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Kotliar D, Raju S, Tabrizi S, Odia I, Goba A, Momoh M, Sandi JD, Nair P, Phelan E, Tariyal R, Eromon PE, Mehta S, Robles-Sikisaka R, Siddle KJ, Stremlau M, Jalloh S, Gire SK, Winnicki S, Chak B, Schaffner SF, Pauthner M, Karlsson EK, Chapin SR, Kennedy SG, Branco LM, Kanneh L, Vitti JJ, Broodie N, Gladden-Young A, Omoniwa O, Jiang PP, Yozwiak N, Heuklom S, Moses LM, Akpede GO, Asogun DA, Rubins K, Kales S, Happi AN, Iruolagbe CO, Dic-Ijiewere M, Iraoyah K, Osazuwa OO, Okonkwo AK, Kunz S, McCormick JB, Khan SH, Honko AN, Lander ES, Oldstone MBA, Hensley L, Folarin OA, Okogbenin SA, Günther S, Ollila HM, Tewhey R, Okokhere PO, Schieffelin JS, Andersen KG, Reilly SK, Grant DS, Garry RF, Barnes KG, Happi CT, Sabeti PC. Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever. Nat Microbiol 2024; 9:751-762. [PMID: 38326571 PMCID: PMC10914620 DOI: 10.1038/s41564-023-01589-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/14/2023] [Indexed: 02/09/2024]
Abstract
Infection with Lassa virus (LASV) can cause Lassa fever, a haemorrhagic illness with an estimated fatality rate of 29.7%, but causes no or mild symptoms in many individuals. Here, to investigate whether human genetic variation underlies the heterogeneity of LASV infection, we carried out genome-wide association studies (GWAS) as well as seroprevalence surveys, human leukocyte antigen typing and high-throughput variant functional characterization assays. We analysed Lassa fever susceptibility and fatal outcomes in 533 cases of Lassa fever and 1,986 population controls recruited over a 7 year period in Nigeria and Sierra Leone. We detected genome-wide significant variant associations with Lassa fever fatal outcomes near GRM7 and LIF in the Nigerian cohort. We also show that a haplotype bearing signatures of positive selection and overlapping LARGE1, a required LASV entry factor, is associated with decreased risk of Lassa fever in the Nigerian cohort but not in the Sierra Leone cohort. Overall, we identified variants and genes that may impact the risk of severe Lassa fever, demonstrating how GWAS can provide insight into viral pathogenesis.
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Affiliation(s)
- Dylan Kotliar
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Siddharth Raju
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Shervin Tabrizi
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ikponmwosa Odia
- Institute of Lassa Fever, Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Augustine Goba
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Mambu Momoh
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Eastern Polytechnic College, Kenema, Sierra Leone
| | - John Demby Sandi
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Parvathy Nair
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | | - Philomena E Eromon
- Institute of Lassa Fever, Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria
| | - Samar Mehta
- Department of Critical Care Medicine, University of Maryland Medical Center, Baltimore, MA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Katherine J Siddle
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | - Simbirie Jalloh
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | | | - Sarah Winnicki
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Bridget Chak
- Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Stephen F Schaffner
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | | | - Elinor K Karlsson
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Sarah R Chapin
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Sharon G Kennedy
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Joseph J Vitti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Nisha Broodie
- New York-Presbyterian Hospital-Columbia and Cornell, New York, NY, USA
| | - Adrianne Gladden-Young
- Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | | | | | - Nathan Yozwiak
- Gene and Cell Therapy Institute, Mass General Brigham, Cambridge, MA, USA
| | - Shannon Heuklom
- San Francisco Community Health Center, San Francisco, CA, USA
| | - Lina M Moses
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - George O Akpede
- Institute of Lassa Fever, Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- Department of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - Danny A Asogun
- Department of Community Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - Kathleen Rubins
- National Aeronautics and Space Administration, Houston, TX, USA
| | | | - Anise N Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria
| | | | - Mercy Dic-Ijiewere
- Department of Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Kelly Iraoyah
- Department of Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Omoregie O Osazuwa
- Department of Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | | | - Stefan Kunz
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Joseph B McCormick
- UTHealth Houston School of Public Health, Brownsville Campus, Brownsville, TX, USA
| | - S Humarr Khan
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Anna N Honko
- Boston University School of Medicine, Boston, MA, USA
| | - Eric S Lander
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Michael B A Oldstone
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lisa Hensley
- National Institutes of Health Integrated Research Facility, Frederick, MA, USA
| | - Onikepe A Folarin
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria
- Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - Sylvanus A Okogbenin
- Institute of Lassa Fever, Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Hanna M Ollila
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Peter O Okokhere
- Institute of Lassa Fever, Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- Department of Medicine, Ambrose Alli University, Ekpoma, Nigeria
- Department of Medicine, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - John S Schieffelin
- Section of Infectious Disease, Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Steven K Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Donald S Grant
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Robert F Garry
- Tulane University School of Medicine, New Orleans, LA, USA
| | - Kayla G Barnes
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Christian T Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Department of Biological Sciences, Redeemer's University, Ede, Nigeria.
| | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.
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Sandi JD, Levy JI, Tapela K, Zeller M, Yeboah JA, Saka DF, Grant DS, Awandare GA, Quashie PK, Andersen KG, Paemka L. Upper Airway Epithelial Tissue Transcriptome Analysis Reveals Immune Signatures Associated with COVID-19 Severity in Ghanaians. J Immunol Res 2024; 2024:6668017. [PMID: 38375062 PMCID: PMC10876312 DOI: 10.1155/2024/6668017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/04/2023] [Accepted: 01/03/2024] [Indexed: 02/21/2024] Open
Abstract
The immunological signatures driving the severity of coronavirus disease 19 (COVID-19) in Ghanaians remain poorly understood. We performed bulk transcriptome sequencing of nasopharyngeal samples from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-infected Ghanaians with mild and severe COVID-19, as well as healthy controls to characterize immune signatures at the primary SARS-CoV-2 infection site and identify drivers of disease severity. Generally, a heightened antiviral response was observed in SARS-CoV-2-infected Ghanaians compared with uninfected controls. COVID-19 severity was associated with immune suppression, overexpression of proinflammatory cytokines, including CRNN, IL1A, S100A7, and IL23A, and activation of pathways involved in keratinocyte proliferation. SAMD9L was among the differentially regulated interferon-stimulated genes in our mild and severe disease cohorts, suggesting that it may play a critical role in SARS-CoV-2 pathogenesis. By comparing our data with a publicly available dataset from a non-African (Indians) (GSE166530), an elevated expression of antiviral response-related genes was noted in COVID-19-infected Ghanaians. Overall, the study describes immune signatures driving COVID-19 severity in Ghanaians and identifies immune drivers that could serve as potential prognostic markers for future outbreaks or pandemics. It further provides important preliminary evidence suggesting differences in antiviral response at the upper respiratory interface in sub-Saharan Africans (Ghanaians) and non-Africans, which could be contributing to the differences in disease outcomes. Further studies using larger datasets from different populations will expand on these findings.
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Affiliation(s)
- John Demby Sandi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology (BCMB), School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Faculty of Laboratory Medicine, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Kenema Government Hospital, Kenema, Sierra Leone
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, San Diego, California 92037, USA
| | - Kesego Tapela
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology (BCMB), School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, San Diego, California 92037, USA
| | - Joshua Afari Yeboah
- Department of Biochemistry, Cell and Molecular Biology (BCMB), School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Daniel Frimpong Saka
- Department of Biochemistry, Cell and Molecular Biology (BCMB), School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Donald S. Grant
- Faculty of Laboratory Medicine, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Kenema Government Hospital, Kenema, Sierra Leone
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology (BCMB), School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Peter K. Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology (BCMB), School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, San Diego, California 92037, USA
| | - Lily Paemka
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology (BCMB), School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
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3
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Smither AR, Koninga J, Kanneh FB, Foday M, Boisen ML, Bond NG, Momoh M, Sandi JD, Kanneh L, Alhasan F, Kanneh IM, Yillah MS, Grant DS, Bush DJ, Nelson DKS, Cruz KM, Klitting R, Pauthner M, Andersen KG, Shaffer JG, Cross RW, Schieffelin JS, Garry RF. Novel Tools for Lassa Virus Surveillance in Peri-domestic Rodents. medRxiv 2023:2023.03.17.23287380. [PMID: 36993465 PMCID: PMC10055574 DOI: 10.1101/2023.03.17.23287380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Background Lassa fever (LF) is a rodent-borne disease endemic to West Africa. In the absence of licensed therapeutics or vaccines, rodent exclusion from living spaces remains the primary method of preventing LF. Zoonotic surveillance of Lassa virus (LASV), the etiologic agent of LF, can assess the burden of LASV in a region and guide public health measures against LF. Methods In this study, we adapted commercially available LASV human diagnostics to assess the prevalence of LASV in peri-domestic rodents in Eastern Sierra Leone. Small mammal trapping was conducted in Kenema district, Sierra Leone between November 2018-July 2019. LASV antigen was detected using a commercially available LASV NP antigen rapid diagnostic test. LASV IgG antibodies against LASV nucleoprotein (NP) and glycoprotein (GP) were tested by adapting a commercially available semi-quantitative enzyme linked immunosorbent assay (ELISA) for detection of mouse-related and rat-related species IgG. Findings Of the 373 tested specimens, 74 (20%) tested positive for LASV antigen. 