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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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [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.
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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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2
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Kumakamba C, Ngay Lukusa I, Mbala Kingebeni P, N'Kawa F, Atibu Losoma J, Mulembakani PM, Makuwa M, Muyembe Tamfum JJ, Belais R, Gillis A, Harris S, Rimoin AW, Hoff NA, Fair JN, Monagin C, Ayukekbong J, Rubin EM, Wolfe ND, Lange CE. DNA indicative of human bocaviruses detected in non-human primates in the Democratic Republic of the Congo. J Gen Virol 2018; 99:676-681. [PMID: 29583115 DOI: 10.1099/jgv.0.001048] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bocaparvoviruses are members of the family Parvovirinae and human bocaviruses have been found to be associated with respiratory and gastrointestinal disease. There are four known human bocaviruses, as well as several distinct ones in great apes. The goal of the presented study was to detect other non-human primate (NHP) bocaviruses in NHP species in the Democratic Republic of the Congo using conventional broad-range PCR. We found bocavirus DNA in blood and tissues samples in 6 out of 620 NHPs, and all isolates showed very high identity (>97 %) with human bocaviruses 2 or 3. These findings suggest cross-species transmission of bocaviruses between humans and NHPs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Joseph N Fair
- Metabiota USA, San Francisco, CA, USA.,VIRION, New Orleans, LA, USA
| | - Corina Monagin
- Metabiota USA, San Francisco, CA, USA.,One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA
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3
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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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4
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O'Hearn AE, Voorhees MA, Fetterer DP, Wauquier N, Coomber MR, Bangura J, Fair JN, Gonzalez JP, Schoepp RJ. Serosurveillance of viral pathogens circulating in West Africa. Virol J 2016; 13:163. [PMID: 27716429 PMCID: PMC5048616 DOI: 10.1186/s12985-016-0621-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 09/22/2016] [Indexed: 01/02/2023] Open
Abstract
Background Sub-Saharan Africa is home to a variety of pathogens, but disease surveillance and the healthcare infrastructure necessary for proper management and control are severely limited. Lassa virus, the cause of Lassa fever, a severe hemorrhagic fever in humans is endemic in West Africa. In Sierra Leone at the Kenema Government Hospital Lassa Diagnostic Laboratory, up to 70 % of acute patient samples suspected of Lassa fever test negative for Lassa virus infection. This large amount of acute undiagnosed febrile illness can be attributed in part to an array of hemorrhagic fever and arthropod-borne viruses causing disease that goes undetected and untreated. Methods To better define the nature and extent of viral pathogens infecting the Sierra Leonean population, we developed a multiplexed MAGPIX® assay to detect IgG antibodies against Lassa, Ebola, Marburg, Rift Valley fever, and Crimean-Congo hemorrhagic fever viruses as well as pan-assays for flaviviruses and alphaviruses. This assay was used to survey 675 human serum samples submitted to the Lassa Diagnostic Laboratory between 2007 and 2014. Results In the study population, 50.2 % were positive for Lassa virus, 5.2 % for Ebola virus, 10.7 % for Marburg virus, 1.8 % for Rift Valley fever virus, 2.0 % for Crimean-Congo hemorrhagic fever virus, 52.9 % for flaviviruses and 55.8 % for alphaviruses. Conclusions These data exemplify the importance of disease surveillance and differential diagnosis for viral diseases in Sierra Leone. We demonstrate the endemic nature of some of these viral pathogens in the region and suggest that unrecognized outbreaks of viral infection have occurred.
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Affiliation(s)
- Aileen E O'Hearn
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD, 21702-5011, USA
| | - Matthew A Voorhees
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD, 21702-5011, USA
| | - David P Fetterer
- Statistics Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | | | - Moinya R Coomber
- Kenema Government Hospital, Lassa Diagnostic Laboratory, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | | | | | | | - Randal J Schoepp
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD, 21702-5011, USA.
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5
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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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6
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Abstract
Sierra Leone in West Africa is in a Lassa fever-hyperendemic region that also includes Guinea and Liberia. Each year, suspected Lassa fever cases result in submission of ≈500-700 samples to the Kenema Government Hospital Lassa Diagnostic Laboratory in eastern Sierra Leone. Generally only 30%-40% of samples tested are positive for Lassa virus (LASV) antigen and/or LASV-specific IgM; thus, 60%-70% of these patients have acute diseases of unknown origin. To investigate what other arthropod-borne and hemorrhagic fever viral diseases might cause serious illness in this region and mimic Lassa fever, we tested patient serum samples that were negative for malaria parasites and LASV. Using IgM-capture ELISAs, we evaluated samples for antibodies to arthropod-borne and other hemorrhagic fever viruses. Approximately 25% of LASV-negative patients had IgM to dengue, West Nile, yellow fever, Rift Valley fever, chikungunya, Ebola, and Marburg viruses but not to Crimean-Congo hemorrhagic fever virus.
