z.W.)
| | - Andreas Filippaios
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., C.P., P.S., T.O., C.W., S.T., S.B., A.F., S.P.)
| | - Bruce Barton
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (E.O., D.A., A.Z., S.W., P.L., B.B., S.C.L.)
| | - Chad J Achenbach
- Division of Infectious Diseases, Department of Medicine, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, Illinois (C.J.A., R.L.M.)
| | - Robert L Murphy
- Division of Infectious Diseases, Department of Medicine, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, Illinois (C.J.A., R.L.M.)
| | - Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland (M.L.R., Y.C.M.)
| | - Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland (M.L.R., Y.C.M.)
| | - Shishir Pandey
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., C.P., P.S., T.O., C.W., S.T., S.B., A.F., S.P.)
| | - Andres Colubri
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts (A.C.)
| | - Laurel O'Connor
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (L.O., J.B.)
| | - Stephenie C Lemon
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (E.O., D.A., A.Z., S.W., P.L., B.B., S.C.L.)
| | - Nisha Fahey
- Program in Digital Medicine, Department of Medicine; Department of Population and Quantitative Health Sciences; and Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, Massachusetts (N.F.)
| | - Katherine L Luzuriaga
- University of Massachusetts Center for Clinical and Translational Science and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (K.L.L., N.H.)
| | - Nathaniel Hafer
- University of Massachusetts Center for Clinical and Translational Science and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (K.L.L., N.H.)
| | - Kristian Roth
- Office of In Vitro Diagnostics, Office of Product Evaluation and Quality, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland (Y.Y., K.R., T.L.)
| | - Toby Lowe
- Office of In Vitro Diagnostics, Office of Product Evaluation and Quality, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland (Y.Y., K.R., T.L.)
| | - Timothy Stenzel
- Division of Microbiology, Office of In Vitro Diagnostics, Office of Product Evaluation and Quality, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, Maryland (T.S.)
| | - William Heetderks
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland (W.H.)
| | - John Broach
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (L.O., J.B.)
| | - David D McManus
- Program in Digital Medicine, Division of Health Systems Science, and Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (D.D.M.)
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Herbert C, Wang B, Lin H, Hafer N, Pretz C, Stamegna P, Tarrant S, Hartin P, Ferranto J, Behar S, Wright C, Orwig T, Suvarna T, Harman E, Schrader S, Nowak C, Kheterpal V, Orvek E, Wong S, Zai A, Barton B, Gerber B, Lemon SC, Filippaios A, D'Amore K, Gibson L, Greene S, Howard-Wilson S, Colubri A, Achenbach C, Murphy R, Heetderks W, Manabe YC, O'Connor L, Fahey N, Luzuriaga K, Broach J, McManus DD, Soni A. Performance of Rapid Antigen Tests Based on Symptom Onset and Close Contact Exposure: A secondary analysis from the Test Us At Home prospective cohort study. medRxiv 2023:2023.02.21.23286239. [PMID: 36865199 PMCID: PMC9980261 DOI: 10.1101/2023.02.21.23286239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Background The performance of rapid antigen tests for SARS-CoV-2 (Ag-RDT) in temporal relation to symptom onset or exposure is unknown, as is the impact of vaccination on this relationship. Objective To evaluate the performance of Ag-RDT compared with RT-PCR based on day after symptom onset or exposure in order to decide on 'when to test'. Design Setting and Participants The Test Us at Home study was a longitudinal cohort study that enrolled participants over 2 years old across the United States between October 18, 2021 and February 4, 2022. All participants were asked to conduct Ag-RDT and RT-PCR testing every 48 hours over a 15-day period. Participants with one or more symptoms during the study period were included in the Day Post Symptom Onset (DPSO) analyses, while those who reported a COVID-19 exposure were included in the Day Post Exposure (DPE) analysis. Exposure Participants were asked to self-report any symptoms or known exposures to SARS-CoV-2 every 48-hours, immediately prior to conducting Ag-RDT and RT-PCR testing. The first day a participant reported one or more symptoms was termed DPSO 0, and the day of exposure was DPE 0. Vaccination status was self-reported. Main Outcome and Measures Results of Ag-RDT were self-reported (positive, negative, or invalid) and RT-PCR results were analyzed by a central laboratory. Percent positivity of SARS-CoV-2 and sensitivity of Ag-RDT and RT-PCR by DPSO and DPE were stratified by vaccination status and calculated with 95% confidence intervals. Results A total of 7,361 participants enrolled in the study. Among them, 2,086 (28.3%) and 546 (7.4%) participants were eligible for the DPSO and DPE analyses, respectively. Unvaccinated participants were nearly twice as likely to test positive for SARS-CoV-2 than vaccinated participants in event of symptoms (PCR+: 27.6% vs 10.1%) or exposure (PCR+: 43.8% vs. 22.2%). The highest proportion of vaccinated and unvaccinated individuals tested positive on DPSO 2 and DPE 5-8. Performance of RT-PCR and Ag-RDT did not differ by vaccination status. Ag-RDT detected 78.0% (95% Confidence Interval: 72.56-82.61) of PCR-confirmed infections by DPSO 4. For exposed participants, Ag-RDT detected 84.9% (95% CI: 75.0-91.4) of PCR-confirmed infections by day five post-exposure (DPE 5). Conclusions and Relevance Performance of Ag-RDT and RT-PCR was highest on DPSO 0-2 and DPE 5 and did not differ by vaccination status. These data suggests that serial testing remains integral to enhancing the performance of Ag-RDT.
