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Sanford A, Bond N, Engel E, Kanneh L, Gbakie M, Kamara F, Grant D, Schieffelin J. Increased frequency of musculoskeletal sequelae in ebola survivors 15–40 years of age in Eastern Sierra Leone. Am J Med Sci 2023. [DOI: 10.1016/s0002-9629(23)00685-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Borrega R, Nelson DKS, Koval AP, Bond NG, Heinrich ML, Rowland MM, Lathigra R, Bush DJ, Aimukanova I, Phinney WN, Koval SA, Hoffmann AR, Smither AR, Bell-Kareem AR, Melnik LI, Genemaras KJ, Chao K, Snarski P, Melton AB, Harrell JE, Smira AA, Elliott DH, Rouelle JA, Sabino-Santos G, Drouin AC, Momoh M, Sandi JD, Goba A, Samuels RJ, Kanneh L, Gbakie M, Branco ZL, Shaffer JG, Schieffelin JS, Robinson JE, Fusco DN, Sabeti PC, Andersen KG, Grant DS, Boisen ML, Branco LM, Garry RF. Cross-Reactive Antibodies to SARS-CoV-2 and MERS-CoV in Pre-COVID-19 Blood Samples from Sierra Leoneans. Viruses 2021; 13:2325. [PMID: 34835131 PMCID: PMC8625389 DOI: 10.3390/v13112325] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 09/29/2021] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Many countries in sub-Saharan Africa have experienced lower COVID-19 caseloads and fewer deaths than countries in other regions worldwide. Under-reporting of cases and a younger population could partly account for these differences, but pre-existing immunity to coronaviruses is another potential factor. Blood samples from Sierra Leonean Lassa fever and Ebola survivors and their contacts collected before the first reported COVID-19 cases were assessed using enzyme-linked immunosorbent assays for the presence of antibodies binding to proteins of coronaviruses that infect humans. Results were compared to COVID-19 subjects and healthy blood donors from the United States. Prior to the pandemic, Sierra Leoneans had more frequent exposures than Americans to coronaviruses with epitopes that cross-react with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), SARS-CoV, and Middle Eastern respiratory syndrome coronavirus (MERS-CoV). The percentage of Sierra Leoneans with antibodies reacting to seasonal coronaviruses was also higher than for American blood donors. Serological responses to coronaviruses by Sierra Leoneans did not differ by age or sex. Approximately a quarter of Sierra Leonian pre-pandemic blood samples had neutralizing antibodies against SARS-CoV-2 pseudovirus, while about a third neutralized MERS-CoV pseudovirus. Prior exposures to coronaviruses that induce cross-protective immunity may contribute to reduced COVID-19 cases and deaths in Sierra Leone.
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Affiliation(s)
- Rodrigo Borrega
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Diana K. S. Nelson
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Anatoliy P. Koval
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Nell G. Bond
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Megan L. Heinrich
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Megan M. Rowland
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Raju Lathigra
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Duane J. Bush
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Irina Aimukanova
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Whitney N. Phinney
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Sophia A. Koval
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Andrew R. Hoffmann
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Allison R. Smither
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Antoinette R. Bell-Kareem
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Lilia I. Melnik
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Kaylynn J. Genemaras
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
- Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA
| | - Karissa Chao
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
- Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA
| | - Patricia Snarski
- Heart and Vascular Institute, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA;
- Department of Physiology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Alexandra B. Melton
- Department of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA;
| | - Jaikin E. Harrell
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Ashley A. Smira
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
| | - Debra H. Elliott
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
| | - Julie A. Rouelle
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
| | - Gilberto Sabino-Santos
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA;
- Centre for Virology Research, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil
| | - Arnaud C. Drouin
- Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.C.D.); (D.N.F.)
| | - Mambu Momoh
- Eastern Polytechnic Institute, Kenema, Sierra Leone;
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - John Demby Sandi
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Robert J. Samuels
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Michael Gbakie
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Zoe L. Branco
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA;
| | - John S. Schieffelin
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
- Department of Internal Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - James E. Robinson
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
| | - Dahlene N. Fusco
- Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.C.D.); (D.N.F.)
| | - Pardis C. Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA;
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbial Science, Scripps Research, La Jolla, CA 92037, USA;
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Matthew L. Boisen
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Luis M. Branco
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Robert F. Garry
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
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Bond NG, Grant DS, Himmelfarb ST, Engel EJ, Al-Hasan F, Gbakie M, Kamara F, Kanneh L, Mustapha I, Okoli A, Fischer W, Wohl D, Garry RF, Samuels R, Shaffer JG, Schieffelin JS. Post-Ebola Syndrome Presents With Multiple Overlapping Symptom Clusters: Evidence From an Ongoing Cohort Study in Eastern Sierra Leone. Clin Infect Dis 2021; 73:1046-1054. [PMID: 33822010 PMCID: PMC8442780 DOI: 10.1093/cid/ciab267] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 08/11/2020] [Accepted: 03/25/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Following the 2013-2016 West African Ebola outbreak, distinct, persistent health complaints were recognized in Ebola virus disease (EVD) survivors. Here we provide an in-depth characterization of post-Ebola syndrome >2.5 years after resolution of disease. Additionally, we report subphenotypes of post-Ebola syndrome with overlapping symptom clusters in survivors from Eastern Sierra Leone. METHODS Participants in Eastern Sierra Leone were identified by the Sierra Leone Association of Ebola survivors. Survivors and their contacts were administered a questionnaire assessing self-reported symptoms and a physical examination. Comparisons between survivors and contacts were conducted using conditional logistic regression. Symptom groupings were identified using hierarchical clustering approaches. Simplified presentation of incredibly complex evaluations (SPICE), correlation analysis, logistic regression, and principal component analysis (PCA) were performed to explore the relationships between symptom clusters. RESULTS Three hundred seventy-five EVD survivors and 1040 contacts were enrolled into the study. At enrollment, EVD survivors reported significantly more symptoms than their contacts in all categories (P < .001). Symptom clusters representing distinct organ systems were identified. Correlation and logistic regression analysis identified relationships between symptom clusters, including stronger relationships between clusters including musculoskeletal symptoms (r = 0.63, P < .001; and P < .001 for correlation and logistic regression, respectively). SPICE and PCA further highlighted subphenotypes with or without musculoskeletal symptoms. CONCLUSIONS This study presents an in-depth characterization of post-Ebola syndrome in Sierra Leonean survivors >2.5 years after disease. The interrelationship between symptom clusters indicates that post-Ebola syndrome is a heterogeneous disease. The distinct musculoskeletal and non-musculoskeletal phenotypes identified likely require targeted therapies to optimize long-term treatment for EVD survivors.
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Affiliation(s)
- Nell G Bond
- Tulane University, New Orleans, Louisiana, USA
| | | | | | | | | | | | | | | | | | | | - William Fischer
- University of North Carolina, Chapel Hill, North Carolina, USA
| | - David Wohl
- University of North Carolina, Chapel Hill, North Carolina, USA
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Shaffer JG, Schieffelin JS, Momoh M, Goba A, Kanneh L, Alhasan F, Gbakie M, Engel EJ, Bond NG, Hartnett JN, Nelson DKS, Bush DJ, Boisen ML, Heinrich ML, Rowland MM, Branco LM, Samuels RJ, Garry RF, Grant DS. Space-Time Trends in Lassa Fever in Sierra Leone by ELISA Serostatus, 2012-2019. Microorganisms 2021; 9:microorganisms9030586. [PMID: 33809204 PMCID: PMC8000031 DOI: 10.3390/microorganisms9030586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 01/03/2023] Open
Abstract
Lassa fever (LF) is a viral hemorrhagic disease found in Sub-Saharan Africa and is responsible for up to 300,000 cases and 5000 deaths annually. LF is highly endemic in Sierra Leone, particularly in its Eastern Province. Kenema Government Hospital (KGH) maintains one of only a few LF isolation facilities in the world with year-round diagnostic testing. Here we focus on space-time trends for LF occurring in Sierra Leone between 2012 and 2019 to provide a current account of LF in the wake of the 2014–2016 Ebola epidemic. Data were analyzed for 3277 suspected LF cases and classified as acute, recent, and non-LF or prior LF exposure using enzyme-linked immunosorbent assays (ELISAs). Presentation rates for acute, recent, and non-LF or prior LF exposure were 6.0% (195/3277), 25.6% (838/3277), and 68.4% (2244/3277), respectively. Among 2051 non-LF or prior LF exposures, 33.2% (682/2051) tested positive for convalescent LF exposure. The overall LF case-fatality rate (CFR) was 78.5% (106/135). Both clinical presentations and confirmed LF cases declined following the Ebola epidemic. These declines coincided with an increased duration between illness onset and clinical presentation, perhaps suggesting more severe disease or presentation at later stages of illness. Acute LF cases and their corresponding CFRs peaked during the dry season (November to April). Subjects with recent (but not acute) LF exposure were more likely to present during the rainy season (May to October) than the dry season (p < 0.001). The findings here suggest that LF remains endemic in Sierra Leone and that caseloads are likely to resume at levels observed prior to the Ebola epidemic. The results provide insight on the current epidemiological profile of LF in Sierra Leone to facilitate LF vaccine studies and accentuate the need for LF cohort studies and continued advancements in LF diagnostics.
