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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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Phillips SR. MHC-B Diversity and Signs of Respiratory Illness in Wild, East African Chimpanzees ( Pan troglodytes schweinfurthii ). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551731. [PMID: 37577711 PMCID: PMC10418158 DOI: 10.1101/2023.08.02.551731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Many traits, intrinsic and extrinsic to an organism, contribute to interindividual variation in immunity in wild habitats. The vertebrate Major Histocompatibility Complex (MHC) includes genes encoding antigen-presenting molecules that are highly variable, and that variation often predicts susceptibility/resistance to and recovery from pathogen infection. I compare MHC-B variation at two long-term chimpanzee research sites, Kibale National Park in Uganda and Gombe National Park in Tanzania. Using decades of respiratory health data available for these chimpanzees, I test hypotheses associated with maintenance of diversity at MHC loci, including heterozygote, divergent allele, and rare allele advantage hypotheses, and predictions for unique function of MHC-B in great apes. I found, despite confirmation of recent shared ancestry between Kibale and Gombe chimpanzees, including an overlapping MHC-B allele repertoire and similar MHC-B phenotype compositions, chimpanzees from the two research sites experienced differences in the occurrence of respiratory signs and had different associations of MHC-B diversity with signs of respiratory illness. Kibale chimpanzees with heterozygous genotypes and different peptide-binding supertypes were observed less often with respiratory signs than those homozygous or possessing the same supertypes, but this same association was not observed among Gombe chimpanzees. Gombe chimpanzees with specific MHC-B phenotypes that enable engagement of Natural Killer (NK) cells were observed more often with respiratory signs than chimpanzees with other phenotypes, but this was not observed at Kanyawara. This study emphasizes local adaptation in shaping genetic and phenotypic traits in different infectious disease contexts, even among close genetic relatives of the same subspecies, and highlights utility for continued and simultaneous tracking of host immune genes and specific pathogens in wild species.
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Olabode AS, Mumby MJ, Wild TA, Muñoz-Baena L, Dikeakos JD, Poon AFY. Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses. Mol Biol Evol 2023; 40:msad164. [PMID: 37463439 PMCID: PMC10400143 DOI: 10.1093/molbev/msad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
Nef is an accessory protein unique to the primate HIV-1, HIV-2, and SIV lentiviruses. During infection, Nef functions by interacting with multiple host proteins within infected cells to evade the immune response and enhance virion infectivity. Notably, Nef can counter immune regulators such as CD4 and MHC-I, as well as the SERINC5 restriction factor in infected cells. In this study, we generated a posterior sample of time-scaled phylogenies relating SIV and HIV Nef sequences, followed by reconstruction of ancestral sequences at the root and internal nodes of the sampled trees up to the HIV-1 Group M ancestor. Upon expression of the ancestral primate lentivirus Nef protein within CD4+ HeLa cells, flow cytometry analysis revealed that the primate lentivirus Nef ancestor robustly downregulated cell-surface SERINC5, yet only partially downregulated CD4 from the cell surface. Further analysis revealed that the Nef-mediated CD4 downregulation ability evolved gradually, while Nef-mediated SERINC5 downregulation was recovered abruptly in the HIV-1/M ancestor. Overall, this study provides a framework to reconstruct ancestral viral proteins and enable the functional characterization of these proteins to delineate how functions could have changed throughout evolutionary history.
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Affiliation(s)
- Abayomi S Olabode
- Department of Pathology & Laboratory Medicine, Western University, London, Canada
| | - Mitchell J Mumby
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Tristan A Wild
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Laura Muñoz-Baena
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Jimmy D Dikeakos
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Art F Y Poon
- Department of Pathology & Laboratory Medicine, Western University, London, Canada
- Department of Microbiology & Immunology, Western University, London, Canada
- Department of Computer Science, Western University, London, Canada
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4
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Sanders JG, Sprockett DD, Li Y, Mjungu D, Lonsdorf EV, Ndjango JBN, Georgiev AV, Hart JA, Sanz CM, Morgan DB, Peeters M, Hahn BH, Moeller AH. Widespread extinctions of co-diversified primate gut bacterial symbionts from humans. Nat Microbiol 2023:10.1038/s41564-023-01388-w. [PMID: 37169918 DOI: 10.1038/s41564-023-01388-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Humans and other primates harbour complex gut bacterial communities that influence health and disease, but the evolutionary histories of these symbioses remain unclear. This is partly due to limited information about the microbiota of ancestral primates. Here, using phylogenetic analyses of metagenome-assembled genomes (MAGs), we show that hundreds of gut bacterial clades diversified in parallel (that is, co-diversified) with primate species over millions of years, but that humans have experienced widespread losses of these ancestral symbionts. Analyses of 9,460 human and non-human primate MAGs, including newly generated MAGs from chimpanzees and bonobos, revealed significant co-diversification within ten gut bacterial phyla, including Firmicutes, Actinobacteriota and Bacteroidota. Strikingly, ~44% of the co-diversifying clades detected in African apes were absent from available metagenomic data from humans and ~54% were absent from industrialized human populations. In contrast, only ~3% of non-co-diversifying clades detected in African apes were absent from humans. Co-diversifying clades present in both humans and chimpanzees displayed consistent genomic signatures of natural selection between the two host species but differed in functional content from co-diversifying clades lost from humans, consistent with selection against certain functions. This study discovers host-species-specific bacterial symbionts that predate hominid diversification, many of which have undergone accelerated extinctions from human populations.
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Affiliation(s)
- Jon G Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Daniel D Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Deus Mjungu
- Gombe Stream Research Center, Kigoma, Tanzania
| | - Elizabeth V Lonsdorf
- Department of Psychology and Biological Foundations of Behavior Program, Franklin and Marshall College, Lancaster, PA, USA
- Department of Anthropology, Emory University, Atlanta, GA, 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
| | - Alexander V Georgiev
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- School of Natural Sciences, Bangor University, Bangor, UK
| | - John A Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, Kinshasa, Democratic Republic of the Congo
| | - Crickette M Sanz
- Department of Anthropology, Washington University in St Louis, Saint Louis, MO, USA
- Wildlife Conservation Society, Congo Program, Brazzaville, Republic of Congo
| | - David B Morgan
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, IL, USA
| | - Martine Peeters
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, Montpellier, France
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
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5
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Jasinska AJ, Apetrei C, Pandrea I. Walk on the wild side: SIV infection in African non-human primate hosts-from the field to the laboratory. Front Immunol 2023; 13:1060985. [PMID: 36713371 PMCID: PMC9878298 DOI: 10.3389/fimmu.2022.1060985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/15/2022] [Indexed: 01/15/2023] Open
Abstract
HIV emerged following cross-species transmissions of simian immunodeficiency viruses (SIVs) that naturally infect non-human primates (NHPs) from Africa. While HIV replication and CD4+ T-cell depletion lead to increased gut permeability, microbial translocation, chronic immune activation, and systemic inflammation, the natural hosts of SIVs generally avoid these deleterious consequences when infected with their species-specific SIVs and do not progress to AIDS despite persistent lifelong high viremia due to long-term coevolution with their SIV pathogens. The benign course of natural SIV infection in the natural hosts is in stark contrast to the experimental SIV infection of Asian macaques, which progresses to simian AIDS. The mechanisms of non-pathogenic SIV infections are studied mainly in African green monkeys, sooty mangabeys, and mandrills, while progressing SIV infection is experimentally modeled in macaques: rhesus macaques, pigtailed macaques, and cynomolgus macaques. Here, we focus on the distinctive features of SIV infection in natural hosts, particularly (1): the superior healing properties of the intestinal mucosa, which enable them to maintain the integrity of the gut barrier and prevent microbial translocation, thus avoiding excessive/pathologic immune activation and inflammation usually perpetrated by the leaking of the microbial products into the circulation; (2) the gut microbiome, the disruption of which is an important factor in some inflammatory diseases, yet not completely understood in the course of lentiviral infection; (3) cell population shifts resulting in target cell restriction (downregulation of CD4 or CCR5 surface molecules that bind to SIV), control of viral replication in the lymph nodes (expansion of natural killer cells), and anti-inflammatory effects in the gut (NKG2a/c+ CD8+ T cells); and (4) the genes and biological pathways that can shape genetic adaptations to viral pathogens and are associated with the non-pathogenic outcome of the natural SIV infection. Deciphering the protective mechanisms against SIV disease progression to immunodeficiency, which have been established through long-term coevolution between the natural hosts and their species-specific SIVs, may prompt the development of novel therapeutic interventions, such as drugs that can control gut inflammation, enhance gut healing capacities, or modulate the gut microbiome. These developments can go beyond HIV infection and open up large avenues for correcting gut damage, which is common in many diseases.
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Affiliation(s)
- Anna J. Jasinska
- Division of Infectious Diseases, Department of Medicine (DOM), School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Cristian Apetrei
- Division of Infectious Diseases, Department of Medicine (DOM), School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States,Department of Infectious Diseases and Immunology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ivona Pandrea
- Department of Infectious Diseases and Immunology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States,Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States,*Correspondence: Ivona Pandrea,
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6
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Sanders JG, Yan W, Mjungu D, Lonsdorf EV, Hart JA, Sanz CM, Morgan DB, Peeters M, Hahn BH, Moeller AH. A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes. Genome Biol 2022; 23:212. [PMID: 36224660 PMCID: PMC9558970 DOI: 10.1186/s13059-022-02777-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
Earth's environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. Here, we present a workflow for bacterial whole-genome sequencing using open-source labware and the OpenTrons robotics platform, reducing costs to approximately $10 per genome. We assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos. We quantify intraspecific genomic diversity and reveal divergence of homologous plasmids between hosts. This enables population genetic analyses of bacterial strains not currently possible with metagenomic data alone.
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Affiliation(s)
- Jon G Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
| | - Weiwei Yan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Deus Mjungu
- Gombe Stream Research Center, Kigoma, Tanzania
| | - Elizabeth V Lonsdorf
- Department of Psychology and Biological Foundations of Behavior Program, Franklin and Marshall College, Lancaster, PA, USA.,Department of Anthropology, Emory University, Atlanta, GA, 30322, USA
| | - John A Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - Crickette M Sanz
- Department of Anthropology, Washington University in St. Louis, 1 Brookings Drive, Saint Louis, MO, USA.,Wildlife Conservation Society, Congo Program, Brazzaville, B.P. 14537, Republic of Congo
| | - David B Morgan
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, IL, USA
| | - Martine Peeters
- Recherche Translationnelle Appliquée Au VIH Et Aux Maladies Infectieuses, Institut de Recherche Pour Le Développement, University of Montpellier, INSERM, 34090, Montpellier, France
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
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7
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Scully EJ, Liu W, Li Y, Ndjango JBN, Peeters M, Kamenya S, Pusey AE, Lonsdorf EV, Sanz CM, Morgan DB, Piel AK, Stewart FA, Gonder MK, Simmons N, Asiimwe C, Zuberbühler K, Koops K, Chapman CA, Chancellor R, Rundus A, Huffman MA, Wolfe ND, Duraisingh MT, Hahn BH, Wrangham RW. The ecology and epidemiology of malaria parasitism in wild chimpanzee reservoirs. Commun Biol 2022; 5:1020. [PMID: 36167977 PMCID: PMC9515101 DOI: 10.1038/s42003-022-03962-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/01/2022] [Indexed: 11/09/2022] Open
Abstract
Chimpanzees (Pan troglodytes) harbor rich assemblages of malaria parasites, including three species closely related to P. falciparum (sub-genus Laverania), the most malignant human malaria parasite. Here, we characterize the ecology and epidemiology of malaria infection in wild chimpanzee reservoirs. We used molecular assays to screen chimpanzee fecal samples, collected longitudinally and cross-sectionally from wild populations, for malaria parasite mitochondrial DNA. We found that chimpanzee malaria parasitism has an early age of onset and varies seasonally in prevalence. A subset of samples revealed Hepatocystis mitochondrial DNA, with phylogenetic analyses suggesting that Hepatocystis appears to cross species barriers more easily than Laverania. Longitudinal and cross-sectional sampling independently support the hypothesis that mean ambient temperature drives spatiotemporal variation in chimpanzee Laverania infection. Infection probability peaked at ~24.5 °C, consistent with the empirical transmission optimum of P. falciparum in humans. Forest cover was also positively correlated with spatial variation in Laverania prevalence, consistent with the observation that forest-dwelling Anophelines are the primary vectors. Extrapolating these relationships across equatorial Africa, we map spatiotemporal variation in the suitability of chimpanzee habitat for Laverania transmission, offering a hypothetical baseline indicator of human exposure risk.