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5
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Soni A, Herbert C, Lin H, Yan Y, Pretz C, Stamegna P, Wang B, Orwig T, Wright C, Tarrant S, Behar S, Suvarna T, Schrader S, Harman E, Nowak C, Kheterpal V, Rao LV, Cashman L, Orvek E, Ayturk D, Gibson L, Zai A, Wong S, Lazar P, Wang Z, Filippaios A, Barton B, Achenbach CJ, Murphy RL, Robinson M, Manabe YC, Pandey S, Colubri A, Oâ Connor L, Lemon SC, Fahey N, Luzuriaga KL, Hafer N, Roth K, Lowe T, Stenzel T, Heetderks W, Broach J, McManus DD. Performance of Rapid Antigen Tests to Detect Symptomatic and Asymptomatic SARS-CoV-2 Infection. medRxiv 2023:2022.08.05.22278466. [PMID: 35982680 PMCID: PMC9387089 DOI: 10.1101/2022.08.05.22278466] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Background Performance of rapid antigen tests for SARS-CoV-2 (Ag-RDT) varies over the course of an infection, and their performance in screening for SARS-CoV-2 is not well established. We aimed to evaluate performance of Ag-RDT for detection of SARS-CoV-2 for symptomatic and asymptomatic participants. Methods Participants >2 years old across the United States enrolled in the study between October 2021 and February 2022. Participants completed Ag-RDT and molecular testing (RT-PCR) for SARS-CoV-2 every 48 hours for 15 days. This analysis was limited to participants who were asymptomatic and tested negative on their first day of study participation. Onset of infection was defined as the day of first positive RT-PCR result. Sensitivity of Ag-RDT was measured based on testing once, twice (after 48-hours), and thrice (after 96 hours). Analysis was repeated for different Days Post Index PCR Positivity (DPIPP) and stratified based on symptom-status. Results In total, 5,609 of 7,361 participants were eligible for this analysis. Among 154 participants who tested positive for SARS-CoV-2, 97 were asymptomatic and 57 had symptoms at infection onset. Serial testing with Ag-RDT twice 48-hours apart resulted in an aggregated sensitivity of 93.4% (95% CI: 89.1-96.1%) among symptomatic participants on DPIPP 0-6. Excluding singleton positives, aggregated sensitivity on DPIPP 0-6 for two-time serial-testing among asymptomatic participants was lower at 62.7% (54.7-70.0%) but improved to 79.0% (71.0-85.3%) with testing three times at 48-hour intervals. Discussion Performance of Ag-RDT was optimized when asymptomatic participants tested three-times at 48-hour intervals and when symptomatic participants tested two-times separated by 48-hours.
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6
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Petros BA, Paull JS, Tomkins-Tinch CH, Loftness BC, DeRuff KC, Nair P, Gionet GL, Benz A, Brock-Fisher T, Hughes M, Yurkovetskiy L, Mulaudzi S, Leenerman E, Nyalile T, Moreno GK, Specht I, Sani K, Adams G, Babet SV, Baron E, Blank JT, Boehm C, Botti-Lodovico Y, Brown J, Buisker AR, Burcham T, Chylek L, Cronan P, Dauphin A, Desreumaux V, Doss M, Flynn B, Gladden-Young A, Glennon O, Harmon HD, Hook TV, Kary A, King C, Loreth C, Marrs L, McQuade KJ, Milton TT, Mulford JM, Oba K, Pearlman L, Schifferli M, Schmidt MJ, Tandus GM, Tyler A, Vodzak ME, Krohn Bevill K, Colubri A, MacInnis BL, Ozsoy AZ, Parrie E, Sholtes K, Siddle KJ, Fry B, Luban J, Park DJ, Marshall J, Bronson A, Schaffner SF, Sabeti PC. Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework. Med 2022; 3:883-900.e13. [PMID: 36198312 PMCID: PMC9482833 DOI: 10.1016/j.medj.2022.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Universities are vulnerable to infectious disease outbreaks, making them ideal environments to study transmission dynamics and evaluate mitigation and surveillance measures. Here, we analyze multimodal COVID-19-associated data collected during the 2020-2021 academic year at Colorado Mesa University and introduce a SARS-CoV-2 surveillance and response framework. METHODS We analyzed epidemiological and sociobehavioral data (demographics, contact tracing, and WiFi-based co-location data) alongside pathogen surveillance data (wastewater and diagnostic testing, and viral genomic sequencing of wastewater and clinical specimens) to characterize outbreak dynamics and inform policy. We applied relative risk, multiple linear regression, and social network assortativity to identify attributes or behaviors associated with contracting SARS-CoV-2. To characterize SARS-CoV-2 transmission, we used viral sequencing, phylogenomic tools, and functional assays. FINDINGS Athletes, particularly those on high-contact teams, had the highest risk of testing positive. On average, individuals who tested positive had more contacts and longer interaction durations than individuals who never tested positive. The distribution of contacts per individual was overdispersed, although not as overdispersed as the distribution of phylogenomic descendants. Corroboration via technical replicates was essential for identification of wastewater mutations. CONCLUSIONS Based on our findings, we formulate a framework that combines tools into an integrated disease surveillance program that can be implemented in other congregate settings with limited resources. FUNDING This work was supported by the National Science Foundation, the Hertz Foundation, the National Institutes of Health, the Centers for Disease Control and Prevention, the Massachusetts Consortium on Pathogen Readiness, the Howard Hughes Medical Institute, the Flu Lab, and the Audacious Project.
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Affiliation(s)
- Brittany A Petros
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Harvard/MIT MD-PhD Program, Boston, MA 02115, USA; Systems, Synthetic, and Quantitative Biology PhD Program, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jillian S Paull
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Systems, Synthetic, and Quantitative Biology PhD Program, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Christopher H Tomkins-Tinch
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Bryn C Loftness
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Computer Science and Engineering, Colorado Mesa University, Grand Junction, CO 81501, USA; Complex Systems and Data Science PhD Program, University of Vermont, Burlington, VT 05405, USA; Vermont Complex Systems Center, University of Vermont, Burlington, VT 05405, USA.
