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A Review on Zoonotic Pathogens Associated with Non-Human Primates: Understanding the Potential Threats to Humans. Microorganisms 2023; 11:microorganisms11020246. [PMID: 36838210 PMCID: PMC9964884 DOI: 10.3390/microorganisms11020246] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/07/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Non-human primates (NHP) share a close relationship with humans due to a genetic homology of 75-98.5%. NHP and humans have highly similar tissue structures, immunity, physiology, and metabolism and thus often can act as hosts to the same pathogens. Agriculture, meat consumption habits, tourism development, religious beliefs, and biological research have led to more extensive and frequent contact between NHPs and humans. Deadly viruses, such as rabies virus, herpes B virus, Marburg virus, Ebola virus, human immunodeficiency virus, and monkeypox virus can be transferred from NHP to humans. Similarly, herpes simplex virus, influenza virus, and yellow fever virus can be transmitted to NHP from humans. Infectious pathogens, including viruses, bacteria, and parasites, can affect the health of both primates and humans. A vast number of NHP-carrying pathogens exhibit a risk of transmission to humans. Therefore, zoonotic infectious diseases should be evaluated in future research. This article reviews the research evidence, diagnostic methods, prevention, and treatment measures that may be useful in limiting the spread of several common viral pathogens via NHP and providing ideas for preventing zoonotic diseases with epidemic potential.
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Russell RM, Bibollet-Ruche F, Liu W, Sherrill-Mix S, Li Y, Connell J, Loy DE, Trimboli S, Smith AG, Avitto AN, Gondim MVP, Plenderleith LJ, Wetzel KS, Collman RG, Ayouba A, Esteban A, Peeters M, Kohler WJ, Miller RA, François-Souquiere S, Switzer WM, Hirsch VM, Marx PA, Piel AK, Stewart FA, Georgiev AV, Sommer V, Bertolani P, Hart JA, Hart TB, Shaw GM, Sharp PM, Hahn BH. CD4 receptor diversity represents an ancient protection mechanism against primate lentiviruses. Proc Natl Acad Sci U S A 2021; 118:e2025914118. [PMID: 33771926 PMCID: PMC8020793 DOI: 10.1073/pnas.2025914118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Infection with human and simian immunodeficiency viruses (HIV/SIV) requires binding of the viral envelope glycoprotein (Env) to the host protein CD4 on the surface of immune cells. Although invariant in humans, the Env binding domain of the chimpanzee CD4 is highly polymorphic, with nine coding variants circulating in wild populations. Here, we show that within-species CD4 diversity is not unique to chimpanzees but found in many African primate species. Characterizing the outermost (D1) domain of the CD4 protein in over 500 monkeys and apes, we found polymorphic residues in 24 of 29 primate species, with as many as 11 different coding variants identified within a single species. D1 domain amino acid replacements affected SIV Env-mediated cell entry in a single-round infection assay, restricting infection in a strain- and allele-specific fashion. Several identical CD4 polymorphisms, including the addition of N-linked glycosylation sites, were found in primate species from different genera, providing striking examples of parallel evolution. Moreover, seven different guenons (Cercopithecus spp.) shared multiple distinct D1 domain variants, pointing to long-term trans-specific polymorphism. These data indicate that the HIV/SIV Env binding region of the primate CD4 protein is highly variable, both within and between species, and suggest that this diversity has been maintained by balancing selection for millions of years, at least in part to confer protection against primate lentiviruses. Although long-term SIV-infected species have evolved specific mechanisms to avoid disease progression, primate lentiviruses are intrinsically pathogenic and have left their mark on the host genome.
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Affiliation(s)
- Ronnie M Russell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Weimin Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Jesse Connell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Dorothy E Loy
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Stephanie Trimboli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Andrew G Smith
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alexa N Avitto
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Marcos V P Gondim
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
- Centre for Immunity, Infection, and Evolution, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
| | - Katherine S Wetzel
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ahidjo Ayouba
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - Amandine Esteban
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - Martine Peeters
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - William J Kohler
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Richard A Miller
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | | | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329
| | - Vanessa M Hirsch
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Preston A Marx
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70118
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433
| | - Alex K Piel
- Department of Anthropology, University College London, WC1H 0BW London, United Kingdom
| | - Fiona A Stewart
- Department of Anthropology, University College London, WC1H 0BW London, United Kingdom
- School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, United Kingdom
| | - Alexander V Georgiev
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Volker Sommer
- Department of Anthropology, University College London, WC1H 0BW London, United Kingdom
| | - Paco Bertolani
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, CB2 1QH Cambridge, United Kingdom
| | - John A Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - Terese B Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Paul M Sharp
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
- Centre for Immunity, Infection, and Evolution, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
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Systematic Review of Important Viral Diseases in Africa in Light of the 'One Health' Concept. Pathogens 2020; 9:pathogens9040301. [PMID: 32325980 PMCID: PMC7238228 DOI: 10.3390/pathogens9040301] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 12/19/2022] Open
Abstract
Emerging and re-emerging viral diseases are of great public health concern. The recent emergence of Severe Acute Respiratory Syndrome (SARS) related coronavirus (SARS-CoV-2) in December 2019 in China, which causes COVID-19 disease in humans, and its current spread to several countries, leading to the first pandemic in history to be caused by a coronavirus, highlights the significance of zoonotic viral diseases. Rift Valley fever, rabies, West Nile, chikungunya, dengue, yellow fever, Crimean-Congo hemorrhagic fever, Ebola, and influenza viruses among many other viruses have been reported from different African countries. The paucity of information, lack of knowledge, limited resources, and climate change, coupled with cultural traditions make the African continent a hotspot for vector-borne and zoonotic viral diseases, which may spread globally. Currently, there is no information available on the status of virus diseases in Africa. This systematic review highlights the available information about viral diseases, including zoonotic and vector-borne diseases, reported in Africa. The findings will help us understand the trend of emerging and re-emerging virus diseases within the African continent. The findings recommend active surveillance of viral diseases and strict implementation of One Health measures in Africa to improve human public health and reduce the possibility of potential pandemics due to zoonotic viruses.