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Affiliation(s)
- Erik J Scully
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Immunology & Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Weimin Liu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jean-Bosco N Ndjango
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, BP 2012, Kisangani, Democratic Republic of the Congo
| | - Martine Peeters
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090, Montpellier, France
| | - Shadrack Kamenya
- Gombe Stream Research Centre, The Jane Goodall Institute, Tanzania, Kigoma, Tanzania
| | - Anne E Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA
| | - Elizabeth V Lonsdorf
- Department of Psychology, Franklin and Marshall College, Lancaster, PA, 17604, USA
| | - Crickette M Sanz
- Department of Anthropology, Washington University in St. Louis, St Louis, MO, 63130, USA.,Congo Program, Wildlife Conservation Society, BP 14537, Brazzaville, Republic of the Congo
| | - David B Morgan
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, IL, 60614, USA
| | - Alex K Piel
- Department of Anthropology, University College London, 14 Taviton St, Bloomsbury, WC1H OBW, London, UK
| | - Fiona A Stewart
- Department of Anthropology, University College London, 14 Taviton St, Bloomsbury, WC1H OBW, London, UK.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Mary K Gonder
- Department of Biology, Drexel University, Philadelphia, PA, 19104, USA
| | - Nicole Simmons
- Zoology Department, Makerere University, P.O. Box 7062, Kampala, Uganda
| | | | - Klaus Zuberbühler
- School of Psychology and Neuroscience, University of St Andrews, St Andrews, UK.,Department of Comparative Cognition, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Kathelijne Koops
- Department of Ape Behaviour & Ecology Group, University of Zurich, Zurich, Switzerland
| | - Colin A Chapman
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, DC, USA.,School of Life Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Rebecca Chancellor
- Department of Anthropology & Sociology, West Chester University, West Chester, PA, USA.,Department of Psychology, West Chester University, West Chester, PA, USA
| | - Aaron Rundus
- Department of Psychology, West Chester University, West Chester, PA, USA
| | - Michael A Huffman
- Center for International Collaboration and Advanced Studies in Primatology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | | | - Manoj T Duraisingh
- Department of Immunology & Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Richard W Wrangham
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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8
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Pawar H, Ostridge HJ, Schmidt JM, Andrés AM. Genetic adaptations to SIV across chimpanzee populations. PLoS Genet 2022; 18:e1010337. [PMID: 36007015 PMCID: PMC9467346 DOI: 10.1371/journal.pgen.1010337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 09/12/2022] [Accepted: 07/12/2022] [Indexed: 11/18/2022] Open
Abstract
Central and eastern chimpanzees are infected with Simian Immunodeficiency Virus (SIV) in the wild, typically without developing acute immunodeficiency. Yet the recent zoonotic transmission of chimpanzee SIV to humans, which were naïve to the virus, gave rise to the Human Immunodeficiency Virus (HIV), which causes AIDS and is responsible for one of the deadliest pandemics in human history. Chimpanzees have likely been infected with SIV for tens of thousands of years and have likely evolved to reduce its pathogenicity, becoming semi-natural hosts that largely tolerate the virus. In support of this view, central and eastern chimpanzees show evidence of positive selection in genes involved in SIV/HIV cell entry and immune response to SIV, respectively. We hypothesise that the population first infected by SIV would have experienced the strongest selective pressure to control the lethal potential of zoonotic SIV, and that population genetics will reveal those first critical adaptations. With that aim we used population genetics to investigate signatures of positive selection in the common ancestor of central-eastern chimpanzees. The genes with signatures of positive selection in the ancestral population are significantly enriched in SIV-related genes, especially those involved in the immune response to SIV and those encoding for host genes that physically interact with SIV/HIV (VIPs). This supports a scenario where SIV first infected the central-eastern ancestor and where this population was under strong pressure to adapt to zoonotic SIV. Interestingly, integrating these genes with candidates of positive selection in the two infected subspecies reveals novel patterns of adaptation to SIV. Specifically, we observe evidence of positive selection in numerous steps of the biological pathway responsible for T-helper cell differentiation, including CD4 and multiple genes that SIV/HIV use to infect and control host cells. This pathway is active only in CD4+ cells which SIV/HIV infects, and it plays a crucial role in shaping the immune response so it can efficiently control the virus. Our results confirm the importance of SIV as a selective factor, identify specific genetic changes that may have allowed our closest living relatives to reduce SIV’s pathogenicity, and demonstrate the potential of population genomics to reveal the evolutionary mechanisms used by naïve hosts to reduce the pathogenicity of zoonotic pathogens. Chimpanzees are at the origin of HIV-1, a virus that generates an incurable disease and that generated a pandemic that has claimed 35 million lives. Chimpanzees have evolved to control the pathogenicity of the virus, which does not typically develop into AIDS in the same way as in humans. Identifying the genetic adaptations responsible for this process provides critical knowledge about SIV and HIV. Our analysis of chimpanzee genetic adaptations identified specific genes and molecular pathways involved in adaptation to SIV, providing important insights into the mechanisms that likely allowed our closest living relatives to control SIV/HIV. Further, we establish SIV as a strong and recurrent selective pressure in central and eastern chimpanzees, two important subspecies of large mammals that are currently endangered.
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Affiliation(s)
- Harvinder Pawar
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Harrison J. Ostridge
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Joshua M. Schmidt
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, Adelaide, Australia
- * E-mail: (JMS); (AMA)
| | - Aida M. Andrés
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- * E-mail: (JMS); (AMA)
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9
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Massaro AP, Gilby IC, Desai N, Weiss A, Feldblum JT, Pusey AE, Wilson ML. Correlates of individual participation in boundary patrols by male chimpanzees. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210151. [PMID: 35369753 DOI: 10.1098/rstb.2021.0151] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Group territory defence poses a collective action problem: individuals can free-ride, benefiting without paying the costs. Individual heterogeneity has been proposed to solve such problems, as individuals high in reproductive success, rank, fighting ability or motivation may benefit from defending territories even if others free-ride. To test this hypothesis, we analysed 30 years of data from chimpanzees (Pan troglodytes) in the Kasekela community, Gombe National Park, Tanzania (1978-2007). We examined the extent to which individual participation in patrols varied according to correlates of reproductive success (mating rate, rank, age), fighting ability (hunting), motivation (scores from personality ratings), costs of defecting (the number of adult males in the community) and gregariousness (sighting frequency). By contrast to expectations from collective action theory, males participated in patrols at consistently high rates (mean ± s.d. = 74.5 ± 11.1% of patrols, n = 23 males). The best predictors of patrol participation were sighting frequency, age and hunting participation. Current and former alpha males did not participate at a higher rate than males that never achieved alpha status. These findings suggest that the temptation to free-ride is low, and that a mutualistic mechanism such as group augmentation may better explain individual participation in group territorial behaviour. This article is part of the theme issue 'Intergroup conflict across taxa'.
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Affiliation(s)
- Anthony P Massaro
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55414, USA
| | - Ian C Gilby
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ 85281, USA
| | - Nisarg Desai
- Department of Anthropology, University of Minnesota, Minneapolis, MN 55414, USA
| | - Alexander Weiss
- National Evolutionary Synthesis Center, Durham, NC 27705, USA.,Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, UK
| | - Joseph T Feldblum
- Department of Anthropology, University of Michigan, Ann Arbor, MI 48109, USA.,Society of Fellows, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anne E Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Michael L Wilson
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55414, USA.,Department of Anthropology, University of Minnesota, Minneapolis, MN 55414, USA.,Institute on the Environment, University of Minnesota, St. Paul, MN 55414, USA
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10
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Zimmerman DM, Mitchell SL, Wolf TM, Deere JR, Noheri JB, Takahashi E, Cranfield MR, Travis DA, Hassell JM. Great ape health watch: Enhancing surveillance for emerging infectious diseases in great apes. Am J Primatol 2022; 84:e23379. [PMID: 35389523 DOI: 10.1002/ajp.23379] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/24/2022] [Accepted: 03/12/2022] [Indexed: 12/27/2022]
Abstract
Infectious diseases have the potential to extirpate populations of great apes. As the interface between humans and great apes expands, zoonoses pose an increasingly severe threat to already endangered great ape populations. Despite recognition of the threat posed by human pathogens to great apes, health monitoring is only conducted for a small fraction of the world's wild great apes (and mostly those that are habituated) meaning that outbreaks of disease often go unrecognized and therefore unmitigated. This lack of surveillance (even in sites where capacity to conduct surveillance is present) is the most significant limiting factor in our ability to quickly detect and respond to emerging infectious diseases in great apes when they first appear. Accordingly, we must create a surveillance system that links disease outbreaks in humans and great apes in time and space, and enables veterinarians, clinicians, conservation managers, national decision makers, and the global health community to respond quickly to these events. Here, we review existing great ape health surveillance programs in African range habitats to identify successes, gaps, and challenges. We use these findings to argue that standardization of surveillance across sites and geographic scales, that monitors primate health in real-time and generates early warnings of disease outbreaks, is an efficient, low-cost step to conserve great ape populations. Such a surveillance program, which we call "Great Ape Health Watch" would lead to long-term improvements in outbreak preparedness, prevention, detection, and response, while generating valuable data for epidemiological research and sustainable conservation planning. Standardized monitoring of great apes would also make it easier to integrate with human surveillance activities. This approach would empower local stakeholders to link wildlife and human health, allowing for near real-time, bidirectional surveillance at the great ape-human interface.
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Affiliation(s)
- Dawn M Zimmerman
- Global Health Program, Smithsonian Conservation Biology Institute, Washington, District of Columbia, USA.,School of Public Health, Yale University, New Haven, Connecticut, USA.,Technical Advisory Board, Gorilla Doctors, Musanze, Rwanda
| | - Stephanie L Mitchell
- Global Health Program, Smithsonian Conservation Biology Institute, Washington, District of Columbia, USA
| | - Tiffany M Wolf
- Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Jessica R Deere
- Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | | | | | - Michael R Cranfield
- Technical Advisory Board, Gorilla Doctors, Musanze, Rwanda.,Mountain Gorilla Veterinary Project, Baltimore, Maryland, USA
| | - Dominic A Travis
- Technical Advisory Board, Gorilla Doctors, Musanze, Rwanda.,Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - James M Hassell
- Global Health Program, Smithsonian Conservation Biology Institute, Washington, District of Columbia, USA.,School of Public Health, Yale University, New Haven, Connecticut, USA
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11
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Interests of the Non-Human Primate Models for HIV Cure Research. Vaccines (Basel) 2021; 9:vaccines9090958. [PMID: 34579195 PMCID: PMC8472852 DOI: 10.3390/vaccines9090958] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/19/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022] Open
Abstract
Non-human primate (NHP) models are important for vaccine development and also contribute to HIV cure research. Although none of the animal models are perfect, NHPs enable the exploration of important questions about tissue viral reservoirs and the development of intervention strategies. In this review, we describe recent advances in the use of these models for HIV cure research and highlight the progress that has been made as well as limitations using these models. The main NHP models used are (i) the macaque, in which simian immunodeficiency virus (SIVmac) infection displays similar replication profiles as to HIV in humans, and (ii) the macaque infected by a recombinant virus (SHIV) consisting of SIVmac expressing the HIV envelope gene serving for studies analyzing the impact of anti-HIV Env broadly neutralizing antibodies. Lessons for HIV cure that can be learned from studying the natural host of SIV are also presented here. An overview of the most promising and less well explored HIV cure strategies tested in NHP models will be given.
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12
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Abstract
Over the last two decades, the viromes of our closest relatives, the African great apes (AGA), have been intensively studied. Comparative approaches have unveiled diverse evolutionary patterns, highlighting both stable host-virus associations over extended evolutionary timescales and much more recent viral emergence events. In this chapter, we summarize these findings and outline how they have shed a new light on the origins and evolution of many human-infecting viruses. We also show how this knowledge can be used to better understand the evolution of human health in relation to viral infections.
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13
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Lonsdorf EV, Travis DA, Raphael J, Kamenya S, Lipende I, Mwacha D, Collins DA, Wilson M, Mjungu D, Murray C, Bakuza J, Wolf TM, Parsons MB, Deere JR, Lantz E, Kinsel MJ, Santymire R, Pintea L, Terio KA, Hahn BH, Pusey AE, Goodall J, Gillespie TR. The Gombe Ecosystem Health Project: 16 years of program evolution and lessons learned. Am J Primatol 2021; 84:e23300. [PMID: 34223656 PMCID: PMC8727649 DOI: 10.1002/ajp.23300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 06/01/2021] [Accepted: 06/15/2021] [Indexed: 12/30/2022]
Abstract
Infectious disease outbreaks pose a significant threat to the conservation of chimpanzees (Pan troglodytes) and all threatened nonhuman primates. Characterizing and mitigating these threats to support the sustainability and welfare of wild populations is of the highest priority. In an attempt to understand and mitigate the risk of disease for the chimpanzees of Gombe National Park, Tanzania, we initiated a long-term health-monitoring program in 2004. While the initial focus was to expand the ongoing behavioral research on chimpanzees to include standardized data on clinical signs of health, it soon became evident that the scope of the project would ideally include diagnostic surveillance of pathogens for all primates (including people) and domestic animals, both within and surrounding the National Park. Integration of these data, along with in-depth post-mortem examinations, have allowed us to establish baseline health indicators to inform outbreak response. Here, we describe the development and expansion of the Gombe Ecosystem Health project, review major findings from the research and summarize the challenges and lessons learned over the past 16 years. We also highlight future directions and present the opportunities and challenges that remain when implementing studies of ecosystem health in a complex, multispecies environment.