40 (11%) specimens tested positive for LASV NP IgG, while an additional 12 (3%) specimens only tested positive for LASV GP IgG. Simultaneous antigen presence and IgG antibody presence was linked in Mastomys sp. specimens (p < 0.01), but not Rattus sp. specimens (p = 1). Despite the link between antigen presence and IgG antibody presence in Mastomys sp., the strength of antigen response did not correlate with the strength of IgG response to either GP IgG or NP IgG. Interpretation The tools developed in this study can aid in the generation of valuable public health data for rapid field assessment of LASV burden during outbreak investigations and general LASV surveillance. Funding Funding for this work was supported by the National Institute of Allergy and Infectious Diseases National Institute of Health, Department of Health and Human Services under the following grants: International Collaboration in Infectious Disease Research on Lassa fever and Ebola - ICIDR - U19 AI115589, Consortium for Viral Systems Biology - CViSB - 5U19AI135995, West African Emerging Infectious Disease Research Center - WARN-ID - U01AI151812, West African Center for Emerging Infectious Diseases: U01AI151801.
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Affiliation(s)
- Allison R. Smither
- Tulane University School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA
- University of Texas Medical Branch, Galveston National Laboratory, Galveston, TX, USA
| | - James Koninga
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Franklyn B. Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Momoh Foday
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | | | - Nell G. Bond
- Tulane University School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA
| | - Mambu Momoh
- Tulane University School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - John Demby Sandi
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Foday Alhasan
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Ibrahim Mustapha Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Mohamed S. Yillah
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone
| | | | | | - Kaitlin M. Cruz
- Tulane University School of Medicine, Department of Pediatrics, Section of Infectious Disease, New Orleans, LA, USA
| | - Raphaëlle Klitting
- The Scripps Research Institute, Department of Microbiology and Immunology, La Jolla, CA, USA
| | - Matthias Pauthner
- The Scripps Research Institute, Department of Microbiology and Immunology, La Jolla, CA, USA
| | - Kristian G. Andersen
- The Scripps Research Institute, Department of Microbiology and Immunology, La Jolla, CA, USA
| | - Jeffrey G. Shaffer
- Tulane University School of Public Health and Tropical Medicine, Department of Biostatistics, New Orleans, LA, USA
| | - Robert W. Cross
- University of Texas Medical Branch, Galveston National Laboratory, Galveston, TX, USA
| | - John S. Schieffelin
- Tulane University School of Medicine, Department of Pediatrics, Section of Infectious Disease, New Orleans, LA, USA
| | - Robert F. Garry
- Tulane University School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA
- Zalgen Labs, LLC, Frederick, MD, USA
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4
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Penfold S, Adegnika AA, Asogun D, Ayodeji O, Azuogu BN, Fischer WA, Garry RF, Grant DS, Happi C, N'Faly M, Olayinka A, Samuels R, Sibley J, Wohl DA, Accrombessi M, Adetifa I, Annibaldis G, Camacho A, Dan-Nwafor C, Deha ARE, DeMarco J, Duraffour S, Goba A, Grais R, Günther S, Honvou ÉJJP, Ihekweazu C, Jacobsen C, Kanneh L, Momoh M, Ndiaye A, Nsaibirni R, Okogbenin S, Ochu C, Ogbaini E, Logbo ÉPMA, Sandi JD, Schieffelin JS, Verstraeten T, Vielle NJ, Yadouleton A, Yovo EK. A prospective, multi-site, cohort study to estimate incidence of infection and disease due to Lassa fever virus in West African countries (the Enable Lassa research programme)-Study protocol. PLoS One 2023; 18:e0283643. [PMID: 36996258 PMCID: PMC10062557 DOI: 10.1371/journal.pone.0283643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/13/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Lassa fever (LF), a haemorrhagic illness caused by the Lassa fever virus (LASV), is endemic in West Africa and causes 5000 fatalities every year. The true prevalence and incidence rates of LF are unknown as infections are often asymptomatic, clinical presentations are varied, and surveillance systems are not robust. The aim of the Enable Lassa research programme is to estimate the incidences of LASV infection and LF disease in five West African countries. The core protocol described here harmonises key study components, such as eligibility