Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes

Nature ◽  
10.1038/17130 ◽  
1999 ◽  
Vol 397 (6718) ◽  
pp. 436-441 ◽  
Author(s):  
Feng Gao ◽  
Elizabeth Bailes ◽  
David L. Robertson ◽  
Yalu Chen ◽  
Cynthia M. Rodenburg ◽  
...  
Keyword(s):  
Pan Troglodytes ◽  
Pan Troglodytes Troglodytes ◽  
Hiv 1

scholarly journals Gene flow in wild chimpanzee populations: what genetic data tell us about chimpanzee movement over space and time

2001 ◽  
Vol 356 (1410) ◽  
pp. 889-897 ◽  
Author(s):  
Pascal Gagneux ◽  
M. Katherine Gonder ◽  
Tony L. Goldberg ◽  
Phillip A. Morin
Keyword(s):  
Gene Flow ◽  
Pan Troglodytes ◽  
Dna Sequences ◽  
Molecular Genetic ◽  
Wild Chimpanzee ◽  
Pan Troglodytes Troglodytes ◽  
Equatorial Africa ◽  
Pan Troglodytes Vellerosus ◽  
Hiv 1 ◽  
Chimpanzee Population

The isolation of phylogenetically distinct primate immunodeficiency viruses from at least seven wild–born, captive chimpanzees indicates that viruses closely related to HIV–1 may be endemic in some wild chimpanzee populations. The search for the chimpanzee population or populations harbouring these viruses is therefore on. This paper attempts to answer the question of whether or not such populations of chimpanzees are likely to exist at all, and, if so, where they are likely to be found. We summarize what is known about gene flow in wild populations of chimpanzees, both between major phylogeographical subdivisions of the species, and within these subdivisions. Our analysis indicates that hitherto undocumented reproductively isolated chimpanzee populations may in fact exist. This conclusion is based on the observation that, despite limited geographical sampling and limited numbers of genetic loci, conventional notions of the nature and extent of chimpanzee gene flow have recently been substantially revised. Molecular genetic studies using mitochondrial DNA sequences and hypervariable nuclear microsatellite markers have indicated the existence of heretofore undocumented barriers to chimpanzee gene flow. These studies have identified at least one population of chimpanzees genetically distinct enough to be classified into a new subspecies ( Pan troglodytes vellerosus ). At the same time, they have called into question the long–accepted genetic distinction between eastern chimpanzees ( Pan troglodytes schweinfurthii ) and western equatorial chimpanzees ( Pan troglodytes troglodytes ). The same studies have further indicated that gene flow between local populations is more extensive than was previously thought, and follows patterns sometimes inconsistent with those documented through direct behavioural observation. Given the apparently incomplete nature of the current understanding of chimpanzee gene flow in equatorial Africa, it seems reasonable to speculate that a chimpanzee population or populations may exist which both harbour the putative HIV–1 ancestor, and which have remained reproductively isolated from other chimpanzee populations over the time–scale relevant to the evolution of the SIVcpz–HIV–1 complex of viruses. Continued extensive sampling of wild chimpanzee populations, both for their genes and their viruses, should be performed quickly considering the high probability of extinction that many wild chimpanzee populations face today. The history of human–chimpanzee contacts is discussed.

scholarly journals Simian Immunodeficiency Virus Infection in Wild-Caught Chimpanzees from Cameroon

2005 ◽  
Vol 79 (2) ◽  
pp. 1312-1319 ◽  
Author(s):  
Eric Nerrienet ◽  
Mario L. Santiago ◽  
Yacouba Foupouapouognigni ◽  
Elizabeth Bailes ◽  
Nicolas I. Mundy ◽  
...  
Keyword(s):  
Pan Troglodytes ◽  
Dna Analysis ◽  
Phylogenetic Analyses ◽  
Central Africa ◽  
Geographic Region ◽  
Pan Troglodytes Troglodytes ◽  
West Central ◽  
Immunodeficiency Virus ◽  
Pan Troglodytes Vellerosus ◽  
Hiv 1