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Affiliation(s)
- Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
- Correspondence: (J.G.S.); (J.S.S.); (D.S.G.); Tel.: +1-504-988-1142 (J.G.S.); +1-504-988-5117 (D.S.G.)
| | - John S. Schieffelin
- Sections of Infectious Disease, Departments of Pediatrics and Internal Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (E.J.E.); (N.G.B.)
- Correspondence: (J.G.S.); (J.S.S.); (D.S.G.); Tel.: +1-504-988-1142 (J.G.S.); +1-504-988-5117 (D.S.G.)
| | - Mambu Momoh
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Augustine Goba
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Lansana Kanneh
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Foday Alhasan
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Michael Gbakie
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Emily J. Engel
- Sections of Infectious Disease, Departments of Pediatrics and Internal Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (E.J.E.); (N.G.B.)
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA 70112, USA; (J.N.H.); (R.F.G.)
| | - Nell G. Bond
- Sections of Infectious Disease, Departments of Pediatrics and Internal Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (E.J.E.); (N.G.B.)
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA 70112, USA; (J.N.H.); (R.F.G.)
| | - Jessica N. Hartnett
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA 70112, USA; (J.N.H.); (R.F.G.)
| | - Diana K. S. Nelson
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Duane J. Bush
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Matthew L. Boisen
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Megan L. Heinrich
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Megan M. Rowland
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Luis M. Branco
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Robert J. Samuels
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, TE 37203, USA
| | - Robert F. Garry
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA 70112, USA; (J.N.H.); (R.F.G.)
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Donald S. Grant
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
- Correspondence: (J.G.S.); (J.S.S.); (D.S.G.); Tel.: +1-504-988-1142 (J.G.S.); +1-504-988-5117 (D.S.G.)
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5
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LaVergne SM, Sakabe S, Kanneh L, Momoh M, Al-Hassan F, Yilah M, Goba A, Sandi JD, Gbakie M, Cubitt B, Boisen M, Mayeux JM, Smira A, Shore K, Bica I, Pollard KM, Carlos de la Torre J, Branco LM, Garry RF, Grant DS, Schieffelin JS, Oldstone MBA, Sullivan BM. Ebola-Specific CD8+ and CD4+ T-Cell Responses in Sierra Leonean Ebola Virus Survivors With or Without Post-Ebola Sequelae. J Infect Dis 2021; 222:1488-1497. [PMID: 32436943 DOI: 10.1093/infdis/jiaa268] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/15/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Ebola virus (EBOV) disease has killed thousands of West and Central Africans over the past several decades. Many who survive the acute disease later experience post-Ebola syndrome, a constellation of symptoms whose causative pathogenesis is unclear. METHODS We investigated EBOV-specific CD8+ and CD4+ T-cell responses in 37 Sierra Leonean EBOV disease survivors with (n = 19) or without (n = 18) sequelae of arthralgia and ocular symptoms. Peripheral blood mononuclear cells were infected with recombinant vesicular stomatitis virus encoding EBOV antigens. We also studied the presence of EBOV-specific immunoglobulin G, antinuclear antibodies, anti-cyclic citrullinated peptide antibodies, rheumatoid factor, complement levels, and cytokine levels in these 2 groups. RESULTS Survivors with sequelae had a significantly higher EBOV-specific CD8+ and CD4+ T-cell response. No differences in EBOV-specific immunoglobulin G, antinuclear antibody, or anti-cyclic citrullinated peptide antibody levels were found. Survivors with sequelae showed significantly higher rheumatoid factor levels. CONCLUSION EBOV-specific CD8+ and CD4+ T-cell responses were significantly higher in Ebola survivors with post-Ebola syndrome. These findings suggest that pathogenesis may occur as an immune-mediated disease via virus-specific T-cell immune response or that persistent antigen exposure leads to increased and sustained T-cell responses.
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Affiliation(s)
- Stephanie M LaVergne
- Viral-Immunobiology Laboratory, Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA.,Division of Infectious Diseases, University of California, San Diego, La Jolla, California, USA
| | - Saori Sakabe
- Viral-Immunobiology Laboratory, Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Mambu Momoh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone.,Eastern Polytechnic Institute, Kenema, Sierra Leone
| | - Foday Al-Hassan
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Mohamed Yilah
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - John Demby Sandi
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Michael Gbakie
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Beatrice Cubitt
- Viral-Immunobiology Laboratory, Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA
| | | | - Jessica M Mayeux
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Ashley Smira
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Kayla Shore
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, USA
| | - Iris Bica
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - K Michael Pollard
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Juan Carlos de la Torre
- Viral-Immunobiology Laboratory, Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA
| | | | - Robert F Garry
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Donald S Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone.,College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - John S Schieffelin
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Michael B A Oldstone
- Viral-Immunobiology Laboratory, Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA
| | - Brian M Sullivan
- Viral-Immunobiology Laboratory, Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA
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6
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Akpogheneta O, Dicks S, Grant D, Kanneh Z, Jusu B, Edem-Hotah J, Kanneh L, Alhasan F, Gbakie M, Schieffelin J, Ijaz S, Tedder R, Bower H. Boosting understanding of Lassa Fever virus epidemiology: Field testing a novel assay to identify past Lassa Fever virus infection in blood and oral fluids of survivors and unexposed controls in Sierra Leone. PLoS Negl Trop Dis 2021; 15:e0009255. [PMID: 33788861 PMCID: PMC8041174 DOI: 10.1371/journal.pntd.0009255] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 04/12/2021] [Accepted: 02/18/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Despite identification 50 years ago, the true burden of Lassa Fever (LF) across Africa remains undefined for reasons including research focus on hospitalised patients, lack of validated field-feasible tools which reliably identify past infection, and the fact that all assays require blood samples making large-scale surveys difficult. Designated a priority pathogen of epidemic potential requiring urgent research by the World Health Organisation, a better understanding of LF sero-epidemiology is essential to developing and evaluating new interventions including vaccines. We describe the first field testing of a novel species-neutral Double Antigen Binding Assay (DABA) designed to detect antibodies to LF in plasma and oral fluid. METHODOLOGY/PRINCIPAL FINDINGS Paired plasma and oral fluid were collected in Sierra Leone from survivors discharged from Kenema Government Hospital Lassa Fever Unit between 1980 and 2018, and from controls recruited in Freetown in 2019. Epidemiological sensitivity and specificity of the DABA measured against historical diagnosis in survivors and self-declared non-exposed controls was 81.7% (95% CI 70.7%- 89.9%) and 83.3% (72.7%- 91.1%) respectively in plasma, and 71.8% (60.0%- 81.9%) and 83.3% (72.7%- 91.1%) respectively in oral fluid. Antibodies were identified in people infected up to 15 years and, in one case, 40 years previously. Participants found oral fluid collection easy and painless with 80% happy to give an oral fluid sample regularly. CONCLUSIONS/SIGNIFICANCE Given the difficulties of assay validation in a resource-limited setting, including unexpected exposures and diagnostics of varying accuracy, the new assay performed well in both plasma and oral fluid. Sensitivity and specificity are expected to be higher when case/control ascertainment is more definitive and further work is planned to investigate this. Even at the performance levels achieved, the species-neutral DABA has the potential to facilitate the large-scale seroprevalence surveys needed to underpin essential developments in LF control, as well as support zoonotic investigations.