criteria, case definitions, outcome measures, and laboratory tests, which will maximise the comparability of data for between-country analyses. METHOD We are conducting a prospective cohort study in Benin, Guinea, Liberia, Nigeria (three sites), and Sierra Leone from 2020 to 2023, with 24 months of follow-up. Each site will assess the incidence of LASV infection, LF disease, or both. When both incidences are assessed the LASV cohort (nmin = 1000 per site) will be drawn from the LF cohort (nmin = 5000 per site). During recruitment participants will complete questionnaires on household composition, socioeconomic status, demographic characteristics, and LF history, and blood samples will be collected to determine IgG LASV serostatus. LF disease cohort participants will be contacted biweekly to identify acute febrile cases, from whom blood samples will be drawn to test for active LASV infection using RT-PCR. Symptom and treatment data will be abstracted from medical records of LF cases. LF survivors will be followed up after four months to assess sequelae, specifically sensorineural hearing loss. LASV infection cohort participants will be asked for a blood sample every six months to assess LASV serostatus (IgG and IgM). DISCUSSION Data on LASV infection and LF disease incidence in West Africa from this research programme will determine the feasibility of future Phase IIb or III clinical trials for LF vaccine candidates.
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Affiliation(s)
| | - Ayola Akim Adegnika
- Fondation pour la Recherche Scientifique (FORS), Cotonou, Bénin
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institut für Tropenmedizin, Universität Tübingen and German Center for Infection Research, Tübingen, Germany
| | - Danny Asogun
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Benedict N Azuogu
- Alex Ekwueme Federal University Teaching Hospital Abakaliki, Abakaliki, Ebonyi State, Nigeria
| | - William A Fischer
- Institute of Global Health and Infectious Diseases, The University of North Carolina (UNC) at Chapel Hill, Chapel Hill, NC, United States of America
| | - Robert F Garry
- Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | | | | | | | | | | | | | - David A Wohl
- Institute of Global Health and Infectious Diseases, The University of North Carolina (UNC) at Chapel Hill, Chapel Hill, NC, United States of America
| | | | | | - Giuditta Annibaldis
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | | | - Jean DeMarco
- Institute of Global Health and Infectious Diseases, The University of North Carolina (UNC) at Chapel Hill, Chapel Hill, NC, United States of America
| | - Sophie Duraffour
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | - Stephan Günther
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | - Christine Jacobsen
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Mambu Momoh
- Kenema Government Hospital (KGH), Kenema, Sierra Leone
| | | | | | - Sylvanus Okogbenin
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Chinwe Ochu
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Ephraim Ogbaini
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | | | - John S Schieffelin
- Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | | | - Nathalie J Vielle
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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5
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Klitting R, Kafetzopoulou LE, Thiery W, Dudas G, Gryseels S, Kotamarthi A, Vrancken B, Gangavarapu K, Momoh M, Sandi JD, Goba A, Alhasan F, Grant DS, Okogbenin S, Ogbaini-Emovo E, Garry RF, Smither AR, Zeller M, Pauthner MG, McGraw M, Hughes LD, Duraffour S, Günther S, Suchard MA, Lemey P, Andersen KG, Dellicour S. Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades. Nat Commun 2022; 13:5596. [PMID: 36167835 PMCID: PMC9515147 DOI: 10.1038/s41467-022-33112-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 09/02/2022] [Indexed: 01/27/2023] Open
Abstract
Lassa fever is a severe viral hemorrhagic fever caused by a zoonotic virus that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate and land use changes could affect the endemic area of this virus, currently limited to parts of West Africa. By exploring the environmental data associated with virus occurrence using ecological niche modelling, we show how temperature, precipitation and the presence of pastures determine ecological suitability for virus circulation. Based on projections of climate, land use, and population changes, we find that regions in Central and East Africa will likely become suitable for Lassa virus over the next decades and estimate that the total population living in ecological conditions that are suitable for Lassa virus circulation may drastically increase by 2070. By analysing geotagged viral genomes using spatially-explicit phylogeography and simulating virus dispersal, we find that in the event of Lassa virus being introduced into a new suitable region, its spread might remain spatially limited over the first decades.