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Ayouba A, Peeters M. Reply to Zhang et al. J Infect Dis 2020; 222:1065-1066. [DOI: 10.1093/infdis/jiaa041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 01/27/2020] [Indexed: 12/14/2022] Open
Affiliation(s)
- Ahidjo Ayouba
- Recherches Translationelles sur le VIH et Maladies Infectieuses/Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement, and University of Montpellier, France
| | - Martine Peeters
- Recherches Translationelles sur le VIH et Maladies Infectieuses/Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche pour le Développement, and University of Montpellier, France
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Nyamota R, Owino V, Murungi EK, Villinger J, Otiende M, Masiga D, Thuita J, Lekolool I, Jeneby M. Broad diversity of simian immunodeficiency virus infecting Chlorocebus species (African green monkey) and evidence of cross-species infection in Papio anubis (olive baboon) in Kenya. J Med Primatol 2020; 49:165-178. [PMID: 32030774 DOI: 10.1111/jmp.12461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/06/2019] [Accepted: 01/19/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND Simian immunodeficiency virus (SIV) naturally infects African non-human primates (NHPs) and poses a threat of transmission to humans through hunting and consumption of monkeys as bushmeat. This study investigated the as of yet unknown molecular diversity of SIV in free-ranging Chlorocebus species (African green monkeys-AGMs) and Papio anubis (olive baboons) within Mombasa, Kisumu and Naivasha urban centres in Kenya. METHODS We collected blood samples from 124 AGMs and 65 olive baboons in situ, and detected SIV by high-resolution melting analysis and sequencing of PCR products. RESULTS Simian immunodeficiency virus prevalence was 32% in AGMs and 3% in baboons. High-resolution melting (HRM) analysis demonstrated distinct melt profiles illustrating virus diversity confirmed by phylogenetic analysis. CONCLUSIONS There is persistent evolutionary diversification of SIVagm strains in its natural host, AGMs and cross-species infection to olive baboons is occurring. Further study is required to establish pathogenesis of the diverse SIVagm variants and baboon immunological responses.
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Affiliation(s)
- Richard Nyamota
- Department of Biochemistry and Molecular Biology, Egerton University, Egerton, Kenya
| | - Vincent Owino
- Department of Biochemistry and Molecular Biology, Egerton University, Egerton, Kenya.,International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | | | - Jandouwe Villinger
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | | | - Daniel Masiga
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - John Thuita
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization (BioRI-KALRO), Kikuyu, Kenya
| | | | - Maamun Jeneby
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya.,Department of Tropical and Infectious Diseases, Institute of Primate Research, Karen, Kenya
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Revisiting human T-cell lymphotropic virus types 1 and 2 infections among rural population in Gabon, central Africa thirty years after the first analysis. PLoS Negl Trop Dis 2018; 12:e0006833. [PMID: 30359373 PMCID: PMC6201875 DOI: 10.1371/journal.pntd.0006833] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/11/2018] [Indexed: 01/03/2023] Open
Abstract
HTLV-1 infection is considered as highly endemic in central Africa. Thirty years ago, a first epidemiological study was performed in Gabon, central Africa, and revealed that the prevalence varied from 5.0 to 10.5%. To evaluate current distribution of HTLVs in Gabon, 4.381 samples were collected from rural population living in 220 villages distributed within the 9 provinces of country. HTLVs prevalence was determined using two ELISA tests and positive results were confirmed by Western Blot. The overall HTLV-1 seroprevalence was of 7.3% among the rural Gabonese population; with 5.4% for men and 9.0% for women. Prevalence of HTLV-1 differed by province, ranging from 2.3% to 12.5% into the rain forest. Being a woman older than 51 years represented a high risk for HTLV-1 acquisition. Hospitalization, operation/surgery, transfusion and medical abortion or fever, arthritis and abdominal pain are also significant risk factors. In addition, 0.1% of samples were found as HTLV-2 positive, while 12.0% had an indeterminate HTLV serological pattern. HTLV-3 and HTLV-4 were not found. Phylogenetic analysis was performed on 87 samples and demonstrated that HTLV-1 present in Gabon belongs mostly to subtype B, however the rare subtype D was also found. Altogether, our results demonstrate that almost thirty years after the first epidemiological study prevention of HTLVs infection is still an issue in Gabon.
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Bell SM, Bedford T. Modern-day SIV viral diversity generated by extensive recombination and cross-species transmission. PLoS Pathog 2017; 13:e1006466. [PMID: 28672035 PMCID: PMC5510905 DOI: 10.1371/journal.ppat.1006466] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 07/14/2017] [Accepted: 06/12/2017] [Indexed: 02/04/2023] Open
Abstract
Cross-species transmission (CST) has led to many devastating epidemics, but is still a poorly understood phenomenon. HIV-1 and HIV-2 (human immunodeficiency virus 1 and 2), which have collectively caused over 35 million deaths, are the result of multiple CSTs from chimpanzees, gorillas, and sooty mangabeys. While the immediate history of HIV is known, there are over 45 lentiviruses that infect specific species of primates, and patterns of host switching are not well characterized. We thus took a phylogenetic approach to better understand the natural history of SIV recombination and CST. We modeled host species as a discrete character trait on the viral phylogeny and inferred historical host switches and the pairwise transmission rates between each pair of 24 primate hosts. We identify 14 novel, well-supported, ancient cross-species transmission events. We also find that lentiviral lineages vary widely in their ability to infect new host species: SIVcol (from colobus monkeys) is evolutionarily isolated, while SIVagms (from African green monkeys) frequently move between host subspecies. We also examine the origins of SIVcpz (the predecessor of HIV-1) in greater detail than previous studies, and find that there are still large portions of the genome with unknown origins. Observed patterns of CST are likely driven by a combination of ecological circumstance and innate immune factors.
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Affiliation(s)
- Sidney M. Bell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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Ahuka-Mundeke S, Mbala-Kingebeni P, Ndimbo-Kumogo SP, Foncelle C, Lunguya-Metila O, Muyembe-Tamfum JJ, Delaporte E, Peeters M, Ayouba A. Full Genome Characterization of a New Simian Immune Deficiency Virus Lineage in a Naturally Infected Cercopithecus ascanius whitesidei in the Democratic Republic of Congo Reveals High Genetic Diversity Among Red-Tailed Monkeys in Central and Eastern Africa. AIDS Res Hum Retroviruses 2017; 33:735-739. [PMID: 28383997 PMCID: PMC5512325 DOI: 10.1089/aid.2017.0027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Our knowledge on simian immune deficiency virus (SIV) diversity and evolution in the different nonhuman primate species is still incomplete. In this study, we report the full genome characterization of a new SIV from a red-tailed monkey (2013DRC-I8), from the Cercopithecus ascanius whitesidei subspecies, in the Democratic Republic of Congo (DRC). The new full-length genome is 9,926 bp long, and the genomic structure is similar to that of other SIVs with the absence of vpx and vpu genes. The new SIVasc-13DRC-I8 strain fell within the Cercopithecus specific SIV lineage. SIVasc-13DRC-I8 and previously reported SIVrtg from the C.a. schmidti subspecies in Uganda did not form a separate species-specific SIV lineage. These observations provide additional evidence for high genetic diversity and the complex evolution of SIVs in the Cercopithecus genus. More studies on a large number of monkeys from a wider geographic area are needed to understand SIV evolution.