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Affiliation(s)
- Onome Akpogheneta
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Steve Dicks
- Blood Borne Virus Unit, Public Health England, Colindale, United Kingdom
- Microbiology Services, NHS Blood and Transplant, London, United Kingdom
| | - Donald Grant
- Kenema Government Hospital Lassa Fever Unit, Kenema, Sierra Leone
| | - Zainab Kanneh
- Kenema Government Hospital Lassa Fever Unit, Kenema, Sierra Leone
| | - Brima Jusu
- Kenema Government Hospital Lassa Fever Unit, Kenema, Sierra Leone
| | - Joseph Edem-Hotah
- Faculty of Nursing, University of Sierra Leone, Freetown, Sierra Leone
| | - Lansana Kanneh
- Kenema Government Hospital Lassa Fever Unit, Kenema, Sierra Leone
| | - Foday Alhasan
- Kenema Government Hospital Lassa Fever Unit, Kenema, Sierra Leone
| | - Michael Gbakie
- Kenema Government Hospital Lassa Fever Unit, Kenema, Sierra Leone
| | - John Schieffelin
- Sections of Infectious Disease, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Samreen Ijaz
- Blood Borne Virus Unit, Public Health England, Colindale, United Kingdom
| | - Richard Tedder
- Department of Infectious Disease, Imperial College, London, United Kingdom
| | - Hilary Bower
- UK Public Health Rapid Support Team, London School of Hygiene & Tropical Medicine/Public Health England, London, United Kingdom
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7
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Li AL, Grant D, Gbakie M, Kanneh L, Mustafa I, Bond N, Engel E, Schieffelin J, Vandy MJ, Yeh S, Shantha JG. Ophthalmic manifestations and vision impairment in Lassa fever survivors. PLoS One 2020; 15:e0243766. [PMID: 33301526 PMCID: PMC7728206 DOI: 10.1371/journal.pone.0243766] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/25/2020] [Indexed: 01/14/2023] Open
Abstract
The purpose of this study was to describe the ocular findings, structural ocular complications, and vision impairment in a cohort of Lassa fever survivors in Kenema, Sierra Leone. A retrospective, uncontrolled, cross-sectional study of 31 Lassa fever survivors (62 eyes) who underwent an ophthalmic evaluation in January 2018 at the Kenema Government Hospital in Kenema, Sierra Leone was performed. Data collection included demographic information, ocular/systemic symptoms, visual acuity (VA), and ophthalmic examination findings. Main outcome measures included anterior and posterior segment ophthalmic manifestations and level of VA impairment in Lassa fever survivors. Anterior segment findings included cataract (18%) and pterygium (2%), while posterior segment manifestations consisted of glaucoma (6%), preretinal hemorrhage (2%), and lattice degeneration (2%). Findings suggestive of prior sequelae of uveitis included chorioretinal scarring (5%), retinal fibrosis (3%), and vitreous opacity (2%). Visual acuity was normal/mildly impaired in 53 eyes (85%), moderately impaired in 6 eyes (10%), and 3 eyes (5%) were considered blind by the World Health Organization (WHO) criteria. Median VA was worse in Lassa fever survivors with ophthalmic disease findings (p<0.0001) for both anterior segment (p<0.0001) and posterior segment disease (p<0.013). Untreated cataract was a significant cause of visual acuity impairment (p<0.0001). Lassa fever survivors in this cohort were found to have cataract and posterior segment findings that potentially represent sequelae of uveitis associated with visual impairment. Future studies are warranted to improve our understanding of the spectrum of ocular disease in this emerging infectious disease of public health consequence.
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Affiliation(s)
- Alexa L. Li
- Section of Vitreoretinal Disease and Surgery, Department of Ophthalmology, Emory Eye Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Donald Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Michael Gbakie
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
| | - Ibrahim Mustafa
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
| | - Nell Bond
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Emily Engel
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - John Schieffelin
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Matthew J. Vandy
- Ministry of Health and Sanitation, National Eye Program, Freetown, Sierra Leone
| | - Steven Yeh
- Section of Vitreoretinal Disease and Surgery, Department of Ophthalmology, Emory Eye Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail: (JGS); (SY)
| | - Jessica G. Shantha
- Section of Vitreoretinal Disease and Surgery, Department of Ophthalmology, Emory Eye Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail: (JGS); (SY)
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8
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Samuels RJ, Moon TD, Starnes JR, Alhasan F, Gbakie M, Goba A, Koroma V, Momoh M, Sandi JD, Garry RF, Engel EJ, Shaffer JG, Schieffelin JS, Grant DS. Lassa Fever among Children in Eastern Province, Sierra Leone: A 7-year Retrospective Analysis (2012-2018). Am J Trop Med Hyg 2020; 104:585-592. [PMID: 33241780 PMCID: PMC7866338 DOI: 10.4269/ajtmh.20-0773] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/01/2020] [Indexed: 01/09/2023] Open
Abstract
Pediatric Lassa fever (LF) usually presents as a nonspecific febrile illness, similar to other endemic diseases in countries like Sierra Leone, where LF is considered to be hyperendemic. The nonspecificity of presentation and lack of research have made it difficult to fully understand best practices for pediatric management. We aim to describe clinical characteristics of hospitalized pediatric patients suspected or diagnosed with LF and assess factors associated with hospital outcomes among those with LF antigen-positive results. We conducted a 7-year retrospective cohort study using routine data for all children younger than 18 years admitted at the Kenema Government Hospital's LF ward. A total of 292 children with suspected or confirmed LF were analyzed. Overall, mortality was high (21%). Children with antigen-positive results had a high case fatality rate of 63% (P < 0.01). In univariate analyses, children who presented with unexplained bleeding (odds ratio [OR]: 3.58; 95% CI: 1.08-11.86; P = 0.040) and confusion (altered sensorium) (OR: 5.37; 95% CI: 1.34-21.48; P = 0.020) had increased odds of death. Abnormal serum levels of alanine aminotransferase (P = 0.001), creatinine (P = 0.004), and potassium (P = 0.003) were associated with increased likelihood of death in these children. Treatment with ribavirin was not significantly associated with survival (P = 0.916). Our findings provide insights into current pediatric LF clinical presentation and management. More evidence-based, high-quality research in creating predictive algorithms of antigen-positivity and hospital outcomes is needed in the management of pediatric LF.
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Affiliation(s)
- Robert J Samuels
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone.,Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Troy D Moon
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joseph R Starnes
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Foday Alhasan
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Michael Gbakie
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Augustine Goba
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Veronica Koroma
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Mambu Momoh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - John Demby Sandi
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Robert F Garry
- Department of Immunology and Microbiology, School of Medicine, Tulane University, New Orleans, Louisiana.,Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Emily J Engel
- Department of Pediatrics and Internal Medicine, Sections of Pediatric and Adult Infectious Diseases, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Jeffrey G Shaffer
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana
| | - John S Schieffelin
- Department of Pediatrics and Internal Medicine, Sections of Pediatric and Adult Infectious Diseases, School of Medicine, Tulane University, New Orleans, Louisiana.,Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Donald S Grant
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone.,Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
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9
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Ficenec SC, Percak J, Arguello S, Bays A, Goba A, Gbakie M, Shaffer JG, Emmett SD, Schieffelin JS, Bausch D. Lassa Fever Induced Hearing Loss: The Neglected Disability of Hemorrhagic Fever. Int J Infect Dis 2020; 100:82-87. [PMID: 32795603 PMCID: PMC7807889 DOI: 10.1016/j.ijid.2020.08.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 06/14/2020] [Revised: 07/27/2020] [Accepted: 08/07/2020] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE Lassa fever (LF) a hemorrhagic fever endemic to Western has an incidence of approximately 500,000 cases per year. Here, we evaluate hearing loss and other sequelae following LF. METHODS This case-control study enrolled laboratory confirmed LF survivors, non-LF Febrile controls and Matched Community controls with no history of LF or recent hospitalization for a febrile illness. Study participants completed a symptom questionnaire. Pure-tone audiometry was completed by a subset of participants. RESULTS One hundred forty-seven subjects were enrolled aged from 3-66 years (mean = 23.3). LF survivors were significantly more likely to report balance difficulties (55% vs 20%, p < 0.001), hair loss (32% vs 7%, p < 0.001), difficulty speaking (19% vs 1%, p < 0.001), social isolation (50% vs 0%, p < 0.001), and hearing loss (17% vs 1%, p = 0.002) in comparison to Matched-Community Controls. Similar trends were noted in comparison to Febrile Controls, although these findings were non-significant. Fifty subjects completed audiometry. Audiometry found that LF survivors had significantly more bilateral hearing loss in comparison to Matched-Community Controls (30% vs 4%, p = 0.029). CONCLUSION This study characterizes the sequelae of LF and highlights the need for increased access to hearing care in West Africa.