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Affiliation(s)
- Raphaëlle Klitting
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Liana E. Kafetzopoulou
- grid.5596.f0000 0001 0668 7884Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium ,grid.424065.10000 0001 0701 3136Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Wim Thiery
- grid.8767.e0000 0001 2290 8069Department of Hydrology and Hydraulic Engineering, Vrije Universiteit Brussel, Brussels, Belgium
| | - Gytis Dudas
- grid.6441.70000 0001 2243 2806Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Sophie Gryseels
- grid.5284.b0000 0001 0790 3681Evolutionary Ecology group, Department of Biology, University of Antwerp, 2610 Antwerp, Belgium ,grid.20478.390000 0001 2171 9581Vertebrate group, Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | - Anjali Kotamarthi
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Bram Vrancken
- grid.5596.f0000 0001 0668 7884Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Karthik Gangavarapu
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Mambu Momoh
- grid.442296.f0000 0001 2290 9707Eastern Technical University of Sierra Leone, Kenema, Sierra Leone ,grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - John Demby Sandi
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Augustine Goba
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Foday Alhasan
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Donald S. Grant
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone ,grid.442296.f0000 0001 2290 9707College of Medicine and Allied Health Sciences, University of Sierra Leone, Kenema, Sierra Leone
| | - Sylvanus Okogbenin
- grid.508091.5Irrua Specialist Teaching Hospital, Irrua, Nigeria ,grid.411357.50000 0000 9018 355XFaculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | | | - Robert F. Garry
- grid.265219.b0000 0001 2217 8588Department of Microbiology and Immunology, Tulane University, School of Medicine, New Orleans, LA 70112 USA ,grid.505518.c0000 0004 5901 1919Zalgen Labs, LCC, Frederick, MD 21703 USA ,grid.475149.aGlobal Virus Network (GVN), Baltimore, MD 21201 USA
| | - Allison R. Smither
- grid.265219.b0000 0001 2217 8588Department of Microbiology and Immunology, Tulane University, School of Medicine, New Orleans, LA 70112 USA
| | - Mark Zeller
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Matthias G. Pauthner
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Michelle McGraw
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Laura D. Hughes
- grid.214007.00000000122199231Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Sophie Duraffour
- grid.424065.10000 0001 0701 3136Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany ,grid.452463.2German Center for Infection Research (DZIF), Partner site Hamburg–Lübeck–Borstel–Riems, Hamburg, Germany
| | - Stephan Günther
- grid.424065.10000 0001 0701 3136Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany ,grid.452463.2German Center for Infection Research (DZIF), Partner site Hamburg–Lübeck–Borstel–Riems, Hamburg, Germany
| | - Marc A. Suchard
- grid.19006.3e0000 0000 9632 6718Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Philippe Lemey
- grid.5596.f0000 0001 0668 7884Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Kristian G. Andersen
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA ,grid.214007.00000000122199231Scripps Research Translational Institute, La Jolla, CA 92037 USA
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium. .,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, 1050, Bruxelles, Belgium.