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Affiliation(s)
- Steve Ahuka-Mundeke
- UMI 233 TransVIHMI/INSERM1175, Institut de Recherche pour le Développement (IRD), University of Montpellier, Montpellier, France
- Institut National de Recherche Biomédicales, Kinshasa, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Placide Mbala-Kingebeni
- Institut National de Recherche Biomédicales, Kinshasa, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | | | - Caroline Foncelle
- UMI 233 TransVIHMI/INSERM1175, Institut de Recherche pour le Développement (IRD), University of Montpellier, Montpellier, France
| | - Octavie Lunguya-Metila
- Institut National de Recherche Biomédicales, Kinshasa, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Jean-Jacques Muyembe-Tamfum
- Institut National de Recherche Biomédicales, Kinshasa, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Eric Delaporte
- UMI 233 TransVIHMI/INSERM1175, Institut de Recherche pour le Développement (IRD), University of Montpellier, Montpellier, France
| | - Martine Peeters
- UMI 233 TransVIHMI/INSERM1175, Institut de Recherche pour le Développement (IRD), University of Montpellier, Montpellier, France
| | - Ahidjo Ayouba
- UMI 233 TransVIHMI/INSERM1175, Institut de Recherche pour le Développement (IRD), University of Montpellier, Montpellier, France
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Steve AM, Ahidjo A, Placide MK, Caroline F, Mukulumanya M, Simon-Pierre NK, Octavie LM, Valentin MA, Jean-Jacques MT, Eric D, Martine P. High Prevalences and a Wide Genetic Diversity of Simian Retroviruses in Non-human Primate Bushmeat in Rural Areas of the Democratic Republic of Congo. ECOHEALTH 2017; 14:100-114. [PMID: 28050688 PMCID: PMC5360875 DOI: 10.1007/s10393-016-1202-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/10/2016] [Accepted: 11/21/2016] [Indexed: 06/06/2023]
Abstract
Like the majority of emerging infectious diseases, HIV and HTLV are of zoonotic origin. Here we assess the risk of cross-species transmissions of their simian counterparts, SIV and STLV, from non-human primates (NHP) to humans in the Democratic Republic of Congo (DRC). A total of 331 samples, derived from NHP bushmeat, were collected as dried blood spots (DBS, n = 283) or as tissue samples (n = 36) at remote forest sites mainly in northern and eastern DRC. SIV antibody prevalences in DBS were estimated with a novel high throughput immunoassay with antigens representing the actual known diversity of HIV/SIV lineages. Antibody-positive samples were confirmed by PCR and sequence analysis. Screening for STLV infection was done with universal primers in tax, and new strains were further characterized in LTR. SIV and STLV infection in tissue samples was done by PCR only. Overall, 5 and 15.4% of NHP bushmeat was infected with SIV and STLV, respectively. A new SIV lineage was identified in Allen's swamp monkeys (Allenopithecus nigroviridis). Three new STLV-1 subtypes were identified in Allen's swamp monkeys (Allenopithecus nigroviridis), blue monkeys (Cercopithecus mitis), red-tailed guenons (Cercopithecus ascanius schmidti) and agile mangabeys (Cercocebus agilis). SIV and STLV prevalences varied according to species and geographic region. Our study illustrates clearly, even on a small sample size from a limited number of geographic areas, that our knowledge on the genetic diversity and geographic distribution of simian retroviruses is still limited and that humans continue to be exposed to relative high proportions on infected NHP bushmeat.
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Affiliation(s)
- Ahuka-Mundeke Steve
- UMI 233 TransVIHMI/INSERM1175, Institut de Recherche pour le Développement (IRD), University of Montpellier, 911 Avenue Agropolis, 34394, Montpellier, Cedex 1, France
- Institut National de Recherche Biomédicales, Kinshasa, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Ayouba Ahidjo
- UMI 233 TransVIHMI/INSERM1175, Institut de Recherche pour le Développement (IRD), University of Montpellier, 911 Avenue Agropolis, 34394, Montpellier, Cedex 1, France
| | - Mbala-Kingebeni Placide
- Institut National de Recherche Biomédicales, Kinshasa, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Foncelle Caroline
- UMI 233 TransVIHMI/INSERM1175, Institut de Recherche pour le Développement (IRD), University of Montpellier, 911 Avenue Agropolis, 34394, Montpellier, Cedex 1, France
| | - Mubonga Mukulumanya
- Institut Supérieur de Techniques Médicales de Walikale, Walikale, Nord Kivu, Democratic Republic of Congo
| | | | - Lunguya-Metila Octavie
- Institut National de Recherche Biomédicales, Kinshasa, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | | | - Muyembe-Tamfum Jean-Jacques
- Institut National de Recherche Biomédicales, Kinshasa, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Delaporte Eric
- UMI 233 TransVIHMI/INSERM1175, Institut de Recherche pour le Développement (IRD), University of Montpellier, 911 Avenue Agropolis, 34394, Montpellier, Cedex 1, France
| | - Peeters Martine
- UMI 233 TransVIHMI/INSERM1175, Institut de Recherche pour le Développement (IRD), University of Montpellier, 911 Avenue Agropolis, 34394, Montpellier, Cedex 1, France.
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Phyloepidemiological Analysis Reveals that Viral Divergence Led to the Paucity of Simian Immunodeficiency Virus SIVmus/gsn/mon Infections in Wild Populations. J Virol 2017; 91:JVI.01884-16. [PMID: 28077632 PMCID: PMC5331790 DOI: 10.1128/jvi.01884-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/06/2016] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is the result of cross-species transmission of simian immunodeficiency virus from chimpanzees (SIVcpz). SIVcpz is a chimeric virus which shares common ancestors with viruses infecting red-capped mangabeys and a subset of guenon species. The epidemiology of SIV infection in hominoids is characterized by low prevalences and an uneven geographic distribution. Surveys in Cameroon indicated that two closely related members of the guenon species subset, mustached guenons and greater spot-nosed guenons, infected with SIVmus and SIVgsn, respectively, also have low rates of SIV infections in their populations. Compared to that for other monkeys, including red-capped mangabeys and closely related guenon species, such an epidemiology is unusual. By intensifying sampling of geographically distinct populations of mustached and greater spot-nosed guenons in Gabon and including large sample sets of mona guenons from Cameroon, we add strong support to the hypothesis that the paucity of SIV infections in wild populations is a general feature of this monophyletic group of viruses. Furthermore, comparative phylogenetic analysis reveals that this phenotype is a feature of this group of viruses infecting phylogenetically disparate hosts, suggesting that this epidemiological phenotype results from infection with these HIV-1-related viruses rather than from a common host factor. Thus, these HIV-1-related viruses, i.e., SIVcpz and the guenon viruses which share an ancestor with part of the SIVcpz genome, have an epidemiology distinct from that found for SIVs in other African primate species.IMPORTANCE Stable virus-host relationships are established over multiple generations. The prevalence of viral infections in any given host is determined by various factors. Stable virus-host relationships of viruses that are able to cause persistent infections and exist with high incidences of infection are generally characterized by a lack of morbidity prior to host reproduction. Such is the case for cytomegalovirus (CMV) and Epstein-Barr virus (EBV) infections of humans. SIV infections of most African primate species also satisfy these criteria, with these infections found at a high prevalence and with rare cases of clinical disease. In contrast, SIVcpz, the ancestor of HIV-1, has a different epidemiology, and it has been reported that infected animals suffer from an AIDS-like disease in the wild. Here we conclusively demonstrate that viruses which are closely related to SIVcpz and infect a subset of guenon monkeys show an epidemiology resembling that of SIVcpz.
