Sequence Analysis of a Highly Divergent HIV-1-Related Lentivirus Isolated from a Wild Captured Chimpanzee

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Current knowledge of the genetic diversity of simian immunodeficiency virus (SIVcpz) infection of wild chimpanzees (Pan troglodytes)is incomplete since few isolates, mostly from captive apes from Cameroon and Gabon, have been characterized; yet this information is critical for understanding the origins of human immunodeficiency virus type 1 (HIV-1) and the circumstances leading to the HIV-1 pandemic. Here, we report the first full-length SIVcpz sequence (TAN1) from a wild chimpanzee (Pan troglodytes schweinfurthii) from Gombe National Park (Tanzania), which was obtained noninvasively by amplification of virion RNA from fecal samples collected under field conditions. Using reverse transcription-PCR and a combination of generic and strain-specific primers, we amplified 13 subgenomic fragments which together spanned the entire TAN1 genome (9,326 bp). Distance and phylogenetic tree analyses identified TAN1 unambiguously as a member of the HIV-1/SIVcpz group of viruses but also revealed an extraordinary degree of divergence from all previously characterized SIVcpz and HIV-1 strains. In Gag, Pol, and Env proteins, TAN1 differed from west-central African SIVcpz and HIV-1 strains on average by 36, 30, and 51% of amino acid sequences, respectively, approaching distance values typically found for SIVs from different primate species. The closest relative was SIVcpzANT, also from a P. t. schweinfurthii ape, which differed by 30, 25, and 44%, respectively, in these same protein sequences but clustered with TAN1 in all major coding regions in a statistically highly significant manner. These data indicate that east African chimpanzees, like those from west-central Africa, are naturally infected by SIVcpz but that their viruses comprise a second, divergent SIVcpz lineage which appears to have evolved in relative isolation for an extended period of time. Our data also demonstrate that noninvasive molecular epidemiological studies of SIVcpz in wild chimpanzees are feasible and that such an approach may prove essential for unraveling the evolutionary history of SIVcpz/HIV-1 as well as that of other pathogens naturally infecting wild primate populations. West-central African chimpanzees (Pan troglodytes troglodytes)are naturally infected with strains of simian immunodeficiency virus (SIVcpz) that represent the closest relatives of human immunodeficiency virus type 1 (HIV-1) groups M, N, and O and have thus been implicated as the primate source of the human infections (12). East African chimpanzees (Pan troglodytes schweinfurthii) are also infected with SIVcpz, but genetic information for these viruses is limited since only two such strains (ANT and TAN1) have so far been identified (32,45). The first of these, SIVcpzANT, was isolated over a decade ago from a wild-caught chimpanzee orphan (Noah) which was confiscated upon illegal exportation from Kinshasa (Democratic Republic of Congo) (26). Although its geographic origin is unknown, this chimpanzee was subsequently typed as an eastern chimpanzee (P. t. schweinfurthii) by mitochondr...

Section: West-central African Chimpanzees (Pan Troglodytes Troglodytes)mentioning

confidence: 99%

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confidence: 99%

Amplification of a Complete Simian Immunodeficiency Virus Genome from Fecal RNA of a Wild Chimpanzee

Santiago

Bibollet-Ruche

Bailes

et al. 2003

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“…SIV and HIV are classified as primate lentiviruses (PLVs), and at the present time six lineages, based upon phylogenetic relationships of full-length genomes, are recognized (5,12). These six designated lineages are (i) SIVcpz from chimpanzees (Pan troglodytes), including HIV-1 (17,25,26,41,55); (ii) SIVsm from sooty mangabeys (Cercocebus atys), including HIV-2 and SIVmac from captive macaques (Macaca spp.) (21,24,36); (iii) SIVagm from African green monkeys (members of the Chlorocebus aethiops superspecies) (1, 2, 14-16, 23, 27, 29, 35); (iv) SIVsyk from Sykes' monkeys (Cercopithecus albogularis); (v) SIVlhoest from L'Hoest monkeys (Cercopithecus lhoesti), including SIVsun from sun-tailed monkeys (Cercopithecus solatus) and SIVmnd type 1 (GB1) from mandrills (Mandrillus sphinx) (3,4,22,54); and (vi) SIVcol from Colobus monkeys (Colobus guereza) (12).…”

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confidence: 99%

Characterization and Comparison of Recombinant Simian Immunodeficiency Virus from Drill ( Mandrillus leucophaeus ) and Mandrill ( Mandrillus sphinx ) Isolates

