1
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Pandit PS, Anthony SJ, Goldstein T, Olival KJ, Doyle MM, Gardner NR, Bird B, Smith W, Wolking D, Gilardi K, Monagin C, Kelly T, Uhart MM, Epstein JH, Machalaba C, Rostal MK, Dawson P, Hagan E, Sullivan A, Li H, Chmura AA, Latinne A, Lange C, O’Rourke T, Olson S, Keatts L, Mendoza AP, Perez A, de Paula CD, Zimmerman D, Valitutto M, LeBreton M, McIver D, Islam A, Duong V, Mouiche M, Shi Z, Mulembakani P, Kumakamba C, Ali M, Kebede N, Tamoufe U, Bel-Nono S, Camara A, Pamungkas J, Coulibaly KJ, Abu-Basha E, Kamau J, Silithammavong S, Desmond J, Hughes T, Shiilegdamba E, Aung O, Karmacharya D, Nziza J, Ndiaye D, Gbakima A, sajali Z, Wacharapluesadee S, Robles EA, Ssebide B, Suzán G, Aguirre LF, Solorio MR, Dhole TN, Nga NTT, Hitchens PL, Joly DO, Saylors K, Fine A, Murray S, Karesh WB, Daszak P, Mazet JAK, Johnson CK. Author Correction: Predicting the potential for zoonotic transmission and host associations for novel viruses. Commun Biol 2023; 6:25. [PMID: 36627372 PMCID: PMC9832161 DOI: 10.1038/s42003-022-04364-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Pranav S. Pandit
- grid.27860.3b0000 0004 1936 9684One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
| | - Simon J. Anthony
- grid.21729.3f0000000419368729Center for Infection and Immunity, Columbia University, New York, NY 10032 USA
| | - Tracey Goldstein
- grid.27860.3b0000 0004 1936 9684One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
| | - Kevin J. Olival
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA
| | - Megan M. Doyle
- grid.27860.3b0000 0004 1936 9684One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
| | - Nicole R. Gardner
- grid.27860.3b0000 0004 1936 9684One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
| | - Brian Bird
- grid.27860.3b0000 0004 1936 9684One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
| | - Woutrina Smith
- grid.27860.3b0000 0004 1936 9684One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
| | - David Wolking
- grid.27860.3b0000 0004 1936 9684One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
| | - Kirsten Gilardi
- grid.27860.3b0000 0004 1936 9684One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
| | - Corina Monagin
- grid.27860.3b0000 0004 1936 9684One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
| | - Terra Kelly
- grid.27860.3b0000 0004 1936 9684One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
| | - Marcela M. Uhart
- grid.27860.3b0000 0004 1936 9684One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
| | - Jonathan H. Epstein
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA
| | - Catherine Machalaba
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA
| | - Melinda K. Rostal
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA
| | - Patrick Dawson
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA
| | - Emily Hagan
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA
| | - Ava Sullivan
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA
| | - Hongying Li
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA
| | - Aleksei A. Chmura
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA
| | - Alice Latinne
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA
| | - Christian Lange
- Labyrinth Global Health, Inc., 546 15th Ave NE, St Petersburg, FL 33704 USA
| | - Tammie O’Rourke
- Labyrinth Global Health, Inc., 546 15th Ave NE, St Petersburg, FL 33704 USA
| | - Sarah Olson
- grid.269823.40000 0001 2164 6888Wildlife Conservation Society, Health Program, Bronx, NY USA
| | - Lucy Keatts
- grid.27860.3b0000 0004 1936 9684One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
| | - A. Patricia Mendoza
- grid.269823.40000 0001 2164 6888Wildlife Conservation Society, Health Program, Bronx, NY USA ,grid.516986.5Wildlife Conservation Society (WCS), Peru Program, Lima, Peru
| | - Alberto Perez
- grid.516986.5Wildlife Conservation Society (WCS), Peru Program, Lima, Peru
| | - Cátia Dejuste de Paula
- grid.269823.40000 0001 2164 6888Wildlife Conservation Society, Health Program, Bronx, NY USA
| | - Dawn Zimmerman
- grid.467700.20000 0001 2182 2028Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC USA
| | - Marc Valitutto
- grid.467700.20000 0001 2182 2028Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC USA
| | | | | | - Ariful Islam
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA
| | - Veasna Duong
- grid.418537.c0000 0004 7535 978XInstitut Pasteur du Cambodge, 5 Monivong Blvd, PO Box 983, Phnom Penh, 12201 Cambodia
| | - Moctar Mouiche
- grid.452492.cMosaic/Global Viral Cameroon, Yaoundé, Cameroon
| | - Zhengli Shi
- grid.9227.e0000000119573309Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Prime Mulembakani
- grid.9783.50000 0000 9927 0991Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | | | - Mohamed Ali
- grid.419725.c0000 0001 2151 8157Egypt National Research Centre, 12311 Dokki, Giza Egypt
| | - Nigatu Kebede
- grid.7123.70000 0001 1250 5688Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Ubald Tamoufe
- grid.452492.cMetabiota Cameroon Ltd, Yaoundé, Centre Region Avenue Mvog-Fouda Ada, Av 1.085, Carrefour Intendance, Yaoundé, BP 15939 Cameroon
| | | | - Alpha Camara
- Centre de Recherche en Virologie (VRV) Projet Fievres Hemoraquiques en Guinée, BP 5680 Nongo/Contéya-Commune de Ratoma, Guinea
| | - Joko Pamungkas
- grid.440754.60000 0001 0698 0773Primate Research Center, Bogor Agricultural University, Bogor, 16151 Indonesia ,grid.440754.60000 0001 0698 0773Faculty of Veterinary Medicine, Bogor Agricultural University, Darmaga Campus, Bogor, 16680 Indonesia
| | - Kalpy J. Coulibaly
- grid.418523.90000 0004 0475 3667Department Environment and Health, Institut Pasteur de Côte d’Ivoire, PO BOX 490, Abidjan 01, Ivory Coast
| | - Ehab Abu-Basha
- grid.37553.370000 0001 0097 5797Department of Basic Medical Veterinary Sciences, College of Veterinary Medicine, Jordan University of Science and Technology, Ar-Ramtha, Jordan
| | - Joseph Kamau
- grid.418948.80000 0004 0566 5415Molecular Biology Laboratory, Institute of Primate Research, Nairobi, Kenya ,grid.10604.330000 0001 2019 0495Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | | | - James Desmond
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA
| | - Tom Hughes
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA ,Conservation Medicine, Sungai Buloh, Selangor Malaysia
| | | | - Ohnmar Aung