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Abstract
Understanding pathogen exchange among human, wildlife, and livestock populations, and the varying ecological and cultural contexts in which this exchange takes place, is a major challenge. The present review contextualizes the risk factors that result from human interactions with livestock, companion animals, animal exhibits, wildlife through nature-based tourism, and wildlife through consumption. Given their phylogenetic relatedness to humans, primates are emphasized in this discussion; primates serve as reservoirs for several human pathogens, and some human pathogens can decimate wild primate populations. Anthropologists must play a central role in understanding cultural variation in attitudes toward other species as well as perceived risks when interacting with animals. I argue that the remediation of emerging infectious diseases will be accomplished primarily through human behavioral changes rather than through efforts in pathogen discovery. Given the history of human interactions with wildlife, candid discussions on zoonotic diseases will be increasingly important for our combined survival.
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Ahuka-Mundeke S, Lunguya-Metila O, Mbenzo-Abokome V, Butel C, Inogwabini BI, Omasombo V, Muyembe-Tamfum JJ, Georgiev AV, Muller MN, Ndjango JBN, Li Y, Delaporte E, Hahn BH, Peeters M, Ayouba A. Genetic diversity of STLV-2 and interspecies transmission of STLV-3 in wild-living bonobos. Virus Evol 2016; 2:vew011. [PMID: 27774304 PMCID: PMC4900509 DOI: 10.1093/ve/vew011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
There are currently four known primate T-cell lymphotropic virus groups (PTLV1-4), each of which comprises closely related simian (STLV) and human (HTLV) viruses. For PTLV-1 and PTLV-3, simian and human viruses are interspersed, suggesting multiple cross-species transmission events; however, for PTLV-2 this is not so clear because HTLV-2 and STLV-2 strains from captive bonobos (Pan paniscus) form two distinct clades. To determine to what extent bonobos are naturally infected with STLV, we screened fecal samples (n = 633) from wild-living bonobos (n = 312) at six different sites in the Democratic Republic of Congo (DRC) for the presence of STLV nucleic acids. STLV infection was detected in 8 of 312 bonobos at four of six field sites, suggesting an overall prevalence of 2.6% (ranging from 0 to 8%). Six samples contained STLV-2, while the two others contained STLV-3, as determined by phylogenetic analysis of partial tax and Long Terminal Repeats (LTR) sequences. The new STLV-2 sequences were highly diverse, but grouped with previously identified STLV-2 strains as a sister clade to HTLV-2. In contrast, the new STLV-3 sequences did not cluster together, but were more closely related to STLVs from sympatric monkey species. These results show for the first time that fecal samples can be used to detect STLV infection in apes. These results also show that wild-living bonobos are endemically infected with STLV-2, but have acquired STLV-3 on at least two occasions most likely by cross-species transmission from monkey species on which they prey. Future studies of bonobos and other non-human primate species in Central Africa are needed to identify the simian precursor of HTLV-2 in humans.
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Affiliation(s)
- Steve Ahuka-Mundeke
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and University of Montpellier, Montpellier, 34394, France; Institut National de Recherches Biomédicales, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Octavie Lunguya-Metila
- Institut National de Recherches Biomédicales, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | | | - Christelle Butel
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and University of Montpellier, Montpellier, 34394, France
| | | | - Valentin Omasombo
- Institut Congolais de Conservation de la Nature (ICCN), Democratic Republic of the Congo
| | - Jean-Jacques Muyembe-Tamfum
- Institut National de Recherches Biomédicales, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Alexander V Georgiev
- Department of Anthropology, Northwestern University, Evanston, IL 60208, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Martin N Muller
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Jean-Bosco N Ndjango
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric Delaporte
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and University of Montpellier, Montpellier, 34394, France
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Martine Peeters
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and University of Montpellier, Montpellier, 34394, France
| | - Ahidjo Ayouba
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and University of Montpellier, Montpellier, 34394, France
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Abstract
Zoonotic diseases are the main contributor to emerging infectious diseases (EIDs) and present a major threat to global public health. Bushmeat is an important source of protein and income for many African people, but bushmeat-related activities have been linked to numerous EID outbreaks, such as Ebola, HIV, and SARS. Importantly, increasing demand and commercialization of bushmeat is exposing more people to pathogens and facilitating the geographic spread of diseases. To date, these linkages have not been systematically assessed. Here we review the literature on bushmeat and EIDs for sub-Saharan Africa, summarizing pathogens (viruses, fungi, bacteria, helminths, protozoan, and prions) by bushmeat taxonomic group to provide for the first time a comprehensive overview of the current state of knowledge concerning zoonotic disease transmission from bushmeat into humans. We conclude by drawing lessons that we believe are applicable to other developing and developed regions and highlight areas requiring further research to mitigate disease risk.