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6
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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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7
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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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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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Horton LE, Cross RW, Hartnett JN, Engel EJ, Sakabe S, Goba A, Momoh M, Sandi JD, Geisbert TW, Garry RF, Schieffelin JS, Grant DS, Sullivan BM. Endotheliopathy and Platelet Dysfunction as Hallmarks of Fatal Lassa Fever. Emerg Infect Dis 2020; 26:2625-2637. [PMID: 33079033 PMCID: PMC7588510 DOI: 10.3201/eid2611.191694] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Lassa fever (LF) causes multisystem disease and has a fatality rate <70%. Severe cases exhibit abnormal coagulation, endothelial barrier disruption, and dysfunctional platelet aggregation but the underlying mechanisms remain poorly understood. In Sierra Leone during 2015-2018, we assessed LF patients' day-of-admission plasma samples for levels of proteins necessary for coagulation, fibrinolysis, and platelet function. P-selectin, soluble endothelial protein C receptor, soluble thrombomodulin, plasminogen activator inhibitor 1, ADAMTS-13, von Willebrand factor, tissue factor, soluble intercellular adhesion molecule 1, and vascular cell adhesion molecule 1 were more elevated in LF patients than in controls. Endothelial protein C receptor, thrombomodulin, intercellular adhesion molecule 1, plasminogen activator inhibitor 1, D-dimer, and hepatocyte growth factor were higher in fatal than nonfatal LF cases. Platelet disaggregation occurred only in samples from fatal LF cases. The impaired homeostasis and platelet dysfunction implicate alterations in the protein C pathway, which might contribute to the loss of endothelial barrier function in fatal infections.
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10
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Gunn BM, Roy V, Karim MM, Hartnett JN, Suscovich TJ, Goba A, Momoh M, Sandi JD, Kanneh L, Andersen KG, Shaffer JG, Schieffelin JS, Garry RF, Grant DS, Alter G. Survivors of Ebola Virus Disease Develop Polyfunctional Antibody Responses. J Infect Dis 2020; 221:156-161. [PMID: 31301137 PMCID: PMC7184900 DOI: 10.1093/infdis/jiz364] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/11/2019] [Indexed: 11/21/2022] Open
Abstract
Monoclonal antibodies can mediate protection against Ebola virus (EBOV) infection through direct neutralization as well as through the recruitment of innate immune effector functions. However, the antibody functional response following survival of acute EBOV disease has not been well characterized. In this study, serum antibodies from Ebola virus disease (EVD) survivors from Sierra Leone were profiled to capture variation in overall subclass/isotype abundance, neutralizing activity, and innate immune effector functions. Antibodies from EVD survivors exhibited robust innate immune effector functions, mediated primarily by IgG1 and IgA1. In conclusion, development of functional antibodies follows survival of acute EVD.
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Affiliation(s)
- Bronwyn M Gunn
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
| | - Vicky Roy
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
| | - Marcus M Karim
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
| | - Jessica N Hartnett
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Todd J Suscovich
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Mambu Momoh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital.,Eastern Polytechnic University, Kenema, Sierra Leone
| | | | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Kristian G Andersen
- Department of Immunology and Microbiology, Scripps Research Institute.,Scripps Research Translational Institute, La Jolla, California
| | - Jeffrey G Shaffer
- Department of Biostatistics and Bioinformatics, Tulane School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - John S Schieffelin
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Donald S Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
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11
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Boisen ML, Uyigue E, Aiyepada J, Siddle KJ, Oestereich L, Nelson DKS, Bush DJ, Rowland MM, Heinrich ML, Eromon P, Kayode AT, Odia I, Adomeh DI, Muoebonam EB, Akhilomen P, Okonofua G, Osiemi B, Omoregie O, Airende M, Agbukor J, Ehikhametalor S, Aire CO, Duraffour S, Pahlmann M, Böhm W, Barnes KG, Mehta S, Momoh M, Sandi JD, Goba A, Folarin OA, Ogbaini-Emovan E, Asogun DA, Tobin EA, Akpede GO, Okogbenin SA, Okokhere PO, Grant DS, Schieffelin JS, Sabeti PC, Günther S, Happi CT, Branco LM, Garry RF. Field evaluation of a Pan-Lassa rapid diagnostic test during the 2018 Nigerian Lassa fever outbreak. Sci Rep 2020; 10:8724. [PMID: 32457420 PMCID: PMC7250850 DOI: 10.1038/s41598-020-65736-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 03/02/2020] [Accepted: 05/08/2020] [Indexed: 01/07/2023] Open
Abstract
Lassa virus (LASV) is the causative agent of Lassa fever (LF), an often-fatal hemorrhagic disease. LF is endemic in Nigeria, Sierra Leone and other West African countries. Diagnosis of LASV infection is challenged by the genetic diversity of the virus, which is greatest in Nigeria. The ReLASV Pan-Lassa Antigen Rapid Test (Pan-Lassa RDT) is a point-of-care, in vitro diagnostic test that utilizes a mixture of polyclonal antibodies raised against recombinant nucleoproteins of representative strains from the three most prevalent LASV lineages (II, III and IV). We compared the performance of the Pan-LASV RDT to available quantitative PCR (qPCR) assays during the 2018 LF outbreak in Nigeria. For patients with acute LF (RDT positive, IgG/IgM negative) during initial screening, RDT performance was 83.3% sensitivity and 92.8% specificity when compared to composite results of two qPCR assays. 100% of samples that gave Ct values below 22 on both qPCR assays were positive on the Pan-Lassa RDT. There were significantly elevated case fatality rates and elevated liver transaminase levels in subjects whose samples were RDT positive compared to RDT negative.