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Affiliation(s)
| | - Jeffrey Percak
- Tulane University School of Medicine, New Orleans, LA, USA
| | - Sara Arguello
- Tulane University School of Medicine, New Orleans, LA, USA
| | - Alison Bays
- Division of Rheumatology, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Jeffrey G Shaffer
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Susan D Emmett
- Department of Head and Neck Surgery and Communication Sciences, Duke University School of Medicine, Durham, NC, USA; Duke Global Health Institute, Durham, NC, USA; Center for Health Policy and Inequalities Research, Duke University, Durham, NC, USA
| | | | - Daniel Bausch
- Tulane Viral Hemorrhagic Fever Research Program, Kenema Government Hospital, Kenema, Sierra Leone
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10
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Shaffer JG, Schieffelin JS, Gbakie M, Alhasan F, Roberts NB, Goba A, Randazzo J, Momoh M, Moon TD, Kanneh L, Levy DC, Podgorski RM, Hartnett JN, Boisen ML, Branco LM, Samuels R, Grant DS, Garry RF. A medical records and data capture and management system for Lassa fever in Sierra Leone: Approach, implementation, and challenges. PLoS One 2019; 14:e0214284. [PMID: 30921383 PMCID: PMC6438490 DOI: 10.1371/journal.pone.0214284] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 03/11/2019] [Indexed: 12/17/2022] Open
Abstract
Situated in southeastern Sierra Leone, Kenema Government Hospital (KGH) maintains one of the world’s only Lassa fever isolation wards and was a strategic Ebola virus disease (EVD) treatment facility during the 2014 EVD outbreak. Since 2006, the Viral Hemorrhagic Fever Consortium (VHFC) has carried out research activities at KGH, capturing clinical and laboratory data for suspected cases of Lassa fever. Here we describe the approach, progress, and challenges in designing and maintaining a data capture and management system (DCMS) at KGH to assist infectious disease researchers in building and sustaining DCMS in low-resource environments. Results on screening patterns and case-fatality rates are provided to illustrate the context and scope of the DCMS covered in this study. A medical records system and DCMS was designed and implemented between 2010 and 2016 linking historical and prospective Lassa fever data sources across KGH Lassa fever units and its peripheral health units. Data were captured using a case report form (CRF) system, enzyme-linked immunosorbent assay (ELISA) plate readers, polymerase chain reaction (PCR) machines, blood chemistry analyzers, and data auditing procedures. Between 2008 and 2016, blood samples for 4,229 suspected Lassa fever cases were screened at KGH, ranging from 219 samples in 2008 to a peak of 760 samples in 2011. Lassa fever case-fatality rates before and following the Ebola outbreak were 65.5% (148/226) and 89.5% (17/19), respectively, suggesting that fewer, but more seriously ill subjects with Lassa fever presented to KGH following the 2014 EVD outbreak (p = .040). DCMS challenges included weak specificity of the Lassa fever suspected case definition, limited capture of patient survival outcome data, internet costs, lapses in internet connectivity, low bandwidth, equipment and software maintenance, lack of computer teaching laboratories, and workload fluctuations due to variable screening activity. DCMS are the backbone of international research efforts and additional literature is needed on the topic for establishing benchmarks and driving goal-based approaches for its advancement in developing countries.
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Affiliation(s)
- Jeffrey G. Shaffer
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail:
| | - John S. Schieffelin
- Departments of Pediatrics and Internal Medicine, Sections of Pediatric & Adult Infectious Diseases, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Michael Gbakie
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Foday Alhasan
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Nicole B. Roberts
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Jessica Randazzo
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Mambu Momoh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Troy D. Moon
- Vanderbilt University Institute for Global Health, Nashville, Tennessee, United States of America
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Danielle C. Levy
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
| | - Rachel M. Podgorski
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
| | - Jessica N. Hartnett
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
| | - Matt L. Boisen
- Zalgen Labs, LLC, Germantown, Maryland, United States of America
| | - Luis M. Branco
- Zalgen Labs, LLC, Germantown, Maryland, United States of America
| | - Robert Samuels
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Robert F. Garry
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
- Zalgen Labs, LLC, Germantown, Maryland, United States of America
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11
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Boisen ML, Cross RW, Hartnett JN, Goba A, Momoh M, Fullah M, Gbakie M, Safa S, Fonnie M, Baimba F, Koroma VJ, Geisbert JB, McCormick S, Nelson DKS, Millett MM, Oottamasathien D, Jones AB, Pham H, Brown BL, Shaffer JG, Schieffelin JS, Kargbo B, Gbetuwa M, Gevao SM, Wilson RB, Pitts KR, Geisbert TW, Branco LM, Khan SH, Grant DS, Garry RF. Field Validation of the ReEBOV Antigen Rapid Test for Point-of-Care Diagnosis of Ebola Virus Infection. J Infect Dis 2016; 214:S203-S209. [PMID: 27521365 DOI: 10.1093/infdis/jiw261] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The 2013-2016 West African Ebola virus disease (EVD) epidemic is the largest recorded. Triage on the basis of clinical signs had limited success, and the time to diagnosis by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) could exceed 5 days. Here we describe the development and field validation of the ReEBOV Antigen Rapid Test (ReEBOV RDT) to aid triage of individuals with suspected EVD. METHODS Samples from patients with suspected EVD were submitted to Kenema Government Hospital, Sierra Leone, for Lassa fever and EVD screening throughout 2014. Banked residual clinical samples were tested in November 2014 and January 2015 in a blinded field trial to estimate the clinical effectiveness of the ReEBOV RDT, compared with EBOV-specific qRT-PCR. RESULTS Preliminary ReEBOV RDT performance demonstrated a positive percentage agreement (PPA) of 91.1% (195 of 214 results; 95% confidence interval [CI], 86.5%-94.6%) and a negative percentage agreement (NPA) of 90.2% (175 of 194; 95% CI, 85.1%-94.0%). The final estimates used by the Food and Drug Administration to determine whether to grant emergency use authorization for the test, which excluded a qRT-PCR reference method threshold cutoff, were a PPA of 62.1% (72 of 116 results; 95% CI, 52.6%-70.9%) and a NPA of 96.7% (58 of 60; 95% CI, 88.5%-99.6%), with a diagnostic likelihood of 18.6. A subsequent, independent evaluation by the World Health Organization generated results consistent with the preliminary performance estimates. CONCLUSIONS The ReEBOV RDT demonstrated the potential to provide clinically effective rapid and accurate point-of-care test results and, thus, to be a powerful tool for increasing triage efficiency.