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7
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Koehler JW, Hall AT, Rolfe PA, Honko AN, Palacios GF, Fair JN, Muyembe JJ, Mulembekani P, Schoepp RJ, Adesokan A, Minogue TD. Development and evaluation of a panel of filovirus sequence capture probes for pathogen detection by next-generation sequencing. PLoS One 2014; 9:e107007. [PMID: 25207553 PMCID: PMC4160210 DOI: 10.1371/journal.pone.0107007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/05/2014] [Indexed: 01/07/2023] Open
Abstract
A detailed understanding of the circulating pathogens in a particular geographic location aids in effectively utilizing targeted, rapid diagnostic assays, thus allowing for appropriate therapeutic and containment procedures. This is especially important in regions prevalent for highly pathogenic viruses co-circulating with other endemic pathogens such as the malaria parasite. The importance of biosurveillance is highlighted by the ongoing Ebola virus disease outbreak in West Africa. For example, a more comprehensive assessment of the regional pathogens could have identified the risk of a filovirus disease outbreak earlier and led to an improved diagnostic and response capacity in the region. In this context, being able to rapidly screen a single sample for multiple pathogens in a single tube reaction could improve both diagnostics as well as pathogen surveillance. Here, probes were designed to capture identifying filovirus sequence for the ebolaviruses Sudan, Ebola, Reston, Taï Forest, and Bundibugyo and the Marburg virus variants Musoke, Ci67, and Angola. These probes were combined into a single probe panel, and the captured filovirus sequence was successfully identified using the MiSeq next-generation sequencing platform. This panel was then used to identify the specific filovirus from nonhuman primates experimentally infected with Ebola virus as well as Bundibugyo virus in human sera samples from the Democratic Republic of the Congo, thus demonstrating the utility for pathogen detection using clinical samples. While not as sensitive and rapid as real-time PCR, this panel, along with incorporating additional sequence capture probe panels, could be used for broad pathogen screening and biosurveillance.
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Affiliation(s)
- Jeffrey W Koehler
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America
| | - Adrienne T Hall
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America
| | | | - Anna N Honko
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America
| | - Gustavo F Palacios
- Center for Genomic Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America
| | - Joseph N Fair
- Metabiota, San Francisco, California, United States of America
| | - Jean-Jacques Muyembe
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Prime Mulembekani
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Randal J Schoepp
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America
| | - Adeyemi Adesokan
- Pathogenica, Inc., Boston, Massachusetts, United States of America
| | - Timothy D Minogue
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America
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8
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Iles JC, Raghwani J, Harrison GLA, Pepin J, Djoko CF, Tamoufe U, LeBreton M, Schneider BS, Fair JN, Tshala FM, Kayembe PK, Muyembe JJ, Edidi-Basepeo S, Wolfe ND, Simmonds P, Klenerman P, Pybus OG. Phylogeography and epidemic history of hepatitis C virus genotype 4 in Africa. Virology 2014; 464-465:233-243. [PMID: 25105489 PMCID: PMC4162651 DOI: 10.1016/j.virol.2014.07.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/04/2014] [Accepted: 07/05/2014] [Indexed: 12/18/2022]
Abstract
HCV genotype 4 is prevalent in many African countries, yet little is known about the genotype׳s epidemic history on the continent. We present a comprehensive study of the molecular epidemiology of genotype 4. To address the deficit of data from the Democratic Republic of the Congo (DRC) we PCR amplified 60 new HCV isolates from the DRC, resulting in 33 core- and 48 NS5B-region sequences. Our data, together with genotype 4 database sequences, were analysed using Bayesian phylogenetic approaches. We find three well-supported intra-genotypic lineages and estimate that the genotype 4 common ancestor existed around 1733 (1650-1805). We show that genotype 4 originated in central Africa and that multiple lineages have been exported to north Africa since ~1850, including subtype 4a which dominates the epidemic in Egypt. We speculate on the causes of the historical intra-continental spread of genotype 4, including population movements during World War 2.
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Affiliation(s)
- James C Iles
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Jayna Raghwani
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - G L Abby Harrison
- Department of Infection & Immunity, Walter & Eliza Hall Institute, Victoria 3052, Australia
| | - Jacques Pepin
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Canada
| | | | | | | | | | | | - Felix M Tshala
- Department of Military Health, Ministry of Defense, Kinshasa, Democratic Republic of the Congo
| | - Patrick K Kayembe
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Jean Jacques Muyembe
- National Institute of Biomedical Research, Kinshasa, Democratic Republic of the Congo
| | - Samuel Edidi-Basepeo
- National AIDS Control Program, Reference Laboratory, Kinshasa, Democratic Republic of the Congo
| | - Nathan D Wolfe
- Metabiota, San Francisco, USA; Stanford University Program in Human Biology, Stanford, USA
| | - Peter Simmonds
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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9
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Naccache SN, Federman S, Veeraraghavan N, Zaharia M, Lee D, Samayoa E, Bouquet J, Greninger AL, Luk KC, Enge B, Wadford DA, Messenger SL, Genrich GL, Pellegrino K, Grard G, Leroy E, Schneider BS, Fair JN, Martínez MA, Isa P, Crump JA, DeRisi JL, Sittler T, Hackett J, Miller S, Chiu CY. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res 2014; 24:1180-92. [PMID: 24899342 PMCID: PMC4079973 DOI: 10.1101/gr.171934.113] [Citation(s) in RCA: 311] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI (“sequence-based ultrarapid pathogen identification”), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. Deployable on both cloud-based and standalone servers, SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7–500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h. SURPI has also directly contributed to real-time microbial diagnosis in acutely ill patients, underscoring its potential key role in the development of unbiased NGS-based clinical assays in infectious diseases that demand rapid turnaround times.