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Affiliation(s)
| | - Eghosa Uyigue
- The African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - John Aiyepada
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Katherine J Siddle
- The Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- The Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Lisa Oestereich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg, Germany
| | | | | | | | | | - Philomena Eromon
- The African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Adeyemi T Kayode
- The African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Ikponmwosa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Donatus I Adomeh
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Ekene B Muoebonam
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Patience Akhilomen
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Grace Okonofua
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Blessing Osiemi
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Omigie Omoregie
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Michael Airende
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Jacqueline Agbukor
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Solomon Ehikhametalor
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Chris Okafi Aire
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Sophie Duraffour
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg, Germany
| | - Meike Pahlmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg, Germany
| | - Wiebke Böhm
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg, Germany
| | - Kayla G Barnes
- The Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Samar Mehta
- The Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Beth Israel Deaconess Medical Center, Division of Infectious Diseases, Boston, MA, USA
| | - Mambu Momoh
- Eastern Polytechnic Institute, Kenema, Sierra Leone
- 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
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Onikepe A Folarin
- The African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Ephraim Ogbaini-Emovan
- 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
| | - Ekaete A Tobin
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - George O Akpede
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Sylvanus A 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
- The Department of Medicine, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
- The Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma, Edo State, Nigeria
| | - 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
- Sections of Infectious Disease, Departments of Pediatrics and Internal Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Pardis C Sabeti
- The Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- The Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard-MIT Health Sciences and Technology, MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg, Germany
| | - Christian T Happi
- The African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
| | | | - Robert F Garry
- Zalgen Labs, LLC, Germantown, MD, USA.
- Tulane Health Sciences Center, Tulane University, New Orleans, LA, USA.
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA.
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12
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Sullivan BM, Sakabe S, Hartnett JN, Nho N, Goba A, Momoh M, Sandi JD, Kanneh L, Cubitt B, Garcia SD, Ware BC, Kotliar D, Robles-Sikisaka R, Gangavarapu K, de la Torre JC, Sabeti PC, Andersen KG, Garry RF, Grant DS, Schieffelin JS, Oldstone MB. Reevaluating HLA-A2-restricted Lassa epitopes in human Lassa fever survivors. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.140.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Many factors contribute to the selection of epitope-specific T cells. Often, candidate epitopes are generated through in silico prediction of various biological processes, mainly peptide generation and MHC binding, that are then tested in relevant biological assays. This is especially true of epitopes derived from BSL-4 pathogens or where relevant patient samples are difficult to obtain. Two previous studies identified CD8+ T cell epitopes from the Lassa virus glycoprotein through in silico prediction, experimental MHC binding assays, and epitope generation in HLA-A2 transgenic mice. Using samples from ten HLA-A*02:01 Lassa fever survivors, we tested whether these previously described epitope-specific CD8+ T cells were present and their relation to the broader Lassa virus-specific T cell response. Using overnight stimulation assays, we detected robust LASV-specific responses to the glycoprotein and nucleoprotein, but only one of the three epitopes (GP60–68)shown to be present and protective in mice made a substantial contribution to the overall LASV-specific response. Using a more sensitive proliferation assay, we detected the remaining two epitopes in some individuals at a very low frequency. Overall, this study shows the limitations of epitope discovery through in silico prediction, MHC binding and transgenic mouse models and highlights the complex nature of T cell selection during natural infection of humans.
