Origin of the HIV-1 group O epidemic in western lowland gorillas

Abstract

HIV-1, the cause of AIDS, is composed of four phylogenetic lineages, groups M, N, O, and P, each of which resulted from an independent cross-species transmission event of simian immunodeficiency viruses (SIVs) infecting African apes. Although groups M and N have been traced to geographically distinct chimpanzee communities in southern Cameroon, the reservoirs of groups O and P remain unknown. Here, we screened fecal samples from western lowland (n = 2,611), eastern lowland (n = 103), and mountain (n = 218) gorillas for gorilla SIV (SIVgor) antibodies and nucleic acids. Despite testing wild troops throughout southern Cameroon (n = 14), northern Gabon (n = 16), the Democratic Republic of Congo (n = 2), and Uganda (n = 1), SIVgor was identified at only four sites in southern Cameroon, with prevalences ranging from 0.8-22%. Amplification of partial and full-length SIVgor sequences revealed extensive genetic diversity, but all SIVgor strains were derived from a single lineage within the chimpanzee SIV (SIVcpz) radiation. Two fully sequenced gorilla viruses from southwestern Cameroon were very closely related to, and likely represent the source population of, HIV-1 group P. Most of the genome of a third SIVgor strain, from central Cameroon, was very closely related to HIV-1 group O, again pointing to gorillas as the immediate source. Functional analyses identified the cytidine deaminase APOBEC3G as a barrier for chimpanzee-to-gorilla, but not gorilla-to-human, virus transmission. These data indicate that HIV-1 group O, which spreads epidemically in west central Africa and is estimated to have infected around 100,000 people, originated by cross-species transmission from western lowland gorillas.

Keywords: AIDS; HIV-1; SIVgor; gorilla; zoonotic transmission.

Fig. 1.

Geographic distribution of SIVgor in wild-living gorillas. Field sites are shown in relation to the ranges of western (G. gorilla, red) and eastern (G. beringei, yellow) gorillas, with subspecies indicated by broken (G. g. gorilla and G. b. graueri) and solid (G. g. diehli and G. b. beringei) lines. Forested areas are shown in dark green, whereas arid and semiarid areas are depicted in yellow and brown, respectively. Major lakes and rivers are shown in blue. Dashed white lines indicate national boundaries. Sites where SIVgor was detected in this study are highlighted in red (yellow border), with SIVgor-positive field sites reported previously shown in yellow (red border) (9, 16). White and gray circles indicate SIVgor-negative sites identified in this and previous studies, respectively (9, 16).

Fig. 2.

Detection of SIVgor antibodies in gorilla fecal samples. INNO-LIA banding patterns are shown, with molecular weight markers of HIV-1 and HIV-2 proteins indicated. IgG control lanes (n = 3) are shown on the top of each strip; plasma from HIV-1–infected (POS) and uninfected (NEG) humans were used for controls (two left lines). Fecal samples are grouped by individuals, with a two-letter code indicating the collection site of origin (Fig. 1).

Fig. 3.

Evolutionary relationships across SIVcpz, SIVgor, and HIV-1 strains based on partial gene sequences. Phylogenetic trees were constructed using partial gag (A), pol (B), and env (C) sequences. Newly identified SIVgor strains (highlighted in green boxes) are compared with previously characterized SIVgor (green), SIVcpzPtt (blue), SIVcpzPts (orange), and HIV-1 (red) strains. Asterisks above branches correspond to nodes supported by bootstrap values over 70% from ML analyses and posterior probabilities over 0.90 from Bayesian analyses. (Scale bar: number of substitutions per site.)

Fig. 4.

Evolutionary relationships across SIVcpz, SIVgor, and HIV-1 strains based on full-length protein sequences. Phylogenetic trees were constructed using complete Gag (A), Pol (B), and concatenated Env and Nef (C) protein sequences. Full-length genome sequences were obtained for SIVgor-BPID1, SIVgor-BPID15, and SIVgor-BQID2; complete gag and pol sequences were obtained for SIVgor-BPID2; and a complete pol sequence was obtained for SIVgor-BPID3. Other details are provided in Fig. 3.

Fig. 5.

Mosaic genome structure of SIVgor-BQID2. (A) Phylogenies are shown for seven genomic regions (a–f) indicated below the genome diagram in B. Genomic regions in which SIVgor-BQID2 clusters with HIV-1 group O, or with SIVgor from site CP, are shown in red and dark green, respectively. (B) In two other regions (light green), BQID2 is not specifically closely related to other strains. Bootstrap values over 70% from ML analyses are shown with an asterisk. (Scale bar: number of substitutions per site.)

Fig. 6.

Gorilla A3G is resistant to degradation by SIVcpz but not SIVgor Vif proteins. Plasmids expressing vif genes from SIVcpzPtt (red), SIVcpzPts (blue), and SIVgor (green) were cotransfected with increasing quantities (0, 25, 50, and 100 ng) of WT gorilla A3G (A), WT chimpanzee A3G (B), and the gorilla A3G mutant Q129P (C), along with a vif-deficient HIV-1 molecular clone (NL4-3 ΔVif) into 293T cells. Two days after transfection, viral supernatants were used to infect TZM-bl reporter cells (a HeLa-derived cell line that constitutively expresses CD4, CCR5, and CXCR4 cell surface receptors) and infectious particle release was measured. (Upper) Virus infectivity (y axis) plotted in the presence of increasing quantities (x axis) of the various Vif expression plasmids (infectivity in the absence of Vif is shown in black) is depicted. Values represent averages (with SDs) from three different transfections. (Lower) Western blots of the corresponding 293T cell lysates (transfected with 50 ng of A3G), probed for A3G and Vif expression (GAPDH represents the loading control), are depicted.