- grid.467700.20000 0001 2182 2028Global Health Program, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC USA
| | - Dibesh Karmacharya
- grid.428196.0Center for Molecular Dynamics Nepal (CMDN), Thapathali -11, Kathmandu, Nepal
| | - Julius Nziza
- Regional Headquarters, Mountain Gorilla Veterinary Project, Musanze, Rwanda
| | - Daouda Ndiaye
- grid.8191.10000 0001 2186 9619Université Cheikh Anta Diop, BP 5005 Dakar, Sénégal
| | - Aiah Gbakima
- Metabiota, Inc. Sierra Leone, Freetown, Sierra Leone
| | - Zikankuba sajali
- grid.11887.370000 0000 9428 8105Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Supaporn Wacharapluesadee
- grid.411628.80000 0000 9758 8584Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Erika Alandia Robles
- grid.516956.8Wildlife Conservation Society (WCS), Bolivia Program, La Paz, Bolivia
| | - Benard Ssebide
- Regional Headquarters, Mountain Gorilla Veterinary Project, Musanze, Rwanda
| | - Gerardo Suzán
- grid.9486.30000 0001 2159 0001Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, México City, 04510 Mexico
| | - Luis F. Aguirre
- grid.10491.3d0000 0001 2176 4059Centro de Biodiversidad y Genética, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Monica R. Solorio
- Laboratório de Epidemiologia e Geoprocessamento (EpiGeo), Instituto de Medicina Veterinária (IMV) Universidade Federal do Pará (UFPA), BR-316 Km 31, Castanhal, Pará 69746-360 Brazil
| | - Tapan N. Dhole
- grid.263138.d0000 0000 9346 7267Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh India
| | - Nguyen T. T. Nga
- Wildlife Conservation Society (WCS), Vietnam Program, Hanoi, Vietnam
| | - Peta L. Hitchens
- grid.1008.90000 0001 2179 088XMelbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Werribee, VIC 3030 Australia
| | - Damien O. Joly
- Nyati Health Consulting, 2175 Dodds Road, Nanaimo, BC V9X0A4 Canada
| | - Karen Saylors
- Labyrinth Global Health, Inc., 546 15th Ave NE, St Petersburg, FL 33704 USA
| | - Amanda Fine
- grid.269823.40000 0001 2164 6888Wildlife Conservation Society, Health Program, Bronx, NY USA
| | - Suzan Murray
- grid.452492.cMosaic/Global Viral Cameroon, Yaoundé, Cameroon
| | - William B. Karesh
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA
| | - Peter Daszak
- grid.420826.a0000 0004 0409 4702EcoHealth Alliance, 520 Eighth Avenue, New York, NY 10018 USA
| | - Jonna A. K. Mazet
- grid.27860.3b0000 0004 1936 9684One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
| | | | - Christine K. Johnson
- grid.27860.3b0000 0004 1936 9684One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 USA
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2
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Hulseberg CE, Kumar R, Di Paola N, Larson P, Nagle ER, Richardson J, Hanson J, Wauquier N, Fair JN, Makuwa M, Mulembakani P, Muyembe-Tamfum JJ, Schoepp RJ, Sanchez-Lockhart M, Palacios GF, Kuhn JH, Kugelman JR. Molecular analysis of the 2012 Bundibugyo virus disease outbreak. Cell Rep Med 2021; 2:100351. [PMID: 34467242 PMCID: PMC8385243 DOI: 10.1016/j.xcrm.2021.100351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/25/2021] [Accepted: 06/24/2021] [Indexed: 01/24/2023]
Abstract
Bundibugyo virus (BDBV) is one of four ebolaviruses known to cause disease in humans. Bundibugyo virus disease (BVD) outbreaks occurred in 2007–2008 in Bundibugyo District, Uganda, and in 2012 in Isiro, Province Orientale, Democratic Republic of the Congo. The 2012 BVD outbreak resulted in 38 laboratory-confirmed cases of human infection, 13 of whom died. However, only 4 BDBV specimens from the 2012 outbreak have been sequenced. Here, we provide BDBV sequences from seven additional patients. Analysis of the molecular epidemiology and evolutionary dynamics of the 2012 outbreak with these additional isolates challenges the current hypothesis that the outbreak was the result of a single spillover event. In addition, one patient record indicates that BDBV’s initial emergence in Isiro occurred 50 days earlier than previously accepted. Collectively, this work demonstrates how retrospective sequencing can be used to elucidate outbreak origins and provide epidemiological contexts to a medically relevant pathogen. In 2012, BDBV was circulating earlier than previously appreciated BDBV genomes from seven additional patients are sequenced Molecular analyses indicate that multiple spillover events fueled the BVD outbreak
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Affiliation(s)
- Christine E Hulseberg
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Raina Kumar
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Nicholas Di Paola
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Peter Larson
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Elyse R Nagle
- National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702, USA
| | - Joshua Richardson
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Jarod Hanson
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Nadia Wauquier
- Metabiota, Inc., Kinshasa, Democratic Republic of the Congo
| | - Joseph N Fair
- Metabiota, Inc., Kinshasa, Democratic Republic of the Congo
| | - Maria Makuwa
- Metabiota, Inc., Kinshasa, Democratic Republic of the Congo
| | | | | | - Randal J Schoepp
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Gustavo F Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Jeffrey R Kugelman
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
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3
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Kumakamba C, Niama FR, Muyembe F, Mombouli JV, Kingebeni PM, Nina RA, Lukusa IN, Bounga G, N'Kawa F, Nkoua CG, Atibu Losoma J, Mulembakani P, Makuwa M, Tamufe U, Gillis A, LeBreton M, Olson SH, Cameron K, Reed P, Ondzie A, Tremeau-Bravard A, Smith BR, Pante J, Schneider BS, McIver DJ, Ayukekbong JA, Hoff NA, Rimoin AW, Laudisoit A, Monagin C, Goldstein T, Joly DO, Saylors K, Wolfe ND, Rubin EM, Bagamboula MPassi R, Muyembe Tamfum JJ, Lange CE. Coronavirus surveillance in wildlife from two Congo basin countries detects RNA of multiple species circulating in bats and rodents. PLoS One 2021; 16:e0236971. [PMID: 34106949 PMCID: PMC8189465 DOI: 10.1371/journal.pone.0236971] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 07/18/2020] [Accepted: 05/19/2021] [Indexed: 12/21/2022] Open
Abstract