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Affiliation(s)
- Samia N Naccache
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Scot Federman
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Narayanan Veeraraghavan
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Matei Zaharia
- Department of Computer Science, University of California, Berkeley, California 94720, USA
| | - Deanna Lee
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Erik Samayoa
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Jerome Bouquet
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | | | - Ka-Cheung Luk
- Abbott Diagnostics, Abbott Park, Illinois 60064, USA
| | - Barryett Enge
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California 94804, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California 94804, USA
| | - Sharon L Messenger
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California 94804, USA
| | - Gillian L Genrich
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA
| | - Kristen Pellegrino
- Department of Family and Community Medicine, UCSF, San Francisco, California 94143, USA
| | - Gilda Grard
- Viral Emergent Diseases Unit, Centre International de Recherches Médicales de Franceville, Franceville, BP 769, Gabon
| | - Eric Leroy
- Viral Emergent Diseases Unit, Centre International de Recherches Médicales de Franceville, Franceville, BP 769, Gabon
| | | | - Joseph N Fair
- Metabiota, Inc., San Francisco, California 94104, USA
| | - Miguel A Martínez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62260, Mexico
| | - Pavel Isa
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62260, Mexico
| | - John A Crump
- Division of Infectious Diseases and International Health and the Duke Global Health Institute, Duke University Medical Center, Durham, North Carolina 27708, USA; Kilimanjaro Christian Medical Centre, Moshi, Kilimanjaro, 7393, Tanzania; Centre for International Health, University of Otago, Dunedin, 9054, New Zealand
| | - Joseph L DeRisi
- Department of Biochemistry, UCSF, San Francisco, California 94107, USA
| | - Taylor Sittler
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA
| | - John Hackett
- Abbott Diagnostics, Abbott Park, Illinois 60064, USA
| | - Steve Miller
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA; Department of Medicine, Division of Infectious Diseases, UCSF, San Francisco, California 94143, USA
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10
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Kugelman JR, Johnston SC, Mulembakani PM, Kisalu N, Lee MS, Koroleva G, McCarthy SE, Gestole MC, Wolfe ND, Fair JN, Schneider BS, Wright LL, Huggins J, Whitehouse CA, Wemakoy EO, Muyembe-Tamfum JJ, Hensley LE, Palacios GF, Rimoin AW. Genomic variability of monkeypox virus among humans, Democratic Republic of the Congo. Emerg Infect Dis 2014; 20:232-9. [PMID: 24457084 PMCID: PMC3901482 DOI: 10.3201/eid2002.130118] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Monkeypox virus is a zoonotic virus endemic to Central Africa. Although active disease surveillance has assessed monkeypox disease prevalence and geographic range, information about virus diversity is lacking. We therefore assessed genome diversity of viruses in 60 samples obtained from humans with primary and secondary cases of infection from 2005 through 2007. We detected 4 distinct lineages and a deletion that resulted in gene loss in 10 (16.7%) samples and that seemed to correlate with human-to-human transmission (p = 0.0544). The data suggest a high frequency of spillover events from the pool of viruses in nonhuman animals, active selection through genomic destabilization and gene loss, and increased disease transmissibility and severity. The potential for accelerated adaptation to humans should be monitored through improved surveillance.
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Affiliation(s)
| | | | - Prime M. Mulembakani
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Neville Kisalu
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Michael S. Lee
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Galina Koroleva
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Sarah E. McCarthy
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Marie C. Gestole
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Nathan D. Wolfe
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Joseph N. Fair
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Bradley S. Schneider
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Linda L. Wright
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - John Huggins
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Chris A. Whitehouse
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Emile Okitolonda Wemakoy
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Jean Jacques Muyembe-Tamfum
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
| | - Lisa E. Hensley
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA (J.R. Kugelman, S.C. Johnston, M.S. Lee, G. Koroleva, S.E. McCarthy, M.C. Gestole, J. Huggins, C.A. Whitehouse, G.F. Palacios)
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo (P.M. Mulembakani, E.O. Wemakoy)
- University of California, Los Angeles, California, USA (N. Kisalu, A.W. Rimoin)
- Global Viral Forecasting (now known as Metabiota), San Francisco, California, USA (N.D. Wolfe, J.N, Fair, B.S. Schneider)
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA (L.L. Wright)
- National Institute of Biomedical Research, Kinshasa (J.J. Muyembe-Tamfum)
- US Food and Drug Administration, Silver Spring, Maryland, USA (L.E. Hensley)
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11
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Iles JC, Abby Harrison G, Lyons S, Djoko CF, Tamoufe U, Lebreton M, Schneider BS, Fair JN, Tshala FM, Kayembe PK, Muyembe JJ, Edidi-Basepeo S, Wolfe ND, Klenerman P, Simmonds P, Pybus OG. Hepatitis C virus infections in the Democratic Republic of Congo exhibit a cohort effect. Infection, Genetics and Evolution 2013; 19:386-94. [DOI: 10.1016/j.meegid.2013.01.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/24/2013] [Accepted: 01/25/2013] [Indexed: 12/26/2022]
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12
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Thomassen HA, Fuller T, Asefi-Najafabady S, Shiplacoff JAG, Mulembakani PM, Blumberg S, Johnston SC, Kisalu NK, Kinkela TL, Fair JN, Wolfe ND, Shongo RL, LeBreton M, Meyer H, Wright LL, Muyembe JJ, Buermann W, Okitolonda E, Hensley LE, Lloyd-Smith JO, Smith TB, Rimoin AW. Pathogen-host associations and predicted range shifts of human monkeypox in response to climate change in central Africa. PLoS One 2013; 8:e66071. [PMID: 23935820 PMCID: PMC3729955 DOI: 10.1371/journal.pone.0066071] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 05/05/2013] [Indexed: 11/18/2022] Open
Abstract
Climate change is predicted to result in changes in the geographic ranges and local prevalence of infectious diseases, either through direct effects on the pathogen, or indirectly through range shifts in vector and reservoir species. To better understand the occurrence of monkeypox virus (MPXV), an emerging Orthopoxvirus in humans, under contemporary and future climate conditions, we used ecological niche modeling techniques in conjunction with climate and remote-sensing variables. We first created spatially explicit probability distributions of its candidate reservoir species in Africa's Congo Basin. Reservoir species distributions were subsequently used to model current and projected future distributions of human monkeypox (MPX). Results indicate that forest clearing and climate are significant driving factors of the transmission of MPX from wildlife to humans under current climate conditions. Models under contemporary climate conditions performed well, as indicated by high values for the area under the receiver operator curve (AUC), and tests on spatially randomly and non-randomly omitted test data. Future projections were made on IPCC 4(th) Assessment climate change scenarios for 2050 and 2080, ranging from more conservative to more aggressive, and representing the potential variation within which range shifts can be expected to occur. Future projections showed range shifts into regions where MPX has not been recorded previously. Increased suitability for MPX was predicted in eastern Democratic Republic of Congo. Models developed here are useful for identifying areas where environmental conditions may become more suitable for human MPX; targeting candidate reservoir species for future screening efforts; and prioritizing regions for future MPX surveillance efforts.