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Affiliation(s)
- Elizabeth V Lonsdorf
- Department of Psychology and Biological Foundations of Behavior Program, Franklin & Marshall College, Lancaster, Pennsylvania, USA
| | - Dominic A Travis
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Jane Raphael
- Gombe National Park, Tanzania Nationals Park, Kigoma, Tanzania
| | - Shadrack Kamenya
- Gombe Stream Research Center, The Jane Goodall Institute, Kigoma, Tanzania
| | - Iddi Lipende
- Tanzania Wildlife Research Institute, Arusha, Tanzania
| | - Dismas Mwacha
- Gombe Stream Research Center, The Jane Goodall Institute, Kigoma, Tanzania
| | - D Anthony Collins
- Gombe Stream Research Center, The Jane Goodall Institute, Kigoma, Tanzania
| | - Michael Wilson
- Departments of Anthropology and Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Deus Mjungu
- Gombe Stream Research Center, The Jane Goodall Institute, Kigoma, Tanzania
| | - Carson Murray
- Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, District of Columbia, USA
| | - Jared Bakuza
- College of Education, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Tiffany M Wolf
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Michele B Parsons
- Division of Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica R Deere
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Emma Lantz
- California Department of Fish and Wildlife, Rancho Cordova, California, USA
| | - Michael J Kinsel
- Zoological Pathology Program, University of Illinois, Brookfield, Illinois, USA
| | - Rachel Santymire
- Davee Center for Epidemiology and Endocrinology, Lincoln Park Zoo, Chicago, Illinois, USA
| | | | - Karen A Terio
- Zoological Pathology Program, University of Illinois, Brookfield, Illinois, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anne E Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Jane Goodall
- The Jane Goodall Institute, Vienna, Virginia, USA
| | - Thomas R Gillespie
- Departments of Environmental Sciences and Environmental Health and Program in Population Biology, Emory University, Atlanta, Georgia, USA
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14
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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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15
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Ayoola AO, Zhang BL, Meisel RP, Nneji LM, Shao Y, Morenikeji OB, Adeola AC, Ng’ang’a SI, Ogunjemite BG, Okeyoyin AO, Roos C, Wu DD. Population Genomics Reveals Incipient Speciation, Introgression, and Adaptation in the African Mona Monkey (Cercopithecus mona). Mol Biol Evol 2021; 38:876-890. [PMID: 32986826 PMCID: PMC7947840 DOI: 10.1093/molbev/msaa248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Guenons (tribe Cercopithecini) are the most widely distributed nonhuman primate in the tropical forest belt of Africa and show considerable phenotypic, taxonomic, and ecological diversity. However, genomic information for most species within this group is still lacking. Here, we present a high-quality de novo genome (total 2.90 Gb, contig N50 equal to 22.7 Mb) of the mona monkey (Cercopithecus mona), together with genome resequencing data of 13 individuals sampled across Nigeria. Our results showed differentiation between populations from East and West of the Niger River ∼84 ka and potential ancient introgression in the East population from other mona group species. The PTPRK, FRAS1, BNC2, and EDN3 genes related to pigmentation displayed signals of introgression in the East population. Genomic scans suggest that immunity genes such as AKT3 and IL13 (possibly involved in simian immunodeficiency virus defense), and G6PD, a gene involved in malaria resistance, are under positive natural selection. Our study gives insights into differentiation, natural selection, and introgression in guenons.
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Affiliation(s)
- Adeola Oluwakemi Ayoola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Olanrewaju B Morenikeji
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY
- Department of Biology, Hamilton College, Clinton, NY
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Said I Ng’ang’a
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Babafemi G Ogunjemite
- Department of Ecotourism and Wildlife Management, Federal University of Technology, Akure, Nigeria
| | - Agboola O Okeyoyin
- National Park Service Headquarters, Federal Capital Territory, Abuja, Nigeria
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
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16
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Wilson ML, Lonsdorf EV, Mjungu DC, Kamenya S, Kimaro EW, Collins DA, Gillespie TR, Travis DA, Lipende I, Mwacha D, Ndimuligo SA, Pintea L, Raphael J, Mtiti ER, Hahn BH, Pusey AE, Goodall J. Research and Conservation in the Greater Gombe Ecosystem: Challenges and Opportunities. BIOLOGICAL CONSERVATION 2020; 252:108853. [PMID: 33343005 PMCID: PMC7743041 DOI: 10.1016/j.biocon.2020.108853] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The study of chimpanzees in Gombe National Park, Tanzania, started by Jane Goodall in 1960, provided pioneering accounts of chimpanzee behavior and ecology. With funding from multiple sources, including the Jane Goodall Institute (JGI) and grants from private foundations and federal programs, the project has continued for sixty years, providing a wealth of information about our evolutionary cousins. These chimpanzees face two main challenges to their survival: infectious disease - including simian immunodeficiency virus (SIVcpz), which can cause Acquired Immune Deficiency Syndrome (AIDS) in chimpanzees - and the deforestation of land outside the park. A health monitoring program has increased understanding of the pathogens affecting chimpanzees and has promoted measures to characterize and reduce disease risk. Deforestation reduces connections between Gombe and other chimpanzee populations, which can cause loss of genetic diversity. To promote habitat restoration, JGI facilitated participatory village land use planning, in which communities voluntarily allocated land to a network of Village Land Forest Reserves. Expected benefits to people include stabilizing watersheds, improving water supplies, and ensuring a supply of forest resources. Surveys and genetic analyses confirm that chimpanzees persist on village lands and remain connected to the Gombe population. Many challenges remain, but the regeneration of natural forest on previously degraded lands provides hope that conservation solutions can be found that benefit both people and wildlife. Conservation work in the Greater Gombe Ecosystem has helped promote broader efforts to plan and work for conservation elsewhere in Tanzania and across Africa.
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Affiliation(s)
- Michael L. Wilson
- Department of Anthropology, University of Minnesota, Minneapolis, MN 55455 USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108 USA
- Institute on the Environment, University of Minnesota, St. Paul, MN 55108 USA
| | | | - Deus C. Mjungu
- Gombe Stream Research Centre, the Jane Goodall Institute – Tanzania, Kigoma, Tanzania
| | - Shadrack Kamenya
- Gombe Stream Research Centre, the Jane Goodall Institute – Tanzania, Kigoma, Tanzania
| | - Elihuruma Wilson Kimaro
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108 USA
- Gombe National Park, Kigoma, Tanzania
| | - D. Anthony Collins
- Gombe Stream Research Centre, the Jane Goodall Institute – Tanzania, Kigoma, Tanzania
| | - Thomas R. Gillespie
- Department of Environmental Sciences, Emory University, Atlanta, Georgia 30322 USA
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322 USA
- Program in Population, Biology, Ecology and Evolution, Emory University, Atlanta, Georgia 30322 USA
| | - Dominic A. Travis
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108 USA
| | - Iddi Lipende
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Dismas Mwacha
- Gombe Stream Research Centre, the Jane Goodall Institute – Tanzania, Kigoma, Tanzania
| | - Sood A. Ndimuligo
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | | | | | | | - Beatrice H. Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708 USA
| | - Jane Goodall
- The Jane Goodall Institute, Vienna, VA, 22182 USA
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17
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Wilson ML, Lonsdorf EV, Mjungu DC, Kamenya S, Kimaro EW, Collins DA, Gillespie TR, Travis DA, Lipende I, Mwacha D, Ndimuligo SA, Pintea L, Raphael J, Mtiti ER, Hahn BH, Pusey AE, Goodall J. Research and Conservation in the Greater Gombe Ecosystem: Challenges and Opportunities. BIOLOGICAL CONSERVATION 2020; 252:108853. [PMID: 33343005 DOI: 10.1016/j.biocon.2020.108731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The study of chimpanzees in Gombe National Park, Tanzania, started by Jane Goodall in 1960, provided pioneering accounts of chimpanzee behavior and ecology. With funding from multiple sources, including the Jane Goodall Institute (JGI) and grants from private foundations and federal programs, the project has continued for sixty years, providing a wealth of information about our evolutionary cousins. These chimpanzees face two main challenges to their survival: infectious disease - including simian immunodeficiency virus (SIVcpz), which can cause Acquired Immune Deficiency Syndrome (AIDS) in chimpanzees - and the deforestation of land outside the park. A health monitoring program has increased understanding of the pathogens affecting chimpanzees and has promoted measures to characterize and reduce disease risk. Deforestation reduces connections between Gombe and other chimpanzee populations, which can cause loss of genetic diversity. To promote habitat restoration, JGI facilitated participatory village land use planning, in which communities voluntarily allocated land to a network of Village Land Forest Reserves. Expected benefits to people include stabilizing watersheds, improving water supplies, and ensuring a supply of forest resources. Surveys and genetic analyses confirm that chimpanzees persist on village lands and remain connected to the Gombe population. Many challenges remain, but the regeneration of natural forest on previously degraded lands provides hope that conservation solutions can be found that benefit both people and wildlife. Conservation work in the Greater Gombe Ecosystem has helped promote broader efforts to plan and work for conservation elsewhere in Tanzania and across Africa.
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Affiliation(s)
- Michael L Wilson
- Department of Anthropology, University of Minnesota, Minneapolis, MN 55455 USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108 USA
- Institute on the Environment, University of Minnesota, St. Paul, MN 55108 USA
| | - Elizabeth V Lonsdorf
- Department of Psychology, Franklin and Marshall College, Lancaster, PA 17604 USA
| | - Deus C Mjungu
- Gombe Stream Research Centre, the Jane Goodall Institute - Tanzania, Kigoma, Tanzania
| | - Shadrack Kamenya
- Gombe Stream Research Centre, the Jane Goodall Institute - Tanzania, Kigoma, Tanzania
| | - Elihuruma Wilson Kimaro
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108 USA
- Gombe National Park, Kigoma, Tanzania
| | - D Anthony Collins
- Gombe Stream Research Centre, the Jane Goodall Institute - Tanzania, Kigoma, Tanzania
| | - Thomas R Gillespie
- Department of Environmental Sciences, Emory University, Atlanta, Georgia 30322 USA
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322 USA
- Program in Population, Biology, Ecology and Evolution, Emory University, Atlanta, Georgia 30322 USA
| | - Dominic A Travis
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108 USA
| | - Iddi Lipende
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Dismas Mwacha
- Gombe Stream Research Centre, the Jane Goodall Institute - Tanzania, Kigoma, Tanzania
| | - Sood A Ndimuligo
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | | | | | | | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, 19104, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Anne E Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708 USA
| | - Jane Goodall
- The Jane Goodall Institute, Vienna, VA, 22182 USA
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18
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The HLA A03 Supertype and Several Pan Species Major Histocompatibility Complex Class I A Allotypes Share a Preference for Binding Positively Charged Residues in the F Pocket: Implications for Controlling Retroviral Infections. J Virol 2020; 94:JVI.01960-19. [PMID: 32075930 DOI: 10.1128/jvi.01960-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/11/2020] [Indexed: 02/02/2023] Open
Abstract
The major histocompatibility complex (MHC) class I region of humans, chimpanzees (Pan troglodytes), and bonobos (Pan paniscus) is highly similar, and orthologues of HLA-A, -B, and -C are present in both Pan species. Based on functional characteristics, the different HLA-A allotypes are classified into different supertypes. One of them, the HLA A03 supertype, is widely distributed among different human populations. All contemporary known chimpanzee and bonobo MHC class I A allotypes cluster genetically into one of the six HLA-A families, the HLA-A1/A3/A11/A30 family. We report here that the peptide-binding motif of the Patr-A*05:01 allotype, which is commonly present in a cohort of western African chimpanzees, has a strong preference for binding peptides with basic amino acids at the carboxyl terminus. This phenomenon is shared with the family members of the HLA A03 supertype. Based on the chemical similarities in the peptide-binding pocket, we inferred that the preference for binding peptides with basic amino acids at the carboxyl terminus is widely present among the human, chimpanzee, and bonobo MHC-A allotypes. Subsequent in silico peptide-binding predictions illustrated that these allotypes have the capacity to target conserved parts of the proteome of human immunodeficiency virus type 1 (HIV-1) and the simian immunodeficiency virus SIVcpz.IMPORTANCE Most experimentally infected chimpanzees seem to control an HIV-1 infection and are therefore considered to be relatively resistant to developing AIDS. Contemporary free-ranging chimpanzees may carry SIVcpz, and there is evidence for AIDS-like symptoms in these free-ranging animals, whereas SIV infections in bonobos appear to be absent. In humans, the natural control of an HIV-1 infection is strongly associated with the presence of particular HLA class I allotypes. The ancestor of the contemporary living chimpanzees and bonobos survived a selective sweep targeting the MHC class I repertoire. We have put forward a hypothesis that this may have been caused by an ancestral retroviral infection similar to SIVcpz. Characterization of the relevant MHC allotypes may contribute to understanding the shaping of their immune repertoire. The abundant presence of MHC-A allotypes that prefer peptides with basic amino acids at the C termini suggests that these molecules may contribute to the control of retroviral infections in humans, chimpanzees, and bonobos.
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19
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Maibach V, Langergraber K, Leendertz FH, Wittig RM, Vigilant L. Differences in MHC-B diversity and KIR epitopes in two populations of wild chimpanzees. Immunogenetics 2019; 71:617-633. [PMID: 31797008 PMCID: PMC6900261 DOI: 10.1007/s00251-019-01148-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/17/2019] [Indexed: 11/26/2022]
Abstract
The major histocompatibility complex (MHC) class I genes play a critical role within the immune system, both by the presentation of antigens from intracellular pathogens to immunocompetent cells and by the interaction with killer cell immunoglobulin-like receptors (KIR) on natural killer cells (NK cells). Genes of the MHC are highly diverse, and MHC variation can have effects on the immune functionality of individuals; hence, comparisons of MHC diversity among closely related phylogenetic taxa may give insight into the factors responsible for the shaping of its diversity. The four geographically separated chimpanzee subspecies differ in their overall genetic diversity, have different population histories, and are confronted with different pathogens in their natural habitat, all of which may affect MHC class I DNA sequence diversity. Here, we compare the MHC-B exon two DNA sequence diversity from 24 wild western and 46 wild eastern chimpanzees using necropsy and noninvasively collected fecal samples, respectively. We found a higher MHC-B exon two nucleotide diversity, in our western than eastern chimpanzees. The inclusion of previously published MHC-B exon two data from other western and eastern chimpanzees supported this finding. In addition, our results confirm and extend the finding of a very low C1 epitope frequency at eastern chimpanzee MHC-B molecules, which likely affects the ability of these molecules to interact with NK cells. While the understanding of the differing pathogen environments encountered by disparate populations of a species is a challenging endeavor, these findings highlight the potential for these pathogens to selectively shape immune system variation.