| | | | - Parvathy Nair
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | - Aaron Benz
- Degree Analytics, Inc., Austin, TX 78758, USA
| | | | | | - Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Shandukani Mulaudzi
- Harvard Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Thomas Nyalile
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Gage K Moreno
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ivan Specht
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kian Sani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gordon Adams
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Simone V Babet
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Emily Baron
- COVIDCheck Colorado, LLC, Denver, CO 80202, USA
| | - Jesse T Blank
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Chloe Boehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Princeton University Molecular Biology Department, Princeton, NJ 08544, USA
| | | | - Jeremy Brown
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | | | | | - Lily Chylek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paul Cronan
- Fathom Information Design, Boston, MA 02114, USA
| | - Ann Dauphin
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Valentine Desreumaux
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Megan Doss
- Warrior Diagnostics, Inc., Loveland, CO 80538, USA
| | - Belinda Flynn
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | | | | | | | - Thomas V Hook
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Anton Kary
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Clay King
- Department of Mathematics and Statistics, Colorado Mesa University, Grand Junction, CO 81501, USA
| | | | - Libby Marrs
- Fathom Information Design, Boston, MA 02114, USA
| | - Kyle J McQuade
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Thorsen T Milton
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Jada M Mulford
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Kyle Oba
- Fathom Information Design, Boston, MA 02114, USA
| | - Leah Pearlman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Grace M Tandus
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Andy Tyler
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Megan E Vodzak
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kelly Krohn Bevill
- Department of Computer Science and Engineering, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Andres Colubri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; University of Massachusetts Medical School, Worcester, MA 01655, USA
| | | | - A Zeynep Ozsoy
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Eric Parrie
- COVIDCheck Colorado, LLC, Denver, CO 80202, USA
| | - Kari Sholtes
- Department of Computer Science and Engineering, Colorado Mesa University, Grand Junction, CO 81501, USA; Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Katherine J Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ben Fry
- Fathom Information Design, Boston, MA 02114, USA
| | - Jeremy Luban
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA; Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John Marshall
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Amy Bronson
- Physician Assistant Program, Department of Kinesiology, Colorado Mesa University, Grand Junction, CO 81501, USA
| | | | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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7
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Soni A, Herbert C, Filippaios A, Broach J, Colubri A, Fahey N, Woods K, Nanavati J, Wright C, Orwig T, Gilliam K, Kheterpal V, Suvarna T, Nowak C, Schrader S, Lin H, O'Connor L, Pretz C, Ayturk D, Orvek E, Flahive J, Lazar P, Shi Q, Achenbach C, Murphy R, Robinson M, Gibson L, Stamegna P, Hafer N, Luzuriaga K, Barton B, Heetderks W, Manabe YC, McManus D. Comparison of Rapid Antigen Tests' Performance Between Delta and Omicron Variants of SARS-CoV-2 : A Secondary Analysis From a Serial Home Self-testing Study. Ann Intern Med 2022; 175:1685-1692. [PMID: 36215709 PMCID: PMC9578286 DOI: 10.7326/m22-0760] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND It is important to document the performance of rapid antigen tests (Ag-RDTs) in detecting SARS-CoV-2 variants. OBJECTIVE To compare the performance of Ag-RDTs in detecting the Delta (B.1.617.2) and Omicron (B.1.1.529) variants of SARS-CoV-2. DESIGN Secondary analysis of a prospective cohort study that enrolled participants between 18 October 2021 and 24 January 2022. Participants did Ag-RDTs and collected samples for reverse transcriptase polymerase chain reaction (RT-PCR) testing every 48 hours for 15 days. SETTING The parent study enrolled participants throughout the mainland United States through a digital platform. All participants self-collected anterior nasal swabs for rapid antigen testing and RT-PCR testing. All Ag-RDTs were completed at home, whereas nasal swabs for RT-PCR were shipped to a central laboratory. PARTICIPANTS Of 7349 participants enrolled in the parent study, 5779 asymptomatic persons who tested negative for SARS-CoV-2 on day 1 of the study were eligible for this substudy. MEASUREMENTS Sensitivity of Ag-RDTs on the same day as the first positive (index) RT-PCR result and 48 hours after the first positive RT-PCR result. RESULTS A total of 207 participants were positive on RT-PCR (58 Delta, 149 Omicron). Differences in sensitivity between variants were not statistically significant (same day: Delta, 15.5% [95% CI, 6.2% to 24.8%] vs. Omicron, 22.1% [CI, 15.5% to 28.8%]; at 48 hours: Delta, 44.8% [CI, 32.0% to 57.6%] vs. Omicron, 49.7% [CI, 41.6% to 57.6%]). Among 109 participants who had RT-PCR-positive results for 48 hours, rapid antigen sensitivity did not differ significantly between Delta- and Omicron-infected participants (48-hour sensitivity: Delta, 81.5% [CI, 66.8% to 96.1%] vs. Omicron, 78.0% [CI, 69.1% to 87.0%]). Only 7.2% of the 69 participants with RT-PCR-positive results for shorter than 48 hours tested positive by Ag-RDT within 1 week; those with Delta infections remained consistently negative on Ag-RDTs. LIMITATION A testing frequency of 48 hours does not allow a finer temporal resolution of the analysis of test performance, and the results of Ag-RDTs are based on self-report. CONCLUSION The performance of Ag-RDTs in persons infected with the SARS-CoV-2 Omicron variant is not inferior to that in persons with Delta infections. Serial testing improved the sensitivity of Ag-RDTs for both variants. The performance of rapid antigen testing varies on the basis of duration of RT-PCR positivity. PRIMARY FUNDING SOURCE National Heart, Lung, and Blood Institute of the National Institutes of Health.
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Affiliation(s)
- Apurv Soni
- Program in Digital Medicine and Division of Clinical Informatics, Department of Medicine, and Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (A.S.)
| | - Carly Herbert
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., A.F., K.W., J.N., C.W., T.O., K.G., C.P.)
| | - Andreas Filippaios
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., A.F., K.W., J.N., C.W., T.O., K.G., C.P.)
| | - John Broach
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (J.B., L.O.)
| | - Andres Colubri
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts (A.C.)
| | - Nisha Fahey
- Program in Digital Medicine, Department of Medicine, Department of Population and Quantitative Health Sciences, and Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, Massachusetts (N.F.)
| | - Kelsey Woods
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., A.F., K.W., J.N., C.W., T.O., K.G., C.P.)
| | - Janvi Nanavati
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., A.F., K.W., J.N., C.W., T.O., K.G., C.P.)
| | - Colton Wright
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., A.F., K.W., J.N., C.W., T.O., K.G., C.P.)
| | - Taylor Orwig
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., A.F., K.W., J.N., C.W., T.O., K.G., C.P.)
| | - Karen Gilliam
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., A.F., K.W., J.N., C.W., T.O., K.G., C.P.)
| | - Vik Kheterpal
- CareEvolution, Ann Arbor, Michigan (V.K., T.S., C.N., S.S.)
| | - Thejas Suvarna
- CareEvolution, Ann Arbor, Michigan (V.K., T.S., C.N., S.S.)
| | - Chris Nowak
- CareEvolution, Ann Arbor, Michigan (V.K., T.S., C.N., S.S.)
| | | | - Honghuang Lin
- Program in Digital Medicine and Division of Clinical Informatics, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (H.L.)
| | - Laurel O'Connor
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (J.B., L.O.)
| | - Caitlin Pretz
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (C.H., A.F., K.W., J.N., C.W., T.O., K.G., C.P.)
| | - Didem Ayturk
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (D.A., E.O., J.F., P.L., B.B.)
| | - Elizabeth Orvek
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (D.A., E.O., J.F., P.L., B.B.)
| | - Julie Flahive
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (D.A., E.O., J.F., P.L., B.B.)
| | - Peter Lazar
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (D.A., E.O., J.F., P.L., B.B.)
| | - Qiming Shi
- Program in Digital Medicine, Department of Medicine, Department of Population and Quantitative Health Sciences, and University of Massachusetts Center for Clinical and Translational Science, University of Massachusetts Chan Medical School, Worcester, Massachusetts (Q.S.)
| | - Chad Achenbach
- Division of Infectious Disease, Department of Medicine, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, Illinois (C.A., R.M.)
| | - Robert Murphy
- Division of Infectious Disease, Department of Medicine, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, Illinois (C.A., R.M.)
| | - Matthew Robinson
- Division of Infectious Disease, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland (M.R., Y.C.M.)
| | - Laura Gibson
- Department of Pediatrics and Division of Infectious Disease, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (L.G.)
| | - Pamela Stamegna
- University of Massachusetts Center for Clinical and Translational Science, University of Massachusetts Chan Medical School, Worcester, Massachusetts (P.S., N.H.)
| | - Nathaniel Hafer
- University of Massachusetts Center for Clinical and Translational Science, University of Massachusetts Chan Medical School, Worcester, Massachusetts (P.S., N.H.)
| | - Katherine Luzuriaga
- University of Massachusetts Center for Clinical and Translational Science and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts (K.L.)
| | - Bruce Barton
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (D.A., E.O., J.F., P.L., B.B.)
| | - William Heetderks
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland (W.H.)
| | - Yukari C Manabe
- Division of Infectious Disease, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland (M.R., Y.C.M.)
| | - David McManus
- Program in Digital Medicine and Division of Cardiology, Department of Medicine, and Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts (D.M.)