Coronaviruses play an important role as pathogens of humans and animals, and the emergence of epidemics like SARS, MERS and COVID-19 is closely linked to zoonotic transmission events primarily from wild animals. Bats have been found to be an important source of coronaviruses with some of them having the potential to infect humans, with other animals serving as intermediate or alternate hosts or reservoirs. Host diversity may be an important contributor to viral diversity and thus the potential for zoonotic events. To date, limited research has been done in Africa on this topic, in particular in the Congo Basin despite frequent contact between humans and wildlife in this region. We sampled and, using consensus coronavirus PCR-primers, tested 3,561 wild animals for coronavirus RNA. The focus was on bats (38%), rodents (38%), and primates (23%) that posed an elevated risk for contact with people, and we found coronavirus RNA in 121 animals, of which all but two were bats. Depending on the taxonomic family, bats were significantly more likely to be coronavirus RNA-positive when sampled either in the wet (Pteropodidae and Rhinolophidae) or dry season (Hipposideridae, Miniopteridae, Molossidae, and Vespertilionidae). The detected RNA sequences correspond to 15 alpha- and 6 betacoronaviruses, with some of them being very similar (>95% nucleotide identities) to known coronaviruses and others being more unique and potentially representing novel viruses. In seven of the bats, we detected RNA most closely related to sequences of the human common cold coronaviruses 229E or NL63 (>80% nucleotide identities). The findings highlight the potential for coronavirus spillover, especially in regions with a high diversity of bats and close human contact, and reinforces the need for ongoing surveillance.
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Affiliation(s)
| | - Fabien R Niama
- National Laboratory of Public Health, Brazzaville, Republic of the Congo
| | | | | | | | - Rock Aime Nina
- Ministry of Agriculture and Livestock, Brazzaville, Republic of the Congo
| | - Ipos Ngay Lukusa
- Metabiota Inc, Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Gerard Bounga
- Wildlife Conversation Society, Bronx, New York, United States of America
| | - Frida N'Kawa
- Metabiota Inc, Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Cynthia Goma Nkoua
- National Laboratory of Public Health, Brazzaville, Republic of the Congo
| | | | | | - Maria Makuwa
- Metabiota Inc, Kinshasa, Kinshasa, Democratic Republic of the Congo.,Labyringth Global Health St. Petersburg, Florida, United States of America
| | - Ubald Tamufe
- Metabiota Cameroon Ltd, Yaoundé, Centre, Cameroon
| | - Amethyst Gillis
- Metabiota Inc, San Francisco, California, United States of America
| | | | - Sarah H Olson
- Wildlife Conversation Society, Bronx, New York, United States of America
| | - Kenneth Cameron
- Wildlife Conversation Society, Bronx, New York, United States of America
| | - Patricia Reed
- Wildlife Conversation Society, Bronx, New York, United States of America
| | - Alain Ondzie
- Wildlife Conversation Society, Bronx, New York, United States of America
| | - Alex Tremeau-Bravard
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Brett R Smith
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Jasmine Pante
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | | | | | | | - Nicole A Hoff
- Fielding School of Public Health, University of California, Los Angeles, California, United States of America
| | - Anne W Rimoin
- Fielding School of Public Health, University of California, Los Angeles, California, United States of America
| | - Anne Laudisoit
- EcoHealth Alliance, New York, New York, United States of America
| | - Corina Monagin
- Metabiota Inc, San Francisco, California, United States of America.,One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Damien O Joly
- Wildlife Conversation Society, Bronx, New York, United States of America.,Metabiota Inc, Nanaimo, British Columbia, Canada
| | - Karen Saylors
- Labyringth Global Health St. Petersburg, Florida, United States of America.,Metabiota Inc, San Francisco, California, United States of America
| | - Nathan D Wolfe
- Metabiota Inc, San Francisco, California, United States of America
| | - Edward M Rubin
- Metabiota Inc, San Francisco, California, United States of America
| | | | - Jean J Muyembe Tamfum
- Institut National de Recherche Biomédicale, Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Christian E Lange
- Labyringth Global Health St. Petersburg, Florida, United States of America.,Metabiota Inc, Nanaimo, British Columbia, Canada
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4
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Doshi RH, Alfonso VH, Morier D, Hoff NA, Sinai C, Mulembakani P, Kisalu N, Cheng A, Ashbaugh H, Gadoth A, Cowell B, Okitolonda EW, Muyembe-Tamfum JJ, Rimoin AW. Monkeypox Rash Severity and Animal Exposures in the Democratic Republic of the Congo. Ecohealth 2020; 17:64-73. [PMID: 31875271 DOI: 10.1007/s10393-019-01459-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 11/07/2019] [Indexed: 05/25/2023]
Abstract
Experimental studies have suggested a larger inoculum of monkeypox virus may be associated with increased rash severity; however, little data are available on the relationship between specific animal exposures and rash severity in endemic regions. Using cross-sectional data from an active surveillance program conducted between 2005 and 2007 in the Sankuru Province of the Democratic Republic of the Congo, we explored the possible relationship between rash severity and exposures to rodents and non-human primates among confirmed MPX cases. Among the 223 PCR-confirmed MPX cases identified during active surveillance, the majority of cases (n = 149) presented with mild rash (5-100 lesions) and 33% had a more serious presentation (> 100 lesions). No association between exposure to rodents and rash severity was found in the multivariable analysis. Those that self-reported hunting NHP 3 weeks prior to onset of MPX symptoms had 2.78 times the odds of severe rash than those that did not report such exposure (95% CI: 1.18, 6.58). This study provides a preliminary step in understanding the association between animal exposure and rash severity and demonstrates correlation with exposure to NHPs and human MPX presentation. Additional research exploring the relationship between rash severity and NHPs is warranted.