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Boué V, Locatelli S, Boucher F, Ayouba A, Butel C, Esteban A, Okouga AP, Ndoungouet A, Motsch P, Le Flohic G, Ngari P, Prugnolle F, Ollomo B, Rouet F, Liégeois F. High Rate of Simian Immunodeficiency Virus (SIV) Infections in Wild Chimpanzees in Northeastern Gabon. Viruses 2015; 7:4997-5015. [PMID: 26389939 PMCID: PMC4584299 DOI: 10.3390/v7092855] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/22/2015] [Accepted: 08/25/2015] [Indexed: 11/17/2022] Open
Abstract
The emergence of HIV-1 groups M, N, O, and P is the result of four independent cross-species transmissions between chimpanzees (cpz) and gorillas (gor) from central/south Cameroon and humans respectively. Although the first two SIVcpz were identified in wild-born captive chimpanzees in Gabon in 1989, no study has been conducted so far in wild chimpanzees in Gabon. To document the SIVcpz infection rate, genetic diversity, and routes of virus transmission, we analyzed 1458 faecal samples collected in 16 different locations across the country, and we conducted follow-up missions in two of them. We found 380 SIV antibody positive samples in 6 different locations in the north and northeast. We determined the number of individuals collected by microsatellite analysis and obtained an adjusted SIV prevalence of 39.45%. We performed parental analysis to investigate viral spread between and within communities and found that SIVs were epidemiologically linked and were transmitted by both horizontal and vertical routes. We amplified pol and gp41 fragments and obtained 57 new SIVcpzPtt strains from three sites. All strains, but one, clustered together within a specific phylogeographic clade. Given that these SIV positive samples have been collected nearby villages and that humans continue to encroach in ape's territories, the emergence of a new HIV in this area needs to be considered.
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Affiliation(s)
- Vanina Boué
- UMI 233 "TransVIHMI", IRD / UM-INSERM U1175/ UM1, 34394 Montpellier, France.
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
| | - Sabrina Locatelli
- UMI 233 "TransVIHMI", IRD / UM-INSERM U1175/ UM1, 34394 Montpellier, France.
| | - Floriane Boucher
- UMI 233 "TransVIHMI", IRD / UM-INSERM U1175/ UM1, 34394 Montpellier, France.
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
| | - Ahidjo Ayouba
- UMI 233 "TransVIHMI", IRD / UM-INSERM U1175/ UM1, 34394 Montpellier, France.
| | - Christelle Butel
- UMI 233 "TransVIHMI", IRD / UM-INSERM U1175/ UM1, 34394 Montpellier, France.
| | - Amandine Esteban
- UMI 233 "TransVIHMI", IRD / UM-INSERM U1175/ UM1, 34394 Montpellier, France.
| | | | | | - Peggy Motsch
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
| | | | - Paul Ngari
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
| | - Franck Prugnolle
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
- Laboratoire Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution, Contrôle, UMR 224IRD/CNRS/UM1, 34394 Montpellier, France4 Institut Pasteur du Cambodge, Phnom-Penh BP 983, Royaume du Cambodge.
| | - Benjamin Ollomo
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
| | - François Rouet
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
- Institut Pasteur du Cambodge, Phnom-Penh BP 983, Royaume du Cambodge.
| | - Florian Liégeois
- UMI 233 "TransVIHMI", IRD / UM-INSERM U1175/ UM1, 34394 Montpellier, France.
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
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Magiorkinis G, Blanco-Melo D, Belshaw R. The decline of human endogenous retroviruses: extinction and survival. Retrovirology 2015; 12:8. [PMID: 25640971 PMCID: PMC4335370 DOI: 10.1186/s12977-015-0136-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/06/2015] [Indexed: 12/21/2022] Open
Abstract
Background Endogenous Retroviruses (ERVs) are retroviruses that over the course of evolution have integrated into germline cells and eventually become part of the host genome. They proliferate within the germline of their host, making up ~5% of the human and mouse genome sequences. Several lines of evidence have suggested a decline in the rate of ERV integration into the human genome in recent evolutionary history but this has not been investigated quantitatively or possible causes explored. Results By dating the integration of ERV loci in 40 mammal species, we show that the human genome and that of other hominoids (great apes and gibbons) have experienced an approximately four-fold decline in the ERV integration rate over the last 10 million years. A major cause is the recent extinction of one very large ERV lineage (HERV-H), which is responsible for most of the integrations over the last 30 million years. The decline however affects most other ERV lineages. Only about 10% of the decline might be attributed to an accompanying increase in body mass (a trait we have shown recently to be negatively correlated with ERV integration rate). Humans are unusual compared to related species – Old World monkeys, great apes and gibbons – in (a) having not acquired any new ERV lineages during the last 30 million years and (b) the possession of an old ERV lineage that has continued to replicate up until at least the last few hundred thousand years – the potentially medically significant HERVK(HML2). Conclusions The human genome shares with the genome of other great apes and gibbons a recent decline in ERV integration that is not typical of other primates and mammals. The human genome differs from that of related species both in maintaining up until at least recently a replicating old ERV lineage and in not having acquired any new lineages. We speculate that the decline in ERV integration in the human genome has been exacerbated by a relatively low burden of horizontally-transmitted retroviruses and subsequent reduced risk of endogenization. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0136-x) contains supplementary material, which is available to authorized users.
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Discovery and characterization of auxiliary proteins encoded by type 3 simian T-cell lymphotropic viruses. J Virol 2014; 89:931-51. [PMID: 25355890 DOI: 10.1128/jvi.02150-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
UNLABELLED Human T-cell lymphotropic virus type 1 (HTLV-1) and HTLV-2 encode auxiliary proteins that play important roles in viral replication, viral latency, and immune escape. The presence of auxiliary protein-encoding open reading frames (ORFs) in HTLV-3, the latest HTLV to be discovered, is unknown. Simian T-cell lymphotropic virus type 3 (STLV-3) is almost identical to HTLV-3. Given the lack of HTLV-3-infected cell lines, we took advantage of STLV-3-infected cells and of an STLV-3 molecular clone to search for the presence of auxiliary transcripts. Using reverse transcriptase PCR (RT-PCR), we first uncovered the presence of three unknown viral mRNAs encoding putative proteins of 5, 8, and 9 kDa and confirmed the presence of the previously reported RorfII transcript. The existence of these viral mRNAs was confirmed by using splice site-specific RT-PCR with ex vivo samples. We showed that p5 is distributed throughout the cell and does not colocalize with a specific organelle. The p9 localization is similar to that of HTLV-1 p12 and induced a strong decrease in the calreticulin signal, similarly to HTLV-1 p12. Although p8, RorfII, and Rex-3 share an N-terminal sequence that is predicted to contain a nucleolar localization signal (NoLS), only p8 is found in the nucleolus. The p8 location in the nucleolus is linked to a bipartite NoLS. p8 and, to a lesser extent, p9 repressed viral expression but did not alter Rex-3-dependent mRNA export. Using a transformation assay, we finally showed that none of the STLV-3 auxiliary proteins had the ability to induce colony formation, while both Tax-3 and antisense protein of HTLV-3 (APH-3) promoted cellular transformation. Altogether, these results complete the characterization of the newly described primate T-lymphotropic virus type 3 (PTLV-3). IMPORTANCE Together with their simian counterparts, HTLVs form the primate T-lymphotropic viruses. HTLVs arose from interspecies transmission between nonhuman primates and humans. HTLV-1 and HTLV-2 encode auxiliary proteins that play important roles in viral replication, viral latency, and immune escape. The presence of ORFs encoding auxiliary proteins in HTLV-3 or STLV-3 genomes was unknown. Using in silico analyses, ex vivo samples, or in vitro experiments, we have uncovered the presence of 3 previously unknown viral mRNAs encoding putative proteins and confirmed the presence of a previously reported viral transcript. We characterized the intracellular localization of the four proteins. We showed that two of these proteins repress viral expression but that none of them have the ability to induce colony formation. However, both Tax and the antisense protein APH-3 promote cell transformation. Our results allowed us to characterize 4 new retroviral proteins for the first time.