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8
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Soni A, Herbert C, Filippaios A, Broach J, Colubri A, Fahey N, Woods K, Nanavati J, Wright C, Orwig T, Gilliam K, Kheterpal V, Suvarna T, Nowak C, Schrader S, Lin H, O'Connor L, Pretz C, Ayturk D, Orvek E, Flahive J, Lazar P, Shi Q, Achenbach C, Murphy R, Robinson M, Gibson L, Stamegna P, Hafer N, Luzuriaga K, Barton B, Heetderks W, Manabe YC, McManus D. Comparison of Rapid Antigen Tests' Performance between Delta (B.1.61.7; AY.X) and Omicron (B.1.1.529; BA1) Variants of SARS-CoV-2: Secondary Analysis from a Serial Home Self-Testing Study. medRxiv 2022. [PMID: 35262091 DOI: 10.1101/2022.02.27.22271090] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background There is a need to understand the performance of rapid antigen tests (Ag-RDT) for detection of the Delta (B.1.61.7; AY.X) and Omicron (B.1.1.529; BA1) SARS-CoV-2 variants. Methods Participants without any symptoms were enrolled from October 18, 2021 to January 24, 2022 and performed Ag-RDT and RT-PCR tests every 48 hours for 15 days. This study represents a non-pre-specified analysis in which we sought to determine if sensitivity of Ag-RDT differed in participants with Delta compared to Omicron variant. Participants who were positive on RT-PCR on the first day of the testing period were excluded. Delta and Omicron variants were defined based on sequencing and date of first RT-PCR positive result (RT-PCR+). Comparison of Ag-RDT performance between the variants was based on sensitivity, defined as proportion of participants with Ag-RDT+ results in relation to their first RT-PCR+ result, for different duration of testing with rapid Ag-RDT. Subsample analysis was performed based on the result of participants' second RT-PCR test within 48 hours of the first RT-PCR+ test. Results From the 7,349 participants enrolled in the parent study, 5,506 met the eligibility criteria for this analysis. A total of 153 participants were RT-PCR+ (61 Delta, 92 Omicron); among this group, 36 (23.5%) tested Ag-RDT+ on the same day, and 84 (54.9%) tested Ag-RDT+ within 48 hours as first RT-PCR+. The differences in sensitivity between variants were not statistically significant (same-day: Delta 16.4% [95% CI: 8.2-28.1] vs Omicron 28.2% [95% CI: 19.4-38.6]; and 48-hours: Delta 45.9% [33.1-59.2] vs. Omicron 60.9% [50.1-70.9]). This trend continued among the 86 participants who had consecutive RT-PCR+ result (48-hour sensitivity: Delta 79.3% [60.3-92.1] vs. Omicron: 89.5% [78.5-96.0]). Conversely, the 38 participants who had an isolated RT-PCR+ remained consistently negative on Ag-RDT, regardless of the variant. Conclusions The performance of Ag-RDT is not inferior among individuals infected with the SARS-CoV-2 Omicron variant as compared to the Delta variant. The improvement in sensitivity of Ag-RDT noted with serial testing is consistent between Delta and Omicron variant. Performance of Ag-RDT varies based on duration of RT-PCR+ results and more studies are needed to understand the clinical and public health significance of individuals who are RT-PCR+ for less than 48 hours.
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9
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Okogbenin S, Okoeguale J, Akpede G, Colubri A, Barnes KG, Mehta S, Eifediyi R, Okogbo F, Eigbefoh J, Momoh M, Rafiu M, Adomeh D, Odia I, Aire C, Atafo R, Okonofua M, Pahlman M, Becker-Ziaja B, Asogun D, Okokhere P, Happi C, Günther S, Sabeti PC, Ogbaini-Emovon E. Retrospective Cohort Study of Lassa Fever in Pregnancy, Southern Nigeria. Emerg Infect Dis 2019; 25. [PMID: 31310586 PMCID: PMC6649346 DOI: 10.3201/eid2508.181299] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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10
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Solano-Roman A, Cruz-Castillo C, Offenhuber D, Colubri A. NX4: a web-based visualization of large multiple sequence alignments. Bioinformatics 2019; 35:4800-4802. [PMID: 31161215 DOI: 10.1093/bioinformatics/btz457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 05/02/2019] [Accepted: 05/29/2019] [Indexed: 11/12/2022] Open
Abstract
SUMMARY Multiple Sequence Alignments (MSAs) are a fundamental operation in genome analysis. However, MSA visualizations such as sequence logos and matrix representations have changed little since the nineties and are not well suited for displaying large-scale alignments. We propose a novel, web-based MSA visualization tool called NX4, which can handle genome alignments comprising thousands of sequences. NX4 calculates the frequency of each nucleotide along the alignment and visually summarizes the results using a color-blind friendly palette that helps identifying regions of high genetic diversity. NX4 also provides the user with additional assistance in finding these regions with a 'focus + context' mechanism that uses a line chart of the Shannon entropy across the alignment. The tool offers geneticists an easy-to-use and scalable analysis for large MSA studies. AVAILABILITY AND IMPLEMENTATION NX4 is freely available at https://www.nx4.io, and its source code at https://github.com/NX4/nx4. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- A Solano-Roman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,College of Arts, Media + Design, Northeastern University, Boston, MA 02115, USA
| | - C Cruz-Castillo
- Department of Computer Science, Universidad Latina de Costa Rica, San José 11501, Costa Rica
| | - D Offenhuber
- College of Arts, Media + Design, Northeastern University, Boston, MA 02115, USA
| | - A Colubri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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11
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Akpede GO, Asogun DA, Okogbenin SA, Dawodu SO, Momoh MO, Dongo AE, Ike C, Tobin E, Akpede N, Ogbaini-Emovon E, Adewale AE, Ochei O, Onyeke F, Okonofua MO, Atafo RO, Odia I, Adomeh DI, Odigie G, Ogbeifun C, Muoebonam E, Ihekweazu C, Ramharter M, Colubri A, Sabeti PC, Happi CT, Günther S, Agbonlahor DE. Corrigendum: Caseload and Case Fatality of Lassa Fever in Nigeria, 2001-2018: A Specialist Center's Experience and Its Implications. Front Public Health 2019; 7:251. [PMID: 31544101 PMCID: PMC6753946 DOI: 10.3389/fpubh.2019.00251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/20/2019] [Indexed: 11/15/2022] Open
Affiliation(s)
- George O Akpede
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Department of Paediatrics, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Danny A Asogun
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Department of Community Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Sylvanus A Okogbenin
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Department of Obstetrics and Gynaecology, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Simeon O Dawodu
- Department of Paediatrics, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Mojeed O Momoh
- Department of Obstetrics and Gynaecology, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Andrew E Dongo
- Department of Surgery, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Chiedozie Ike
- Department of Community Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Ekaete Tobin
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Nosa Akpede
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Ephraim Ogbaini-Emovon
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Adetunji E Adewale
- Department of Paediatrics, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Oboratare Ochei
- Department of Community Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Frank Onyeke
- Department of Paediatrics, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Martha O Okonofua
- Department of Nursing Services, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Rebecca O Atafo
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Department of Nursing Services, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Ikponmwosa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Donatus I Adomeh
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - George Odigie
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Caroline Ogbeifun
- Department of Medical Records, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Ekene Muoebonam
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | | | - Michael Ramharter