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Affiliation(s)
- Reena H Doshi
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, USA
| | - Vivian H Alfonso
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, USA
| | - Douglas Morier
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, USA
| | - Nicole A Hoff
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, USA
| | - Cyrus Sinai
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, USA
| | - Prime Mulembakani
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Neville Kisalu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Alvan Cheng
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, USA
| | - Hayley Ashbaugh
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, USA
| | - Adva Gadoth
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, USA
| | - Brian Cowell
- Texas A&M School of Public Health, College Station, TX, USA
| | - Emile W Okitolonda
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | | | - Anne W Rimoin
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, USA.
- , Los Angeles, USA.
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5
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Steffen I, Lu K, Hoff NA, Mulembakani P, Okitolonda Wemakoy E, Muyembe-Tamfum JJ, Ndembi N, Brennan CA, Hackett J, Switzer WM, Saragosti S, Mbensa GO, Laperche S, Rimoin AW, Simmons G. Seroreactivity against Marburg or related filoviruses in West and Central Africa. Emerg Microbes Infect 2020; 9:124-128. [PMID: 31913767 PMCID: PMC6968259 DOI: 10.1080/22221751.2019.1709563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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] [Indexed: 12/03/2022]
Abstract
A serological survey of 2,430 archived serum samples collected between 1997 and 2012 was conducted to retrospectively determine the prevalence of Marburg virus in five African countries. Serum samples were screened for neutralizing antibodies in a pseudotype micro-neutralization assay and confirmed by enzyme-linked immunosorbent assay (ELISA). Surprisingly, a seroprevalence for Marburg virus of 7.5 and 6.3% was found in Cameroon and Ghana, respectively, suggesting the circulation of filoviruses or related viruses outside of known endemic areas that remain undetected by current surveillance efforts. However, due to the lack of validated assays and appropriate positive controls, these results must be considered preliminary.
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Affiliation(s)
- Imke Steffen
- Vitalant Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kai Lu
- Vitalant Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Nicole A Hoff
- Department of Epidemiology, School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Prime Mulembakani
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Emile Okitolonda Wemakoy
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | | | | | | | | | | | | | - Guy O Mbensa
- Centre National de Transfusion Sanguine, Kinshasa, Democratic Republic of Congo
| | - Syria Laperche
- Institut National de la Transfusion Sanguine, Paris, France
| | - Anne W Rimoin
- Department of Epidemiology, School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Graham Simmons
- Vitalant Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
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6
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Kumakamba C, N'Kawa F, Kingebeni PM, Losoma JA, Lukusa IN, Muyembe F, Mulembakani P, Makuwa M, LeBreton M, Gillis A, Rimoin AW, Hoff NA, Schneider BS, Monagin C, Joly DO, Wolfe ND, Rubin EM, Tamfum JJM, Lange CE. Analysis of adenovirus DNA detected in rodent species from the Democratic Republic of the Congo indicates potentially novel adenovirus types. New Microbes New Infect 2019; 34:100640. [PMID: 32025309 PMCID: PMC6997563 DOI: 10.1016/j.nmni.2019.100640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/16/2019] [Accepted: 12/24/2019] [Indexed: 11/25/2022] Open
Abstract
Different species of adenoviruses (AdVs) infect humans and animals and are known for their role as pathogens, especially in humans, with animals, primarily rodents, often serving as model systems. However, although we know over 100 types of human AdVs, we know comparatively little about the diversity of animal AdVs. Due to the fact that rodents are the most diverse family of mammals and a standard model system for human disease, we set out to sample African rodents native to the Democratic Republic of the Congo and test them for AdV DNA using a semi-nested consensus PCR. A total of 775 animals were tested, and viral DNA was detected in four of them. The AdV DNA found belongs to three different AdVs, all being closely related to murine adenovirus 2 (MAdV-2). Considering the genetic differences of the amplicon were 9%, 11% and 19% from MAdV-2 and at least 10% from each other, they seem to belong to up to three different novel types within the Murine mastadenovirus B species. This evidence of genetic diversity highlights the opportunities to isolate and study additional AdVs that infect rodents as models for AdV biology and pathology.
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Affiliation(s)
- C Kumakamba
- Metabiota DRC, Kinshasa, Democratic Republic of the Congo
| | - F N'Kawa
- Metabiota DRC, Kinshasa, Democratic Republic of the Congo
| | | | - J Atibu Losoma
- School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - I Ngay Lukusa
- Metabiota DRC, Kinshasa, Democratic Republic of the Congo
| | - F Muyembe
- Metabiota DRC, Kinshasa, Democratic Republic of the Congo
| | - P Mulembakani
- Metabiota DRC, Kinshasa, Democratic Republic of the Congo
| | - M Makuwa
- Metabiota DRC, Kinshasa, Democratic Republic of the Congo
| | | | - A Gillis
- Metabiota Inc., San Francisco, CA, USA
| | - A W Rimoin
- University of California, Los Angeles, CA, USA
| | | | - B S Schneider
- Metabiota Inc., San Francisco, CA, USA.,Etiologic, Oakland, CA, USA.,Pinpoint Science, San Francisco, CA, USA
| | - C Monagin
- Metabiota Inc., San Francisco, CA, USA.,One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - D O Joly
- Metabiota Inc., Nanaimo, Canada.,British Columbia Ministry of Environment and Climate Change Strategy, Victoria, Canada
| | - N D Wolfe
- Metabiota Inc., San Francisco, CA, USA
| | - E M Rubin
- Metabiota Inc., San Francisco, CA, USA
| | - J J Muyembe Tamfum
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
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7
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Steffen I, Lu K, Yamamoto LK, Hoff NA, Mulembakani P, Wemakoy EO, Muyembe-Tamfum JJ, Ndembi N, Brennan CA, Hackett J, Stramer SL, Switzer WM, Saragosti S, Mbensa GO, Laperche S, Rimoin AW, Simmons G. Serologic Prevalence of Ebola Virus in Equatorial Africa. Emerg Infect Dis 2019; 25:911-918. [PMID: 31002071 PMCID: PMC6478206 DOI: 10.3201/eid2505.180115] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 01/29/2023] Open
Abstract
We conducted a serologic survey of 2,430 serum samples collected during 1997-2012 for various studies to determine the prevalence of the hemorrhagic fever virus Ebola virus (EBOV) in equatorial Africa. We screened serum samples for neutralizing antibodies by using a pseudotype microneutralization assay and a newly developed luciferase immunoprecipitation system assay. Specimens seroreactive for EBOV were confirmed by using an ELISA. Our results suggest a serologic prevalence of 2%-3.5% in the Republic of the Congo and the Democratic Republic of the Congo, which have reported outbreaks of infection with EBOV. In addition we detected a seroprevalence of 1.3% in southern Cameroon, which indicated a low risk for exposure in this region.
