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Tebit DM, Nickel G, Gibson R, Rodriguez M, Hathaway NJ, Bain K, Reyes-Rodriguez AL, Ondoa P, Heeney JL, Li Y, Bongorno J, Canaday D, McDonald D, Bailey JA, Arts EJ. Replicative fitness and pathogenicity of primate lentiviruses in lymphoid tissue, primary human and chimpanzee cells: relation to possible jumps to humans. EBioMedicine 2024; 100:104965. [PMID: 38215691 PMCID: PMC10827413 DOI: 10.1016/j.ebiom.2023.104965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Simian immunodeficiency viruses (SIV) have been jumping between non-human primates in West/Central Africa for thousands of years and yet, the HIV-1 epidemic only originated from a primate lentivirus over 100 years ago. METHODS This study examined the replicative fitness, transmission, restriction, and cytopathogenicity of 22 primate lentiviruses in primary human lymphoid tissue and both primary human and chimpanzee peripheral blood mononuclear cells. FINDINGS Pairwise competitions revealed that SIV from chimpanzees (cpz) had the highest replicative fitness in human or chimpanzee peripheral blood mononuclear cells, even higher fitness than HIV-1 group M strains responsible for worldwide epidemic. The SIV strains belonging to the "HIV-2 lineage" (including SIVsmm, SIVmac, SIVagm) had the lowest replicative fitness. SIVcpz strains were less inhibited by human restriction factors than the "HIV-2 lineage" strains. SIVcpz efficiently replicated in human tonsillar tissue but did not deplete CD4+ T-cells, consistent with the slow or nonpathogenic disease observed in most chimpanzees. In contrast, HIV-1 isolates and SIV of the HIV-2 lineage were pathogenic to the human tonsillar tissue, almost independent of the level of virus replication. INTERPRETATION Of all primate lentiviruses, SIV from chimpanzees appears most capable of infecting and replicating in humans, establishing HIV-1. SIV from other Old World monkeys, e.g. the progenitor of HIV-2, replicate slowly in humans due in part to restriction factors. Nonetheless, many of these SIV strains were more pathogenic than SIVcpz. Either SIVcpz evolved into a more pathogenic virus while in humans or a rare SIVcpz, possibly extinct in chimpanzees, was pathogenic immediately following the jump into human. FUNDING Support for this study to E.J.A. was provided by the NIH/NIAID R01 AI49170 and CIHR project grant 385787. Infrastructure support was provided by the NIH CFAR AI36219 and Canadian CFI/Ontario ORF 36287. Efforts of J.A.B. and N.J.H. was provided by NIH AI099473 and for D.H.C., by VA and NIH AI AI080313.
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Affiliation(s)
- Denis M Tebit
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Global Biomed Scientific, LLC, P.O. Box 2368, Forest, VA, USA
| | - Gabrielle Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Richard Gibson
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Myriam Rodriguez
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Nicolas J Hathaway
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Katie Bain
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Angel L Reyes-Rodriguez
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Pascal Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia; Department of Global Health, Institute of Global Health and Development, University of Amsterdam, Amsterdam, the Netherlands
| | - Jonathan L Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Yue Li
- Department of Microbiology and Immunology, Western University, Ontario, Canada
| | - Jennifer Bongorno
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - David Canaday
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - David McDonald
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Eric J Arts
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Microbiology and Immunology, Western University, Ontario, Canada.
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2
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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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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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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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5
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The well-tempered SIV infection: Pathogenesis of SIV infection in natural hosts in the wild, with emphasis on virus transmission and early events post-infection that may contribute to protection from disease progression. INFECTION GENETICS AND EVOLUTION 2016; 46:308-323. [PMID: 27394696 DOI: 10.1016/j.meegid.2016.07.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 07/04/2016] [Accepted: 07/05/2016] [Indexed: 12/25/2022]
Abstract
African NHPs are infected by over 40 different simian immunodeficiency viruses. These viruses have coevolved with their hosts for long periods of time and, unlike HIV in humans, infection does not generally lead to disease progression. Chronic viral replication is maintained for the natural lifespan of the host, without loss of overall immune function. Lack of disease progression is not correlated with transmission, as SIV infection is highly prevalent in many African NHP species in the wild. The exact mechanisms by which these natural hosts of SIV avoid disease progression are still unclear, but a number of factors might play a role, including: (i) avoidance of microbial translocation from the gut lumen by preventing or repairing damage to the gut epithelium; (ii) control of immune activation and apoptosis following infection; (iii) establishment of an anti-inflammatory response that resolves chronic inflammation; (iv) maintenance of homeostasis of various immune cell populations, including NK cells, monocytes/macrophages, dendritic cells, Tregs, Th17 T-cells, and γδ T-cells; (v) restriction of CCR5 availability at mucosal sites; (vi) preservation of T-cell function associated with down-regulation of CD4 receptor. Some of these mechanisms might also be involved in protection of natural hosts from mother-to-infant SIV transmission during breastfeeding. The difficulty of performing invasive studies in the wild has prohibited investigation of the exact events surrounding transmission in natural hosts. Increased understanding of the mechanisms of SIV transmission in natural hosts, and of the early events post-transmission which may contribute to avoidance of disease progression, along with better comprehension of the factors involved in protection from SIV breastfeeding transmission in the natural hosts, could prove invaluable for the development of new prevention strategies for HIV.