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine & I. Department of Medicine University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andres Colubri
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Pardis C Sabeti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Christian T Happi
- Department of Biological Sciences and African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
| | - Stephan Günther
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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12
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Akpede GO, Asogun DA, Okogbenin SA, Dawodu SO, Momoh MO, Dongo AE, Ike C, Tobin E, Akpede N, Ogbaini-Emovon E, Adewale AE, Ochei O, Onyeke F, Okonofua MO, Atafo RO, Odia I, Adomeh DI, Odigie G, Ogbeifun C, Muebonam E, Ihekweazu C, Ramharter M, Colubri A, Sarbeti PC, Happi CT, Günther S, Agbonlahor DE. Caseload and Case Fatality of Lassa Fever in Nigeria, 2001-2018: A Specialist Center's Experience and Its Implications. Front Public Health 2019; 7:170. [PMID: 31294014 PMCID: PMC6603170 DOI: 10.3389/fpubh.2019.00170] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 01/26/2019] [Accepted: 06/06/2019] [Indexed: 12/29/2022] Open
Abstract
Background: The general lack of comprehensive data on the trends of Lassa fever (LF) outbreaks contrasts with its widespread occurrence in West Africa and is an important constraint in the design of effective control measures. We reviewed the contribution of LF to admissions and mortality among hospitalized patients from 2001 to 2018 in the bid to address this gap. Methods: Observational study of LF caseload and mortality from 2001 to 18 in terms of the contribution of confirmed LF to admissions and deaths, and case fatality (CF) among patients with confirmed LF at a specialist center in Nigeria. The diagnosis of LF was confirmed using reverse transcription polymerase chain reaction (RT-PCR) test, and medians and frequencies were compared using Kruskal-Wallis, Mann-Whitney and χ2 tests, with p-values <0.05 taken as significant. Results: The contribution of confirmed LF to deaths (362/9057, 4.0%) was significantly higher than to admissions (1,298/185,707, 0.7%; OR [95% CI] = 5.9 [5.3, 6.7], p < 0.001). The average CF among patients with confirmed LF declined from 154/355 (43%) in 2001–09 to 183/867 (21.1%) (OR [95% CI] = 2.9 [2.2, 3.7], p < 0.001) in 2011–18. The annual CF declined from 94% in 2001 to 15% in 2018 whereas the caseload increased from 0.3 to 3.4%. The outbreaks were characterized by irregular cycles of high caseload in 2005–2007, 2012–2014, and 2016–2018, and progressive blurring of the seasonality. Conclusion: LF outbreaks in Nigeria have upgraded spatially and temporally, with the potential for cycles of increasing severity. The strategic establishment of LF surveillance and clinical case management centers could be a pragmatic and cost-effective approach to mitigating the outbreaks, particularly in reducing the associated CF. Urgent efforts are needed in reinvigorating extant control measures while the search for sustainable solutions continues.
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Affiliation(s)
- George O Akpede
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Department of Paediatrics, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Danny A Asogun
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Department of Community Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Sylvanus A Okogbenin
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Department of Obstetrics and Gynaecology, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Simeon O Dawodu
- Department of Paediatrics, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Mojeed O Momoh
- Department of Obstetrics and Gynaecology, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Andrew E Dongo
- Department of Surgery, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Chiedozie Ike
- Department of Community Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Ekaete Tobin
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Nosa Akpede
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Ephraim Ogbaini-Emovon
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Adetunji E Adewale
- Department of Paediatrics, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Oboratare Ochei
- Department of Community Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Frank Onyeke
- Department of Paediatrics, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Martha O Okonofua
- Department of Nursing Services, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Rebecca O Atafo
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Department of Nursing Services, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Ikponmwosa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Donatus I Adomeh
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - George Odigie
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Caroline Ogbeifun
- Department of Medical Records, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Ekene Muebonam
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | | | - Michael Ramharter
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine & I. Department of Medicine University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andres Colubri
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Pardis C Sarbeti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Christian T Happi
- Department of Biological Sciences and African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
| | - Stephan Günther
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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13
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Colubri A, Hartley MA, Siakor M, Wolfman V, Felix A, Sesay T, Shaffer JG, Garry RF, Grant DS, Levine AC, Sabeti PC. Machine-learning Prognostic Models from the 2014-16 Ebola Outbreak: Data-harmonization Challenges, Validation Strategies, and mHealth Applications. EClinicalMedicine 2019; 11:54-64. [PMID: 31312805 PMCID: PMC6610774 DOI: 10.1016/j.eclinm.2019.06.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 05/02/2019] [Accepted: 06/07/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Ebola virus disease (EVD) plagues low-resource and difficult-to-access settings. Machine learning prognostic models and mHealth tools could improve the understanding and use of evidence-based care guidelines in such settings. However, data incompleteness and lack of interoperability limit model generalizability. This study harmonizes diverse datasets from the 2014-16 EVD epidemic and generates several prognostic models incorporated into the novel Ebola Care Guidelines app that provides informed access to recommended evidence-based guidelines. METHODS Multivariate logistic regression was applied to investigate survival outcomes in 470 patients admitted to five Ebola treatment units in Liberia and Sierra Leone at various timepoints during 2014-16. We generated a parsimonious model (viral load, age, temperature, bleeding, jaundice, dyspnea, dysphagia, and time-to-presentation) and several fallback models for when these variables are unavailable. All were externally validated against two independent datasets and compared to further models including expert observational wellness assessments. Models were incorporated into an app highlighting the signs/symptoms with the largest contribution to prognosis. FINDINGS The parsimonious model approached the predictive power of observational assessments by experienced clinicians (Area-Under-the-Curve, AUC = 0.70-0.79, accuracy = 0.64-0.74) and maintained its performance across subcohorts with different healthcare seeking behaviors. Age and viral load contributed > 5-fold the weighting of other features and including them in a minimal model had a similar AUC, albeit at the cost of specificity. INTERPRETATION Clinically guided prognostic models can recapitulate clinical expertise and be useful when such expertise is unavailable. Incorporating these models into mHealth tools may facilitate their interpretation and provide informed access to comprehensive clinical guidelines. FUNDING Howard Hughes Medical Institute, US National Institutes of Health, Bill & Melinda Gates Foundation, International Medical Corps, UK Department for International Development, and GOAL Global.