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Affiliation(s)
- Matthew L Boisen
- Corgenix, Broomfield, Colorado Department of Microbiology and Immunology
| | - Robert W Cross
- Galveston National Laboratory, University of Texas Medical Branch
| | | | - Augustine Goba
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Mambu Momoh
- Lassa Fever Program, Kenema Government Hospital Eastern Polytechnic Institute, Kenema Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Mohamed Fullah
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Michael Gbakie
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Sidiki Safa
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Mbalu Fonnie
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Francis Baimba
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Veronica J Koroma
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Joan B Geisbert
- Galveston National Laboratory, University of Texas Medical Branch
| | | | | | | | | | | | - Ha Pham
- Corgenix, Broomfield, Colorado
| | | | - Jeffrey G Shaffer
- Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - John S Schieffelin
- Department of Pediatrics, Section of Infectious Diseases, Tulane University
| | - Brima Kargbo
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | - Sahr M Gevao
- Lassa Fever Program, Kenema Government Hospital Eastern Polytechnic Institute, Kenema Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | | | | | | | - Sheik H Khan
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Donald S Grant
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Robert F Garry
- Department of Microbiology and Immunology Zalgen Labs, Germantown, Maryland
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12
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Goba A, Khan SH, Fonnie M, Fullah M, Moigboi A, Kovoma A, Sinnah V, Yoko N, Rogers H, Safai S, Momoh M, Koroma V, Kamara FK, Konowu E, Yillah M, French I, Mustapha I, Kanneh F, Foday M, McCarthy H, Kallon T, Kallon M, Naiebu J, Sellu J, Jalloh AA, Gbakie M, Kanneh L, Massaly JLB, Kargbo D, Kargbo B, Vandi M, Gbetuwa M, Gevao SM, Sandi JD, Jalloh SC, Grant DS, Blyden SO, Crozier I, Schieffelin JS, McLellan SL, Jacob ST, Boisen ML, Hartnett JN, Cross RW, Branco LM, Andersen KG, Yozwiak NL, Gire SK, Tariyal R, Park DJ, Haislip AM, Bishop CM, Melnik LI, Gallaher WR, Wimley WC, He J, Shaffer JG, Sullivan BM, Grillo S, Oman S, Garry CE, Edwards DR, McCormick SJ, Elliott DH, Rouelle JA, Kannadka CB, Reyna AA, Bradley BT, Yu H, Yenni RE, Hastie KM, Geisbert JB, Kulakosky PC, Wilson RB, Oldstone MBA, Pitts KR, Henderson LA, Robinson JE, Geisbert TW, Saphire EO, Happi CT, Asogun DA, Sabeti PC, Garry RF. An Outbreak of Ebola Virus Disease in the Lassa Fever Zone. J Infect Dis 2016; 214:S110-S121. [PMID: 27402779 DOI: 10.1093/infdis/jiw239] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Kenema Government Hospital (KGH) has developed an advanced clinical and laboratory research capacity to manage the threat of Lassa fever, a viral hemorrhagic fever (VHF). The 2013-2016 Ebola virus (EBOV) disease (EVD) outbreak is the first to have occurred in an area close to a facility with established clinical and laboratory capacity for study of VHFs. METHODS Because of its proximity to the epicenter of the EVD outbreak, which began in Guinea in March 2014, the KGH Lassa fever Team mobilized to establish EBOV surveillance and diagnostic capabilities. RESULTS Augustine Goba, director of the KGH Lassa laboratory, diagnosed the first documented case of EVD in Sierra Leone, on 25 May 2014. Thereafter, KGH received and cared for numbers of patients with EVD that quickly overwhelmed the capacity for safe management. Numerous healthcare workers contracted and lost their lives to EVD. The vast majority of subsequent EVD cases in West Africa can be traced back to a single transmission chain that includes this first diagnosed case. CONCLUSIONS Responding to the challenges of confronting 2 hemorrhagic fever viruses will require continued investments in the development of countermeasures (vaccines, therapeutic agents, and diagnostic assays), infrastructure, and human resources.
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Affiliation(s)
- Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - S Humarr Khan
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Mbalu Fonnie
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Mohamed Fullah
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Alex Moigboi
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Alice Kovoma
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Vandi Sinnah
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Nancy Yoko
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Hawa Rogers
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Siddiki Safai
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Mambu Momoh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | | | | | - Edwin Konowu
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Mohamed Yillah
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Issa French
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | | | | | - Momoh Foday
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | | | - Tiangay Kallon
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | | | - Jenneh Naiebu
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | | | - Abdul A Jalloh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Michael Gbakie
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | | | | | | | | | | | | | - John D Sandi
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | | | - Donald S Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital Ministry of Health and Sanitation
| | | | - Ian Crozier
- World Health Organization Sierra Leone Ebola Response Team, Freetown, Sierra Leone Infectious Diseases Institute, Mulago Hospital Complex, Kampala, Uganda
| | - John S Schieffelin
- Section of Infectious Disease, Department of Pediatrics Section of Infectious Disease, Department of Internal Medicine, School of Medicine
| | - Susan L McLellan
- Section of Infectious Disease, Department of Pediatrics Section of Infectious Disease, Department of Internal Medicine, School of Medicine Department of Tropical Medicine
| | - Shevin T Jacob
- Division of Allergy and Infectious Diseases, University of Washington, Seattle
| | - Matt L Boisen
- Corgenix, Broomfield, Colorado Zalgen Labs, Germantown, Maryland
| | | | - Robert W Cross
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston
| | | | | | | | | | | | | | | | | | | | - William R Gallaher
- Department of Microbiology, Immunology, and Parasitology, LSU Health Mockingbird Nature Research Group, Pearl River, Louisiana
| | | | - Jing He
- Department of Biochemistry, Tulane University
| | - Jeffrey G Shaffer
- Department of Biostatistics and Bioinformatics, Tulane School of Public Health and Tropical Medicine
| | | | - Sonia Grillo
- Naval Engineering Facilities Command, Naples, Italy
| | | | - Courtney E Garry
- Section of Infectious Disease, Department of Pediatrics Section of Infectious Disease, Department of Internal Medicine, School of Medicine Autoimmune Technologies, New Orleans
| | | | | | - Deborah H Elliott
- Section of Infectious Disease, Department of Pediatrics Section of Infectious Disease, Department of Internal Medicine, School of Medicine
| | - Julie A Rouelle
- Section of Infectious Disease, Department of Pediatrics Section of Infectious Disease, Department of Internal Medicine, School of Medicine
| | - Chandrika B Kannadka
- Section of Infectious Disease, Department of Pediatrics Section of Infectious Disease, Department of Internal Medicine, School of Medicine
| | - Ashley A Reyna
- Section of Infectious Disease, Department of Pediatrics Section of Infectious Disease, Department of Internal Medicine, School of Medicine
| | - Benjamin T Bradley
- Section of Infectious Disease, Department of Pediatrics Section of Infectious Disease, Department of Internal Medicine, School of Medicine
| | - Haini Yu
- Section of Infectious Disease, Department of Pediatrics Section of Infectious Disease, Department of Internal Medicine, School of Medicine
| | | | | | - Joan B Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston
| | | | | | | | | | | | - James E Robinson
- Section of Infectious Disease, Department of Pediatrics Section of Infectious Disease, Department of Internal Medicine, School of Medicine
| | - Thomas W Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston
| | - Erica Ollmann Saphire
- Department of Immunology and Microbial Science The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla
| | - Christian T Happi
- Redeemer's University, Ede Irrua Specialist Teaching Hospital, Nigeria
| | | | - Pardis C Sabeti
- Broad Institute of MIT and Harvard Department of Organismic and Evolutionary Biology, Center for Systems Biology, Harvard University, Cambridge, Massachusetts
| | - Robert F Garry
- Department of Microbiology and Immunology Zalgen Labs, Germantown, Maryland
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13
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Robinson JE, Hastie KM, Cross RW, Yenni RE, Elliott DH, Rouelle JA, Kannadka CB, Smira AA, Garry CE, Bradley BT, Yu H, Shaffer JG, Boisen ML, Hartnett JN, Zandonatti MA, Rowland MM, Heinrich ML, Martínez-Sobrido L, Cheng B, de la Torre JC, Andersen KG, Goba A, Momoh M, Fullah M, Gbakie M, Kanneh L, Koroma VJ, Fonnie R, Jalloh SC, Kargbo B, Vandi MA, Gbetuwa M, Ikponmwosa O, Asogun DA, Okokhere PO, Follarin OA, Schieffelin JS, Pitts KR, Geisbert JB, Kulakoski PC, Wilson RB, Happi CT, Sabeti PC, Gevao SM, Khan SH, Grant DS, Geisbert TW, Saphire EO, Branco LM, Garry RF. Most neutralizing human monoclonal antibodies target novel epitopes requiring both Lassa virus glycoprotein subunits. Nat Commun 2016; 7:11544. [PMID: 27161536 PMCID: PMC4866400 DOI: 10.1038/ncomms11544] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/07/2016] [Indexed: 01/19/2023] Open
Abstract
Lassa fever is a severe multisystem disease that often has haemorrhagic manifestations. The epitopes of the Lassa virus (LASV) surface glycoproteins recognized by naturally infected human hosts have not been identified or characterized. Here we have cloned 113 human monoclonal antibodies (mAbs) specific for LASV glycoproteins from memory B cells of Lassa fever survivors from West Africa. One-half bind the GP2 fusion subunit, one-fourth recognize the GP1 receptor-binding subunit and the remaining fourth are specific for the assembled glycoprotein complex, requiring both GP1 and GP2 subunits for recognition. Notably, of the 16 mAbs that neutralize LASV, 13 require the assembled glycoprotein complex for binding, while the remaining 3 require GP1 only. Compared with non-neutralizing mAbs, neutralizing mAbs have higher binding affinities and greater divergence from germline progenitors. Some mAbs potently neutralize all four LASV lineages. These insights from LASV human mAb characterization will guide strategies for immunotherapeutic development and vaccine design.