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Affiliation(s)
- Vincent Maibach
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.
| | - Kevin Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ, 85281, USA
| | | | - Roman M Wittig
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Taï Chimpanzee Project, CSRS, Abidjan, 01, Côte d'Ivoire
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
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20
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Schmidt JM, de Manuel M, Marques-Bonet T, Castellano S, Andrés AM. The impact of genetic adaptation on chimpanzee subspecies differentiation. PLoS Genet 2019; 15:e1008485. [PMID: 31765391 PMCID: PMC6901233 DOI: 10.1371/journal.pgen.1008485] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 12/09/2019] [Accepted: 10/17/2019] [Indexed: 12/25/2022] Open
Abstract
Chimpanzees, humans' closest relatives, are in danger of extinction. Aside from direct human impacts such as hunting and habitat destruction, a key threat is transmissible disease. As humans continue to encroach upon their habitats, which shrink in size and grow in density, the risk of inter-population and cross-species viral transmission increases, a point dramatically made in the reverse with the global HIV/AIDS pandemic. Inhabiting central Africa, the four subspecies of chimpanzees differ in demographic history and geographical range, and are likely differentially adapted to their particular local environments. To quantitatively explore genetic adaptation, we investigated the genic enrichment for SNPs highly differentiated between chimpanzee subspecies. Previous analyses of such patterns in human populations exhibited limited evidence of adaptation. In contrast, chimpanzees show evidence of recent positive selection, with differences among subspecies. Specifically, we observe strong evidence of recent selection in eastern chimpanzees, with highly differentiated SNPs being uniquely enriched in genic sites in a way that is expected under recent adaptation but not under neutral evolution or background selection. These sites are enriched for genes involved in immune responses to pathogens, and for genes inferred to differentiate the immune response to infection by simian immunodeficiency virus (SIV) in natural vs. non-natural host species. Conversely, central chimpanzees exhibit an enrichment of signatures of positive selection only at cytokine receptors, due to selective sweeps in CCR3, CCR9 and CXCR6 -paralogs of CCR5 and CXCR4, the two major receptors utilized by HIV to enter human cells. Thus, our results suggest that positive selection has contributed to the genetic and phenotypic differentiation of chimpanzee subspecies, and that viruses likely play a predominate role in this differentiation, with SIV being a likely selective agent. Interestingly, our results suggest that SIV has elicited distinctive adaptive responses in these two chimpanzee subspecies.
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MESH Headings
- Adaptation, Physiological/genetics
- Adaptation, Physiological/immunology
- Animals
- Demography
- Genetic Drift
- Genetic Speciation
- HIV/genetics
- HIV/immunology
- HIV/pathogenicity
- Humans
- Immunity, Innate/genetics
- Pan troglodytes/genetics
- Pan troglodytes/immunology
- Pan troglodytes/virology
- Polymorphism, Single Nucleotide/genetics
- Receptors, CCR/genetics
- Receptors, CCR3/genetics
- Receptors, CCR5/genetics
- Receptors, CXCR4/genetics
- Receptors, CXCR6/immunology
- Selection, Genetic/genetics
- Simian Immunodeficiency Virus/genetics
- Simian Immunodeficiency Virus/immunology
- Simian Immunodeficiency Virus/pathogenicity
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Affiliation(s)
- Joshua M. Schmidt
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
- * E-mail: (JMS); (AMA)
| | - Marc de Manuel
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona, Spain
- National Centre for Genomic Analysis–Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Sergi Castellano
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
- Genetics and Genomic Medicine Programme, Great Ormond Street Institute of Child Health, University College London (UCL), London, United Kingdom
- UCL Genomics, London, United Kingdom
| | - Aida M. Andrés
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
- * E-mail: (JMS); (AMA)
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21
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Bibollet-Ruche F, Russell RM, Liu W, Stewart-Jones GBE, Sherrill-Mix S, Li Y, Learn GH, Smith AG, Gondim MVP, Plenderleith LJ, Decker JM, Easlick JL, Wetzel KS, Collman RG, Ding S, Finzi A, Ayouba A, Peeters M, Leendertz FH, van Schijndel J, Goedmakers A, Ton E, Boesch C, Kuehl H, Arandjelovic M, Dieguez P, Murai M, Colin C, Koops K, Speede S, Gonder MK, Muller MN, Sanz CM, Morgan DB, Atencia R, Cox D, Piel AK, Stewart FA, Ndjango JBN, Mjungu D, Lonsdorf EV, Pusey AE, Kwong PD, Sharp PM, Shaw GM, Hahn BH. CD4 receptor diversity in chimpanzees protects against SIV infection. Proc Natl Acad Sci U S A 2019; 116:3229-3238. [PMID: 30718403 PMCID: PMC6386711 DOI: 10.1073/pnas.1821197116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Human and simian immunodeficiency viruses (HIV/SIVs) use CD4 as the primary receptor to enter target cells. Here, we show that the chimpanzee CD4 is highly polymorphic, with nine coding variants present in wild populations, and that this diversity interferes with SIV envelope (Env)-CD4 interactions. Testing the replication fitness of SIVcpz strains in CD4+ T cells from captive chimpanzees, we found that certain viruses were unable to infect cells from certain hosts. These differences were recapitulated in CD4 transfection assays, which revealed a strong association between CD4 genotypes and SIVcpz infection phenotypes. The most striking differences were observed for three substitutions (Q25R, Q40R, and P68T), with P68T generating a second N-linked glycosylation site (N66) in addition to an invariant N32 encoded by all chimpanzee CD4 alleles. In silico modeling and site-directed mutagenesis identified charged residues at the CD4-Env interface and clashes between CD4- and Env-encoded glycans as mechanisms of inhibition. CD4 polymorphisms also reduced Env-mediated cell entry of monkey SIVs, which was dependent on at least one D1 domain glycan. CD4 allele frequencies varied among wild chimpanzees, with high diversity in all but the western subspecies, which appeared to have undergone a selective sweep. One allele was associated with lower SIVcpz prevalence rates in the wild. These results indicate that substitutions in the D1 domain of the chimpanzee CD4 can prevent SIV cell entry. Although some SIVcpz strains have adapted to utilize these variants, CD4 diversity is maintained, protecting chimpanzees against infection with SIVcpz and other SIVs to which they are exposed.
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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
| | - Guillaume B E Stewart-Jones
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - 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
| | - Gerald H Learn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Andrew G Smith
- 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
| | - Julie M Decker
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Juliet L Easlick
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - 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
| | - Shilei Ding
- Département de Microbiologie, Infectiologie et Immunologie, Centre de Recherche du Centre Hospitalier de L'Université de Montréal, Montréal, QC H2X0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H2X0A9, Canada
| | - Andrés Finzi
- Département de Microbiologie, Infectiologie et Immunologie, Centre de Recherche du Centre Hospitalier de L'Université de Montréal, Montréal, QC H2X0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H2X0A9, Canada
| | - Ahidjo Ayouba
- 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
| | - Fabian H Leendertz
- Research Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, 13353 Berlin, Germany
| | - Joost van Schijndel
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Chimbo Foundation, 1011 PW Amsterdam, The Netherlands
| | | | - Els Ton
- Chimbo Foundation, 1011 PW Amsterdam, The Netherlands
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Hjalmar Kuehl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Paula Dieguez
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mizuki Murai
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christelle Colin
- Projet Primates France, Centre de Conservation pour Chimpanzés, BP 36 Faranah, Republic of Guinea
| | - Kathelijne Koops
- Department of Anthropology, University of Zurich, CH-8006 Zurich, Switzerland
| | - Sheri Speede
- Sanaga-Yong Chimpanzee Rescue Center, In Defense of Animals-Africa, Portland, OR 97204
| | - Mary K Gonder
- Department of Biology, Drexel University, Philadelphia, PA 19104
| | - Martin N Muller
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131
| | - Crickette M Sanz
- Department of Anthropology, Washington University in St. Louis, St Louis, MO 63130
- Congo Program, Wildlife Conservation Society, BP 14537 Brazzaville, Republic of the Congo
| | - David B Morgan
- Congo Program, Wildlife Conservation Society, BP 14537 Brazzaville, Republic of the Congo
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, IL 60614
| | - Rebecca Atencia
- Tchimpounga Chimpanzee Rehabilitation Center, The Jane Goodall Institute-Congo, BP 1206 Pointe Noire, Republic of Congo
| | - Debby Cox
- Tchimpounga Chimpanzee Rehabilitation Center, The Jane Goodall Institute-Congo, BP 1206 Pointe Noire, Republic of Congo
- Africa Programs, The Jane Goodall Institute, Vienna, VA 22182
| | - Alex K Piel
- School of Natural Sciences and Psychology, Liverpool John Moores University, L3 3AF Liverpool, United Kingdom
| | - Fiona A Stewart
- School of Natural Sciences and Psychology, Liverpool John Moores University, L3 3AF Liverpool, United Kingdom
| | - Jean-Bosco N Ndjango
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, BP 2012 Kisangani, Democratic Republic of the Congo
| | - Deus Mjungu
- Gombe Stream Research Centre, The Jane Goodall Institute, Kigoma, Tanzania
| | | | - Anne E Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - 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
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - 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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22
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Veazey RS, Lackner AA. Nonhuman Primate Models and Understanding the Pathogenesis of HIV Infection and AIDS. ILAR J 2018; 58:160-171. [PMID: 29228218 DOI: 10.1093/ilar/ilx032] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/04/2017] [Indexed: 12/16/2022] Open
Abstract
Research using nonhuman primates (NHPs) as models for human immunodeficiency virus (HIV) infection and acquired immunodeficiency syndrome (AIDS) has resulted in tremendous achievements not only in the prevention and treatment of HIV, but also in biomedical research more broadly. Once considered a death sentence, HIV infection is now fairly well controlled with combination antiretroviral treatments, almost all of which were first tested for efficacy and safety in nonhuman primates or other laboratory animals. Research in NHP has led to "dogma changing" discoveries in immunology, infectious disease, and even our own genetics. We now know that many of our genes are retroviral remnants, or developed in response to archaic HIV-like retroviral infections. Early studies involving blood from HIV patients and in experiments in cultured tissues contributed to confusion regarding the cause of AIDS and impeded progress in the development of effective interventions. Research on the many retroviruses of different NHP species have broadened our understanding of human immunology and perhaps even our origins and evolution as a species. In combination with recent advances in molecular biology and computational analytics, research in NHPs has unique potential for discoveries that will directly lead to new cures for old human and animal diseases, including HIV/AIDS.
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Affiliation(s)
- Ronald S Veazey
- Division of Comparative Pathology, Tulane National Primate Research Center, Tulane University School of Medicine.,Department of Pathology and Laboratory Medicine, Tulane University School of Medicine
| | - Andrew A Lackner
- Tulane National Primate Research Center, Tulane University School of Medicine.,Department of Microbiology and Pathology and Laboratory Medicine, Tulane University School of Medicine
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23
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Villabona‐Arenas CJ, Ayouba A, Esteban A, D'arc M, Mpoudi Ngole E, Peeters M. Noninvasive western lowland gorilla's health monitoring: A decade of simian immunodeficiency virus surveillance in southern Cameroon. Ecol Evol 2018; 8:10698-10710. [PMID: 30519399 PMCID: PMC6262910 DOI: 10.1002/ece3.4478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/18/2018] [Accepted: 07/27/2018] [Indexed: 11/21/2022] Open
Abstract
Simian immunodeficiency virus (SIVgor) causes persistent infection in critically endangered western lowland gorillas (Gorilla gorilla gorilla) from west central Africa. SIVgor is closely related to chimpanzee and human immunodeficiency viruses (SIVcpz and HIV-1, respectively). We established a noninvasive method that does not interfere with gorillas' natural behaviour to provide wildlife pathogen surveillance and health monitoring for conservation. A total of 1,665 geo-referenced fecal samples were collected at regular intervals from February 2006 to December 2014 (123 sampling days) in the Campo-Ma'an National Park (southwest Cameroon). Host genotyping was performed using microsatellite markers, SIVgor infection was identified by serology and genetic amplification was attempted on seropositive individuals. We identified at least 125 distinct gorillas, 50 were resampled (observed 3.5 times in average) and 38 were SIVgor+ (seven individuals were seroconverters). Six groups of gorillas were identified based on the overlapping occurrence of individuals with apparent high rates of gene flow. We obtained SIVgor genetic sequences from 25 of 38 seropositive genotyped gorillas and showed that the virus follows exponential growth dynamics under a strict molecular clock. Different groups shared SIVgor lineages demonstrating intergroup viral spread and recapture of positive individuals illustrated intra-host viral evolution. Relatedness and relationship genetic analysis of gorillas together with Bayesian phylogenetic inference of SIVgor provided evidence suggestive of vertical transmission. In conclusion, we provided insights into gorilla social dynamics and SIVgor evolution and emphasized the utility of noninvasive sampling to study wildlife health populations. These findings contribute to prospective planning for better monitoring and conservation.