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Affiliation(s)
- Andres Colubri
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Howard Hughes Medical Institute, Chevy Chase, USA
- Correspondence to: A. Colubri, Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, USA.
| | - Mary-Anne Hartley
- University of Lausanne, Faculty of Biology and Medicine, Lausanne, Switzerland
- GOAL Global, Dublin, Ireland
| | | | | | - August Felix
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Tom Sesay
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Jeffrey G. Shaffer
- Tulane University, School of Public Health and Tropical Medicine, New Orleans, USA
| | - Robert F. Garry
- Tulane University, Department of Microbiology and Immunology, New Orleans, USA
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
| | - Adam C. Levine
- International Medical Corps, Los Angeles, USA
- Brown University, Warren Alpert School of Medicine, Providence, USA
- Correspondence to: A. C. Levine, International Medical Corps, Los Angeles, USA.
| | - Pardis C. Sabeti
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Howard Hughes Medical Institute, Chevy Chase, USA
- Harvard School of Public Health, Boston, USA
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14
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Okokhere P, Colubri A, Azubike C, Iruolagbe C, Osazuwa O, Tabrizi S, Chin E, Asad S, Ediale E, Rafiu M, Adomeh D, Odia I, Atafo R, Aire C, Okogbenin S, Pahlman M, Becker-Ziaja B, Asogun D, Fradet T, Fry B, Schaffner SF, Happi C, Akpede G, Günther S, Sabeti PC. Clinical and laboratory predictors of Lassa fever outcome in a dedicated treatment facility in Nigeria: a retrospective, observational cohort study. Lancet Infect Dis 2018; 18:684-695. [PMID: 29523497 PMCID: PMC5984133 DOI: 10.1016/s1473-3099(18)30121-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 01/17/2018] [Accepted: 01/19/2018] [Indexed: 12/01/2022]
Abstract
BACKGROUND Lassa fever is a viral haemorrhagic disease endemic to west Africa. No large-scale studies exist from Nigeria, where the Lassa virus (LASV) is most diverse. LASV diversity, coupled with host genetic and environmental factors, might cause differences in disease pathophysiology. Small-scale studies in Nigeria suggest that acute kidney injury is an important clinical feature and might be a determinant of survival. We aimed to establish the demographic, clinical, and laboratory factors associated with mortality in Nigerian patients with Lassa fever, and hypothesised that LASV was the direct cause of intrinsic renal damage for a subset of the patients with Lassa fever. METHODS We did a retrospective, observational cohort study of consecutive patients in Nigeria with Lassa fever, who tested positive for LASV with RT-PCR, and were treated in Irrua Specialist Teaching Hospital. We did univariate and multivariate statistical analyses, including logistic regression, of all demographic, clinical, and laboratory variables available at presentation to identify the factors associated with patient mortality. FINDINGS Of 291 patients treated in Irrua Specialist Teaching Hospital between Jan 3, 2011, and Dec 11, 2015, 284 (98%) had known outcomes (died or survived) and seven (2%) were discharged against medical advice. Overall case-fatality rate was 24% (68 of 284 patients), with a 1·4 times increase in mortality risk for each 10 years of age (p=0·00017), reaching 39% (22 of 57) for patients older than 50 years. Of 284 patients, 81 (28%) had acute kidney injury and 104 (37%) had CNS manifestations and thus both were considered important complications of acute Lassa fever in Nigeria. Acute kidney injury was strongly associated with poor outcome (case-fatality rate of 60% [49 of 81 patients]; odds ratio [OR] 15, p<0·00001). Compared with patients without acute kidney injury, those with acute kidney injury had higher incidence of proteinuria (32 [82%] of 39 patients) and haematuria (29 [76%] of 38) and higher mean serum potassium (4·63 [SD 1·04] mmol/L) and lower blood urea nitrogen to creatinine ratio (8·6 for patients without clinical history of fluid loss), suggesting intrinsic renal damage. Normalisation of creatinine concentration was associated with recovery. Elevated serum creatinine (OR 1·3; p=0·046), aspartate aminotransferase (OR 1·5; p=0·075), and potassium (OR 3·6; p=0·0024) were independent predictors of death. INTERPRETATION Our study presents detailed clinical and laboratory data for Nigerian patients with Lassa fever and provides strong evidence for intrinsic renal dysfunction in acute Lassa fever. Early recognition and treatment of acute kidney injury might significantly reduce mortality. FUNDING German Research Foundation, German Center for Infection Research, Howard Hughes Medical Institute, US National Institutes of Health, and World Bank.
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Affiliation(s)
- Peter Okokhere
- Department of Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria; Institute of Lassa fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria; Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma, Edo, Nigeria.
| | - Andres Colubri
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Maryland, MD, USA.