ABSTRACT Simian immunodeficiency viruses (SIVcpz) infecting chimpanzees (Pan troglodytes) in west central Africa are the closest relatives to all major variants of human immunodeficiency virus type 1 ([HIV-1]; groups M, N and O), and have thus been implicated as the source of the human infections; however, information concerning the prevalence, geographic distribution, and subspecies association of SIVcpz still remains limited. In this study, we tested 71 wild-caught chimpanzees from Cameroon for evidence of SIVcpz infection. Thirty-nine of these were of the central subspecies (Pan troglodytes troglodytes), and 32 were of the Nigerian subspecies (Pan troglodytes vellerosus), as determined by mitochondrial DNA analysis. Serological analysis determined that one P. t. troglodytes ape (CAM13) harbored serum antibodies that cross-reacted strongly with HIV-1 antigens; all other apes were seronegative. To characterize the newly identified virus, 14 partially overlapping viral fragments were amplified from fecal virion RNA and concatenated to yield a complete SIVcpz genome (9,284 bp). Phylogenetic analyses revealed that SIVcpzCAM13 fell well within the radiation of the SIVcpzPtt group of viruses, as part of a clade including all other SIVcpzPtt strains as well as HIV-1 groups M and N. However, SIVcpzCAM13 clustered most closely with SIVcpzGAB1 from Gabon rather than with SIVcpzCAM3 and SIVcpzCAM5 from Cameroon, indicating the existence of divergent SIVcpzPtt lineages within the same geographic region. These data, together with evidence of recombination among ancestral SIVcpzPtt lineages, indicate long-standing endemic infection of central chimpanzees and reaffirm a west central African origin of HIV-1. Whether P. t. vellerosus apes are naturally infected with SIVcpz requires further study.

scholarly journals Intercommunity interactions and killings in central chimpanzees (Pan troglodytes troglodytes) from Loango National Park, Gabon

Primates ◽  
2021 ◽  
Author(s):  
Laura Martínez-Íñigo ◽  
Pauline Baas ◽  
Harmonie Klein ◽  
Simone Pika ◽  
Tobias Deschner
Keyword(s):  
Pan Troglodytes ◽  
National Park ◽  
Camera Traps ◽  
Encounter Rate ◽  
Visual Contact ◽  
Intergroup Interactions ◽  
Killing Rate ◽  
The Core ◽  
Pan Troglodytes Troglodytes

AbstractIntercommunity competition in chimpanzees (Pan troglodytes) has been widely studied in eastern (P. t. schweinfurthii) and western (P. t. verus) communities. Both subspecies show hostility towards neighboring communities but differ in rates of lethal attacks and female involvement. However, relatively little is known about the territorial behavior of the two other subspecies, central (P. t. troglodytes) and Nigeria-Cameroon chimpanzees (P. t. ellioti). Here, we present the first insights into intercommunity interactions of individuals of a community of central chimpanzees living in the Loango National Park in Gabon. The presence of individuals of neighboring communities in the Rekambo home range was assessed using 27 camera traps. Information was compiled on intergroup interactions recorded before (2005–2016) and after (January 2017–June 2019) the habituation of the community. Individuals from neighboring communities entered the core area, where nine out of 16 recorded intercommunity encounters occurred. Males were the main participants in territorial patrols and intercommunity aggressions. Females were part of all six territorial patrols recorded and dependent offspring participated in five patrols. Females were involved in intercommunity aggression in five out of twelve recorded encounters in which there was visual contact between communities. While the intercommunity encounter rate was lower than that reported across most other long-term chimpanzee sites, the annual intercommunity killing rate was among the highest. These results suggest that the frequency of lethal attacks at Loango is comparable to that reported for the eastern subspecies. In contrast, female involvement in intercommunity interactions mirrors that of the western subspecies.

scholarly journals Cell Type-Dependent Escape of Capsid Inhibitors by Simian Immunodeficiency Virus SIVcpz