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Affiliation(s)
- Christian Julian Villabona‐Arenas
- TransVIHMIInstitut de Recherche pour le Développement (IRD)Institut national de la santé et de la recherche médicale (INSERM)Université de MontpellierMontpellierFrance
| | - Ahidjo Ayouba
- TransVIHMIInstitut de Recherche pour le Développement (IRD)Institut national de la santé et de la recherche médicale (INSERM)Université de MontpellierMontpellierFrance
| | - Amandine Esteban
- TransVIHMIInstitut de Recherche pour le Développement (IRD)Institut national de la santé et de la recherche médicale (INSERM)Université de MontpellierMontpellierFrance
| | - Mirela D'arc
- TransVIHMIInstitut de Recherche pour le Développement (IRD)Institut national de la santé et de la recherche médicale (INSERM)Université de MontpellierMontpellierFrance
| | - Eitel Mpoudi Ngole
- Centre de recherche sur les maladies émergentes et réémergentes (CREMER)Institut de Recherches Médicales et d'Etudes des Plantes Médicinales (IMPM)YaoundéCameroun
| | - Martine Peeters
- TransVIHMIInstitut de Recherche pour le Développement (IRD)Institut national de la santé et de la recherche médicale (INSERM)Université de MontpellierMontpellierFrance
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24
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Barbian HJ, Connell AJ, Avitto AN, Russell RM, Smith AG, Gundlapally MS, Shazad AL, Li Y, Bibollet‐Ruche F, Wroblewski EE, Mjungu D, Lonsdorf EV, Stewart FA, Piel AK, Pusey AE, Sharp PM, Hahn BH. CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees. Ecol Evol 2018; 8:7946-7963. [PMID: 30250675 PMCID: PMC6145012 DOI: 10.1002/ece3.4302] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/14/2018] [Accepted: 05/29/2018] [Indexed: 12/29/2022] Open
Abstract
Short tandem repeats (STRs), also known as microsatellites, are commonly used to noninvasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq-based approach for genotyping nonhabituated populations and performing comparative analyses across field sites. The new automated high-throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.
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Affiliation(s)
- Hannah J. Barbian
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Andrew Jesse Connell
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Alexa N. Avitto
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Ronnie M. Russell
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Andrew G. Smith
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Madhurima S. Gundlapally
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Alexander L. Shazad
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Yingying Li
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Frederic Bibollet‐Ruche
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Emily E. Wroblewski
- Department of AnthropologyWashington University in St. LouisSt. LouisMissouri
| | | | | | - Fiona A. Stewart
- School of Natural Sciences and PsychologyLiverpool John Moores UniversityLiverpoolUK
| | - Alexander K. Piel
- School of Natural Sciences and PsychologyLiverpool John Moores UniversityLiverpoolUK
| | - Anne E. Pusey
- Department of Evolutionary AnthropologyDuke UniversityDurhamNorth Carolina
| | - Paul M. Sharp
- Institute of Evolutionary Biology and Centre for ImmunityInfection and EvolutionUniversity of EdinburghEdinburghUK
| | - Beatrice H. Hahn
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
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McCarthy MS, Lester JD, Langergraber KE, Stanford CB, Vigilant L. Genetic analysis suggests dispersal among chimpanzees in a fragmented forest landscape in Uganda. Am J Primatol 2018; 80:e22902. [PMID: 30052284 DOI: 10.1002/ajp.22902] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/26/2018] [Accepted: 07/07/2018] [Indexed: 11/05/2022]
Abstract
Habitat fragmentation is a leading threat to global biodiversity. Dispersal plays a key role in gene flow and population viability, but the impact of fragmentation on dispersal patterns remains poorly understood. Among chimpanzees, males typically remain in their natal communities while females often disperse. However, habitat loss and fragmentation may cause severe ecological disruptions, potentially resulting in decreased fitness benefits of male philopatry and limited female dispersal ability. To investigate this issue, we genotyped nearly 900 non-invasively collected chimpanzee fecal samples across a fragmented forest habitat that may function as a corridor between two large continuous forests in Uganda, and used the spatial associations among co-sampled genotypes to attribute a total of 229 individuals to 10 distinct communities, including 9 communities in the corridor habitat and 1 in continuous forest. We then used parentage analyses to infer instances of between-community dispersal. Of the 115 parent-offspring dyads detected with confidence, members of 39% (N = 26) of mother-daughter dyads were found in different communities, while members of 10% (N = 5) of father-son dyads were found in different communities. We also found direct evidence for one dispersal event that occurred during the study period, as a female's sample found first in one community was found multiple times in another community 19 months later. These findings suggest that even in fragmented habitats, chimpanzee males remain in their natal communities while females tend to disperse. Corridor enhancement in unprotected forest fragments could help maintain gene flow in chimpanzees and other species amid anthropogenic pressures.
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Affiliation(s)
- Maureen S McCarthy
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jack D Lester
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona.,Institute of Human Origins, Arizona State University, Tempe, Arizona
| | - Craig B Stanford
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Bowder D, Thompson J, Durst K, Hollingsead H, Hu D, Wei W, Xiang SH. Characterization of twin-cysteine motif in the V2-loop region of gp120 in primate lentiviruses. Virology 2018; 519:180-189. [DOI: 10.1016/j.virol.2018.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/15/2018] [Accepted: 04/17/2018] [Indexed: 10/17/2022]
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D'arc M, Furtado C, Siqueira JD, Seuánez HN, Ayouba A, Peeters M, Soares MA. Assessment of the gorilla gut virome in association with natural simian immunodeficiency virus infection. Retrovirology 2018; 15:19. [PMID: 29402305 PMCID: PMC5800045 DOI: 10.1186/s12977-018-0402-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/28/2018] [Indexed: 01/10/2023] Open
Abstract
Background Simian immunodeficiency viruses (SIVs) of chimpanzees and gorillas from Central Africa crossed the species barrier at least four times giving rise to human immunodeficiency virus type 1 (HIV-1) groups M, N, O and P. The paradigm of non-pathogenic lentiviral infections has been challenged by observations of naturally infected chimpanzees with SIVcpz associated with a negative impact on their life span and reproduction, CD4+ T-lymphocyte loss and lymphoid tissue destruction. With the advent and dissemination of new generation sequencing technologies, novel promising markers of immune deficiency have been explored in human and nonhuman primate species, showing changes in the microbiome (dysbiosis) that might be associated with pathogenic conditions. The aim of the present study was to identify and compare enteric viromes of SIVgor-infected and uninfected gorillas using noninvasive sampling and ultradeep sequencing, and to assess the association of virome composition with potential SIVgor pathogenesis in their natural hosts. Results We analyzed both RNA and DNA virus libraries of 23 fecal samples from 11 SIVgor-infected (two samples from one animal) and 11 uninfected western lowland gorillas from Campo-Ma’an National Park (CP), in southwestern Cameroon. Three bacteriophage families (Siphoviridae, Myoviridae and Podoviridae) represented 67.5 and 68% of the total annotated reads in SIVgor-infected and uninfected individuals, respectively. Conversely, mammalian viral families, such as Herpesviridae and Reoviridae, previously associated with gut- and several mammalian diseases were significantly more abundant (p < 0.003) in the SIVgor-infected group. In the present study, we analyzed, for the first time, the enteric virome of gorillas and their association with SIVgor status. This also provided the first evidence of association of specific mammalian viral families and SIVgor in a putative dysbiosis context. Conclusions Our results suggested that viromes might be potentially used as markers of lentiviral disease progression in wild gorilla populations. The diverse mammalian viral families, herein described in SIVgor-infected gorillas, may play a pivotal role in a disease progression still unclear in these animals but already well characterized in pathogenic lentiviral infections in other organisms. Larger sample sets should be further explored to reduce intrinsic sampling variation.
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Affiliation(s)
- Mirela D'arc
- Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.,Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | | | - Héctor N Seuánez
- Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.,Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ahidjo Ayouba
- UMI233/INSERM1175 Institut de Recherche pour le Développement (IRD), University of Montpellier, Montpellier, France
| | - Martine Peeters
- UMI233/INSERM1175 Institut de Recherche pour le Développement (IRD), University of Montpellier, Montpellier, France
| | - Marcelo A Soares
- Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil. .,Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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LONSDORF ELIZABETHV, GILLESPIE THOMASR, WOLF TIFFANYM, LIPENDE IDDI, RAPHAEL JANE, BAKUZA JARED, MURRAY CARSONM, WILSON MICHAELL, KAMENYA SHADRACK, MJUNGU DEUS, COLLINS DANTHONY, GILBY IANC, STANTON MARGARETA, TERIO KARENA, BARBIAN HANNAHJ, LI YINGYING, RAMIREZ MIGUEL, KRUPNICK ALEXANDER, SEIDL EMILY, GOODALL JANE, HAHN BEATRICEH, PUSEY ANNEE, TRAVIS DOMINICA. Socioecological correlates of clinical signs in two communities of wild chimpanzees (Pan troglodytes) at Gombe National Park, Tanzania. Am J Primatol 2018; 80:10.1002/ajp.22562. [PMID: 27182786 PMCID: PMC5112147 DOI: 10.1002/ajp.22562] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 03/14/2016] [Accepted: 04/23/2016] [Indexed: 11/06/2022]
Abstract
Disease and other health hazards pose serious threats to the persistence of wild ape populations. The total chimpanzee population at Gombe National Park, Tanzania, has declined from an estimated 120 to 150 individuals in the 1960's to around 100 individuals by the end of 2013, with death associated with observable signs of disease as the leading cause of mortality. In 2004, we began a non-invasive health-monitoring program in the two habituated communities in the park (Kasekela and Mitumba) with the aim of understanding the prevalence of health issues in the population, and identifying the presence and impacts of various pathogens. Here we present prospectively collected data on clinical signs (observable changes in health) in the chimpanzees of the Kasekela (n = 81) and Mitumba (n = 32) communities over an 8-year period (2005-2012). First, we take a population approach and analyze prevalence of clinical signs in five different categories: gastrointestinal system (diarrhea), body condition (estimated weight loss), respiratory system (coughing, sneezing etc.), wounds/lameness, and dermatologic issues by year, month, and community membership. Mean monthly prevalence of each clinical sign per community varied, but typically affected <10% of observed individuals. Secondly, we analyze the presence of clinical signs in these categories as they relate to individual demographic and social factors (age, sex, and dominance rank) and simian immunodeficiency virus (SIVcpz) infection status. Adults have higher odds of being observed with diarrhea, loss of body condition, and wounds or lameness when compared to immatures, while males have a higher probability of being observed with wounds or lameness than females. In contrast, signs of respiratory illness appear not to be related to chimpanzee-specific factors and skin abnormalities are very rare. For a subset of known-rank individuals, dominance rank predicts the probability of wounding/lameness in adult males, but does not predict any adverse clinical signs in adult females. Instead, adult females with SIVcpz infection are more likely to be observed with diarrhea, a finding that warrants further investigation. Comparable data are needed from other sites to determine whether the prevalence of clinical signs we observe are relatively high or low, as well as to more fully understand the factors influencing health of wild apes at both the population and individual level. Am. J. Primatol. 80:e22562, 2018. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - THOMAS R. GILLESPIE
- Department of Environmental Sciences and Program in Population Biology, Ecology and Evolution, Rollins School of Public Health, Emory University, Atlanta, Georgia
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - TIFFANY M. WOLF
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| | - IDDI LIPENDE
- Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania
| | - JANE RAPHAEL
- Gombe National Park, Tanzania National Parks, Kigoma, Tanzania
| | - JARED BAKUZA
- College of Education, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - CARSON M. MURRAY
- Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, District of Columbia
| | - MICHAEL L. WILSON
- Departments of Anthropology and Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota
| | - SHADRACK KAMENYA
- Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania
| | - DEUS MJUNGU
- Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania
| | | | - IAN C. GILBY
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona
| | - MARGARET A. STANTON
- Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, District of Columbia
| | - KAREN A. TERIO
- Zoological Pathology Program, University of Illinois, Brookfield, Illinois
| | - HANNAH J. BARBIAN
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - YINGYING LI
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - MIGUEL RAMIREZ
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - ALEXANDER KRUPNICK
- Department of Psychology, Franklin and Marshall College, Lancaster, Pennsylvania
| | - EMILY SEIDL
- Department of Psychology, Franklin and Marshall College, Lancaster, Pennsylvania
| | | | - BEATRICE H. HAHN
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - ANNE E. PUSEY
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - DOMINIC A. TRAVIS
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
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Lowenstine LJ, McManamon R, Terio KA. Apes. PATHOLOGY OF WILDLIFE AND ZOO ANIMALS 2018. [PMCID: PMC7173580 DOI: 10.1016/b978-0-12-805306-5.00015-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Kirchhoff CA, Wilson ML, Mjungu DC, Raphael J, Kamenya S, Collins DA. Infanticide in chimpanzees: Taphonomic case studies from Gombe. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 165:108-122. [PMID: 29072310 DOI: 10.1002/ajpa.23335] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 07/01/2017] [Accepted: 09/20/2017] [Indexed: 11/07/2022]
Abstract
OBJECTIVES We present a study of skeletal damage to four chimpanzee (Pan troglodytes) infanticide victims from Gombe National Park, Tanzania. Skeletal analysis may provide insight into the adaptive significance of infanticide by examining whether nutritional benefits sufficiently explain infanticidal behavior. The nutritional hypothesis would be supported if bone survivorship rates and skeletal damage patterns are comparable to those of monkey prey. If not, other explanations, such as the resource competition hypothesis, should be considered. METHODS Taphonomic assessment of two chimpanzee infants included description of breakage and surface modification, data on MNE, %MNE, and bone survivorship. Two additional infants were assessed qualitatively. The data were compared to published information on monkey prey. We also undertook a review of published infanticide cases. RESULTS The cases were intercommunity infanticides (one male and three female infants) committed by males. Attackers partially consumed two of the victims. Damage to all four infants included puncture marks and compression fractures to the cranium, crenulated breaks to long bones, and incipient fractures on ribs. Compared to monkey prey, the chimpanzee infants had an abundance of vertebrae and hand/foot bones. CONCLUSIONS The cases described here suggest that chimpanzees may not always completely consume infanticide victims, while reports on chimpanzee predation indicated that complete consumption of monkey prey usually occurred. Infanticidal chimpanzees undoubtedly gain nutritional benefits when they consume dead infants, but this benefit may not sufficiently explain infanticide in this species. Continued study of infanticidal and hunting behavior, including skeletal analysis, is likely to be of interest.