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Affiliation(s)
- Henri A. Thomassen
- Center for Tropical Research, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Comparative Zoology, University of Tübingen, Tübingen, Germany
| | - Trevon Fuller
- Center for Tropical Research, University of California Los Angeles, Los Angeles, California, United States of America
| | - Salvi Asefi-Najafabady
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, California, United States of America
| | - Julia A. G. Shiplacoff
- Center for Tropical Research, University of California Los Angeles, Los Angeles, California, United States of America
| | | | - Seth Blumberg
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Sara C. Johnston
- United States Army Medical Research Institute of Infectious Diseases, Fredrick, Maryland, United States of America
| | - Neville K. Kisalu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | | | - Joseph N. Fair
- Global Viral Forecasting, San Francisco, California, United States of America
| | - Nathan D. Wolfe
- Global Viral Forecasting, San Francisco, California, United States of America
- Stanford University, Program in Human Biology, Stanford, California, United States of America
| | | | - Matthew LeBreton
- Global Viral Forecasting, San Francisco, California, United States of America
| | - Hermann Meyer
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Linda L. Wright
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, United States of America
| | - Jean-Jacques Muyembe
- National Institute of Biomedical Research, Kinshasa, Democratic Republic of Congo
| | - Wolfgang Buermann
- Center for Tropical Research, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Atmospheric and Oceanic Sciences, University of California Los Angeles, Los Angeles, California, United States of America
| | - Emile Okitolonda
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | - Lisa E. Hensley
- Medical Countermeasures Initiative, Silver Spring, Maryland, United States of America
| | - James O. Lloyd-Smith
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Thomas B. Smith
- Center for Tropical Research, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Anne W. Rimoin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Epidemiology, School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
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13
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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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14
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Harvala H, McIntyre CL, Imai N, Clasper L, Djoko CF, LeBreton M, Vermeulen M, Saville A, Mutapi F, Tamoufé U, Kiyang J, Biblia TG, Midzi N, Mduluza T, Pépin J, Njouom R, Njoum R, Smura T, Fair JN, Wolfe ND, Roivainen M, Simmonds P. High seroprevalence of enterovirus infections in apes and old world monkeys. Emerg Infect Dis 2012; 18:283-6. [PMID: 22305156 PMCID: PMC3310466 DOI: 10.3201/eid1802.111363] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [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] [Indexed: 12/02/2022] Open
Abstract
To estimate population exposure of apes and Old World monkeys in Africa to enteroviruses (EVs), we conducted a seroepidemiologic study of serotype-specific neutralizing antibodies against 3 EV types. Detection of species A, B, and D EVs infecting wild chimpanzees demonstrates their potential widespread circulation in primates.
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Affiliation(s)
- Heli Harvala
- Royal Infirmary of Edinburgh, Edinburgh, Scotland.
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15
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Djoko CF, Wolfe ND, Aghokeng AF, Lebreton M, Liegeois F, Tamoufe U, Schneider BS, Ortiz N, Mbacham WF, Carr JK, Rimoin AW, Fair JN, Pike BL, Mpoudi-Ngole E, Delaporte E, Burke DS, Peeters M. Failure to detect simian immunodeficiency virus infection in a large Cameroonian cohort with high non-human primate exposure. Ecohealth 2012; 9:17-23. [PMID: 22395958 DOI: 10.1007/s10393-012-0751-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 01/31/2012] [Accepted: 02/03/2012] [Indexed: 05/31/2023]
Abstract
Hunting and butchering of wildlife in Central Africa are known risk factors for a variety of human diseases, including HIV/AIDS. Due to the high incidence of human exposure to body fluids of non-human primates, the significant prevalence of simian immunodeficiency virus (SIV) in non-human primates, and hunting/butchering associated cross-species transmission of other retroviruses in Central Africa, it is possible that SIV is actively transmitted to humans from primate species other than mangabeys, chimpanzees, and/or gorillas. We evaluated SIV transmission to humans by screening 2,436 individuals that hunt and butcher non-human primates, a population in which simian foamy virus and simian T-lymphotropic virus were previously detected. We identified 23 individuals with high seroreactivity to SIV. Nucleic acid sequences of SIV genes could not be detected, suggesting that SIV infection in humans could occur at a lower frequency than infections with other retroviruses, including simian foamy virus and simian T-lymphotropic virus. Additional studies on human populations at risk for non-human primate zoonosis are necessary to determine whether these results are due to viral/host characteristics or are indicative of low SIV prevalence in primate species consumed as bushmeat as compared to other retroviruses in Cameroon.
