SIVagm infection in wild African green monkeys from South Africa: epidemiology, natural history, and evolutionary considerations

Abstract

Pathogenesis studies of SIV infection have not been performed to date in wild monkeys due to difficulty in collecting and storing samples on site and the lack of analytical reagents covering the extensive SIV diversity. We performed a large scale study of molecular epidemiology and natural history of SIVagm infection in 225 free-ranging AGMs from multiple locations in South Africa. SIV prevalence (established by sequencing pol, env, and gag) varied dramatically between infant/juvenile (7%) and adult animals (68%) (p<0.0001), and between adult females (78%) and males (57%). Phylogenetic analyses revealed an extensive genetic diversity, including frequent recombination events. Some AGMs harbored epidemiologically linked viruses. Viruses infecting AGMs in the Free State, which are separated from those on the coastal side by the Drakensberg Mountains, formed a separate cluster in the phylogenetic trees; this observation supports a long standing presence of SIV in AGMs, at least from the time of their speciation to their Plio-Pleistocene migration. Specific primers/probes were synthesized based on the pol sequence data and viral loads (VLs) were quantified. VLs were of 10(4)-10(6) RNA copies/ml, in the range of those observed in experimentally-infected monkeys, validating the experimental approaches in natural hosts. VLs were significantly higher (10(7)-10(8) RNA copies/ml) in 10 AGMs diagnosed as acutely infected based on SIV seronegativity (Fiebig II), which suggests a very active transmission of SIVagm in the wild. Neither cytokine levels (as biomarkers of immune activation) nor sCD14 levels (a biomarker of microbial translocation) were different between SIV-infected and SIV-uninfected monkeys. This complex algorithm combining sequencing and phylogeny, VL quantification, serology, and testing of surrogate markers of microbial translocation and immune activation permits a systematic investigation of the epidemiology, viral diversity and natural history of SIV infection in wild African natural hosts.

Figure 1. Satellite map of the Republic of South Africa indicating the geographical origin of the samples included in this study.

Vervet samples from areas from three provinces (Free State, KwaZulu Natal and Eastern Cape) were included, as indicated. Sex and age-group coverage is illustrated.

Figure 2. SIVagmVer diversity in wild AGMs from different parks and game reserves in the Republic of South Africa.

Maximum likelihood tree for pol gene. Sequences are colored depending on the region in which the sequences were sampled, with red indicating sequences from Free State, green indicating sequences from KwaZulu-Natal, and blue indicating sequences from Eastern Cape territories. Reference SIVagm strains from vervet monkeys in Kenya are shown in black. The tree is based on a 592 bp pol sequence alignment (after gap-containing sites were removed). Maximum likelihood estimates were performed using 1000 replicate bootstrap analysis. Internal nodes indicate level of support values for internal branching. Bar represents number of amino acid replacements (0.09) per site. The strain nomenclature includes the identification number, monkey status (M-male, F-female; I-infant; J-juvenile and A-adult),and the site and state of origin (FS-Free State; KZN-KwaZulu Natal; EC-Eastern Cape). Putative heterosexual transmission cases documented to be of recent occurrence based on VL and serology testing are underlined. Putative maternal-to-infant transmission cases are boxed.

Figure 3. Molecular clock trees for pol gene based on the newly derived SIVagmVer sequences from vervets in South Africa.

Relaxed molecular clock tree show the ultrametric divergence pattern between lineages. Calibration was based on internal nodes indicated with a red circle, by setting priors that span the presumed divergence MRCA date ranges, 100,000–3,000,000 years for SIVagm sequences surrounding the Drakensberg Mountains in South Africa, and 10,000±1,000 for SIVdrl sequences sampled from Bioko Island . Internal nodes show divergence date estimates. Sequences are colored based on the territory from which they were sampled, with South African sequences colored red, green and blue, for Free State, KwaZulu Natal and Eastern Cape, respectively, and Bioko sequences colored in yellow.

Figure 4. Alignment of partial envelope protein sequences from multiple SIVagmVer isolates.

PCR-derived env nucleotide sequences were translated, aligned with previously reported SIVAGM env sequences and compared with a consensus sequence generated by BioEdit. Dots denote sequence identity with the consensus sequence, while dashes represent gaps introduced to optimize the alignment. Triangles (∧) denote N-linked glycosylation sites. Bullets (•) mark CD4 binding sites. V3, V4 and V5 designate hypervariable SIVagm Env domains as previously described . The envelope precursor cleavage site is indicated by an arrow above the consensus sequence. Strain nomenclature includes the identification number, monkey status (M-male, F-female; I-infant; J-juvenile and A-adult), and the site and the state of origin (FS-Free State; KZN-KwaZulu Natal; EC-Eastern Cape).

Figure 5. Cross-sectional analysis of SIVagm RNA levels in plasma of naturally infected AGM using a real-time RT-PCR assay.

No significant difference could be observed between infant, juvenile and adult AGM or between female and male monkeys. Samples with high VLs assessed as acutely infected are shown. VLs of lactating dams are depicted in lighter colors. Detection limit: 100 copies/ml.

Figure 6. anti-SIVagmVer IgG antibody seroprevalence in vervets from South Africa.

Testing was done by peptide ELISA (mapping the immunodominant region of gp41 of SIVagmVer). Samples were grouped based on PCR and VL quantification results as originating from uninfected vervets, SIV-infected vervets with VLs>10⁶ SIVagmVer RNA copies/ml, SIV-infected vervets with VLs ranging from 10⁴ to 10⁶ SIVagmVer RNA copies/ml and samples from infant vervets. Samples in the latter group are negative by PCR but show different levels of anti-SIVagm IgG, therefore being suggestive of transplacental crossing of maternal antibodies. Values on the Y-axis represent fold increases of the optical density of the samples (measured at 492 nm) over the cut-off value (established at an optical density of 0.2).

Figure 7. Plasma sCD14 levels in uninfected and SIVagmVer-infected vervets from South Africa.

P value was calculated by the Mann-Whitney U-test. Animals diagnosed as acutely infected are denoted by light red circles.

Figure 8. Cytokine and chemokine levels in uninfected and SIVagmVer-infected vervets from South Africa.

P value was calculated by the Mann-Whitney U-test. Animals diagnosed as acutely infected are denoted by light red circles.