Switzer

Foley

et al. 2003

Since simian immunodeficiency virus (SIV) was found to be the source of the human AIDS pandemic, a major goal has been to characterize the diversity of SIV strains in the wild and to assess their potential for crossover into humans. In the present study, SIV was isolated from a seropositive drill (Mandrillus leucophaeus) and three seropositive mandrills (Mandrillus sphinx) by using macaque peripheral blood mononuclear cells (PBMC). Full-length sequences were obtained from a drill and mandrill and designated SIVdrl1FAO and SIVmnd5440, respectively. A 182-bp fragment of the pol genes of the two remaining mandrill SIV isolates was also analyzed. Phylogenetic analyses demonstrated that SIVdrl1FAO formed a monophyletic clade with SIVmnd5440 and SIVmndM14, recently designated SIVmnd type 2. Both the SIVdrl and SIVmnd type 2 genomes carried a vpx gene and appeared to share a common ancestor with SIVrcm in the 5 region of the genome and with SIVmndGB1 (type 1) in the 3 region of the genome. A statistically significant recombination breakpoint was detected at the beginning of envelope, suggesting that the viruses were descendents of the same recombinant. Phylogenetic analysis of vpx and vpr genes demonstrated that the vpx genes formed a monophyletic cluster that grouped with vpr from SIVagm. In addition, both SIVdrl1FAO and SIVmnd5440 replicated in human PBMC and therefore could pose a risk of transmission to the human population.

“…The six known primate lineages are approximately equidistant from one another, differing by approximately 40 to 50% in the Pol protein. These lineages are represented by (i) SIVcpz from chimpanzees (Pan troglodytes) including HIV-1 (13,21,22,38,46), (ii) SIVsm from sooty mangabeys (Cercocebus atys) including HIV-2 and SIVmac from macaques (Macaca spp.) (17,20,33), (iii) SIVagm from African green monkeys (members of the Chlorocebus aethiops superspecies) (1, 2, 9-11, 19, 23, 24, 32), (iv) SIVsyk from Sykes' monkeys (Cercopithecus albogularis), (v) SIVlhoest from L'Hoest monkeys (Cercopithecus l'hoesti) including SIVsun from sun-tailed monkeys (Cercopithecus solatus) and SIVmnd from mandrills (Mandrillus sphinx) (3,4,18,45), and most recently discovered (vi) SIVcol from Colobus monkeys (Colobus guereza) (8).…”

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confidence: 99%

Characterization of Novel Simian Immunodeficiency Viruses from Red-Capped Mangabeys from Nigeria (SIVrcmNG409 and -NG411)

Beer

Foley

Kuiken

et al. 2001

Two novel simian immunodeficiency virus (SIV) strains from wild-caught red-capped mangabeys (Cercocebus torquatus torquatus) from Nigeria were characterized. Sequence analysis of the fully sequenced SIV strain rcmNG411 (SIVrcmNG411) and gag and pol sequence of SIVrcmNG409 revealed that they were genetically most closely related to the recently characterized SIVrcm from Gabon (SIVrcmGB1). Thus, red-capped mangabeys from distant geographic locations harbor a common lineage of SIV. SIVrcmNG411 carried a vpx gene in addition to vpr, suggesting a common evolutionary ancestor with SIVsm (from sooty mangabeys). However, SIVrcm was only marginally closer to SIVsm in that region than to any of the other lentiviruses. SIVrcm showed the highest similarity in pol with SIVdrl, isolated from a drill, a primate that is phylogenetically distinct from mangabey monkeys, and clustered with other primate lentiviruses (primarily SIVcpz [from chimpanzees] and SIVagmSab [from African green monkeys]) discordantly in different regions of the genome, suggesting a history of recombination. Despite the genetic relationship to SIVcpz in the pol gene, SIVrcmNG411 did not replicate in chimpanzee peripheral blood mononuclear cells (PBMC), although two other viruses unrelated to SIVcpz, SIVmndGB1 (from mandrills) and SIVlhoest (from L'Hoest monkeys), were able to grow in chimpanzee PBMC. The CCR5 24-bp deletion previously described in red-capped mangabeys from Gabon was also observed in Nigerian red-capped mangabeys, and SIVrcmNG411, like SIVrcmGB1, used CCR2B and STRL33 as coreceptors for virus entry. SIVrcm, SIVsm, SIVmndGB1, and all four SIVlhoest isolates but not SIVsun (from sun-tailed monkeys) replicated efficiently in human PBMC, suggesting that the ability to infect the human host can vary within one lineage.