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8
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Mulangu S, Alfonso VH, Hoff NA, Doshi RH, Mulembakani P, Kisalu NK, Okitolonda-Wemakoy E, Kebela BI, Marcus H, Shiloach J, Phue JN, Wright LL, Muyembe-Tamfum JJ, Sullivan NJ, Rimoin AW. Serologic Evidence of Ebolavirus Infection in a Population With No History of Outbreaks in the Democratic Republic of the Congo. J Infect Dis 2019; 217:529-537. [PMID: 29329455 DOI: 10.1093/infdis/jix619] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/29/2017] [Indexed: 11/13/2022] Open
Abstract
Background Previous studies suggest that cases of Ebola virus disease (EVD) may go unreported because they are asymptomatic or unrecognized, but evidence is limited by study designs and sample size. Methods A large population-based survey was conducted (n = 3415) to assess animal exposures and behaviors associated with Ebolavirus antibody prevalence in rural Kasai Oriental province of the Democratic Republic of Congo (DRC). Fourteen villages were randomly selected and all healthy individuals ≥1 year of age were eligible. Results Overall, 11% of subjects tested positive for Zaire Ebolavirus (EBOV) immunoglobulin G antibodies. Odds of seropositivity were higher for study participants older than 15 years of age and for males. Those residing in Kole (closer to the outbreak site) tested positive at a rate 1.6× higher than Lomela, with seropositivity peaking at a site located between Kole and Lomela. Multivariate analyses of behaviors and animal exposures showed that visits to the forest or hunting and exposure to rodents or duikers predicted a higher likelihood of EBOV seropositivity. Conclusions These results provide serologic evidence of Ebolavirus exposure in a population residing in non-EBOV outbreak locations in the DRC and define statistically significant activities and animal exposures that associate with EBOV seropositivity.
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Affiliation(s)
- Sabue Mulangu
- National Institute of Allergy and Infectious Diseases, Vaccine Research Center, Bethesda, Maryland.,Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of the Congo
| | | | - Nicole A Hoff
- UCLA Fielding School of Public Health, Los Angeles, California
| | - Reena H Doshi
- UCLA Fielding School of Public Health, Los Angeles, California
| | | | - Neville K Kisalu
- National Institute of Allergy and Infectious Diseases, Vaccine Research Center, Bethesda, Maryland
| | | | - Benoit Ilunga Kebela
- Division de la Lutte Contre les Maladies, Ministere de la Santé, Kinshasa, Democratic Republic of the Congo
| | - Hadar Marcus
- National Institute of Allergy and Infectious Diseases, Vaccine Research Center, Bethesda, Maryland
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Disease, Bethesda, Maryland
| | - Je-Nie Phue
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Disease, Bethesda, Maryland
| | - Linda L Wright
- National Institute of Child Health and Human Development, Bethesda, Maryland
| | | | - Nancy J Sullivan
- National Institute of Allergy and Infectious Diseases, Vaccine Research Center, Bethesda, Maryland
| | - Anne W Rimoin
- UCLA Fielding School of Public Health, Los Angeles, California
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9
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Ntumvi NF, Mbala Kingebeni P, Tamoufe U, Kumakamba C, Ndze V, Ngay Lukusa I, LeBreton M, Atibu Losoma J, Le Doux Diffo J, N'Kawa F, Takuo JM, Mulembakani P, Nwobegahay J, Makuwa M, Muyembe Tamfum JJ, Gillis A, Harris S, Rimoin AW, Hoff NA, Fair JM, Monagin C, Ayukekbong J, Rubin EM, Wolfe ND, Lange CE. High Herpesvirus Diversity in Wild Rodent and Shrew Species in Central Africa. Intervirology 2018; 61:155-165. [PMID: 30448834 DOI: 10.1159/000493796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/16/2018] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Herpesviruses belong to a diverse order of large DNA viruses that can cause diseases in humans and animals. With the goal of gathering information about the distribution and diversity of herpesviruses in wild rodent and shrew species in central Africa, animals in Cameroon and the Democratic Republic of the Congo were sampled and tested by PCR for the presence of herpesvirus DNA. METHODS A broad range PCRs targeting either the Polymerase or the terminase gene were used for virus detection. Amplified products from PCR were sequenced and isolates analysed for phylogenetic placement. RESULTS Overall, samples of 1,004 animals of various rodent and shrew species were tested and 24 were found to be positive for herpesvirus DNA. Six of these samples contained strains of known viruses, while the other positive samples revealed DNA sequences putatively belonging to 11 previously undescribed herpesviruses. The new isolates are beta- and gammaherpesviruses and the shrew isolates appear to form a separate cluster within the Betaherpesvirinae subfamily. CONCLUSION The diversity of viruses detected is higher than in similar studies in Europe and Asia. The high diversity of rodent and shrew species occurring in central Africa may be the reason for a higher diversity in herpesviruses in this area.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jean J Muyembe Tamfum
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | | | - Anne W Rimoin
- University of California, Los Angeles, California, USA
| | - Nicole A Hoff
- University of California, Los Angeles, California, USA
| | - Joseph M Fair
- Metabiota, San Francisco, California, USA.,VIRION, New Orleans, Louisiana, USA
| | - Corina Monagin
- Metabiota, San Francisco, California, USA.,One Health Institute, School of Veterinary Medicine, University of California, Davis, California, USA
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10
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Mbala P, Baguelin M, Ngay I, Rosello A, Mulembakani P, Demiris N, Edmunds WJ, Muyembe JJ. Evaluating the frequency of asymptomatic Ebola virus infection. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0303. [PMID: 28396474 DOI: 10.1098/rstb.2016.0303] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2016] [Indexed: 11/12/2022] Open
Abstract
The potential for asymptomatic infection from Ebola viruses has long been questioned. Knowing the proportion of infections that are asymptomatic substantially changes the predictions made by mathematical models and alters the corresponding decisions based upon these models. To assess the degree of asymptomatic infection occurring during an Ebola virus disease (EVD) outbreak, we carried out a serological survey in the Djera district of the Equateur province of the Democratic Republic of the Congo affected by an Ebola outbreak in 2014. We sampled all asymptomatic residents (n = 182) of 48 households where at least one case of EVD was detected. To control for potential background seroprevalence of Ebola antibodies in the population, we also sampled 188 individuals from 92 households in an unaffected area with a similar demographic background. We tested the sera collected for anti-Ebola IgG and IgM antibodies at four different dilutions. We then developed a mixture model to estimate the likely number of asymptomatic patients who developed IgM and IgG responses to Ebola antigens in both groups. While we detected an association between medium to high titres and age, we did not detect any evidence of increased asymptomatic infection in the individuals who resided in the same household as cases.This article is part of the themed issue 'The 2013-2016 West African Ebola epidemic: data, decision-making and disease control'.