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16
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Grove JN, Branco LM, Boisen ML, Muncy IJ, Henderson LA, Schieffellin JS, Robinson JE, Bangura JJ, Fonnie M, Schoepp RJ, Hensley LE, Seisay A, Fair JN, Garry RF. Capacity building permitting comprehensive monitoring of a severe case of Lassa hemorrhagic fever in Sierra Leone with a positive outcome: case report. Virol J 2011; 8:314. [PMID: 21689444 PMCID: PMC3283910 DOI: 10.1186/1743-422x-8-314] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 06/20/2011] [Indexed: 11/29/2022] Open
Abstract
Lassa fever is a neglected tropical disease with a significant impact on the health care system of endemic West African nations. To date, case reports of Lassa fever have focused on laboratory characterisation of serological, biochemical and molecular aspects of the disease imported by infected individuals from Western Africa to the United States, Canada, Europe, Japan and Israel. Our report presents the first comprehensive real time diagnosis and characterization of a severe, hemorrhagic Lassa fever case in a Sierra Leonean individual admitted to the Kenema Government Hospital Lassa Fever Ward. Fever, malaise, unresponsiveness to anti-malarial and antibiotic drugs, followed by worsening symptoms and onset of haemorrhaging prompted medical officials to suspect Lassa fever. A recombinant Lassa virus protein based diagnostic was employed in diagnosing Lassa fever upon admission. This patient experienced a severe case of Lassa hemorrhagic fever with dysregulation of overall homeostasis, significant liver and renal system involvement, the interplay of pro- and anti-inflammatory cytokines during the course of hospitalization and an eventual successful outcome. These studies provide new insights into the pathophysiology and management of this viral illness and outline the improved infrastructure, research and real-time diagnostic capabilities within LASV endemic areas.
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Affiliation(s)
- Jessica N Grove
- Tulane University Department of Microbiology and Immunology, New Orleans, LA, USA
| | - Luis M Branco
- Tulane University Department of Microbiology and Immunology, New Orleans, LA, USA
- Autoimmune Technologies, LLC, New Orleans, LA, USA
| | | | | | | | - John S Schieffellin
- Tulane University Department of Pediatrics, Section of Infectious Disease, New Orleans, LA, USA
| | - James E Robinson
- Tulane University Department of Pediatrics, Section of Infectious Disease, New Orleans, LA, USA
| | - James J Bangura
- Ministry of Health and Sanitation Workplace Health, Sierra Leone
- The Global Viral Forecasting Initiative, San Francisco, CA
| | - Mbalu Fonnie
- Kenema Government Hospital Lassa Fever Ward, Kenema, Sierra Leone
| | - Randal J Schoepp
- Applied Diagnostics Branch, Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - Lisa E Hensley
- Viral Therapeutics Branch, Virology Division, U.S. Army Medical Research Institute of Infectious Diseases Diagnostic Systems Division, Fort Detrick, MD, USA
| | - Alhassan Seisay
- Ministry of Health and Sanitation Workplace Health, Sierra Leone
| | - Joseph N Fair
- The Global Viral Forecasting Initiative, San Francisco, CA
| | - Robert F Garry
- Tulane University Department of Microbiology and Immunology, New Orleans, LA, USA
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17
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Djoko CF, Rimoin AW, Vidal N, Tamoufe U, Wolfe ND, Butel C, LeBreton M, Tshala FM, Kayembe PK, Muyembe JJ, Edidi-Basepeo S, Pike BL, Fair JN, Mbacham WF, Saylors KE, Mpoudi-Ngole E, Delaporte E, Grillo M, Peeters M. High HIV type 1 group M pol diversity and low rate of antiretroviral resistance mutations among the uniformed services in Kinshasa, Democratic Republic of the Congo. AIDS Res Hum Retroviruses 2011; 27:323-9. [PMID: 20954909 DOI: 10.1089/aid.2010.0201] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
For the first time the genetic diversity among the uniformed personnel in Kinshasa, the capital city of the Democratic Republic of Congo (DRC), a country that has experienced military conflicts since 1998 and in which the global HIV-1/M pandemic started, has now been documented. A total of 94 HIV-1-positive samples, collected in 2007 in Kinshasa garrison settings from informed consenting volunteers, were genetically characterized in the pol region (protease and RT). An extensive diversity was observed, with 51% of the strains corresponding to six pure subtypes (A 23%, C 13.8%, D, G, H, J, and untypable), 15% corresponding to nine different CRFs (01, 02, 11, 13, 25, 26, 37, 43, and 45), and 34% being unique recombinants with one-third being complex mosaic viruses involving three or more different subtypes/CRFs. Only one strain harbored a single mutation, I54V, associated with drug resistance to protease inhibitors. Due to their high mobility and potential risk behavior, HIV infections in military personnel can lead to an even more complex epidemic in the DRC and to a possible increase of subtype C.