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Full-length genome analyses of two new simian immunodeficiency virus (SIV) strains from mustached monkeys (C. Cephus) in Gabon illustrate a complex evolutionary history among the SIVmus/mon/gsn lineage. Viruses 2014; 6:2880-98. [PMID: 25054885 PMCID: PMC4113797 DOI: 10.3390/v6072880] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/04/2014] [Accepted: 07/08/2014] [Indexed: 12/22/2022] Open
Abstract
The Simian Immunodeficiency Virus (SIV) mus/mon/gsn lineage is a descendant of one of the precursor viruses to the HIV-1/SIVcpz/gor viral lineage. SIVmus and SIVgsn were sequenced from mustached and greater spot nosed monkeys in Cameroon and SIVmon from mona monkeys in Cameroon and Nigeria. In order to further document the genetic diversity of SIVmus, we analyzed two full-length genomes of new strains identified in Gabon. The whole genomes obtained showed the expected reading frames for gag, pol, vif, vpr, tat, rev, env, nef, and also for a vpu gene. Analyses showed that the Gabonese SIVmus strains were closely related and formed a monophyletic clade within the SIVmus/mon/gsn lineage. Nonetheless, within this lineage, the position of both new SIVmus differed according to the gene analyzed. In pol and nef gene, phylogenetic topologies suggested different evolutions for each of the two new SIVmus strains whereas in the other nucleic fragments studied, their positions fluctuated between SIVmon, SIVmus-1, and SIVgsn. In addition, in C1 domain of env, we identified an insertion of seven amino acids characteristic for the SIVmus/mon/gsn and HIV‑1/SIVcpz/SIVgor lineages. Our results show a high genetic diversity of SIVmus in mustached monkeys and suggest cross-species transmission events and recombination within SIVmus/mon/gsn lineage. Additionally, in Central Africa, hunters continue to be exposed to these simian viruses, and this represents a potential threat to humans.
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18
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LeBreton M, Switzer WM, Djoko CF, Gillis A, Jia H, Sturgeon MM, Shankar A, Zheng H, Nkeunen G, Tamoufe U, Nana A, Le Doux Diffo J, Tafon B, Kiyang J, Schneider BS, Burke DS, Wolfe ND. A gorilla reservoir for human T-lymphotropic virus type 4. Emerg Microbes Infect 2014; 3:e7. [PMID: 26038495 PMCID: PMC3913825 DOI: 10.1038/emi.2014.7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/05/2013] [Accepted: 12/10/2013] [Indexed: 12/18/2022]
Abstract
Of the seven known species of human retroviruses only one, human T-cell lymphotropic virus type 4 (HTLV-4), lacks a known animal reservoir. We report the largest screening for simian T-cell lymphotropic virus (STLV-4) to date in a wide range of captive and wild non-human primate (NHP) species from Cameroon. Among the 681 wild and 426 captive NHPs examined, we detected STLV-4 infection only among gorillas by using HTLV-4-specific quantitative polymerase chain reaction. The large number of samples analyzed, the diversity of NHP species examined, the geographic distribution of infected animals relative to the known HTLV-4 case, as well as detailed phylogenetic analyses on partial and full genomes, indicate that STLV-4 is endemic to gorillas, and that rather than being an ancient virus among humans, HTLV-4 emerged from a gorilla reservoir, likely through the hunting and butchering of wild gorillas. Our findings shed further light on the importance of gorillas as keystone reservoirs for the evolution and emergence of human infectious diseases and provide a clear course for preventing HTLV-4 emergence through management of human contact with wild gorillas, the development of improved assays for HTLV-4/STLV-4 detection and the ongoing monitoring of STLV-4 among gorillas and for HTLV-4 zoonosis among individuals exposed to gorilla populations.
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Affiliation(s)
- Matthew LeBreton
- Mosaic, (Environment, Health, Data, Technology) , Yaoundé, Cameroon ; Global Viral Cameroon , BP 7039 Yaounde, Cameroon ; Metabiota , San Francisco, CA 94104, USA
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, GA 30333, USA
| | | | - Amethyst Gillis
- Global Viral Cameroon , BP 7039 Yaounde, Cameroon ; Metabiota , San Francisco, CA 94104, USA
| | - Hongwei Jia
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, GA 30333, USA
| | - Michele M Sturgeon
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, GA 30333, USA
| | - Anupama Shankar
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, GA 30333, USA
| | - Haoqiang Zheng
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, GA 30333, USA
| | | | - Ubald Tamoufe
- Global Viral Cameroon , BP 7039 Yaounde, Cameroon ; Metabiota , San Francisco, CA 94104, USA
| | - Ahmadou Nana
- Global Viral Cameroon , BP 7039 Yaounde, Cameroon
| | | | - Babila Tafon
- Ape Action Africa, Cameroon , BP 20072 Yaounde, Cameroon
| | | | | | - Donald S Burke
- Graduate School of Public Health, University of Pittsburgh , Pittsburgh, PA 15213, USA
| | - Nathan D Wolfe
- Metabiota , San Francisco, CA 94104, USA ; Program in Human Biology, Stanford University , Stanford, CA 94305, USA ; Global Viral , San Francisco, CA 94104, USA
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Peeters M, D’Arc M, Delaporte E. Origin and diversity of human retroviruses. AIDS Rev 2014; 16:23-34. [PMID: 24584106 PMCID: PMC4289907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Simian immunodeficiency viruses, simian T‑cell lymphotropic viruses, and simian foamy viruses from nonhuman primates have crossed the species barrier to humans at several time points, leading to the HIV and human T lymphotropic virus epidemic and to sporadic cases of human infections with simian foamy viruses, respectively. Efficient infection and spread in humans differs between simian foamy virus, simian lymphotropic virus, and simian immunodeficiency virus, but seems also to differ among the different viruses from the same simian lineage, as illustrated by the different spread of HIV‑1 M, N O, P or for the different HIV‑2 groups. Among the four HIV‑1 groups, only HIV‑1 group M has spread worldwide, and the actual diversity within HIV‑1 M (subtypes, circulating recombinants) is the result of subsequent evolution and spread in the human population. HIV‑2 only spread to some extent in West Africa, and similarly as for HIV‑1, the nine HIV‑2 groups have also a different epidemic history. Four types of human T lymphotropic virus, type 1 to 4, have been described in humans and for three of them simian counterparts (simian T lymphotropic virus‑1, ‑2, ‑3) have been identified in multiple nonhuman primate species. The majority of human infections are with human T lymphotropic virus‑1, which is present throughout the world as clusters of high endemicity. Humans are susceptible to a wide variety of simian foamy viruses and seem to acquire these viruses more readily than simian immunodeficiency viruses or simian T lymphotropic viruses, but neither signs of disease in humans nor human‑to‑human transmission of simian foamy virus have been documented yet. The current HIV‑1 M epidemic illustrates the impact of a single cross‑species transmission. The recent discovery of HIV‑1 P, HIV‑2 I, new human T lymphotropic virus‑1 and ‑3 variants, as well as simian foamy virus infections in humans in Central Africa, show that our knowledge of genetic diversity and cross‑species transmissions of simian retroviruses is still incomplete.