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Affiliation(s)
- Placide Mbala
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo.,METABIOTA, Kinshasa, Democratic Republic of Congo
| | - Marc Baguelin
- Modelling and Economics Department, Public Health England, London NW9 5EQ, UK .,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Ipos Ngay
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo.,METABIOTA, Kinshasa, Democratic Republic of Congo
| | - Alicia Rosello
- Modelling and Economics Department, Public Health England, London NW9 5EQ, UK.,Institute of Health Informatics, University College London, London WC1E 6BT, UK
| | | | - Nikolaos Demiris
- Department of Statistics, Athens University of Economics and Business, Athens 10434, Greece
| | - W John Edmunds
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Jean-Jacques Muyembe
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
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11
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Mbala PK, Huggins JW, Riu-Rovira T, Ahuka SM, Mulembakani P, Rimoin AW, Martin JW, Muyembe JJT. Maternal and Fetal Outcomes Among Pregnant Women With Human Monkeypox Infection in the Democratic Republic of Congo. J Infect Dis 2017; 216:824-828. [PMID: 29029147 DOI: 10.1093/infdis/jix260] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/25/2017] [Indexed: 11/13/2022] Open
Abstract
Human monkeypox is an endemic disease in rain-forested regions of central Democratic Republic of Congo. We report fetal outcomes for 1 of 4 pregnant women who participated in an observational study at the General Hospital of Kole (Sankuru Province), where 222 symptomatic subjects were followed between 2007 and 2011. Of the 4 pregnant women, 1 gave birth to a healthy infant, 2 had miscarriages in the first trimester, and 1 had fetal death, with the macerated stillborn showing diffuse cutaneous maculopapillary skin lesions involving the head, trunk and extremities, including palms of hands and soles of feet.
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Affiliation(s)
- Placide K Mbala
- L'Institut National de Recherche Biomédicale
- Metabiota, Kinshasa
| | - John W Huggins
- Divisions of Medicine, US Army Medical Institute of Infectious Diseases, Fort Detrick, Maryland
| | - Therese Riu-Rovira
- L'Hôpital Général de Référence de Kole, Kole-sur-Lukenie, Democratic Republic of Congo
| | | | | | - Anne W Rimoin
- Department of Epidemiology, Jonathan and Karin Fielding School of Public Health, University of California-Los Angeles
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12
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Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe JJ, Sittler T, Veeraraghavan N, Ruby JG, Wang C, Makuwa M, Mulembakani P, Tesh RB, Mazet J, Rimoin AW, Taylor T, Schneider BS, Simmons G, Delwart E, Wolfe ND, Chiu CY, Leroy EM. Correction: Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa. PLoS Pathog 2017; 13:e1006583. [PMID: 28880960 PMCID: PMC5589260 DOI: 10.1371/journal.ppat.1006583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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13
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Rimoin AW, Alfonso VH, Hoff NA, Doshi RH, Mulembakani P, Kisalu NK, Muyembe JJ, Okitolonda EW, Wright LL. Human Exposure to Wild Animals in the Sankuru Province of the Democratic Republic of the Congo. Ecohealth 2017; 14:552-563. [PMID: 28831639 DOI: 10.1007/s10393-017-1262-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 05/11/2017] [Accepted: 06/15/2017] [Indexed: 05/25/2023]
Abstract
Due to the high level of biological diversity in the Congo Basin and human population dependence on bushmeat, the DRC represents an ideal location for expanding knowledge on wild animal exposures and thus the potential for transmission of zoonotic pathogens. However, limited information exists on patterns and extent of contact with wildlife in such communities. Using a cross-sectional study, 14 villages in the Sankuru Province of the DRC were surveyed between August and September 2007. Villagers ≥ 1 year of age and at home of the time of the survey were eligible and enrolled to describe and assess factors associated with animal exposures (both activity and type of animal). Among respondents, 91% reported exposure to rodents, 89% to duikers, 78% to non-human primates (NHPs), and 32% reported contact with bats in the month prior to the survey. The most frequently reported activities included eating (95%), cooking (70%), and butchering or skinning of animals (55%). The activities and animals to which subjects had contact varied by sex and age. Moreover, we observed a high correlation of the same activities across animal types. In this and other populations that rely on bushmeat, there is a high frequency of exposure to multiple animal species through various modalities. In the event of future zoonotic disease outbreaks, effective public health interventions and campaigns that mitigate the risk of animal contact during outbreaks need to be broad to include various modes of contact and should be directed to both men and women across all age groups. As available information is limited, further studies are necessary to better understand the complex relationships and exposures individuals have with animals.
