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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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2
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Critchley HOD, Babayev E, Bulun SE, Clark S, Garcia-Grau I, Gregersen PK, Kilcoyne A, Kim JYJ, Lavender M, Marsh EE, Matteson KA, Maybin JA, Metz CN, Moreno I, Silk K, Sommer M, Simon C, Tariyal R, Taylor HS, Wagner GP, Griffith LG. Menstruation: science and society. Am J Obstet Gynecol 2020; 223:624-664. [PMID: 32707266 PMCID: PMC7661839 DOI: 10.1016/j.ajog.2020.06.004] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/13/2020] [Accepted: 06/03/2020] [Indexed: 12/11/2022]
Abstract
Women's health concerns are generally underrepresented in basic and translational research, but reproductive health in particular has been hampered by a lack of understanding of basic uterine and menstrual physiology. Menstrual health is an integral part of overall health because between menarche and menopause, most women menstruate. Yet for tens of millions of women around the world, menstruation regularly and often catastrophically disrupts their physical, mental, and social well-being. Enhancing our understanding of the underlying phenomena involved in menstruation, abnormal uterine bleeding, and other menstruation-related disorders will move us closer to the goal of personalized care. Furthermore, a deeper mechanistic understanding of menstruation-a fast, scarless healing process in healthy individuals-will likely yield insights into a myriad of other diseases involving regulation of vascular function locally and systemically. We also recognize that many women now delay pregnancy and that there is an increasing desire for fertility and uterine preservation. In September 2018, the Gynecologic Health and Disease Branch of the Eunice Kennedy Shriver National Institute of Child Health and Human Development convened a 2-day meeting, "Menstruation: Science and Society" with an aim to "identify gaps and opportunities in menstruation science and to raise awareness of the need for more research in this field." Experts in fields ranging from the evolutionary role of menstruation to basic endometrial biology (including omic analysis of the endometrium, stem cells and tissue engineering of the endometrium, endometrial microbiome, and abnormal uterine bleeding and fibroids) and translational medicine (imaging and sampling modalities, patient-focused analysis of menstrual disorders including abnormal uterine bleeding, smart technologies or applications and mobile health platforms) to societal challenges in health literacy and dissemination frameworks across different economic and cultural landscapes shared current state-of-the-art and future vision, incorporating the patient voice at the launch of the meeting. Here, we provide an enhanced meeting report with extensive up-to-date (as of submission) context, capturing the spectrum from how the basic processes of menstruation commence in response to progesterone withdrawal, through the role of tissue-resident and circulating stem and progenitor cells in monthly regeneration-and current gaps in knowledge on how dysregulation leads to abnormal uterine bleeding and other menstruation-related disorders such as adenomyosis, endometriosis, and fibroids-to the clinical challenges in diagnostics, treatment, and patient and societal education. We conclude with an overview of how the global agenda concerning menstruation, and specifically menstrual health and hygiene, are gaining momentum, ranging from increasing investment in addressing menstruation-related barriers facing girls in schools in low- to middle-income countries to the more recent "menstrual equity" and "period poverty" movements spreading across high-income countries.
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Affiliation(s)
- Hilary O D Critchley
- Medical Research Council Centre for Reproductive Health, The University of Edinburgh, United Kingdom.
| | - Elnur Babayev
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Serdar E Bulun
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | | | - Iolanda Garcia-Grau
- Igenomix Foundation-Instituto de Investigación Sanitaria Hospital Clínico, INCLIVA, Valencia, Spain; Department of Pediatrics, Obstetrics and Gynecology, School of Medicine, University of Valencia, Valencia, Spain
| | - Peter K Gregersen
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY
| | | | | | | | - Erica E Marsh
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI
| | - Kristen A Matteson
- Division of Research, Department of Obstetrics and Gynecology, Women and Infants Hospital, Warren Alpert Medical School of Brown University, Providence, RI
| | - Jacqueline A Maybin
- Medical Research Council Centre for Reproductive Health, The University of Edinburgh, United Kingdom
| | - Christine N Metz
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY
| | - Inmaculada Moreno
- Igenomix Foundation-Instituto de Investigación Sanitaria Hospital Clínico, INCLIVA, Valencia, Spain
| | - Kami Silk
- Department of Communication, University of Delaware, Newark, DE
| | - Marni Sommer
- Department of Sociomedical Sciences, Columbia University Mailman School of Public Health, New York, NY
| | - Carlos Simon
- Igenomix Foundation-Instituto de Investigación Sanitaria Hospital Clínico, INCLIVA, Valencia, Spain; Department of Pediatrics, Obstetrics and Gynecology, School of Medicine, University of Valencia, Valencia, Spain; Beth Israel Deaconess Medical Center, Harvard University, Boston, MA; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX
| | | | - Hugh S Taylor
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Department of Obstetrics, Gynecology and Reproductive Sciences, Systems Biology Institute, Yale University, New Haven, CT; Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI
| | - Linda G Griffith
- Center for Gynepathology Research, Massachusetts Institute of Technology, Cambridge, MA
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3
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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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4
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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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5
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Boisen ML, Schieffelin JS, Goba A, Oottamasathien D, Jones AB, Shaffer JG, Hastie KM, Hartnett JN, Momoh M, Fullah M, Gabiki M, Safa S, Zandonatti M, Fusco M, Bornholdt Z, Abelson D, Gire SK, Andersen KG, Tariyal R, Stremlau M, Cross RW, Geisbert JB, Pitts KR, Geisbert TW, Kulakoski P, Wilson RB, Henderson L, Sabeti PC, Grant DS, Garry RF, Saphire EO, Branco LM, Khan SH. Multiple circulating infections can mimic the early stages of viral hemorrhagic fevers and possible human exposure to filoviruses in Sierra Leone prior to the 2014 outbreak. Viral Immunol 2015; 28:19-31. [PMID: 25531344 DOI: 10.1089/vim.2014.0108] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Lassa fever (LF) is a severe viral hemorrhagic fever caused by Lassa virus (LASV). The LF program at the Kenema Government Hospital (KGH) in Eastern Sierra Leone currently provides diagnostic services and clinical care for more than 500 suspected LF cases per year. Nearly two-thirds of suspected LF patients presenting to the LF Ward test negative for either LASV antigen or anti-LASV immunoglobulin M (IgM), and therefore are considered to have a non-Lassa febrile illness (NLFI). The NLFI patients in this study were generally severely ill, which accounts for their high case fatality rate of 36%. The current studies were aimed at determining possible causes of severe febrile illnesses in non-LF cases presenting to the KGH, including possible involvement of filoviruses. A seroprevalence survey employing commercial enzyme-linked immunosorbent assay tests revealed significant IgM and IgG reactivity against dengue virus, chikungunya virus, West Nile virus (WNV), Leptospira, and typhus. A polymerase chain reaction-based survey using sera from subjects with acute LF, evidence of prior LASV exposure, or NLFI revealed widespread infection with Plasmodium falciparum malaria in febrile patients. WNV RNA was detected in a subset of patients, and a 419 nt amplicon specific to filoviral L segment RNA was detected at low levels in a single patient. However, 22% of the patients presenting at the KGH between 2011 and 2014 who were included in this survey registered anti-Ebola virus (EBOV) IgG or IgM, suggesting prior exposure to this agent. The 2014 Ebola virus disease (EVD) outbreak is already the deadliest and most widely dispersed outbreak of its kind on record. Serological evidence reported here for possible human exposure to filoviruses in Sierra Leone prior to the current EVD outbreak supports genetic analysis that EBOV may have been present in West Africa for some time prior to the 2014 outbreak.
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