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Affiliation(s)
- James E Robinson
- Section of Infectious Disease, Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana 70112, USA
| | - Kathryn M Hastie
- Department of Immunology and Microbial Science, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Robert W Cross
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, Texas 77555, USA
| | - Rachael E Yenni
- Department of Microbiology and Immunology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana 70112, USA
| | - Deborah H Elliott
- Section of Infectious Disease, Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana 70112, USA
| | - Julie A Rouelle
- Section of Infectious Disease, Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana 70112, USA
| | - Chandrika B Kannadka
- Section of Infectious Disease, Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana 70112, USA
| | - Ashley A Smira
- Section of Infectious Disease, Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana 70112, USA
| | - Courtney E Garry
- Section of Infectious Disease, Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana 70112, USA.,Autoimmune Technologies, LLC, 1010 Common St #1705, New Orleans, Louisiana 70112, USA
| | - Benjamin T Bradley
- Section of Infectious Disease, Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana 70112, USA
| | - Haini Yu
- Section of Infectious Disease, Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana 70112, USA
| | - Jeffrey G Shaffer
- Department of Biostatistics and Bioinformatics, Tulane School of Public Health and Tropical Medicine, New Orleans, Louisiana 70112, USA
| | - Matt L Boisen
- Corgenix, Inc., 11575 Main Street #400, Broomfield, Colorado 80020, USA
| | - Jessica N Hartnett
- Department of Microbiology and Immunology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana 70112, USA
| | - Michelle A Zandonatti
- Department of Immunology and Microbial Science, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Megan M Rowland
- Zalgen Labs, LLC, 20271 Goldenrod Lane, Suite 2083, Germantown, Maryland 20876, USA
| | - Megan L Heinrich
- Zalgen Labs, LLC, 20271 Goldenrod Lane, Suite 2083, Germantown, Maryland 20876, USA
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, 601 Elmwood Avenue, Rochester, New York 14642, USA
| | - Benson Cheng
- Department of Microbiology and Immunology, University of Rochester, 601 Elmwood Avenue, Rochester, New York 14642, USA
| | - Juan C de la Torre
- Department of Immunology and Microbial Science, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Kristian G Andersen
- Department of Immunology and Microbial Science, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
| | - Mambu Momoh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone.,Department of Laboratory Sciences Polytechnic College, 2 Combema Road, Kenema, Sierra Leone
| | - Mohamed Fullah
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone.,Department of Laboratory Sciences Polytechnic College, 2 Combema Road, Kenema, Sierra Leone
| | - Michael Gbakie
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
| | - Veronica J Koroma
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
| | - Richard Fonnie
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
| | - Simbirie C Jalloh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
| | - Brima Kargbo
- Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Mohamed A Vandi
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone.,Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Momoh Gbetuwa
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone.,Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Odia Ikponmwosa
- Department of Medicine, Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Km. 87, Benin/Auchi Road, Irrua, Nigeria
| | - Danny A Asogun
- Department of Medicine, Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Km. 87, Benin/Auchi Road, Irrua, Nigeria
| | - Peter O Okokhere
- Department of Medicine, Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Km. 87, Benin/Auchi Road, Irrua, Nigeria
| | - Onikepe A Follarin
- Department of Medicine, Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Km. 87, Benin/Auchi Road, Irrua, Nigeria.,Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Off Gbongan-Oshogbo Road, Ede, Nigeria.,African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer's University, Off Gbongan-Oshogbo Road, Ede, Nigeria
| | - John S Schieffelin
- Section of Infectious Disease, Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana 70112, USA.,Section of Infectious Disease, Department of Internal Medicine, Tulane University School of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana 70112, USA
| | - Kelly R Pitts
- Corgenix, Inc., 11575 Main Street #400, Broomfield, Colorado 80020, USA
| | - Joan B Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, Texas 77555, USA
| | - Peter C Kulakoski
- Autoimmune Technologies, LLC, 1010 Common St #1705, New Orleans, Louisiana 70112, USA
| | - Russell B Wilson
- Autoimmune Technologies, LLC, 1010 Common St #1705, New Orleans, Louisiana 70112, USA
| | - Christian T Happi
- Department of Medicine, Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Km. 87, Benin/Auchi Road, Irrua, Nigeria.,Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Off Gbongan-Oshogbo Road, Ede, Nigeria.,African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer's University, Off Gbongan-Oshogbo Road, Ede, Nigeria
| | - Pardis C Sabeti
- Department of Organismic and Evolutionary Biology, Center for Systems Biology, Harvard University, 1350 Massachusetts Avenue, Cambridge, Massachusetts 02138, USA.,Center for Systems Biology, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, USA.,Department of Immunology and Infectious Disease, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA
| | - Sahr M Gevao
- Department of Medicine, University of Sierra Leone, Freetown, Sierra Leone
| | - S Humarr Khan
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone.,Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Donald S Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone.,Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
| | - Thomas W Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, Texas 77555, USA
| | - Erica Ollmann Saphire
- Department of Immunology and Microbial Science, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Luis M Branco
- Zalgen Labs, LLC, 20271 Goldenrod Lane, Suite 2083, Germantown, Maryland 20876, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana 70112, USA.,Zalgen Labs, LLC, 20271 Goldenrod Lane, Suite 2083, Germantown, Maryland 20876, USA
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14
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Andersen KG, Shapiro BJ, Matranga CB, Sealfon R, Lin AE, Moses LM, Folarin OA, Goba A, Odia I, Ehiane PE, Momoh M, England EM, Winnicki S, Branco LM, Gire SK, Phelan E, Tariyal R, Tewhey R, Omoniwa O, Fullah M, Fonnie R, Fonnie M, Kanneh L, Jalloh S, Gbakie M, Saffa S, Karbo K, Gladden AD, Qu J, Stremlau M, Nekoui M, Finucane HK, Tabrizi S, Vitti JJ, Birren B, Fitzgerald M, McCowan C, Ireland A, Berlin AM, Bochicchio J, Tazon-Vega B, Lennon NJ, Ryan EM, Bjornson Z, Milner DA, Lukens AK, Broodie N, Rowland M, Heinrich M, Akdag M, Schieffelin JS, Levy D, Akpan H, Bausch DG, Rubins K, McCormick JB, Lander ES, Günther S, Hensley L, Okogbenin S, Schaffner SF, Okokhere PO, Khan SH, Grant DS, Akpede GO, Asogun DA, Gnirke A, Levin JZ, Happi CT, Garry RF, Sabeti PC. Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus. Cell 2016; 162:738-50. [PMID: 26276630 DOI: 10.1016/j.cell.2015.07.020] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/26/2015] [Accepted: 06/12/2015] [Indexed: 12/25/2022]
Abstract
The 2013-2015 West African epidemic of Ebola virus disease (EVD) reminds us of how little is known about biosafety level 4 viruses. Like Ebola virus, Lassa virus (LASV) can cause hemorrhagic fever with high case fatality rates. We generated a genomic catalog of almost 200 LASV sequences from clinical and rodent reservoir samples. We show that whereas the 2013-2015 EVD epidemic is fueled by human-to-human transmissions, LASV infections mainly result from reservoir-to-human infections. We elucidated the spread of LASV across West Africa and show that this migration was accompanied by changes in LASV genome abundance, fatality rates, codon adaptation, and translational efficiency. By investigating intrahost evolution, we found that mutations accumulate in epitopes of viral surface proteins, suggesting selection for immune escape. This catalog will serve as a foundation for the development of vaccines and diagnostics. VIDEO ABSTRACT.