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Affiliation(s)
- Anne W Rimoin
- Department of Epidemiology, UCLA Fielding School of Public Health, 650 S Charles E Young Drive, Los Angeles, CA, USA.
| | - Vivian Helena Alfonso
- Department of Epidemiology, UCLA Fielding School of Public Health, 650 S Charles E Young Drive, Los Angeles, CA, USA
| | - Nicole A Hoff
- Department of Epidemiology, UCLA Fielding School of Public Health, 650 S Charles E Young Drive, Los Angeles, CA, USA
| | - Reena H Doshi
- Department of Epidemiology, UCLA Fielding School of Public Health, 650 S Charles E Young Drive, Los Angeles, CA, USA
| | - Prime Mulembakani
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Nevile K Kisalu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jean-Jacques Muyembe
- Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of the Congo
| | - Emile W Okitolonda
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Linda L Wright
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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14
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Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe JJ, Sittler T, Veeraraghavan N, Ruby JG, Wang C, Makuwa M, Mulembakani P, Tesh RB, Mazet J, Rimoin AW, Taylor T, Schneider BS, Simmons G, Delwart E, Wolfe ND, Chiu CY, Leroy EM. Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa. PLoS Pathog 2016; 12:e1005503. [PMID: 26991269 PMCID: PMC4798281 DOI: 10.1371/journal.ppat.1005503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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15
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Greninger AL, Naccache SN, Federman S, Yu G, Mbala P, Bres V, Stryke D, Bouquet J, Somasekar S, Linnen JM, Dodd R, Mulembakani P, Schneider BS, Muyembe-Tamfum JJ, Stramer SL, Chiu CY. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med 2015; 7:99. [PMID: 26416663 PMCID: PMC4587849 DOI: 10.1186/s13073-015-0220-9] [Citation(s) in RCA: 325] [Impact Index Per Article: 36.1] [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: 06/12/2015] [Accepted: 09/03/2015] [Indexed: 12/16/2022] Open
Abstract
We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), and hepatitis C virus (HCV) from four human blood samples by MinION nanopore sequencing coupled to a newly developed, web-based pipeline for real-time bioinformatics analysis on a computational server or laptop (MetaPORE). At titers ranging from 107–108 copies per milliliter, reads to EBOV from two patients with acute hemorrhagic fever and CHIKV from an asymptomatic blood donor were detected within 4 to 10 min of data acquisition, while lower titer HCV virus (1 × 105 copies per milliliter) was detected within 40 min. Analysis of mapped nanopore reads alone, despite an average individual error rate of 24 % (range 8–49 %), permitted identification of the correct viral strain in all four isolates, and 90 % of the genome of CHIKV was recovered with 97–99 % accuracy. Using nanopore sequencing, metagenomic detection of viral pathogens directly from clinical samples was performed within an unprecedented <6 hr sample-to-answer turnaround time, and in a timeframe amenable to actionable clinical and public health diagnostics.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | - Samia N Naccache
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | - Placide Mbala
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo, Africa.,Metabiota, Inc, San Francisco, CA, 94104, USA
| | | | - Doug Stryke
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | - Jerome Bouquet
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | - Sneha Somasekar
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | | | - Roger Dodd
- American Red Cross, Gaithersburg, MD, 2087, USA
| | | | | | | | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA. .,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA. .,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA.
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16
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Switzer WM, Tang S, Ahuka-Mundeke S, Shankar A, Hanson DL, Zheng H, Ayouba A, Wolfe ND, LeBreton M, Djoko CF, Tamoufe U, Esteban A, Heneine W, Peeters M, Wright LL, Muyembe-Tamfum JJ, Wemakoy EO, Mulembakani P, Hoff NA, Rimoin AW. Novel simian foamy virus infections from multiple monkey species in women from the Democratic Republic of Congo. Retrovirology 2012; 9:100. [PMID: 23217108 PMCID: PMC3524035 DOI: 10.1186/1742-4690-9-100] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [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: 08/10/2012] [Accepted: 11/11/2012] [Indexed: 12/02/2022] Open
Abstract
Background Zoonotic transmission of simian retroviruses in Central Africa is ongoing and can result in pandemic human infection. While simian foamy virus (SFV) infection was reported in primate hunters in Cameroon and Gabon, little is known about the distribution of SFV in Africa and whether human-to-human transmission and disease occur. We screened 3,334 plasmas from persons living in rural villages in central Democratic Republic of Congo (DRC) using SFV-specific EIA and Western blot (WB) tests. PCR amplification of SFV polymerase sequences from DNA extracted from buffy coats was used to measure proviral loads. Phylogenetic analysis was used to define the NHP species origin of SFV. Participants completed questionnaires to capture NHP exposure information. Results Sixteen (0.5%) samples were WB-positive; 12 of 16 were from women (75%, 95% confidence limits 47.6%, 92.7%). Sequence analysis detected SFV in three women originating from Angolan colobus or red-tailed monkeys; both monkeys are hunted frequently in DRC. NHP exposure varied and infected women lived in distant villages suggesting a wide and potentially diverse distribution of SFV infections across DRC. Plasmas from 22 contacts of 8 WB-positive participants were all WB negative suggesting no secondary viral transmission. Proviral loads in the three women ranged from 14 – 1,755 copies/105 cells. Conclusions Our study documents SFV infection in rural DRC for the first time and identifies infections with novel SFV variants from Colobus and red-tailed monkeys. Unlike previous studies, women were not at lower risk for SFV infection in our population, providing opportunities for spread of SFV both horizontally and vertically. However, limited testing of close contacts of WB-positive persons did not identify human-to-human transmission. Combined with the broad behavioral risk and distribution of NHPs across DRC, our results suggest that SFV infection may have a wider geographic distribution within DRC. These results also reinforce the potential for an increased SFV prevalence throughout the forested regions of Africa where humans and simians co-exist. Our finding of endemic foci of SFV infection in DRC will facilitate longitudinal studies to determine the potential for person-to-person transmissibility and pathogenicity of these zoonotic retroviral infections.