2020 ◽  
Vol 94 (23) ◽  
Author(s):  
Augustin Penda Twizerimana ◽  
Rachel Scheck ◽  
Daniel Becker ◽  
Zeli Zhang ◽  
Marianne Wammers ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Simian Immunodeficiency Virus ◽  
Pan Troglodytes ◽  
Hela Cells ◽  
Cyclophilin A ◽  
Human Pbmcs ◽  
Cell Type ◽  
Content Type ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACT Pandemic human immunodeficiency virus type 1 (HIV-1) is the result of the zoonotic transmission of simian immunodeficiency virus (SIV) from the chimpanzee subspecies Pan troglodytes troglodytes (SIVcpzPtt). The related subspecies Pan troglodytes schweinfurthii is the host of a similar virus, SIVcpzPts, which did not spread to humans. We tested these viruses with small-molecule capsid inhibitors (PF57, PF74, and GS-CA1) that interact with a binding groove in the capsid that is also used by CPSF6. While HIV-1 was sensitive to capsid inhibitors in cell lines, human macrophages, and peripheral blood mononuclear cells (PBMCs), SIVcpzPtt was resistant in rhesus FRhL-2 cells and human PBMCs but was sensitive to PF74 in human HOS and HeLa cells. SIVcpzPts was insensitive to PF74 in FRhL-2 cells, HeLa cells, PBMCs, and macrophages but was inhibited by PF74 in HOS cells. A truncated version of CPSF6 (CPSF6-358) inhibited SIVcpzPtt and HIV-1, while in contrast, SIVcpzPts was resistant to CPSF6-358. Homology modeling of HIV-1, SIVcpzPtt, and SIVcpzPts capsids and binding energy estimates suggest that these three viruses bind similarly to the host proteins cyclophilin A (CYPA) and CPSF6 as well as the capsid inhibitor PF74. Cyclosporine treatment, mutation of the CYPA-binding loop in the capsid, or CYPA knockout eliminated the resistance of SIVcpzPts to PF74 in HeLa cells. These experiments revealed that the antiviral capacity of PF74 is controlled by CYPA in a virus- and cell type-specific manner. Our data indicate that SIVcpz viruses can use infection pathways that escape the antiviral activity of PF74. We further suggest that the antiviral activity of PF74 capsid inhibitors depends on cellular cofactors. IMPORTANCE HIV-1 originated from SIVcpzPtt but not from the related virus SIVcpzPts, and thus, it is important to describe molecular infection by SIVcpzPts in human cells to understand the zoonosis of SIVs. Pharmacological HIV-1 capsid inhibitors (e.g., PF74) bind a capsid groove that is also a binding site for the cellular protein CPSF6. SIVcpzPts was resistant to PF74 in HeLa cells but sensitive in HOS cells, thus indicating cell line-specific resistance. Both SIVcpz viruses showed resistance to PF74 in human PBMCs. Modulating the presence of cyclophilin A or its binding to capsid in HeLa cells overcame SIVcpzPts resistance to PF74. These results indicate that early cytoplasmic infection events of SIVcpzPts may differ between cell types and affect, in an unknown manner, the antiviral activity of capsid inhibitors. Thus, capsid inhibitors depend on the activity or interaction of currently uncharacterized cellular factors.

scholarly journals Neutralization Properties of Simian Immunodeficiency Viruses Infecting Chimpanzees and Gorillas

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Hannah J. Barbian ◽  
Julie M. Decker ◽  
Frederic Bibollet-Ruche ◽  
Rachel P. Galimidi ◽  
Anthony P. West ◽  
...  
Keyword(s):  
T Cells ◽  
Binding Site ◽  
Pan Troglodytes ◽  
Neutralizing Antibodies ◽  
Gorilla Gorilla ◽  
Protective Capacity ◽  
Content Type ◽  
Ccr5 Receptor ◽  
Cd4 Binding Site ◽  
Hiv 1

ABSTRACTBroadly 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 troglodytestroglodytes) (SIVcpzPtt) and eastern (Pan troglodytesschweinfurthii) (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 SIVcpzPttstrains. In contrast, one antibody targeting the membrane-proximal external region (MPER) of gp41 (10E8), functional CD4 and CCR5 receptor mimetics (eCD4-Ig, eCD4-Igmim2, 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.IMPORTANCESIVcpz 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.