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Affiliation(s)
- Cyrille F. Djoko
- Global Viral Forecasting Initiative (GVF), San Francisco, California, and Yaoundé, Cameroon
- Biotechnology Center and Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
| | | | - Nicole Vidal
- Laboratoire Retrovirus, UMR 145, Institute for Research and Development (IRD) and University of Montpellier 1, Montpellier, France
| | - Ubald Tamoufe
- Global Viral Forecasting Initiative (GVF), San Francisco, California, and Yaoundé, Cameroon
| | - Nathan D. Wolfe
- Global Viral Forecasting Initiative (GVF), San Francisco, California, and Yaoundé, Cameroon
- Stanford University, Program in Human Biology, Stanford, California
| | - Christelle Butel
- Laboratoire Retrovirus, UMR 145, Institute for Research and Development (IRD) and University of Montpellier 1, Montpellier, France
| | - Matthew LeBreton
- Global Viral Forecasting Initiative (GVF), San Francisco, California, and Yaoundé, Cameroon
| | - Felix M. Tshala
- Military Health Services, Ministry of Defence, Kinshasa, Democratic Republic of the Congo
| | - Patrick K. Kayembe
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Jean Jacques Muyembe
- National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
| | - Samuel Edidi-Basepeo
- National AIDS Control Program Laboratory, Kinshasa, Democratic Republic of the Congo
| | - Brian L. Pike
- Global Viral Forecasting Initiative (GVF), San Francisco, California, and Yaoundé, Cameroon
| | - Joseph N. Fair
- Global Viral Forecasting Initiative (GVF), San Francisco, California, and Yaoundé, Cameroon
| | - Wilfred F. Mbacham
- Biotechnology Center and Department of Biochemistry, University of Yaoundé I, Yaoundé, Cameroon
| | - Karen E. Saylors
- Global Viral Forecasting Initiative (GVF), San Francisco, California, and Yaoundé, Cameroon
| | | | - Eric Delaporte
- Laboratoire Retrovirus, UMR 145, Institute for Research and Development (IRD) and University of Montpellier 1, Montpellier, France
- Department of Infectious Diseases, CHU, Montpellier, France
| | - Michael Grillo
- Department of Defense HIV AIDS Prevention Program (DHAPP), San Diego, California
| | - Martine Peeters
- Laboratoire Retrovirus, UMR 145, Institute for Research and Development (IRD) and University of Montpellier 1, Montpellier, France
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18
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Fuller T, Thomassen HA, Mulembakani PM, Johnston SC, Lloyd-Smith JO, Kisalu NK, Lutete TK, Blumberg S, Fair JN, Wolfe ND, Shongo RL, Formenty P, Meyer H, Wright LL, Muyembe JJ, Buermann W, Saatchi SS, Okitolonda E, Hensley L, Smith TB, Rimoin AW. Using remote sensing to map the risk of human monkeypox virus in the Congo Basin. Ecohealth 2011; 8:14-25. [PMID: 21069425 PMCID: PMC3237841 DOI: 10.1007/s10393-010-0355-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [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: 05/10/2010] [Revised: 09/12/2010] [Accepted: 09/30/2010] [Indexed: 05/23/2023]
Abstract
Although the incidence of human monkeypox has greatly increased in Central Africa over the last decade, resources for surveillance remain extremely limited. We conducted a geospatial analysis using existing data to better inform future surveillance efforts. Using active surveillance data collected between 2005 and 2007, we identified locations in Sankuru district, Democratic Republic of Congo (DRC) where there have been one or more cases of human monkeypox. To assess what taxa constitute the main reservoirs of monkeypox, we tested whether human cases were associated with (i) rope squirrels (Funisciurus sp.), which were implicated in monkeypox outbreaks elsewhere in the DRC in the 1980s, or (ii) terrestrial rodents in the genera Cricetomys and Graphiurus, which are believed to be monkeypox reservoirs in West Africa. Results suggest that the best predictors of human monkeypox cases are proximity to dense forests and associated habitat preferred by rope squirrels. The risk of contracting monkeypox is significantly greater near sites predicted to be habitable for squirrels (OR = 1.32; 95% CI 1.08-1.63). We recommend that semi-deciduous rainforests with oil-palm, the rope squirrel's main food source, be prioritized for monitoring.
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Affiliation(s)
- Trevon Fuller
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, 619 Charles E. Young Dr. East, Los Angeles, CA 90095-1496 USA
| | - Henri A. Thomassen
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, 619 Charles E. Young Dr. East, Los Angeles, CA 90095-1496 USA
| | | | - Sara C. Johnston
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD USA
| | - James O. Lloyd-Smith
- Fogarty International Center, National Institutes of Health, Bethesda, MD USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA USA
| | - Neville K. Kisalu
- Department of Microbiology, University of California, Los Angeles, CA USA
| | - Timothee K. Lutete
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | - Seth Blumberg
- Fogarty International Center, National Institutes of Health, Bethesda, MD USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA USA
| | - Joseph N. Fair
- Global Viral Forecasting Initiative, San Francisco, CA USA
| | | | | | - Pierre Formenty
- Department of Global Alert and Response, World Health Organization, Geneva, Switzerland
| | - Hermann Meyer
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Linda L. Wright
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD USA
| | - Jean-Jacques Muyembe
- National Institute of Biomedical Research, Kinshasa, Democratic Republic of Congo
| | - Wolfgang Buermann
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, 619 Charles E. Young Dr. East, Los Angeles, CA 90095-1496 USA
- Department of Atmospheric and Oceanic Sciences, University of California, Los Angeles, CA USA
| | - Sassan S. Saatchi
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, 619 Charles E. Young Dr. East, Los Angeles, CA 90095-1496 USA
- Radar Science Technical Group, Radar Science and Engineering Section, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Emile Okitolonda