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Affiliation(s)
- William M Switzer
- Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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17
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Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe JJ, Sittler T, Veeraraghavan N, Ruby JG, Wang C, Makuwa M, Mulembakani P, Tesh RB, Mazet J, Rimoin AW, Taylor T, Schneider BS, Simmons G, Delwart E, Wolfe ND, Chiu CY, Leroy EM. A novel rhabdovirus associated with acute hemorrhagic fever in central Africa. PLoS Pathog 2012; 8:e1002924. [PMID: 23028323 PMCID: PMC3460624 DOI: 10.1371/journal.ppat.1002924] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 08/08/2012] [Indexed: 12/01/2022] Open
Abstract
Deep sequencing was used to discover a novel rhabdovirus (Bas-Congo virus, or BASV) associated with a 2009 outbreak of 3 human cases of acute hemorrhagic fever in Mangala village, Democratic Republic of Congo (DRC), Africa. The cases, presenting over a 3-week period, were characterized by abrupt disease onset, high fever, mucosal hemorrhage, and, in two patients, death within 3 days. BASV was detected in an acute serum sample from the lone survivor at a concentration of 1.09×106 RNA copies/mL, and 98.2% of the genome was subsequently de novo assembled from ∼140 million sequence reads. Phylogenetic analysis revealed that BASV is highly divergent and shares less than 34% amino acid identity with any other rhabdovirus. High convalescent neutralizing antibody titers of >1∶1000 were detected in the survivor and an asymptomatic nurse directly caring for him, both of whom were health care workers, suggesting the potential for human-to-human transmission of BASV. The natural animal reservoir host or arthropod vector and precise mode of transmission for the virus remain unclear. BASV is an emerging human pathogen associated with acute hemorrhagic fever in Africa. We used deep sequencing, a method for generating millions of DNA sequence reads from clinical samples, to discover a novel rhabdovirus (Bas-Congo virus, or BASV) associated with a 2009 outbreak of 3 human cases of acute hemorrhagic fever in Mangala village, Democratic Republic of Congo (DRC), Africa. The cases, presenting over a 3-week period, were characterized by abrupt disease onset, high fever, bloody vomiting and diarrhea, and, in two patients, death within 3 days. BASV was present in the blood of the lone survivor at a concentration of over a million copies per milliliter. The genome of BASV, assembled from over 140 million sequence reads, reveals that it is very different from any other rhabdovirus. The lone survivor and a nurse caring for him (with no symptoms), both health care workers, were found to have high levels of antibodies to BASV, indicating that they both had been infected by the virus. Although the source of the virus remains unclear, our study findings suggest that BASV may be spread by human-to-human contact and is an emerging pathogen associated with acute hemorrhagic fever in Africa.
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Affiliation(s)
- Gilda Grard
- Viral Emergent Diseases unit, Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- MIVEGEC, UMR (IRD 224 - CNRS 5290 - UM1 - UM2), Institut de Recherche pour le Développement, Montpellier, France
| | - Joseph N. Fair
- Global Viral Forecasting, Incorporated, San Francisco, California, United States of America
| | - Deanna Lee
- Department of Laboratory Medicine, University of California, San Francisco, California, United States of America
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Elizabeth Slikas
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Imke Steffen
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Jean-Jacques Muyembe
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Taylor Sittler
- Department of Laboratory Medicine, University of California, San Francisco, California, United States of America
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Narayanan Veeraraghavan
- Department of Laboratory Medicine, University of California, San Francisco, California, United States of America
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - J. Graham Ruby
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Department of Biochemistry, University of California, San Francisco, California, United States of America
| | - Chunlin Wang
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Maria Makuwa
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Prime Mulembakani
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Robert B. Tesh
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jonna Mazet
- Department of Epidemiology, University of California at Davis, Davis, California, United States of America
| | - Anne W. Rimoin
- Department of Epidemiology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Travis Taylor
- Global Viral Forecasting, Incorporated, San Francisco, California, United States of America
| | - Bradley S. Schneider
- Global Viral Forecasting, Incorporated, San Francisco, California, United States of America
| | - Graham Simmons
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Nathan D. Wolfe
- Global Viral Forecasting, Incorporated, San Francisco, California, United States of America
| | - Charles Y. Chiu
- Department of Laboratory Medicine, University of California, San Francisco, California, United States of America
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (CYC); (EML)
| | - Eric M. Leroy
- Viral Emergent Diseases unit, Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- MIVEGEC, UMR (IRD 224 - CNRS 5290 - UM1 - UM2), Institut de Recherche pour le Développement, Montpellier, France
- * E-mail: (CYC); (EML)
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Muyembe-Tamfum JJ, Mulembakani P, Lekie RB, Szczeniowski M, Ježek Z, Doshi R, Hoff N, Rimoin AW. Smallpox and its eradication in the Democratic Republic of Congo: Lessons learned. Vaccine 2011; 29 Suppl 4:D13-8. [PMID: 22188930 PMCID: PMC9628709 DOI: 10.1016/j.vaccine.2011.10.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 10/04/2011] [Accepted: 10/20/2011] [Indexed: 11/20/2022]
Abstract
Smallpox eradication is considered to be one of the most remarkable accomplishments of the 20th century. Lessons learned from the campaign during the 1960s and 1970s in the Democratic Republic of Congo (DRC) can provide important information for the development of other eradication programs including polio. The DRC is the third largest country in Africa; the population suffers from extreme poverty, deteriorating infrastructure and health systems, and long periods of civil strife. Despite these challenges, DRC's smallpox eradication campaign was successful, eradicating smallpox only 41 months after initiation. DRC had been polio free since 2001; however, in 2006, imported cases were identified in the country. Polio transmission has since been re-established and DRC now has the second greatest number of reported polio cases in the world. Challenges which existed during the smallpox campaign in DRC are still present today; additionally, the polio vaccine itself poses unique challenges which include requiring multiple doses to confer immunity. In the fight against polio in DRC, it will be important to draw from the smallpox eradication experience. A number of important themes emerged during the campaign that could be beneficial to eradicating polio and future eradication programs that may follow. During the smallpox campaign, a standard vaccination program was implemented, surveillance was intensified, and there were strong collaborative programs with community involvement. These successful elements of the smallpox campaign should be adapted and applied in DRC in polio eradication programs.
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Switzer WM, Ahuka-Mundeke S, Tang S, Shankar A, Wolfe ND, Heneine W, Peeters M, Ayouba A, Mulembakani P, Rimoin AW. Simian Foamy Virus (SFV) infection from multiple monkey species in women from the Democratic Republic of Congo. Retrovirology 2011. [PMCID: PMC3112713 DOI: 10.1186/1742-4690-8-s1-a233] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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