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Affiliation(s)
- Claire A Kirchhoff
- Department of Anthropology, University of Minnesota, Minneapolis, Minnesota 55455.,Department of Biomedical Sciences, Marquette University, Milwaukee, Wisconsin 53201-1881
| | - Michael L Wilson
- Department of Anthropology, University of Minnesota, Minneapolis, Minnesota 55455.,Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota 55108
| | - Deus C Mjungu
- Gombe Stream Research Center, the Jane Goodall Institute, Kigoma, Tanzania
| | - Jane Raphael
- Gombe Stream Research Center, the Jane Goodall Institute, Kigoma, Tanzania
| | - Shadrack Kamenya
- Gombe Stream Research Center, the Jane Goodall Institute, Kigoma, Tanzania
| | - D Anthony Collins
- Gombe Stream Research Center, the Jane Goodall Institute, Kigoma, Tanzania
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Abstract
Major histocompatibility complex (MHC) class I genes are critically involved in the defense against intracellular pathogens. MHC diversity comparisons among samples of closely related taxa may reveal traces of past or ongoing selective processes. The bonobo and chimpanzee are the closest living evolutionary relatives of humans and last shared a common ancestor some 1 mya. However, little is known concerning MHC class I diversity in bonobos or in central chimpanzees, the most numerous and genetically diverse chimpanzee subspecies. Here, we used a long-read sequencing technology (PacBio) to sequence the classical MHC class I genes A, B, C, and A-like in 20 and 30 wild-born bonobos and chimpanzees, respectively, with a main focus on central chimpanzees to assess and compare diversity in those two species. We describe in total 21 and 42 novel coding region sequences for the two species, respectively. In addition, we found evidence for a reduced MHC class I diversity in bonobos as compared to central chimpanzees as well as to western chimpanzees and humans. The reduced bonobo MHC class I diversity may be the result of a selective process in their evolutionary past since their split from chimpanzees.
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Affiliation(s)
- Vincent Maibach
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.
| | - Jörg B Hans
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | | | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
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Barbian HJ, Jackson-Jewett R, Brown CS, Bibollet-Ruche F, Learn GH, Decker T, Kreider EF, Li Y, Denny TN, Sharp PM, Shaw GM, Lifson J, Acosta EP, Saag MS, Bar KJ, Hahn BH. Effective treatment of SIVcpz-induced immunodeficiency in a captive western chimpanzee. Retrovirology 2017; 14:35. [PMID: 28576126 PMCID: PMC5457593 DOI: 10.1186/s12977-017-0359-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/25/2017] [Indexed: 01/20/2023] Open
Abstract
Background Simian immunodeficiency virus of chimpanzees (SIVcpz), the progenitor of human immunodeficiency virus type 1 (HIV-1), is associated with increased mortality and AIDS-like immunopathology in wild-living chimpanzees (Pan troglodytes). Surprisingly, however, similar findings have not been reported for chimpanzees experimentally infected with SIVcpz in captivity, raising questions about the intrinsic pathogenicity of this lentivirus. Findings Here, we report progressive immunodeficiency and clinical disease in a captive western chimpanzee (P. t. verus) infected twenty years ago by intrarectal inoculation with an SIVcpz strain (ANT) from a wild-caught eastern chimpanzee (P. t. schweinfurthii). With sustained plasma viral loads of 105 to 106 RNA copies/ml for the past 15 years, this chimpanzee developed CD4+ T cell depletion (220 cells/μl), thrombocytopenia (90,000 platelets/μl), and persistent soft tissue infections refractory to antibacterial therapy. Combination antiretroviral therapy consisting of emtricitabine (FTC), tenofovir disoproxil fumarate (TDF), and dolutegravir (DTG) decreased plasma viremia to undetectable levels (<200 copies/ml), improved CD4+ T cell counts (509 cell/μl), and resulted in the rapid resolution of all soft tissue infections. However, initial lack of adherence and/or differences in pharmacokinetics led to low plasma drug concentrations, which resulted in transient rebound viremia and the emergence of FTC resistance mutations (M184V/I) identical to those observed in HIV-1 infected humans. Conclusions These data demonstrate that SIVcpz can cause immunodeficiency and other hallmarks of AIDS in captive chimpanzees, including P. t. verus apes that are not naturally infected with this virus. Moreover, SIVcpz-associated immunodeficiency can be effectively treated with antiretroviral therapy, although sufficiently high plasma concentrations must be maintained to prevent the emergence of drug resistance. These findings extend a growing body of evidence documenting the immunopathogenicity of SIVcpz and suggest that experimentally infected chimpanzees may benefit from clinical monitoring and therapeutic intervention.
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Affiliation(s)
- Hannah J Barbian
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | | | | | - Frederic Bibollet-Ruche
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Timothy Decker
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Edward F Kreider
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Paul M Sharp
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - George M Shaw
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Jeffrey Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Edward P Acosta
- Department of Medicine and Center for AIDS Research, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michael S Saag
- Department of Medicine and Center for AIDS Research, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Katharine J Bar
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Beatrice H Hahn
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 409 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.
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De Nys H, Löhrich T, Wu D, Calvignac-Spencer S, Leendertz F. Wild African great apes as natural hosts of malaria parasites: current knowledge and research perspectives. Primate Biol 2017; 4:47-59. [PMID: 32110692 PMCID: PMC7041518 DOI: 10.5194/pb-4-47-2017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 02/24/2017] [Indexed: 11/24/2022] Open
Abstract
Humans and African great apes (AGAs) are naturally infected with several species of closely related malaria parasites. The need to understand the origins of human malaria as well as the risk of zoonotic transmissions and emergence of new malaria strains in human populations has markedly encouraged research on great ape Plasmodium parasites. Progress in the use of non-invasive methods has rendered investigations into wild ape populations possible. Present knowledge is mainly focused on parasite diversity and phylogeny, with still large gaps to fill on malaria parasite ecology. Understanding what malaria infection means in terms of great ape health is also an important, but challenging avenue of research and has been subject to relatively few research efforts so far. This paper reviews current knowledge on African great ape malaria and identifies gaps and future research perspectives.
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Affiliation(s)
- Hélène Marie De Nys
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
- current address: UMI 233, Institut de Recherche pour le Développement (IRD), INSERM U1175, and University of Montpellier, Montpellier, France
| | - Therese Löhrich
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Doris Wu
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | | | - Fabian Hubertus Leendertz
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
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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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Faillace CA, Lorusso NS, Duffy S. Overlooking the smallest matter: viruses impact biological invasions. Ecol Lett 2017; 20:524-538. [PMID: 28176452 DOI: 10.1111/ele.12742] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/28/2016] [Accepted: 01/05/2017] [Indexed: 12/12/2022]
Abstract
Parasites and pathogens have recently received considerable attention for their ability to affect biological invasions, however, researchers have largely overlooked the distinct role of viruses afforded by their unique ability to rapidly mutate and adapt to new hosts. With high mutation and genomic substitution rates, RNA and single-stranded DNA (ssDNA) viruses may be important constituents of invaded ecosystems, and could potentially behave quite differently from other pathogens. We review evidence suggesting that rapidly evolving viruses impact invasion dynamics in three key ways: (1) Rapidly evolving viruses may prevent exotic species from establishing self-sustaining populations. (2) Viruses can cause population collapses of exotic species in the introduced range. (3) Viruses can alter the consequences of biological invasions by causing population collapses and extinctions of native species. The ubiquity and frequent host shifting of viruses make their ability to influence invasion events likely. Eludicating the viral ecology of biological invasions will lead to an improved understanding of the causes and consequences of invasions, particularly as regards establishment success and changes to community structure that cannot be explained by direct interspecific interactions among native and exotic species.
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Affiliation(s)
- Cara A Faillace
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ, 08901, USA
| | - Nicholas S Lorusso
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ, 08901, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ, 08901, USA
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Walker KK, Rudicell RS, Li Y, Hahn BH, Wroblewski E, Pusey AE. Chimpanzees breed with genetically dissimilar mates. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160422. [PMID: 28280546 DOI: 10.5061/dryad.d7g4c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/23/2016] [Indexed: 05/22/2023]
Abstract
Inbreeding adversely affects fitness, whereas heterozygosity often augments it. Therefore, mechanisms to avoid inbreeding and increase genetic distance between mates should be advantageous in species where adult relatives reside together. Here we investigate mate choice for genetic dissimilarity in chimpanzees, a species in which many females avoid inbreeding through dispersal, but where promiscuous mating and sexual coercion can limit choice when related adults reside together. We take advantage of incomplete female dispersal in Gombe National Park, Tanzania to compare mate choice for genetic dissimilarity among immigrant and natal females in two communities using pairwise relatedness measures in 135 genotyped chimpanzees. As expected, natal females were more related to adult males in their community than were immigrant females. However, among 62 breeding events, natal females were not more related to the sires of their offspring than immigrant females, despite four instances of close inbreeding. Moreover, females were generally less related to the sires of their offspring than to non-sires. These results demonstrate that chimpanzees may be capable of detecting relatedness and selecting mates on the basis of genetic distance.
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Affiliation(s)
- Kara K Walker
- Department of Evolutionary Anthropology , Duke University , Durham, NC , USA
| | | | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine , University of Pennsylvania , Philadelphia, PA , USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine , University of Pennsylvania , Philadelphia, PA , USA
| | - Emily Wroblewski
- Department of Structural Biology , Stanford University School of Medicine , Stanford, CA , USA
| | - Anne E Pusey
- Department of Evolutionary Anthropology , Duke University , Durham, NC , USA
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38
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Walker KK, Rudicell RS, Li Y, Hahn BH, Wroblewski E, Pusey AE. Chimpanzees breed with genetically dissimilar mates. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160422. [PMID: 28280546 PMCID: PMC5319312 DOI: 10.1098/rsos.160422] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/23/2016] [Indexed: 05/05/2023]
Abstract
Inbreeding adversely affects fitness, whereas heterozygosity often augments it. Therefore, mechanisms to avoid inbreeding and increase genetic distance between mates should be advantageous in species where adult relatives reside together. Here we investigate mate choice for genetic dissimilarity in chimpanzees, a species in which many females avoid inbreeding through dispersal, but where promiscuous mating and sexual coercion can limit choice when related adults reside together. We take advantage of incomplete female dispersal in Gombe National Park, Tanzania to compare mate choice for genetic dissimilarity among immigrant and natal females in two communities using pairwise relatedness measures in 135 genotyped chimpanzees. As expected, natal females were more related to adult males in their community than were immigrant females. However, among 62 breeding events, natal females were not more related to the sires of their offspring than immigrant females, despite four instances of close inbreeding. Moreover, females were generally less related to the sires of their offspring than to non-sires. These results demonstrate that chimpanzees may be capable of detecting relatedness and selecting mates on the basis of genetic distance.