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | - Lisa Hensley
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD USA
| | - Thomas B. Smith
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, 619 Charles E. Young Dr. East, Los Angeles, CA 90095-1496 USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA USA
| | - Anne W. Rimoin
- Fogarty International Center, National Institutes of Health, Bethesda, MD USA
- Department of Epidemiology, School of Public Health, University of California, 650 Charles E. Young Drive South, CHS 41-275, Los Angeles, CA 90095 USA
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19
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Rimoin AW, Mulembakani PM, Johnston SC, Lloyd Smith JO, Kisalu NK, Kinkela TL, Blumberg S, Thomassen HA, Pike BL, Fair JN, Wolfe ND, Shongo RL, Graham BS, Formenty P, Okitolonda E, Hensley LE, Meyer H, Wright LL, Muyembe JJ. Major increase in human monkeypox incidence 30 years after smallpox vaccination campaigns cease in the Democratic Republic of Congo. Proc Natl Acad Sci U S A 2010; 107:16262-7. [PMID: 20805472 PMCID: PMC2941342 DOI: 10.1073/pnas.1005769107] [Citation(s) in RCA: 446] [Impact Index Per Article: 31.9] [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] [Indexed: 11/18/2022] Open
Abstract
Studies on the burden of human monkeypox in the Democratic Republic of the Congo (DRC) were last conducted from 1981 to 1986. Since then, the population that is immunologically naïve to orthopoxviruses has increased significantly due to cessation of mass smallpox vaccination campaigns. To assess the current risk of infection, we analyzed human monkeypox incidence trends in a monkeypox-enzootic region. Active, population-based surveillance was conducted in nine health zones in central DRC. Epidemiologic data and biological samples were obtained from suspected cases. Cumulative incidence (per 10,000 population) and major determinants of infection were compared with data from active surveillance in similar regions from 1981 to 1986. Between November 2005 and November 2007, 760 laboratory-confirmed human monkeypox cases were identified in participating health zones. The average annual cumulative incidence across zones was 5.53 per 10,000 (2.18-14.42). Factors associated with increased risk of infection included: living in forested areas, male gender, age < 15, and no prior smallpox vaccination. Vaccinated persons had a 5.2-fold lower risk of monkeypox than unvaccinated persons (0.78 vs. 4.05 per 10,000). Comparison of active surveillance data in the same health zone from the 1980s (0.72 per 10,000) and 2006-07 (14.42 per 10,000) suggests a 20-fold increase in human monkeypox incidence. Thirty years after mass smallpox vaccination campaigns ceased, human monkeypox incidence has dramatically increased in rural DRC. Improved surveillance and epidemiological analysis is needed to better assess the public health burden and develop strategies for reducing the risk of wider spread of infection.
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Affiliation(s)
- Anne W Rimoin
- University of California, Los Angeles School of Public Health, Los Angeles, CA 90095, USA.
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20
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Abstract
Despite the fact that most emerging diseases stem from the transmission of pathogenic agents from animals to humans, the factors that mediate this process are still ill defined. What is known, however, is that the interface between humans and animals is of paramount importance in the process. This review will discuss the importance of the human-animal interface to the disease emergence process. We also provide an overview of factors that are believed to contribute to the origin and global spread of emerging infectious diseases and offer suggestions that may serve as future prevention strategies, such as social mobilization, public health education, behavioral change, and communication strategies. Because there exists no comprehensive global surveillance system to monitor zoonotic disease emergence, the intervention measures discussed herein may prove effective temporary alternatives.
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Affiliation(s)
- Brian L Pike
- Global Viral Forecasting Initiative, San Francisco, California, USA
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21
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Trombley AR, Wachter L, Garrison J, Buckley-Beason VA, Jahrling J, Hensley LE, Schoepp RJ, Norwood DA, Goba A, Fair JN, Kulesh DA. Comprehensive panel of real-time TaqMan polymerase chain reaction assays for detection and absolute quantification of filoviruses, arenaviruses, and New World hantaviruses. Am J Trop Med Hyg 2010; 82:954-60. [PMID: 20439981 DOI: 10.4269/ajtmh.2010.09-0636] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Viral hemorrhagic fever is caused by a diverse group of single-stranded, negative-sense or positive-sense RNA viruses belonging to the families Filoviridae (Ebola and Marburg), Arenaviridae (Lassa, Junin, Machupo, Sabia, and Guanarito), and Bunyaviridae (hantavirus). Disease characteristics in these families mark each with the potential to be used as a biological threat agent. Because other diseases have similar clinical symptoms, specific laboratory diagnostic tests are necessary to provide the differential diagnosis during outbreaks and for instituting acceptable quarantine procedures. We designed 48 TaqMan-based polymerase chain reaction (PCR) assays for specific and absolute quantitative detection of multiple hemorrhagic fever viruses. Forty-six assays were determined to be virus-specific, and two were designated as pan assays for Marburg virus. The limit of detection for the assays ranged from 10 to 0.001 plaque-forming units (PFU)/PCR. Although these real-time hemorrhagic fever virus assays are qualitative (presence of target), they are also quantitative (measure a single DNA/RNA target sequence in an unknown sample and express the final results as an absolute value (e.g., viral load, PFUs, or copies/mL) on the basis of concentration of standard samples and can be used in viral load, vaccine, and antiviral drug studies.