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Alcala N, Jensen JD, Telenti A, Vuilleumier S. The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV. G3 (BETHESDA, MD.) 2015; 6:107-20. [PMID: 26546308 PMCID: PMC4704709 DOI: 10.1534/g3.115.024208] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 11/02/2015] [Indexed: 01/19/2023]
Abstract
Ease of worldwide travel provides increased opportunities for organisms not only to colonize new environments but also to encounter related but diverged populations. Such events of reconnection and secondary contact of previously isolated populations are widely observed at different time scales. For example, during the quaternary glaciation, sea water level fluctuations caused temporal isolation of populations, often to be followed by secondary contact. At shorter time scales, population isolation and reconnection of viruses are commonly observed, and such events are often associated with epidemics and pandemics. Here, using coalescent theory and simulations, we describe the temporal impact of population reconnection after isolation on nucleotide differences and the site frequency spectrum, as well as common summary statistics of DNA variation. We identify robust genomic signatures of population reconnection after isolation. We utilize our development to infer the recent evolutionary history of human immunodeficiency virus 1 (HIV-1) in Asia and South America, successfully retrieving the successive HIV subtype colonization events in these regions. Our analysis reveals that divergent HIV-1 subtype populations are currently admixing in these regions, suggesting that HIV-1 may be undergoing a process of homogenization, contrary to popular belief.
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Affiliation(s)
- Nicolas Alcala
- Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland Department of Biology, Stanford University, Stanford, California 94305-5020
| | - Jeffrey D Jensen
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Amalio Telenti
- Genomic Medicine, The J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037
| | - Séverine Vuilleumier
- Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland Institute of Microbiology, University Hospital and University of Lausanne, Lausanne CH-1011, Switzerland
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7
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Abstract
PURPOSE OF REVIEW An improved understanding of how recombination affects the evolutionary history of HIV is crucial to understand its current and future evolution. The present review aims to disentangle the manifold effects of recombination on HIV by discussing its effects on the evolutionary history and the adaptive potential of HIV in the context of concepts from evolutionary genetics and genomics. RECENT FINDINGS The increasing occurrence of secondary contacts between divergent subtype populations (during coinfection) results in increased observations of recombinants worldwide. Recombination is heterogeneous along the HIV genome. Consequences of recombination of HIV evolution are, in combination with other demographic processes, expected to either homogenize the genetic composition of HIV populations (homogenization) or provide the potential for novel adaptations (diversification). New methods in population genomics allow deep characterization of recombinant genome (the segment composition and origin) and their evolutionary trajectories. SUMMARY HIV recombinants increase worldwide and invade geographical regions where pure subtypes were previously predominant. This trend is expected to continue in the future, as ease to travel worldwide increases opportunities for recombination between divergent HIV strains. While the effects of recombination in HIV are much researched, more effort is required to characterize current HIV recombinant composition and dynamics. This can be achieved with new population genetic and genomic methods.
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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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9
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Ayouba A, Njouom R, Chia JE, Ahuka-Mundeke S, Kfutwah A, Ngole EM, Nerrienet E, Delaporte E, Peeters M. Molecular characterization of a new mosaic Simian Immunodeficiency Virus in a naturally infected tantalus monkey (Chlorocebus tantalus) from Cameroon: a challenge to the virus-host co-evolution of SIVagm in African green monkeys. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 30:65-73. [PMID: 25500294 PMCID: PMC4680966 DOI: 10.1016/j.meegid.2014.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/21/2014] [Accepted: 12/02/2014] [Indexed: 10/24/2022]
Abstract
African green monkeys (AGMs) represent the most widely distributed non-human primates species in Africa. SIVagm naturally infects four of the 6 AGMs species at high prevalence in a species-specific manner. To date, only limited information is available on molecular characteristics of SIVagm infecting Chlorocebus tantalus. Here, we characterized the full-length genome of a virus infecting a naturally infected captive C. tantalus from Cameroon by amplifying and sequencing sub-genomic PCR fragments. The isolate (SIVagmTAN-CM545) is 9923bp long and contained all canonical genes of a functional SIV. SIVagmTAN-CM545 showed a mosaic structure, with gag, pol, nef and accessory genes closely related to SIVagmSAB infecting Chlorocebus sabaeus monkeys from west Africa, and the env gene, closely related to SIVagmTAN infecting tantalus monkeys from Central Africa. Thus SIVagmTAN-CM545 is SIVagmSAB/SIVagmTAN recombinant. These unexpected findings suggest that the evolution of SIVagm is more complex than previously thought and warrant further studies.
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Affiliation(s)
- Ahidjo Ayouba
- UMI 233, IRD and University of Montpellier 1, Montpellier, France.
| | - Richard Njouom
- Service de Virologie, Centre Pasteur du Cameroun, Yaoundé, Cameroon
| | | | | | - Anfumbom Kfutwah
- Service de Virologie, Centre Pasteur du Cameroun, Yaoundé, Cameroon
| | | | - Eric Nerrienet
- Service de Virologie, Centre Pasteur du Cameroun, Yaoundé, Cameroon
| | - Eric Delaporte
- UMI 233, IRD and University of Montpellier 1, Montpellier, France
| | - Martine Peeters
- UMI 233, IRD and University of Montpellier 1, Montpellier, France; Institut de Biologie Computationnelle, Montpellier, France
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