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

Abstract

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...

Foci of Endemic Simian Immunodeficiency Virus Infection in Wild-Living Eastern Chimpanzees ( Pan troglodytes schweinfurthii )

“…For Ch-64 and Ch-45, amplification was successful for both regions, and the corresponding viruses were designated TAN2 and TAN3, respectively. For the remaining two chimpanzees, only one of the two genomic regions could be amplified: a pol fragment for Ch-70 (TAN4) and a gp41/nef fragment for Ch-71 (TAN5 newly derived sequences were compared to each other as well as to the previously reported SIVcpz TAN1 strain (48). In pairwise sequence comparisons, the nucleotide sequences of all five Gombe SIVcpz strains (TAN1 to TAN5) differed by 5.9 to 9.6% in the pol region and by 9.5 to 14.6% in the gp41/nef region (Table 6), while pol sequences obtained from Ch-06 at different time points (TAN1a to TAN1c) differed by only 0.7 to 1.4% (not shown).…”

“…Analysis of urine samples from 24 wild chimpanzees from the Kanyawara community in Kibale National Park (Uganda) failed to detect evidence of SIVcpz infection, whereas testing of only six apes from the Kasekela community in Gombe National Park identified one chimpanzee (Ch-06) to be both urine antibody and fecal vRNA positive. Subsequent molecular analyses confirmed SIVcpz infection in this individual (49) and even permitted the amplification of a complete viral genome from fecal samples (48). While these studies established the utility of the noninvasive assays for the detection and characterization of SIVcpz under field conditions, they did not examine the sensitivity and specificity of the assays, nor did they address the frequency of SIVcpz infection in these wild chimpanzee communities.…”

“…Only P. t. troglodytes and P. t. schweinfurthii are known to be naturally infected with SIVcpz (13,42,49). We have explained the absence of SIVcpz from P. t. verus by postulating that chimpanzees as a species acquired SIVcpz infection after the geographic separation and isolation of P. t. verus from the other subspecies (2,26,48,49). Recent data concerning the origin of SIVcpz are consistent with this interpretation, indicating that SIVcpz is actually a recombinant of ancestral viruses that infected west central African monkey species upon which chimpanzees prey (3).…”

“…Sequences were analyzed with the Sequencher program (Gene Codes Corporation, Ann Arbor, Mich.), and deposited at GenBank: SIVcpzTAN2 (AY181990, AY181991), SIVcpzTAN3 (AY181988, AY181992), SIVcpzTAN4 (AY181989), and SIVcpzTAN5 (AY181993). The full-length SIVcpzTAN1 sequence (AF447763) has been reported previously (48).…”

Molecular genetic approaches to the study of primate behavior, social organization, and reproduction

“…For example, Ling et al (2003) and Santiago et al (2003) recently used PCR to amplify viron RNA from simian immunodeficiency virus (SIV) from the feces of captive sooty mangebeys and wild chimpan-zees, demonstrating the feasibility of such noninvasive epidemiological surveys.…”