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Affiliation(s)
- Kristian G Andersen
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; The Scripps Research Institute, Scripps Translational Science Institute, La Jolla, CA 92037, USA.
| | - B Jesse Shapiro
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Department of Biological Sciences, University of Montréal, Montréal, QC H2V 2S9, Canada
| | | | - Rachel Sealfon
- Broad Institute, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aaron E Lin
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Lina M Moses
- Tulane Health Sciences Center, Tulane University, New Orleans, LA 70118, USA
| | - Onikepe A Folarin
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria; Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Redemption City, Osun State, Nigeria
| | - Augustine Goba
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Eastern Province, Sierra Leone
| | - Ikponmwonsa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Philomena E Ehiane
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Mambu Momoh
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Eastern Province, Sierra Leone; Eastern Polytechnic College, Kenema, Eastern Province, Sierra Leone
| | | | - Sarah Winnicki
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA
| | | | - Stephen K Gire
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA
| | | | | | - Ryan Tewhey
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Omowunmi Omoniwa
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Mohammed Fullah
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Eastern Province, Sierra Leone; Eastern Polytechnic College, Kenema, Eastern Province, Sierra Leone
| | - Richard Fonnie
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Eastern Province, Sierra Leone
| | - Mbalu Fonnie
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Eastern Province, Sierra Leone
| | - Lansana Kanneh
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Eastern Province, Sierra Leone
| | - Simbirie Jalloh
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Eastern Province, Sierra Leone
| | - Michael Gbakie
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Eastern Province, Sierra Leone
| | - Sidiki Saffa
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Eastern Province, Sierra Leone
| | - Kandeh Karbo
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Eastern Province, Sierra Leone
| | | | - James Qu
- Broad Institute, Cambridge, MA 02142, USA
| | - Matthew Stremlau
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Mahan Nekoui
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA
| | | | - Shervin Tabrizi
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Joseph J Vitti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | | | | | | | | | | | | | | | | | - Zach Bjornson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Danny A Milner
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA 02115, USA
| | - Amanda K Lukens
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA 02115, USA
| | - Nisha Broodie
- College of Medicine, Columbia University, New York, NY 10032, USA
| | | | | | | | - John S Schieffelin
- Tulane Health Sciences Center, Tulane University, New Orleans, LA 70118, USA
| | - Danielle Levy
- Tulane Health Sciences Center, Tulane University, New Orleans, LA 70118, USA
| | - Henry Akpan
- Nigerian Federal Ministry of Health, Abuja, Federal Capital Territory, Nigeria
| | - Daniel G Bausch
- Tulane Health Sciences Center, Tulane University, New Orleans, LA 70118, USA
| | - Kathleen Rubins
- The National Aeronautics and Space Administration, Johnson Space Center, Houston, TX 77058, USA
| | - Joseph B McCormick
- The University of Texas School of Public Health, Brownsville, TX 77030, USA
| | | | - Stephan Günther
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, 20259 Hamburg, Germany
| | - Lisa Hensley
- NIAID Integrated Research Facility, Frederick, MD 21702, USA
| | - Sylvanus Okogbenin
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | | | - Peter O Okokhere
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - S Humarr Khan
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Eastern Province, Sierra Leone
| | - Donald S Grant
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Eastern Province, Sierra Leone
| | - George O Akpede
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Danny A Asogun
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | | | - Christian T Happi
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria; Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Redemption City, Osun State, Nigeria.
| | - Robert F Garry
- Tulane Health Sciences Center, Tulane University, New Orleans, LA 70118, USA
| | - Pardis C Sabeti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA 02115, USA.
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Park DJ, Dudas G, Wohl S, Goba A, Whitmer SLM, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR, Matranga CB, Winnicki SM, Qu J, Gire SK, Gladden-Young A, Jalloh S, Nosamiefan D, Yozwiak NL, Moses LM, Jiang PP, Lin AE, Schaffner SF, Bird B, Towner J, Mamoh M, Gbakie M, Kanneh L, Kargbo D, Massally JLB, Kamara FK, Konuwa E, Sellu J, Jalloh AA, Mustapha I, Foday M, Yillah M, Erickson BR, Sealy T, Blau D, Paddock C, Brault A, Amman B, Basile J, Bearden S, Belser J, Bergeron E, Campbell S, Chakrabarti A, Dodd K, Flint M, Gibbons A, Goodman C, Klena J, McMullan L, Morgan L, Russell B, Salzer J, Sanchez A, Wang D, Jungreis I, Tomkins-Tinch C, Kislyuk A, Lin MF, Chapman S, MacInnis B, Matthews A, Bochicchio J, Hensley LE, Kuhn JH, Nusbaum C, Schieffelin JS, Birren BW, Forget M, Nichol ST, Palacios GF, Ndiaye D, Happi C, Gevao SM, Vandi MA, Kargbo B, Holmes EC, Bedford T, Gnirke A, Ströher U, Rambaut A, Garry RF, Sabeti PC. Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone. Cell 2015; 161:1516-26. [PMID: 26091036 PMCID: PMC4503805 DOI: 10.1016/j.cell.2015.06.007] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 05/26/2015] [Accepted: 06/01/2015] [Indexed: 11/29/2022]
Abstract
The 2013–2015 Ebola virus disease (EVD) epidemic is caused by the Makona variant of Ebola virus (EBOV). Early in the epidemic, genome sequencing provided insights into virus evolution and transmission and offered important information for outbreak response. Here, we analyze sequences from 232 patients sampled over 7 months in Sierra Leone, along with 86 previously released genomes from earlier in the epidemic. We confirm sustained human-to-human transmission within Sierra Leone and find no evidence for import or export of EBOV across national borders after its initial introduction. Using high-depth replicate sequencing, we observe both host-to-host transmission and recurrent emergence of intrahost genetic variants. We trace the increasing impact of purifying selection in suppressing the accumulation of nonsynonymous mutations over time. Finally, we note changes in the mucin-like domain of EBOV glycoprotein that merit further investigation. These findings clarify the movement of EBOV within the region and describe viral evolution during prolonged human-to-human transmission. In Sierra Leone, transmission has primarily been within-country, not between-country Infectious doses are large enough for intrahost variants to transmit between hosts A prolonged epidemic removes deleterious mutations from the viral population There is preliminary evidence for human RNA editing effects on the Ebola genome
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Affiliation(s)
- Daniel J Park
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
| | - Gytis Dudas
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Shirlee Wohl
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | | | - Shannon L M Whitmer
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Kristian G Andersen
- Scripps Translational Science Institute, The Scripps Research Institute, 3344 N Torrey Pines Court, La Jolla, CA 92037, USA
| | - Rachel S Sealfon
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jason T Ladner
- US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Jeffrey R Kugelman
- US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | | | - Sarah M Winnicki
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - James Qu
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Stephen K Gire
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | | | | | - Dolo Nosamiefan
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Nathan L Yozwiak
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Lina M Moses
- Tulane University, 1430 Tulane Avenue, SL-38, New Orleans, LA 70112, USA
| | - Pan-Pan Jiang
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Aaron E Lin
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Brian Bird
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Jonathan Towner
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Mambu Mamoh
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | | | - David Kargbo
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | | | - Edwin Konuwa
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | | | | | - Momoh Foday
- Kenema Government Hospital, Kenema, Sierra Leone
| | | | - Bobbie R Erickson
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Tara Sealy
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Dianna Blau
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Christopher Paddock
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Aaron Brault
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Brian Amman
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Jane Basile
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Scott Bearden
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Jessica Belser
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Eric Bergeron
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Shelley Campbell
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Ayan Chakrabarti
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Kimberly Dodd
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Mike Flint
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Aridth Gibbons
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Christin Goodman
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - John Klena
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Laura McMullan
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Laura Morgan
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Brandy Russell
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Johanna Salzer
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Angela Sanchez
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - David Wang
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Irwin Jungreis
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | | | - Andrey Kislyuk
- DNAnexus, 1975 West El Camino Real, Suite 101, Mountain View, CA 94040, USA
| | - Michael F Lin
- DNAnexus, 1975 West El Camino Real, Suite 101, Mountain View, CA 94040, USA
| | - Sinead Chapman
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Bronwyn MacInnis
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Ashley Matthews
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - James Bochicchio
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Lisa E Hensley
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Chad Nusbaum
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - John S Schieffelin
- Tulane University, 1430 Tulane Avenue, SL-38, New Orleans, LA 70112, USA
| | - Bruce W Birren
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Marc Forget
- Médecins Sans Frontières, Rue de l'Arbre Bénit 46, 1050 Bruxelles, Belgium
| | - Stuart T Nichol
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Gustavo F Palacios
- US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Daouda Ndiaye
- Université Cheikh Anta Diop, BP 5005, Dakar, Sénégal
| | - Christian Happi
- Redeemers University Nigeria, KM 46 Lagos-Ibadan Expressway, Redemption City, Ogun State, Nigeria
| | - Sahr M Gevao
- University of Sierra Leone, A.J. Momoh St, Tower Hill, Freetown, Sierra Leone
| | - Mohamed A Vandi
- Sierra Leone Ministry of Health and Sanitation, Youyi Building, Freetown, Sierra Leone
| | - Brima Kargbo
- Sierra Leone Ministry of Health and Sanitation, Youyi Building, Freetown, Sierra Leone
| | - Edward C Holmes
- University of Sydney, Johns Hopkins Drive, Camperdown NSW 2050, Australia
| | - Trevor Bedford
- Fred Hutchinson Cancer Research Center, 110 Fairview Avenue North, Seattle, WA 98109, USA
| | - Andreas Gnirke
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
| | - Ute Ströher
- National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH9 3FL, UK; Centre for Immunology, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3FL, UK; Fogarty International Center, National Institutes of Health, 31 Center Drive, MSC 2220 Bethesda, MD 20892, USA.