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Affiliation(s)
- Martine Peeters
- UMI 233, Institut de Recherche pour le Développement (IRD) and University of Montpellier 1, Montpellier, France
- Computational Biology Institute, Montpellier, France
| | - Mirela D’Arc
- UMI 233, Institut de Recherche pour le Développement (IRD) and University of Montpellier 1, Montpellier, France
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eric Delaporte
- UMI 233, Institut de Recherche pour le Développement (IRD) and University of Montpellier 1, Montpellier, France
- Universitary Hospital Gui de Chauliac, Montpellier, France
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20
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Lauck M, Switzer WM, Sibley SD, Hyeroba D, Tumukunde A, Weny G, Taylor B, Shankar A, Ting N, Chapman CA, Friedrich TC, Goldberg TL, O'Connor DH. Discovery and full genome characterization of two highly divergent simian immunodeficiency viruses infecting black-and-white colobus monkeys (Colobus guereza) in Kibale National Park, Uganda. Retrovirology 2013; 10:107. [PMID: 24139306 PMCID: PMC4016034 DOI: 10.1186/1742-4690-10-107] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/03/2013] [Indexed: 01/06/2023] Open
Abstract
Background African non-human primates (NHPs) are natural hosts for simian immunodeficiency viruses (SIV), the zoonotic transmission of which led to the emergence of HIV-1 and HIV-2. However, our understanding of SIV diversity and evolution is limited by incomplete taxonomic and geographic sampling of NHPs, particularly in East Africa. In this study, we screened blood specimens from nine black-and-white colobus monkeys (Colobus guereza occidentalis) from Kibale National Park, Uganda, for novel SIVs using a combination of serology and “unbiased” deep-sequencing, a method that does not rely on genetic similarity to previously characterized viruses. Results We identified two novel and divergent SIVs, tentatively named SIVkcol-1 and SIVkcol-2, and assembled genomes covering the entire coding region for each virus. SIVkcol-1 and SIVkcol-2 were detected in three and four animals, respectively, but with no animals co-infected. Phylogenetic analyses showed that SIVkcol-1 and SIVkcol-2 form a lineage with SIVcol, previously discovered in black-and-white colobus from Cameroon. Although SIVkcol-1 and SIVkcol-2 were isolated from the same host population in Uganda, SIVkcol-1 is more closely related to SIVcol than to SIVkcol-2. Analysis of functional motifs in the extracellular envelope glycoprotein (gp120) revealed that SIVkcol-2 is unique among primate lentiviruses in containing only 16 conserved cysteine residues instead of the usual 18 or more. Conclusions Our results demonstrate that the genetic diversity of SIVs infecting black-and-white colobus across equatorial Africa is greater than previously appreciated and that divergent SIVs can co-circulate in the same colobine population. We also show that the use of “unbiased” deep sequencing for the detection of SIV has great advantages over traditional serological approaches, especially for studies of unknown or poorly characterized viruses. Finally, the detection of the first SIV containing only 16 conserved cysteines in the extracellular envelope protein gp120 further expands the range of functional motifs observed among SIVs and highlights the complex evolutionary history of simian retroviruses.
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Ayouba A, Duval L, Liégeois F, Ngin S, Ahuka-Mundeke S, Switzer WM, Delaporte E, Ariey F, Peeters M, Nerrienet E. Nonhuman primate retroviruses from Cambodia: high simian foamy virus prevalence, identification of divergent STLV-1 strains and no evidence of SIV infection. INFECTION GENETICS AND EVOLUTION 2013; 18:325-34. [PMID: 23612320 DOI: 10.1016/j.meegid.2013.04.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 04/05/2013] [Accepted: 04/06/2013] [Indexed: 10/26/2022]
Abstract
Nonhuman primates (NHPs) carry retroviruses such as simian immunodeficiency viruses (SIV), simian T-cell lymphotropic viruses (STLV) and simian foamy viruses (SFV). Here, we revisited NHPs from Cambodia to assess the prevalence and diversity of these retroviruses using updated viral detection tools. We screened blood from 118 NHPs consisting of six species (Macaca fascicularis (n=91), Macaca leonine (n=8), Presbytis cristata (n=3), Nycticebus coucang (n=1), Hylobates pileatus (n=14), and Pongo pygmaeus) (n=1) by using a Luminex-based multiplex serology assay that allows the detection of all known SIV/HIV and SFV lineages. We also used highly sensitive PCR assays to detect each simian retrovirus group. Positive PCR products were sequenced and phylogenetically analyzed to infer evolutionary histories. Fifty-three of 118 (44.9%) NHPs tested positive for SFV by serology and 8/52 (15.4%), all from M. fascicularis, were PCR-confirmed. The 8 novel SFV sequences formed a highly supported distinct lineage within a clade composed of other macaque SFV. We observed no serological or molecular evidence of SIV infection among the 118 NHP samples tested. Four of 118 (3.3%) NHPs were PCR-positive for STLV, including one M. fascicularis, one P. cristata, and two H. pileatus. Phylogenetic analyses revealed that the four novel STLV belonged to the PTLV-1 lineage, outside the African radiation of PTLV-1, like all Asian PTLV identified so far. Sequence analysis of the whole STLV-1 genome from a H. pileatus (C578_Hp) revealed a genetic structure characteristic of PTLV. Similarity analysis comparing the STLV-1 (C578_Hp) sequence with prototype PTLVs showed that C578_Hp is closer to PTLV-1s than to all other types across the entire genome. In conclusion, we showed a high frequency of SFV infection but found no evidence of SIV infection in NHPs from Cambodia. We identified for the first time STLV-1 in a P. cristata and in two H. pileatus.