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Affiliation(s)
- Adrienne R Trombley
- Diagnostic Systems Division, and Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21701-5011, USA
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22
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Illick MM, Branco LM, Fair JN, Illick KA, Matschiner A, Schoepp R, Garry RF, Guttieri MC. Uncoupling GP1 and GP2 expression in the Lassa virus glycoprotein complex: implications for GP1 ectodomain shedding. Virol J 2008; 5:161. [PMID: 19105844 PMCID: PMC2645378 DOI: 10.1186/1743-422x-5-161] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2008] [Accepted: 12/23/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sera from convalescent Lassa fever patients often contains antibodies to Lassa virus (LASV) glycoprotein 1 (GP1), and glycoprotein 2 (GP2); Immunization of non-human primates with viral vectors expressing the arenaviral glycoprotein complex (GPC) confers full protective immunity against a lethal challenge with LASV. Thus, the development of native or quasi native recombinant LASV GP1 and GP2 as soluble, uncoupled proteins will improve current diagnostics, treatment, and prevention of Lassa fever. To this end, mammalian expression systems were engineered for production and purification of secreted forms of soluble LASV GP1 and GP2 proteins. RESULTS Determinants for mammalian cell expression of secreted uncoupled Lassa virus (LASV) glycoprotein 1 (GP1) and glycoprotein 2 (GP2) were established. Soluble GP1 was generated using either the native glycoprotein precursor (GPC) signal peptide (SP) or human IgG signal sequences (s.s.). GP2 was secreted from cells only when (1) the transmembrane (TM) domain was deleted, the intracellular domain (IC) was fused to the ectodomain, and the gene was co-expressed with a complete GP1 gene in cis; (2) the TM and IC domains were deleted and GP1 was co-expressed in cis; (3) expression of GP1 was driven by the native GPC SP. These data implicate GP1 as a chaperone for processing and shuttling GP2 to the cell surface. The soluble forms of GP1 and GP2 generated through these studies were secreted as homogeneously glycosylated proteins that contained high mannose glycans. Furthermore, observation of GP1 ectodomain shedding from cells expressing wild type LASV GPC represents a novel aspect of arenaviral glycoprotein expression. CONCLUSION These results implicate GP1 as a chaperone for the correct processing and shuttling of GP2 to the cell surface, and suggest that native GPC SP plays a role in this process. In the absence of GP1 and GPC SP the GP2 protein may be processed by an alternate pathway that produces heterogeneously glycosylated protein, or the polypeptide may not fully mature in the secretory cascade in mammalian cells. The expression constructs developed in these studies resulted in the generation and purification of soluble, uncoupled GP1 and GP2 proteins from mammalian cells with quasi-native properties. The observation of GP1 ectodomain shedding from cells expressing wild type LASV GPC establishes new correlates of disease progression and highlights potential opportunities for development of diagnostics targeting the early stages of Lassa fever.
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Affiliation(s)
| | - Luis M Branco
- Tulane University Health Sciences Center, New Orleans, LA, USA
| | - Joseph N Fair
- Tulane University Health Sciences Center, New Orleans, LA, USA
- Tulane University School of Public Health & Tropical Medicine, New Orleans, LA, USA
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - Kerry A Illick
- BioFactura, Inc., Rockville, MD, USA
- Department of Science, Cedar Crest College, Allentown, PA, USA
| | | | - Randal Schoepp
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - Robert F Garry
- Tulane University Health Sciences Center, New Orleans, LA, USA
| | - Mary C Guttieri
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
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23
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Branco LM, Matschiner A, Fair JN, Goba A, Sampey DB, Ferro PJ, Cashman KA, Schoepp RJ, Tesh RB, Bausch DG, Garry RF, Guttieri MC. Bacterial-based systems for expression and purification of recombinant Lassa virus proteins of immunological relevance. Virol J 2008; 5:74. [PMID: 18538016 PMCID: PMC2435526 DOI: 10.1186/1743-422x-5-74] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Accepted: 06/06/2008] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND There is a significant requirement for the development and acquisition of reagents that will facilitate effective diagnosis, treatment, and prevention of Lassa fever. In this regard, recombinant Lassa virus (LASV) proteins may serve as valuable tools in diverse antiviral applications. Bacterial-based systems were engineered for expression and purification of recombinant LASV nucleoprotein (NP), glycoprotein 1 (GP1), and glycoprotein 2 (GP2). RESULTS Full-length NP and the ectodomains of GP1 and GP2 were generated as maltose-binding protein (MBP) fusions in the Rosetta strains of Escherichia coli (E. coli) using pMAL-c2x vectors. Average fusion protein yields per liter of culture for MBP-NP, MBP-GP1, and MBP-GP2 were 10 mg, 9 mg, and 9 mg, respectively. Each protein was captured from cell lysates using amylose resin, cleaved with Factor Xa, and purified using size-exclusion chromatography (SEC). Fermentation cultures resulted in average yields per liter of 1.6 mg, 1.5 mg, and 0.7 mg of purified NP, GP1 and GP2, respectively. LASV-specific antibodies in human convalescent sera specifically detected each of the purified recombinant LASV proteins, highlighting their utility in diagnostic applications. In addition, mouse hyperimmune ascitic fluids (MHAF) against a panel of Old and New World arenaviruses demonstrated selective cross reactivity with LASV proteins in Western blot and enzyme-linked immunosorbent assay (ELISA). CONCLUSION These results demonstrate the potential for developing broadly reactive immunological assays that employ all three arenaviral proteins individually and in combination.
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Affiliation(s)
| | | | - Joseph N Fair
- Tulane University Health Sciences Center, New Orleans, Louisiana, USA
- Tulane University School of Public Health & Tropical Medicine, New Orleans, Louisiana, USA
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Augustine Goba
- Tulane University School of Public Health & Tropical Medicine, New Orleans, Louisiana, USA
- Lassa Fever Laboratory – Kenema Government Hospital, Kenema, Sierra Leone
| | | | - Philip J Ferro
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Kathleen A Cashman
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Randal J Schoepp
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Ft. Detrick, Maryland, USA
| | - Robert B Tesh
- University of Texas Medical Branch, Department of Pathology, Galveston, Texas, USA
| | - Daniel G Bausch
- Tulane University School of Public Health & Tropical Medicine, New Orleans, Louisiana, USA
| | - Robert F Garry
- Tulane University Health Sciences Center, New Orleans, Louisiana, USA
| | - Mary C Guttieri
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
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