| | - Robert F Garry
- Tulane University, 1430 Tulane Avenue, SL-38, New Orleans, LA 70112, USA
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
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16
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Boisen ML, Oottamasathien D, Jones AB, Millett MM, Nelson DS, Bornholdt ZA, Fusco ML, Abelson DM, Oda SI, Hartnett JN, Rowland MM, Heinrich ML, Akdag M, Goba A, Momoh M, Fullah M, Baimba F, Gbakie M, Safa S, Fonnie R, Kanneh L, Cross RW, Geisbert JB, Geisbert TW, Kulakosky PC, Grant DS, Shaffer JG, Schieffelin JS, Wilson RB, Saphire EO, Branco LM, Garry RF, Khan SH, Pitts KR. Development of Prototype Filovirus Recombinant Antigen Immunoassays. J Infect Dis 2015; 212 Suppl 2:S359-67. [PMID: 26232440 DOI: 10.1093/infdis/jiv353] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Throughout the 2014-2015 Ebola outbreak in West Africa, major gaps were exposed in the availability of validated rapid diagnostic platforms, protective vaccines, and effective therapeutic agents. These gaps potentiated the development of prototype rapid lateral flow immunodiagnostic (LFI) assays that are true point-of-contact platforms, for the detection of active Ebola infections in small blood samples. METHODS Recombinant Ebola and Marburg virus matrix VP40 and glycoprotein (GP) antigens were used to derive a panel of monoclonal and polyclonal antibodies. Antibodies were tested using a multivariate approach to identify antibody-antigen combinations suitable for enzyme-linked immunosorbent assay (ELISA) and LFI assay development. RESULTS Polyclonal antibodies generated in goats were superior reagents for capture and detection of recombinant VP40 in test sample matrices. These antibodies were optimized for use in antigen-capture ELISA and LFI assay platforms. Prototype immunoglobulin M (IgM)/immunoglobulin G (IgG) ELISAs were similarly developed that specifically detect Ebola virus-specific antibodies in the serum of experimentally infected nonhuman primates and in blood samples obtained from patients with Ebola from Sierra Leone. CONCLUSIONS The prototype recombinant Ebola LFI assays developed in these studies have sensitivities that are useful for clinical diagnosis of acute ebolavirus infections. The antigen-capture and IgM/IgG ELISAs provide additional confirmatory assay platforms for detecting VP40 and other ebolavirus-specific immunoglobulins.
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Affiliation(s)
- Matt L Boisen
- Corgenix, Broomfield, Colorado Department of Microbiology and Immunology, School of Medicine
| | | | | | | | | | - Zachary A Bornholdt
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California
| | - Marnie L Fusco
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California
| | - Dafna M Abelson
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California
| | - Shun-Ichiro Oda
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California
| | | | | | | | | | | | - Mambu Momoh
- Lassa Fever Program, Kenema Government Hospital Eastern Polytechnic College, Kenema
| | | | | | - Michael Gbakie
- Section of Infectious Disease, Department of Internal Medicine, School of Medicine, Tulane University
| | - Sadiki Safa
- Lassa Fever Program, Kenema Government Hospital
| | | | | | - Robert W Cross
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston
| | - Joan B Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston
| | - Thomas W Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston
| | | | - Donald S Grant
- Zalgen Labs, Germantown, Maryland Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Jeffery G Shaffer
- Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine
| | - John S Schieffelin
- Section of Infectious Disease, Department of Pediatrics Section of Infectious Disease, Department of Internal Medicine, School of Medicine, Tulane University
| | | | - Erica Ollmann Saphire
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California
| | | | - Robert F Garry
- Department of Microbiology and Immunology, School of Medicine Zalgen Labs, Germantown, Maryland
| | - S Humarr Khan
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation, Freetown, Sierra Leone
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17
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Wauquier N, Bangura J, Moses L, Humarr Khan S, Coomber M, Lungay V, Gbakie M, Sesay MSK, Gassama IAK, Massally JLB, Gbakima A, Squire J, Lamin M, Kanneh L, Yillah M, Kargbo K, Roberts W, Vandi M, Kargbo D, Vincent T, Jambai A, Guttieri M, Fair J, Souris M, Gonzalez JP. Understanding the emergence of ebola virus disease in sierra leone: stalking the virus in the threatening wake of emergence. PLoS Curr 2015; 7. [PMID: 25969797 PMCID: PMC4423925 DOI: 10.1371/currents.outbreaks.9a6530ab7bb9096b34143230ab01cdef] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Since Ebola Virus Disease (EVD) was first identified in 1976 in what is now the Democratic Republic of Congo, and despite the numerous outbreaks recorded to date, rarely has an epidemic origin been identified. Indeed, among the twenty-one most documented EVD outbreaks in Africa, an index case has been identified four times, and hypothesized in only two other instances. The initial steps of emergence and spread of a virus are critical in the development of a potential outbreak and need to be thoroughly dissected and understood in order to improve on preventative strategies. In the current West African outbreak of EVD, a unique index case has been identified, pinpointing the geographical origin of the epidemic in Guinea. Herein, we provide an accounting of events that serve as the footprint of EVD emergence in Sierra Leone and a road map for risk mitigation fueled by lessons learned.
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Affiliation(s)
| | | | - Lina Moses
- Tulane University, New Orleans, Louisiana, USA
| | | | - Moinya Coomber
- Metabiota Inc., Kenema Government Hospital, Kenema, Sierra Leone
| | - Victor Lungay
- Metabiota Inc., Freetown, Sierra Leone; Ministry of Heath and Sanitation, Sierra Leone
| | - Michael Gbakie
- Tulane University, New Orleans, Louisiana, USA; Ministry of Heath and Sanitation, Sierra Leone
| | | | | | | | | | | | | | | | | | | | - Willie Roberts
- Metabiota Inc., Freetown, Sierra Leone; Ministry of Heath and Sanitation, Sierra Leone
| | | | - David Kargbo
- Directorate of Disease Prevention and Control, DPC Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Tom Vincent
- Metabiota Inc., Silver Spring and San Francisco, USA
| | | | - Mary Guttieri
- Metabiota Inc., Silver Spring and San Francisco, USA
| | | | - Marc Souris
- UMRD 190 Emergence des Pathologies Virales, IRD, Aix-Marseille University, Vientiane, Laos
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18
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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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19
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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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