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Affiliation(s)
- Ahidjo Ayouba
- UM1 233, Institut de Recherche pour le Développement-IRD and University of Montpellier 1, Montpellier, France.
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22
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Nagel M, Dischinger J, Türck M, Verrier D, Oedenkoven M, Ngoubangoye B, Le Flohic G, Drexler JF, Bierbaum G, Gonzalez JP. Human-associated Staphylococcus aureus strains within great ape populations in Central Africa (Gabon). Clin Microbiol Infect 2013; 19:1072-7. [PMID: 23398468 DOI: 10.1111/1469-0691.12119] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 11/02/2012] [Accepted: 11/25/2012] [Indexed: 12/12/2022]
Abstract
The risk of serious infections caused by Staphylococcus aureus is well-known. However, most studies regarding the distribution of (clinically relevant) S. aureus among humans and animals took place in the western hemisphere and only limited data are available from (Central) Africa. In this context, recent studies focused on S. aureus strains in humans and primates, but the question of whether humans and monkeys share related S. aureus strains or may interchange strains remained largely unsolved. In this study we aimed to evaluate the distribution and spread of human-like S. aureus strains among great apes living in captivity. Therefore, a primate facility at the International Centre for Medical Research of Franceville (Gabon) was screened. We detected among the primates a common human S. aureus strain, belonging to the spa-type t148. It was isolated from three different individuals of the western lowland gorilla (Gorilla gorilla gorilla), of which one individual showed a large necrotizing wound. This animal died, most probably of a staphylococcal sepsis. Additionally, we discovered the t148 type among chimpanzees (Pan troglodytes) that were settled in the immediate neighbourhood of the infected gorillas. A detailed analysis by pulsed field gel electrophoresis showed that the gorilla and chimpanzee isolates represented two closely related strains. To our knowledge, this is the first report of a human-associated S. aureus strain causing disease in great apes. The simultaneous detection in gorillas and chimpanzees indicated an interspecies transmission of this S. aureus strain. Our results recommend that protection of wild animals must not only be based on habitat conservation, but also on the assessment of the risk of contact with human pathogens.
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Affiliation(s)
- M Nagel
- International Centre for Medical Research of Franceville, Franceville, Gabon
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23
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Gessain A, Rua R, Betsem E, Turpin J, Mahieux R. HTLV-3/4 and simian foamy retroviruses in humans: discovery, epidemiology, cross-species transmission and molecular virology. Virology 2013; 435:187-99. [PMID: 23217627 PMCID: PMC7111966 DOI: 10.1016/j.virol.2012.09.035] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 09/28/2012] [Indexed: 12/20/2022]
Abstract
Non-human primates are considered to be likely sources of viruses that can infect humans and thus pose a significant threat to human population. This is well illustrated by some retroviruses, as the simian immunodeficiency viruses and the simian T lymphotropic viruses, which have the ability to cross-species, adapt to a new host and sometimes spread. This leads to a pandemic situation for HIV-1 or an endemic one for HTLV-1. Here, we present the available data on the discovery, epidemiology, cross-species transmission and molecular virology of the recently discovered HTLV-3 and HTLV-4 deltaretroviruses, as well as the simian foamy retroviruses present in different human populations at risk, especially in central African hunters. We discuss also the natural history in humans of these retroviruses of zoonotic origin (magnitude and geographical distribution, possible inter-human transmission). In Central Africa, the increase of the bushmeat trade during the last decades has opened new possibilities for retroviral emergence in humans, especially in immuno-compromised persons.
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Affiliation(s)
- Antoine Gessain
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, France, Département de Virologie, Institut Pasteur, 25-28 rue du Dr Roux, 75724 Paris, Cedex 15, France.
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24
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Convergence and divergence in the evolution of the APOBEC3G-Vif interaction reveal ancient origins of simian immunodeficiency viruses. PLoS Pathog 2013; 9:e1003135. [PMID: 23359341 PMCID: PMC3554591 DOI: 10.1371/journal.ppat.1003135] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 12/03/2012] [Indexed: 01/05/2023] Open
Abstract
Naturally circulating lentiviruses are abundant in African primate species today, yet their origins and history of transmitting between hosts remain obscure. As a means to better understand the age of primate lentiviruses, we analyzed primate genomes for signatures of lentivirus-driven evolution. Specifically, we studied the adaptive evolution of host restriction factor APOBEC3G (A3G) in Old World Monkey (OWM) species. We find recurrent mutation of A3G in multiple primate lineages at sites that determine susceptibility to antagonism by the lentiviral accessory protein Vif. Using a broad panel of SIV Vif isolates, we demonstrate that natural variation in OWM A3G confers resistance to Vif-mediated degradation, suggesting that adaptive variants of the host factor were selected upon exposure to pathogenic lentiviruses at least 5–6 million years ago (MYA). Furthermore, in members of the divergent Colobinae subfamily of OWM, a multi-residue insertion event in A3G that arose at least 12 MYA blocks the activity of Vif, suggesting an even more ancient origin of SIV. Moreover, analysis of the lentiviruses associated with Colobinae monkeys reveal that the interface of the A3G-Vif interaction has shifted and given rise to a second genetic conflict. Our analysis of virus-driven evolution describes an ancient yet ongoing genetic conflict between simian primates and lentiviruses on a million-year time scale. The emergence of AIDS in the late 20th century has provoked studies to better understand the evolutionary history of viruses and the factors that govern their spread. Pandemic human immunodeficiency virus-type 1 (HIV-1), which currently infects 34 million people worldwide, emerged following the transmission of a lentivirus between chimpanzees and humans. A growing list of apparently nonpathogenic, species-specific strains has now been characterized in dozens of African primates, suggesting that primate lentiviruses are older and more widespread than originally thought. To estimate the extent to which primates and lentiviruses have coexisted, we examined the interaction between host and virus on a molecular level and tracked its dynamics over evolutionary time. We report that the immunity factor APOBEC3G is evolving in tandem with the lentiviral accessory gene vif, allowing us to associate instances of host evolution with instances of lentivirus infection in deep and shallow timescales. Specifically, we show that the region of APOBEC3G targeted by Vif is adaptively diversifying in independent primate lineages in a manner that suggests that lentiviruses are millions of years old. Our study reveals that, while primate lentiviruses may have modern consequences for human health, they have ancient origins in our non-human primate relatives.
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