| | | | | | - Omoregie Osazuwa
- Department of Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | | | - Elizabeth Chin
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; University of California, Los Angeles, CA, USA; Department of Bioinformatics, Los Angeles, CA, USA
| | - Sara Asad
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ehi Ediale
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mojeed Rafiu
- Department of Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Donatus Adomeh
- Institute of Lassa fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Ikponmwosa Odia
- Institute of Lassa fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Rebecca Atafo
- Lassa fever Ward, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Chris Aire
- Institute of Lassa fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Sylvanus Okogbenin
- Department of Obstetrics and Gynaecology, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Meike Pahlman
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Centre for Infection Research, Partner site, Hamburg, Germany
| | - Beate Becker-Ziaja
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Centre for Infection Research, Partner site, Hamburg, Germany
| | - Danny Asogun
- Institute of Lassa fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | | | - Ben Fry
- Fathom Information Design, Boston, MA, USA
| | - Stephen F Schaffner
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard School of Public Health, Boston, MA, USA
| | - Christian Happi
- Department of Biological Sciences and African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Edo, Nigeria
| | - George Akpede
- Department of Paediatrics, Irrua Specialist Teaching Hospital, Irrua, Nigeria; Department of Paediatrics, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma, Edo, Nigeria
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; German Centre for Infection Research, Partner site, Hamburg, Germany
| | - Pardis C Sabeti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Maryland, MD, USA; Harvard School of Public Health, Boston, MA, USA
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15
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Colubri A, Silver T, Fradet T, Retzepi K, Fry B, Sabeti P. Transforming Clinical Data into Actionable Prognosis Models: Machine-Learning Framework and Field-Deployable App to Predict Outcome of Ebola Patients. PLoS Negl Trop Dis 2016; 10:e0004549. [PMID: 26991501 PMCID: PMC4798608 DOI: 10.1371/journal.pntd.0004549] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [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: 11/03/2015] [Accepted: 02/24/2016] [Indexed: 11/19/2022] Open
Abstract
Background Assessment of the response to the 2014–15 Ebola outbreak indicates the need for innovations in data collection, sharing, and use to improve case detection and treatment. Here we introduce a Machine Learning pipeline for Ebola Virus Disease (EVD) prognosis prediction, which packages the best models into a mobile app to be available in clinical care settings. The pipeline was trained on a public EVD clinical dataset, from 106 patients in Sierra Leone. Methods/Principal Findings We used a new tool for exploratory analysis, Mirador, to identify the most informative clinical factors that correlate with EVD outcome. The small sample size and high prevalence of missing records were significant challenges. We applied multiple imputation and bootstrap sampling to address missing data and quantify overfitting. We trained several predictors over all combinations of covariates, which resulted in an ensemble of predictors, with and without viral load information, with an area under the receiver operator characteristic curve of 0.8 or more, after correcting for optimistic bias. We ranked the predictors by their F1-score, and those above a set threshold were compiled into a mobile app, Ebola CARE (Computational Assignment of Risk Estimates). Conclusions/Significance This method demonstrates how to address small sample sizes and missing data, while creating predictive models that can be readily deployed to assist treatment in future outbreaks of EVD and other infectious diseases. By generating an ensemble of predictors instead of relying on a single model, we are able to handle situations where patient data is partially available. The prognosis app can be updated as new data become available, and we made all the computational protocols fully documented and open-sourced to encourage timely data sharing, independent validation, and development of better prediction models in outbreak response. We introduce a machine-learning framework and field-deployable app to predict outcome of Ebola patients from their initial clinical symptoms. Recent work from other authors also points out to the clinical factors that can be used to better understand patient prognosis, but there is currently no predictive model that can be deployed in the field to assist health care workers. Mobile apps for clinical diagnosis and prognosis allow using more complex models than the scoring protocols that have been traditionally favored by clinicians, such as Apgar and MTS. Furthermore, the WHO Ebola Interim Assessment Panel has recently concluded that innovative tools for data collection, reporting, and monitoring are needed for better response in future outbreaks. However, incomplete clinical data will continue to be a serious problem until more robust and standardized data collection systems are in place. Our app demonstrates how systematic data collection could lead to actionable knowledge, which in turn would trigger more and better collection, further improving the prognosis models and the app, essentially creating a virtuous cycle.
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Affiliation(s)
- Andres Colubri
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail:
| | - Tom Silver
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Harvard College, Cambridge, Massachusetts, United States of America
| | - Terrence Fradet
- Fathom Information Design, Boston, Massachusetts, United States of America
| | - Kalliroi Retzepi
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Ben Fry
- Fathom Information Design, Boston, Massachusetts, United States of America
| | - Pardis Sabeti
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts, United States of America
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16
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Schieffelin JS, Shaffer JG, Goba A, Gbakie M, Gire SK, Colubri A, Sealfon RSG, Kanneh L, Moigboi A, Momoh M, Fullah M, Moses LM, Brown BL, Andersen KG, Winnicki S, Schaffner SF, Park DJ, Yozwiak NL, Jiang PP, Kargbo D, Jalloh S, Fonnie M, Sinnah V, French I, Kovoma A, Kamara FK, Tucker V, Konuwa E, Sellu J, Mustapha I, Foday M, Yillah M, Kanneh F, Saffa S, Massally JLB, Boisen ML, Branco LM, Vandi MA, Grant DS, Happi C, Gevao SM, Fletcher TE, Fowler RA, Bausch DG, Sabeti PC, Khan SH, Garry RF. Clinical illness and outcomes in patients with Ebola in Sierra Leone. N Engl J Med 2014; 371:2092-100. [PMID: 25353969 PMCID: PMC4318555 DOI: 10.1056/nejmoa1411680] [Citation(s) in RCA: 416] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Limited clinical and laboratory data are available on patients with Ebola virus disease (EVD). The Kenema Government Hospital in Sierra Leone, which had an existing infrastructure for research regarding viral hemorrhagic fever, has received and cared for patients with EVD since the beginning of the outbreak in Sierra Leone in May 2014. METHODS We reviewed available epidemiologic, clinical, and laboratory records of patients in whom EVD was diagnosed between May 25 and June 18, 2014. We used quantitative reverse-transcriptase-polymerase-chain-reaction assays to assess the load of Ebola virus (EBOV, Zaire species) in a subgroup of patients. RESULTS Of 106 patients in whom EVD was diagnosed, 87 had a known outcome, and 44 had detailed clinical information available. The incubation period was estimated to be 6 to 12 days, and the case fatality rate was 74%. Common findings at presentation included fever (in 89% of the patients), headache (in 80%), weakness (in 66%), dizziness (in 60%), diarrhea (in 51%), abdominal pain (in 40%), and vomiting (in 34%). Clinical and laboratory factors at presentation that were associated with a fatal outcome included fever, weakness, dizziness, diarrhea, and elevated levels of blood urea nitrogen, aspartate aminotransferase, and creatinine. Exploratory analyses indicated that patients under the age of 21 years had a lower case fatality rate than those over the age of 45 years (57% vs. 94%, P=0.03), and patients presenting with fewer than 100,000 EBOV copies per milliliter had a lower case fatality rate than those with 10 million EBOV copies per milliliter or more (33% vs. 94%, P=0.003). Bleeding occurred in only 1 patient. CONCLUSIONS The incubation period and case fatality rate among patients with EVD in Sierra Leone are similar to those observed elsewhere in the 2014 outbreak and in previous outbreaks. Although bleeding was an infrequent finding, diarrhea and other gastrointestinal manifestations were common. (Funded by the National Institutes of Health and others.).
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17
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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.
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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.