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Affiliation(s)
- Kara K Walker
- Department of Evolutionary Anthropology , Duke University , Durham, NC , USA
| | | | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine , University of Pennsylvania , Philadelphia, PA , USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine , University of Pennsylvania , Philadelphia, PA , USA
| | - Emily Wroblewski
- Department of Structural Biology , Stanford University School of Medicine , Stanford, CA , USA
| | - Anne E Pusey
- Department of Evolutionary Anthropology , Duke University , Durham, NC , USA
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Locatelli S, Harrigan RJ, Sesink Clee PR, Mitchell MW, McKean KA, Smith TB, Gonder MK. Why Are Nigeria-Cameroon Chimpanzees (Pan troglodytes ellioti) Free of SIVcpz Infection? PLoS One 2016; 11:e0160788. [PMID: 27505066 PMCID: PMC4978404 DOI: 10.1371/journal.pone.0160788] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/24/2016] [Indexed: 12/26/2022] Open
Abstract
Simian immunodeficiency virus (SIV) naturally infects two subspecies of chimpanzee: Pan troglodytes troglodytes from Central Africa (SIVcpzPtt) and P. t. schweinfurtii from East Africa (SIVcpzPts), but is absent in P. t. verus from West Africa and appears to be absent in P. t. ellioti inhabiting Nigeria and western Cameroon. One explanation for this pattern is that P. t. troglodytes and P. t schweinfurthii may have acquired SIVcpz after their divergence from P. t. verus and P. t. ellioti. However, all of the subspecies, except P. t. verus, still occasionally exchange migrants making the absence of SIVcpz in P. t. ellioti puzzling. Sampling of P. t. ellioti has been minimal to date, particularly along the banks of the Sanaga River, where its range abuts that of P. t. troglodytes. This study had three objectives. First, we extended the sampling of SIVcpz across the range of chimpanzees north of the Sanaga River to address whether under-sampling might account for the absence of evidence for SIVcpz infection in P. t. ellioti. Second, we investigated how environmental variation is associated with the spread and prevalence of SIVcpz in the two chimpanzee subspecies inhabiting Cameroon since environmental variation has been shown to contribute to their divergence from one another. Finally, we compared the prevalence and distribution of SIVcpz with that of Simian Foamy Virus (SFV) to examine the role of ecology and behavior in shaping the distribution of diseases in wild host populations. The dataset includes previously published results on SIVcpz infection and SFVcpz as well as newly collected data, and represents over 1000 chimpanzee fecal samples from 41 locations across Cameroon. Results revealed that none of the 181 P. t. ellioti fecal samples collected across the range of P. t. ellioti tested positive for SIVcpz. In addition, species distribution models suggest that environmental variation contributes to differences in the distribution and prevalence of SIVcpz and SFVcpz. The ecological niches of these two viruses are largely non-overlapping, although stronger statistical support for this conclusion will require more sampling. Overall this study demonstrates that SIVcpz infection is absent or very rare in P. t. ellioti, despite multiple opportunities for transmission. The reasons for its absence remain unclear, but might be explained by one or more factors, including environmental variation, viral competition, and/or local adaptation—all of which should be explored in greater detail through continued surveillance of this region.
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Affiliation(s)
- Sabrina Locatelli
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and University of Montpellier, 34394 Montpellier, France
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- * E-mail:
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA, 90095, United States of America
| | - Paul R. Sesink Clee
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- Department of Biology, Drexel University, Philadelphia, PA, 19104, United States of America
| | - Matthew W Mitchell
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- Department of Biology, Drexel University, Philadelphia, PA, 19104, United States of America
| | - Kurt A. McKean
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
| | - Thomas B. Smith
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA, 90095, United States of America
| | - Mary Katherine Gonder
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- Department of Biology, Drexel University, Philadelphia, PA, 19104, United States of America
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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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Foerster S, Zhong Y, Pintea L, Murray CM, Wilson ML, Mjungu DC, Pusey AE. Feeding habitat quality and behavioral trade-offs in chimpanzees: a case for species distribution models. Behav Ecol 2016; 27:1004-1016. [PMID: 27418751 PMCID: PMC4943107 DOI: 10.1093/beheco/arw004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 12/18/2015] [Accepted: 12/22/2015] [Indexed: 11/12/2022] Open
Abstract
The distribution and abundance of food resources are among the most important factors that influence animal behavioral strategies. Yet, spatial variation in feeding habitat quality is often difficult to assess with traditional methods that rely on extrapolation from plot survey data or remote sensing. Here, we show that maximum entropy species distribution modeling can be used to successfully predict small-scale variation in the distribution of 24 important plant food species for chimpanzees at Gombe National Park, Tanzania. We combined model predictions with behavioral observations to quantify feeding habitat quality as the cumulative dietary proportion of the species predicted to occur in a given location. This measure exhibited considerable spatial heterogeneity with elevation and latitude, both within and across main habitat types. We used model results to assess individual variation in habitat selection among adult chimpanzees during a 10-year period, testing predictions about trade-offs between foraging and reproductive effort. We found that nonswollen females selected the highest-quality habitats compared with swollen females or males, in line with predictions based on their energetic needs. Swollen females appeared to compromise feeding in favor of mating opportunities, suggesting that females rather than males change their ranging patterns in search of mates. Males generally occupied feeding habitats of lower quality, which may exacerbate energetic challenges of aggression and territory defense. Finally, we documented an increase in feeding habitat quality with community residence time in both sexes during the dry season, suggesting an influence of familiarity on foraging decisions in a highly heterogeneous landscape.
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Affiliation(s)
- Steffen Foerster
- Department of Evolutionary Anthropology, Duke University , Box 90383, Durham, NC 27708 , USA
| | - Ying Zhong
- Master of Environmental Management Program, Nicholas School of the Environment, Duke University, 450 Research Drive, Durham, NC 27708, USA
| | - Lilian Pintea
- Conservation Science Department, The Jane Goodall Institute, 1595 Spring Hill Road, Suite 550, Vienna, VA 22182, USA
| | - Carson M Murray
- Center for the Advanced Study of Human Paleobiology, The George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Michael L Wilson
- Department of Anthropology, University of Minnesota, 395 Humphrey Center, 301 19th Ave S, Minneapolis, MN 55455, USA; Department of Ecology, Evolution and Behavior, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St Paul, MN 55108, USA, and
| | - Deus C Mjungu
- Gombe Stream Research Centre, The Jane Goodall Institute, PO Box 1182, Kigoma, Tanzania
| | - Anne E Pusey
- Department of Evolutionary Anthropology, Duke University , Box 90383, Durham, NC 27708 , USA
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42
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Wolf TM, Sreevatsan S, Singer RS, Lipende I, Collins A, Gillespie TR, Lonsdorf EV, Travis DA. Noninvasive Tuberculosis Screening in Free-Living Primate Populations in Gombe National Park, Tanzania. ECOHEALTH 2016; 13:139-144. [PMID: 26419483 DOI: 10.1007/s10393-015-1063-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 06/05/2023]
Abstract
Recent advances in noninvasive detection methods for mycobacterial infection in primates create new opportunities for exploring the epidemiology of tuberculosis in free-living species. Chimpanzees (Pan troglodytes schweinfurthii) and baboons (Papio anubis) in Gombe National Park, Tanzania, were screened for infection with pathogens of the Mycobacterium tuberculosis Complex using Fecal IS6110 PCR; none was positive. This study demonstrates the feasibility of large-scale mycobacterial screening in wild primates.
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Affiliation(s)
- Tiffany M Wolf
- Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA.
- Minnesota Zoological Gardens, Apple Valley, MN, USA.
| | - Srinand Sreevatsan
- Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
| | - Randall S Singer
- Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA
| | | | | | | | | | - Dominic A Travis
- Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
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Barbian HJ, Li Y, Ramirez M, Klase Z, Lipende I, Mjungu D, Moeller AH, Wilson ML, Pusey AE, Lonsdorf EV, Bushman FD, Hahn BH. Destabilization of the gut microbiome marks the end-stage of simian immunodeficiency virus infection in wild chimpanzees. Am J Primatol 2015; 80. [PMID: 26676710 DOI: 10.1002/ajp.22515] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/20/2015] [Accepted: 12/01/2015] [Indexed: 12/17/2022]
Abstract
Enteric dysbiosis is a characteristic feature of progressive human immunodeficiency virus type 1 (HIV-1) infection but has not been observed in simian immunodeficiency virus (SIVmac)-infected macaques, including in animals with end-stage disease. This has raised questions concerning the mechanisms underlying the HIV-1 associated enteropathy, with factors other than virus infection, such as lifestyle and antibiotic use, implicated as playing possible causal roles. Simian immunodeficiency virus of chimpanzees (SIVcpz) is also associated with increased mortality in wild-living communities, and like HIV-1 and SIVmac, can cause CD4+ T cell depletion and immunodeficiency in infected individuals. Given the central role of the intestinal microbiome in mammalian health, we asked whether gut microbial constituents could be identified that are indicative of SIVcpz status and/or disease progression. Here, we characterized the gut microbiome of SIVcpz-infected and -uninfected chimpanzees in Gombe National Park, Tanzania. Subjecting a small number of fecal samples (N = 9) to metagenomic (shotgun) sequencing, we found bacteria of the family Prevotellaceae to be enriched in SIVcpz-infected chimpanzees. However, 16S rRNA gene sequencing of a larger number of samples (N = 123) failed to show significant differences in both the composition and diversity (alpha and beta) of gut bacterial communities between infected (N = 24) and uninfected (N = 26) chimpanzees. Similarly, chimpanzee stool-associated circular virus (Chi-SCV) and chimpanzee adenovirus (ChAdV) identified by metagenomic sequencing were neither more prevalent nor more abundant in SIVcpz-infected individuals. However, fecal samples collected from SIVcpz-infected chimpanzees within 5 months before their AIDS-related death exhibited significant compositional changes in their gut bacteriome. These data indicate that SIVcpz-infected chimpanzees retain a stable gut microbiome throughout much of their natural infection course, with a significant destabilization of bacterial (but not viral) communities observed only in individuals with known immunodeficiency within the last several months before their death. Am. J. Primatol. 80:e22515, 2018. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Hannah J Barbian
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Miguel Ramirez
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zachary Klase
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania
| | | | - Deus Mjungu
- Gombe Stream Research Center, Kigoma, Tanzania
| | - Andrew H Moeller
- Department of Integrative Biology, University of California, Berkeley, California.,Miller Institute for Basic Research, University of California, Berkeley, California
| | - Michael L Wilson
- Department of Anthropology, University of Minnesota, Minneapolis, Minnesota.,Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota
| | - Anne E Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Elizabeth V Lonsdorf
- Department of Psychology, Franklin and Marshall College, Lancaster, Pennsylvania
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania
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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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McCarthy KR, Kirmaier A, Autissier P, Johnson WE. Evolutionary and Functional Analysis of Old World Primate TRIM5 Reveals the Ancient Emergence of Primate Lentiviruses and Convergent Evolution Targeting a Conserved Capsid Interface. PLoS Pathog 2015; 11:e1005085. [PMID: 26291613 PMCID: PMC4546234 DOI: 10.1371/journal.ppat.1005085] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/15/2015] [Indexed: 12/29/2022] Open
Abstract
The widespread distribution of lentiviruses among African primates, and the lack of severe pathogenesis in many of these natural reservoirs, are taken as evidence for long-term co-evolution between the simian immunodeficiency viruses (SIVs) and their primate hosts. Evidence for positive selection acting on antiviral restriction factors is consistent with virus-host interactions spanning millions of years of primate evolution. However, many restriction mechanisms are not virus-specific, and selection cannot be unambiguously attributed to any one type of virus. We hypothesized that the restriction factor TRIM5, because of its unique specificity for retrovirus capsids, should accumulate adaptive changes in a virus-specific fashion, and therefore, that phylogenetic reconstruction of TRIM5 evolution in African primates should reveal selection by lentiviruses closely related to modern SIVs. We analyzed complete TRIM5 coding sequences of 22 Old World primates and identified a tightly-spaced cluster of branch-specific adaptions appearing in the Cercopithecinae lineage after divergence from the Colobinae around 16 million years ago. Functional assays of both extant TRIM5 orthologs and reconstructed ancestral TRIM5 proteins revealed that this cluster of adaptations in TRIM5 specifically resulted in the ability to restrict Cercopithecine lentiviruses, but had no effect (positive or negative) on restriction of other retroviruses, including lentiviruses of non-Cercopithecine primates. The correlation between lineage-specific adaptations and ability to restrict viruses endemic to the same hosts supports the hypothesis that lentiviruses closely related to modern SIVs were present in Africa and infecting the ancestors of Cercopithecine primates as far back as 16 million years ago, and provides insight into the evolution of TRIM5 specificity. Old World primates in Africa are reservoir hosts for more than 40 species of simian immunodeficiency viruses (SIVs), including the sources of the human immunodeficiency viruses, HIV-1 and HIV-2. To investigate the prehistoric origins of these lentiviruses, we looked for patterns of evolution in the antiviral host gene TRIM5 that would reflect selection by lentiviruses during evolution of African primates. We identified a pattern of adaptive changes unique to the TRIM5 proteins of a subset of African monkeys that suggests that the ancestors of these viruses emerged between 11–16 million years ago, and by reconstructing and comparing the function of ancestral TRIM5 proteins with extant TRIM5 proteins, we confirmed that these adaptations confer specificity for their modern descendants, the SIVs.
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Affiliation(s)
- Kevin R. McCarthy
- Harvard Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Andrea Kirmaier
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Patrick Autissier
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Welkin E. Johnson
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
- * E-mail:
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Rushmore J, Allison AB, Edwards EE, Bagal U, Altizer S, Cranfield MR, Glenn TC, Liu H, Mudakikwa A, Mugisha L, Muller MN, Stumpf RM, Thompson ME, Wrangham R, Yabsley MJ. Screening wild and semi-free ranging great apes for putative sexually transmitted diseases: Evidence of Trichomonadidae infections. Am J Primatol 2015; 77:1075-85. [PMID: 26119266 DOI: 10.1002/ajp.22442] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 06/02/2015] [Indexed: 11/07/2022]
Abstract
Sexually transmitted diseases (STDs) can persist endemically, are known to cause sterility and infant mortality in humans, and could have similar impacts in wildlife populations. African apes (i.e., chimpanzees, bonobos, and to a lesser extent gorillas) show multi-male mating behavior that could offer opportunities for STD transmission, yet little is known about the prevalence and impact of STDs in this endangered primate group. We used serology and PCR-based detection methods to screen biological samples from wild and orphaned eastern chimpanzees and gorillas (N = 172 individuals, including adults, and juveniles) for four classes of pathogens that either commonly cause human STDs or were previously detected in captive apes: trichomonads, Chlamydia spp., Treponema pallidum (syphilis and yaws), and papillomaviruses. Based on results from prior modeling and comparative research, we expected STD prevalence to be highest in females versus males and in sexually mature versus immature individuals. All samples were negative for Chlamydia, Treponema pallidum, and papillomaviruses; however, a high percentage of wild chimpanzee urine and fecal samples showed evidence of trichomonads (protozoa). Analysis revealed that females were more likely than males to have positive urine-but not fecal-samples; however, there was no evidence of age (sexual maturity) differences in infection status. Sequence analysis of chimpanzee trichomonad samples revealed a close relationship to previously described trichomonads within the genus Tetratrichomonas. Phylogenetic comparisons to archived sequences from multiple vertebrate hosts suggests that many of the chimpanzee parasites from our study are likely transmitted via fecal-oral contact, but the transmission of some Tetratrichomonas sequence-types remains unknown and could include sexual contact. Our work emphasizes that only a fraction of infectious agents affecting wild apes are presently known to science, and that further work on great ape STDs could offer insights for the management of endangered great apes and for understanding human STD origins.