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Affiliation(s)
| | - Saori Sakabe
- 1Department of Immunology and Microbiology, The Scripps Research Institute
| | | | - Nhi Nho
- 1Department of Immunology and Microbiology, The Scripps Research Institute
| | - Augustine Goba
- 3Viral Hemorrhagic Fever Program, Kenema Government Hospital
- 4Ministry of Health and Sanitation, Sierra Leone, Sierra Leone
| | - Mambu Momoh
- 4Ministry of Health and Sanitation, Sierra Leone, Sierra Leone
- 5Viral Hemorrhagic Fever Program, Kenema Government Hospital, Sierra Leone
- 6Eastern Polytechnic Institute, Sierra Leone
| | - John Demby Sandi
- 4Ministry of Health and Sanitation, Sierra Leone, Sierra Leone
- 5Viral Hemorrhagic Fever Program, Kenema Government Hospital, Sierra Leone
- 7Njala University, Sierra Leone
| | - Lansana Kanneh
- 4Ministry of Health and Sanitation, Sierra Leone, Sierra Leone
- 5Viral Hemorrhagic Fever Program, Kenema Government Hospital, Sierra Leone
| | - Beatrice Cubitt
- 1Department of Immunology and Microbiology, The Scripps Research Institute
| | - Selma D Garcia
- 1Department of Immunology and Microbiology, The Scripps Research Institute
| | - Brian C Ware
- 1Department of Immunology and Microbiology, The Scripps Research Institute
| | - Dylan Kotliar
- 8FAS Center for Systems Biology, Broad Institute of MIT and Harvard
| | - Refugio Robles-Sikisaka
- 1Department of Immunology and Microbiology, The Scripps Research Institute
- 9Scripps Translational Research Institute, The Scripps Research Institute
| | - Karthik Gangavarapu
- 10Department of Molecular and Experimental Medicine, The Scripps Research Institute
| | | | - Pardis C Sabeti
- 8FAS Center for Systems Biology, Broad Institute of MIT and Harvard
| | - Kristian G Andersen
- 1Department of Immunology and Microbiology, The Scripps Research Institute
- 9Scripps Translational Research Institute, The Scripps Research Institute
| | | | - Donald S Grant
- 4Ministry of Health and Sanitation, Sierra Leone, Sierra Leone
- 5Viral Hemorrhagic Fever Program, Kenema Government Hospital, Sierra Leone
- 11College of Medicine and Allied Health Sciences, University of Sierra Leone, Sierra Leone
| | | | - Michael B Oldstone
- 1Department of Immunology and Microbiology, The Scripps Research Institute
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13
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Sullivan BM, Sakabe S, Hartnett J, Goba A, Momoh M, Sandi JD, Schieffelin JS, de la Torre JC, Grant DS, Garry RF, Oldstone MB. Memory T cell responses in survivors of the 2013–2016 West African Ebola outbreak. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.126.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Primary infection with Ebola virus protects against subsequent challenge, thus an optimal vaccine should generate immune responses similar to those found in disease survivors. To this end, we characterized CD8 and CD4 T cell responses in Ebola survivors to uncover the immunogenicity of seven of eight Ebola virus proteins. T cell responses of 33 Sierra Leonean Ebola survivors were examined. Nearly all individuals studied harbored nucleoprotein (NP)-specific CD8 T cell responses. Moreover, NP-specific T cells responded more strongly and were more numerous in 65% of NP responders compared to responses to other EBOV proteins in the same individual. Conversely, we found glycoprotein (GP) CD8+ T cell responses in only 37% of EBOV responders. GP responses were also weaker and less numerous than other responses in the same individual. Specificity of the CD4+ T cell responses were more evenly distributed. Altogether, our data indicate that NP is among the most immunogenic EBOV proteins while only VP30 was less immunogenic than GP in our cohort of Sierra Leonean survivors. An optimal vaccine designed to elicit both humoral and cell mediated immune responses in a broad human population should contain both NP and the GP.
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Affiliation(s)
| | | | | | - Augustine Goba
- 3Kenema Government Hospital, Sierra Leone
- 4Ministry of Health and Sanitation, Sierra Leone
| | - Mambu Momoh
- 3Kenema Government Hospital, Sierra Leone
- 4Ministry of Health and Sanitation, Sierra Leone
| | - John Demby Sandi
- 3Kenema Government Hospital, Sierra Leone
- 4Ministry of Health and Sanitation, Sierra Leone
| | | | | | - Donald S. Grant
- 3Kenema Government Hospital, Sierra Leone
- 4Ministry of Health and Sanitation, Sierra Leone
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