scholarly journals Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 276 ◽  
Author(s):  
Daniela C. Soto ◽  
Colin Shew ◽  
Mira Mastoras ◽  
Joshua M. Schmidt ◽  
Ruta Sahasrabudhe ◽  
...  
Keyword(s):  
Pan Troglodytes ◽  
Optical Mapping ◽  
Demographic History ◽  
Cell Types ◽  
Genome Project ◽  
Nanopore Sequencing ◽  
Great Ape ◽  
Single Nucleotide Variants ◽  
Short Read ◽  
Pan Troglodytes Troglodytes

Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits. Structural variants (SVs), including deletions and inversions, comprise a larger proportion of genetic differences between and within species, making them an important yet understudied source of trait divergence. Here, we used a combination of long-read and -range sequencing approaches to characterize the structural variant landscape of two additional Pan troglodytes verus individuals, one of whom carries 13% admixture from Pan troglodytes troglodytes. We performed optical mapping of both individuals followed by nanopore sequencing of one individual. Filtering for larger variants (>10 kbp) and combined with genotyping of SVs using short-read data from the Great Ape Genome Project, we identified 425 deletions and 59 inversions, of which 88 and 36, respectively, were novel. Compared with gene expression in humans, we found a significant enrichment of chimpanzee genes with differential expression in lymphoblastoid cell lines and induced pluripotent stem cells, both within deletions and near inversion breakpoints. We examined chromatin-conformation maps from human and chimpanzee using these same cell types and observed alterations in genomic interactions at SV breakpoints. Finally, we focused on 56 genes impacted by SVs in >90% of chimpanzees and absent in humans and gorillas, which may contribute to chimpanzee-specific features. Sequencing a greater set of individuals from diverse subspecies will be critical to establish the complete landscape of genetic variation in chimpanzees.

scholarly journals Assessment of gastrointestinal parasites in wild chimpanzees (Pan troglodytes troglodytes) in southeast Cameroon

2014 ◽  
Vol 113 (7) ◽  
pp. 2541-2550 ◽  
Author(s):  
Pascal Drakulovski ◽  
Sébastien Bertout ◽  
Sabrina Locatelli ◽  
Christelle Butel ◽  
Sébastien Pion ◽  
...  
Keyword(s):  
Pan Troglodytes ◽  
Gastrointestinal Parasites ◽  
Pan Troglodytes Troglodytes

scholarly journals The evolution of HIV-1 and the origin of AIDS

2010 ◽  
Vol 365 (1552) ◽  
pp. 2487-2494 ◽  
Author(s):  
Paul M. Sharp ◽  
Beatrice H. Hahn
Keyword(s):  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Central Africa ◽  
Immune Deficiency Syndrome ◽  
Deficiency Syndrome ◽  
Gorilla Gorilla ◽  
Genetic Changes ◽  
Pan Troglodytes Troglodytes ◽  
Species Specific ◽  
Hiv 1

The major cause of acquired immune deficiency syndrome (AIDS) is human immunodeficiency virus type 1 (HIV-1). We have been using evolutionary comparisons to trace (i) the origin(s) of HIV-1 and (ii) the origin(s) of AIDS. The closest relatives of HIV-1 are simian immunodeficiency viruses (SIVs) infecting wild-living chimpanzees ( Pan troglodytes troglodytes ) and gorillas ( Gorilla gorilla gorilla ) in west central Africa. Phylogenetic analyses have revealed the origins of HIV-1: chimpanzees were the original hosts of this clade of viruses; four lineages of HIV-1 have arisen by independent cross-species transmissions to humans and one or two of those transmissions may have been via gorillas. However, SIVs are primarily monkey viruses: more than 40 species of African monkeys are infected with their own, species-specific, SIV and in at least some host species, the infection seems non-pathogenic. Chimpanzees acquired from monkeys two distinct forms of SIVs that recombined to produce a virus with a unique genome structure. We have found that SIV infection causes CD4 + T-cell depletion and increases mortality in wild chimpanzees, and so the origin of AIDS is more ancient than the origin of HIV-1. Tracing the genetic changes that occurred as monkey viruses adapted to infect first chimpanzees and then humans may provide insights into the causes of the pathogenicity of these viruses.

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