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Affiliation(s)
- Julie Rushmore
- Odum School of Ecology, The University of Georgia, Athens, Georgia
- College of Veterinary Medicine, The University of Georgia, Athens, Georgia
| | - Andrew B Allison
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Erin E Edwards
- College of Veterinary Medicine, The University of Georgia, Athens, Georgia
| | - Ujwal Bagal
- Institute of Bioinformatics, The University of Georgia, Athens, Georgia
| | - Sonia Altizer
- Odum School of Ecology, The University of Georgia, Athens, Georgia
| | - Mike R Cranfield
- Gorilla Doctors, Wildlife Health Center, University of California Davis, Davis, California
- The Department of Molecular and Pathobiology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Travis C Glenn
- Department of Environmental Health Science, The University of Georgia, Athens, Georgia
| | - Hsi Liu
- National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control, Athens, Georgia
| | - Antoine Mudakikwa
- Rwanda Development Board, Department of Tourism and Conservation, Kigali, Rwanda
| | - Lawrence Mugisha
- Conservation and Ecosystem Health Alliance (CEHA), Kampala, Uganda
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Martin N Muller
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico
| | - Rebecca M Stumpf
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | | | - Richard Wrangham
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Michael J Yabsley
- Warnell School of Forestry and Natural Resources, The University of Georgia and the Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, The University of Georgia, Athens, Georgia
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47
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Piel AK, Cohen N, Kamenya S, Ndimuligo SA, Pintea L, Stewart FA. Population status of chimpanzees in the Masito-Ugalla Ecosystem, Tanzania. Am J Primatol 2015; 77:1027-35. [PMID: 26119006 DOI: 10.1002/ajp.22438] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 05/27/2015] [Indexed: 12/24/2022]
Abstract
More than 75 percent of Tanzania's chimpanzees live at low densities on land outside national parks. Chimpanzees are one of the key conservation targets in the region and long-term monitoring of these populations is essential for assessing the overall status of ecosystem health and the success of implemented conservation strategies. We aimed to assess change in chimpanzee density within the Masito-Ugalla Ecosystem (MUE) by comparing results of re-walking the same line transects in 2007 and 2014. We further used published remote sensing data derived from Landsat satellites to assess forest cover change within a 5 km buffer of these transects over that same period. We detected no statistically significant decline in chimpanzee density across the surveyed areas of MUE between 2007 and 2014, although the overall mean density of chimpanzees declined from 0.09 individuals/km(2) in 2007 to 0.05 individuals/km(2) in 2014. Whether this change is biologically meaningful cannot be determined due to small sample sizes and large, entirely overlapping error margins. It is therefore possible that the MUE chimpanzee population has been stable over this period and indeed in some areas (Issa Valley, Mkanga, Kamkulu) even showed an increase in chimpanzee density. Variation in chimpanzee habitat preference for ranging or nesting could explain variation in density at some of the survey sites between 2007 and 2014. We also found a relationship between increasing habitat loss and lower mean chimpanzee density. Future surveys will need to ensure a larger sample size, broader geographic effort, and random survey design, to more precisely determine trends in MUE chimpanzee density and population size over time.
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Affiliation(s)
- Alex K Piel
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 3QG, United Kingdom.,Ugalla Primate Project, Kigoma, Tanzania
| | | | | | - Sood A Ndimuligo
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Blindern, Oslo, Norway
| | - Lilian Pintea
- The Jane Goodall Institute, 1595 Spring Hill Road, Suite 550 Vienna, Virginia
| | - Fiona A Stewart
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 3QG, United Kingdom.,Ugalla Primate Project, Kigoma, Tanzania
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48
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De Nys HM, Madinda NF, Merkel K, Robbins M, Boesch C, Leendertz FH, Calvignac-Spencer S. A cautionary note on fecal sampling and molecular epidemiology in predatory wild great apes. Am J Primatol 2015; 77:833-40. [PMID: 26031302 DOI: 10.1002/ajp.22418] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/18/2015] [Accepted: 03/22/2015] [Indexed: 11/06/2022]
Abstract
Fecal samples are an important source of information on parasites (viruses, prokaryotes, or eukaryotes) infecting wild great apes. Molecular analysis of fecal samples has already been used for deciphering the origins of major human pathogens such as HIV-1 or Plasmodium falciparum. However, for apes that hunt (chimpanzees and bonobos), detection of parasite nucleic acids may reflect either true infection of the host of interest or ingestion of an infected prey, for example, another non-human primate. To determine the potential magnitude of this issue, we estimated the prevalence of prey DNA in fecal samples obtained from two wild chimpanzee communities. We observed values >15%, which are higher than or close to the fecal detection rates of many great ape parasites. Contamination of fecal samples with parasite DNA from dietary origin may therefore occasionally impact non-invasive epidemiological studies. This problem can be addressed (at least partially) by monitoring the presence of prey DNA.
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Affiliation(s)
- Hélène Marie De Nys
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Nordufer, Berlin, Germany.,Department of Primatology, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany.,Laboratory of Parasitology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan, Merelbeke, Belgium
| | - Nadège Freda Madinda
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Nordufer, Berlin, Germany.,Department of Primatology, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany.,Institut de Recherches en Ecologie Tropicale, Libreville, Gabon
| | - Kevin Merkel
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Nordufer, Berlin, Germany
| | - Martha Robbins
- Department of Primatology, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
| | - Christophe Boesch
- Department of Primatology, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
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49
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Wroblewski EE, Norman PJ, Guethlein LA, Rudicell RS, Ramirez MA, Li Y, Hahn BH, Pusey AE, Parham P. Signature Patterns of MHC Diversity in Three Gombe Communities of Wild Chimpanzees Reflect Fitness in Reproduction and Immune Defense against SIVcpz. PLoS Biol 2015; 13:e1002144. [PMID: 26020813 PMCID: PMC4447270 DOI: 10.1371/journal.pbio.1002144] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 04/02/2015] [Indexed: 11/19/2022] Open
Abstract
Major histocompatibility complex (MHC) class I molecules determine immune responses to viral infections. These polymorphic cell-surface glycoproteins bind peptide antigens, forming ligands for cytotoxic T and natural killer cell receptors. Under pressure from rapidly evolving viruses, hominoid MHC class I molecules also evolve rapidly, becoming diverse and species-specific. Little is known of the impact of infectious disease epidemics on MHC class I variant distributions in human populations, a context in which the chimpanzee is the superior animal model. Population dynamics of the chimpanzees inhabiting Gombe National Park, Tanzania have been studied for over 50 years. This population is infected with SIVcpz, the precursor of human HIV-1. Because HLA-B is the most polymorphic human MHC class I molecule and correlates strongly with HIV-1 progression, we determined sequences for its ortholog, Patr-B, in 125 Gombe chimpanzees. Eleven Patr-B variants were defined, as were their frequencies in Gombe's three communities, changes in frequency with time, and effect of SIVcpz infection. The growing populations of the northern and central communities, where SIVcpz is less prevalent, have stable distributions comprising a majority of low-frequency Patr-B variants and a few high-frequency variants. Driving the latter to high frequency has been the fecundity of immigrants to the northern community, whereas in the central community, it has been the fecundity of socially dominant individuals. In the declining population of the southern community, where greater SIVcpz prevalence is associated with mortality and emigration, Patr-B variant distributions have been changing. Enriched in this community are Patr-B variants that engage with natural killer cell receptors. Elevated among SIVcpz-infected chimpanzees, the Patr-B*06:03 variant has striking structural and functional similarities to HLA-B*57, the human allotype most strongly associated with delayed HIV-1 progression. Like HLA-B*57, Patr-B*06:03 correlates with reduced viral load, as assessed by detection of SIVcpz RNA in feces.
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Affiliation(s)
- Emily E. Wroblewski
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (EEW); (PP)
| | - Paul J. Norman
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Lisbeth A. Guethlein
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Rebecca S. Rudicell
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
- Sanofi, Cambridge, Massachusetts, United States of America
| | - Miguel A. Ramirez
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
| | - Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (EEW); (PP)
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50
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Barbian HJ, Decker JM, Bibollet-Ruche F, Galimidi RP, West AP, Learn GH, Parrish NF, Iyer SS, Li Y, Pace CS, Song R, Huang Y, Denny TN, Mouquet H, Martin L, Acharya P, Zhang B, Kwong PD, Mascola JR, Verrips CT, Strokappe NM, Rutten L, McCoy LE, Weiss RA, Brown CS, Jackson R, Silvestri G, Connors M, Burton DR, Shaw GM, Nussenzweig MC, Bjorkman PJ, Ho DD, Farzan M, Hahn BH. Neutralization properties of simian immunodeficiency viruses infecting chimpanzees and gorillas. mBio 2015; 6:e00296-15. [PMID: 25900654 PMCID: PMC4453581 DOI: 10.1128/mbio.00296-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 03/19/2015] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED Broadly cross-reactive neutralizing antibodies (bNabs) represent powerful tools to combat human immunodeficiency virus type 1 (HIV-1) infection. Here, we examined whether HIV-1-specific bNabs are capable of cross-neutralizing distantly related simian immunodeficiency viruses (SIVs) infecting central (Pan troglodytes troglodytes) (SIVcpzPtt) and eastern (Pan troglodytes schweinfurthii) (SIVcpzPts) chimpanzees (n = 11) as well as western gorillas (Gorilla gorilla gorilla) (SIVgor) (n = 1). We found that bNabs directed against the CD4 binding site (n = 10), peptidoglycans at the base of variable loop 3 (V3) (n = 5), and epitopes at the interface of surface (gp120) and membrane-bound (gp41) envelope glycoproteins (n = 5) failed to neutralize SIVcpz and SIVgor strains. In addition, apex V2-directed bNabs (n = 3) as well as llama-derived (heavy chain only) antibodies (n = 6) recognizing both the CD4 binding site and gp41 epitopes were either completely inactive or neutralized only a fraction of SIVcpzPtt strains. In contrast, one antibody targeting the membrane-proximal external region (MPER) of gp41 (10E8), functional CD4 and CCR5 receptor mimetics (eCD4-Ig, eCD4-Ig(mim2), CD4-218.3-E51, and CD4-218.3-E51-mim2), as well as mono- and bispecific anti-human CD4 (iMab and LM52) and CCR5 (PRO140, PRO140-10E8) receptor antibodies neutralized >90% of SIVcpz and SIVgor strains with low-nanomolar (0.13 to 8.4 nM) potency. Importantly, the latter antibodies blocked virus entry not only in TZM-bl cells but also in Cf2Th cells expressing chimpanzee CD4 and CCR5 and neutralized SIVcpz in chimpanzee CD4(+) T cells, with 50% inhibitory concentrations (IC50s) ranging from 3.6 to 40.5 nM. These findings provide new insight into the protective capacity of anti-HIV-1 bNabs and identify candidates for further development to combat SIVcpz infection. IMPORTANCE SIVcpz is widespread in wild-living chimpanzees and can cause AIDS-like immunopathology and clinical disease. HIV-1 infection of humans can be controlled by antiretroviral therapy; however, treatment of wild-living African apes with current drug regimens is not feasible. Nonetheless, it may be possible to curb the spread of SIVcpz in select ape communities using vectored immunoprophylaxis and/or therapy. Here, we show that antibodies and antibody-like inhibitors developed to combat HIV-1 infection in humans are capable of neutralizing genetically diverse SIVcpz and SIVgor strains with considerable breadth and potency, including in primary chimpanzee CD4(+) T cells. These reagents provide an important first step toward translating intervention strategies currently developed to treat and prevent AIDS in humans to SIV-infected apes.
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Affiliation(s)
- Hannah J Barbian
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Julie M Decker
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Frederic Bibollet-Ruche
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rachel P Galimidi
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, USA
| | - Anthony P West
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, USA
| | - Gerald H Learn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nicholas F Parrish
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shilpa S Iyer
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yingying Li
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Ruijiang Song
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, USA
| | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Loic Martin
- CEA, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, Gif-sur-Yvette, France
| | - Priyamvada Acharya
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Nika M Strokappe
- Biomolecular Imaging (BMI), Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Lucy Rutten
- Biomolecular Imaging (BMI), Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Robin A Weiss
- Division of Infection and Immunity, University College London, London, United Kingdom
| | | | | | - Guido Silvestri
- Yerkes Regional Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology and Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, USA
| | - Michael Farzan
- Department of Immunology and Microbial Science, The Scripps Research Institute, Jupiter, Florida, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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