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18
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Fitzgerald JE, Jha AK, Colubri A, Sosnick TR, Freed KF. Reduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification. Protein Sci 2007; 16:2123-39. [PMID: 17893359 PMCID: PMC2204143 DOI: 10.1110/ps.072939707] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [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] [Indexed: 10/22/2022]
Abstract
We developed a series of statistical potentials to recognize the native protein from decoys, particularly when using only a reduced representation in which each side chain is treated as a single C(beta) atom. Beginning with a highly successful all-atom statistical potential, the Discrete Optimized Protein Energy function (DOPE), we considered the implications of including additional information in the all-atom statistical potential and subsequently reducing to the C(beta) representation. One of the potentials includes interaction energies conditional on backbone geometries. A second potential separates sequence local from sequence nonlocal interactions and introduces a novel reference state for the sequence local interactions. The resultant potentials perform better than the original DOPE statistical potential in decoy identification. Moreover, even upon passing to a reduced C(beta) representation, these statistical potentials outscore the original (all-atom) DOPE potential in identifying native states for sets of decoys. Interestingly, the backbone-dependent statistical potential is shown to retain nearly all of the information content of the all-atom representation in the C(beta) representation. In addition, these new statistical potentials are combined with existing potentials to model hydrogen bonding, torsion energies, and solvation energies to produce even better performing potentials. The ability of the C(beta) statistical potentials to accurately represent protein interactions bodes well for computational efficiency in protein folding calculations using reduced backbone representations, while the extensions to DOPE illustrate general principles for improving knowledge-based potentials.
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Affiliation(s)
- James E Fitzgerald
- Department of Physics, The University of Chicago, Chicago, Illinois 60637, USA
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19
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Jha AK, Colubri A, Zaman MH, Koide S, Sosnick TR, Freed KF. Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. Biochemistry 2005; 44:9691-702. [PMID: 16008354 DOI: 10.1021/bi0474822] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.9] [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: 11/29/2022]
Abstract
A central issue in protein folding is the degree to which each residue's backbone conformational preferences stabilize the native state. We have studied the conformational preferences of each amino acid when the amino acid is not constrained to be in a regular secondary structure. In this large but highly restricted coil library, the backbone preferentially adopts dihedral angles consistent with the polyproline II conformation rather than alpha or beta conformations. The preference for the polyproline II conformation is independent of the degree of solvation. In conjunction with a new masking procedure, the frequencies in our coil library accurately recapitulate both helix and sheet frequencies for the amino acids in structured regions, as well as polyproline II propensities. Therefore, structural propensities for alpha-helices and beta-sheets and for polyproline II conformations in unfolded peptides can be rationalized solely by local effects. In addition, these propensities are often strongly affected by both the chemical nature and the conformation of neighboring residues, contrary to the Flory isolated residue hypothesis.
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Affiliation(s)
- Abhishek K Jha
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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20
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Fernández A, Colubri A, Appignanesi G. Semiempirical prediction of protein folds. Phys Rev E Stat Nonlin Soft Matter Phys 2001; 64:021901. [PMID: 11497614 DOI: 10.1103/physreve.64.021901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2000] [Revised: 11/14/2000] [Indexed: 05/23/2023]
Abstract
We introduce a semiempirical approach to predict ab initio expeditious pathways and native backbone geometries of proteins that fold under in vitro renaturation conditions. The algorithm is engineered to incorporate a discrete codification of local steric hindrances that constrain the movements of the peptide backbone throughout the folding process. Thus, the torsional state of the chain is assumed to be conditioned by the fact that hopping from one basin of attraction to another in the Ramachandran map (local potential energy surface) of each residue is energetically more costly than the search for a specific (Phi, Psi) torsional state within a single basin. A combinatorial procedure is introduced to evaluate coarsely defined torsional states of the chain defined "modulo basins" and translate them into meaningful patterns of long range interactions. Thus, an algorithm for structure prediction is designed based on the fact that local contributions to the potential energy may be subsumed into time-evolving conformational constraints defining sets of restricted backbone geometries whereupon the patterns of nonbonded interactions are constructed. The predictive power of the algorithm is assessed by (a) computing ab initio folding pathways for mammalian ubiquitin that ultimately yield a stable structural pattern reproducing all of its native features, (b) determining the nucleating event that triggers the hydrophobic collapse of the chain, and (c) comparing coarse predictions of the stable folds of moderately large proteins (N approximately 100) with structural information extracted from the protein data bank.
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Affiliation(s)
- A Fernández
- Instituto de Matemática, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Sur, Avenida Alem 1253, Bahía Blanca 8000, Argentina.
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21
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Abstract
Evolution of protein structure from random coil to native is first represented topologically by its time-dependent sequences of discretized Ramachandran basins occupied by successive backbone residues. Introducing energetic and entropic criteria at each instant of observation transforms the description from a structurally ambiguous topological representation to an unambiguous geometric picture of the folding process. The method is applied with success to folding of beta-lactoglobulin, traditionally perplexing because of its reputed nonhierarchical folding pattern. This molecule passes through a stage, ca. 0.1 microseconds duration, of transient, "flickering" alpha-helical structure, until a bit of tertiary structure forms that stabilizes the system long enough to allow it to pass to its native beta-sheet.
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Affiliation(s)
- A Fernández
- James Franck Institute and Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
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22
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Fernández A, Colubri A. Nucleation theory for helix unfolding in peptide chains. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 1999; 60:4645-51. [PMID: 11970326 DOI: 10.1103/physreve.60.4645] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/1999] [Indexed: 04/18/2023]
Abstract
This work introduces a microscopic nucleation theory of helix unfolding in peptide chains aimed at obtaining a semiempirical estimation of the critical-size bubble of structural distortion which may function as the kernel for helix destruction. A dynamic nucleation model for helix-coil transition has been previously introduced as an ansatz to estimate the kinetic barrier of the helix-unfolding event [A. Fernández and A. Colubri, J. Math. Phys. 39, 3167 (1998)]. However, the critical size of the helix-destruction bubble, empirically obtained from computer simulations of favored folding pathways, has not been hitherto justified or determined from first principles. This requires introducing a microscopic treatment of the long-time torsional dynamics to assess its bearing on the formation of structural-distortion bubbles which eventually trigger the helix-unfolding process. To reach this goal we introduce two operational tenets: (a) The torsional dynamics of the chain may be coarse grained according to a discretization of the conformational state of each unit, resolved according to its significant torsional isomers; (b) the semiempirical formulation accounts for the known dependence of the enthalpy increment due to helix unfolding on the change in the effective solvent-exposed surface area. The functional dependence on bubble size of the mean time of completion of the rate-determining step for helix unwinding is shown to be in agreement with previous ad hoc macroscopic models. However, in contrast with such treatments, we infer the existence of a denaturation temperature from the dynamics of critical bubble formation, rather than introducing it as an a priori postulate. Our determination of the critical temperature based on nucleation kinetics theory of critical bubble formation coincides with those obtained from calorimetric and spectroscopic measurements.
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Affiliation(s)
- A Fernández
- Instituto de Matemática, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Sur, Avenida Alem 1253, Bahía Blanca 8000, Argentina
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