Noninvasive follow-up of simian immunodeficiency virus infection in wild-living nonhabituated western lowland gorillas in Cameroon

Abstract

Simian immunodeficiency viruses infecting western lowland gorillas (SIVgor) are closely related to HIV-1 and are most likely the ancestors of HIV-1 groups O and P. At present, limited data are available on genetic diversity, transmission, viral evolution, and pathogenicity of SIVgor in its natural host. Between 2004 and 2011, 961 putative gorilla fecal samples were collected at the Campo Ma'an National Park, Cameroon. Among them, 16% cross-reacted with HIV-1 antibodies, corresponding to at least 34 infected gorillas. Combining host genotyping and field data, we identified four social groups composed of 7 to 15 individuals each, with SIV rates ranging from 13% to 29%. Eleven SIVgor-infected gorillas were sampled multiple times; two most likely seroconverted during the study period, showing that SIVgor continues to spread. Phylogenetic analysis of partial env and pol sequences revealed cocirculation of closely related and divergent strains among gorillas from the same social group, indicating SIVgor transmissions within and between groups. Parental links could be inferred for some gorillas infected with closely related strains, suggesting vertical transmission, but horizontal transmission by sexual or aggressive behavior was also suspected. Intrahost molecular evolution in one gorilla over a 5-year period showed viral adaptations characteristic of escape mutants, i.e., V1V2 loop elongation and an increased number of glycosylation sites. Here we show for the first time the feasibility of noninvasive monitoring of nonhabituated gorillas to study SIVgor infection over time at both the individual and population levels. This approach can also be applied more generally to study other pathogens in wildlife.

Fig 1

Inferred composition of gorilla groups of interest at the Campo Ma'an field site over the 7.5-year study period, underlining the follow-up of SIVgor-positive individuals and social groups. For each studied group, data on sampled individuals are shown, with information on sex (F, female; M, male; ?, unknown) and SIV serology (data for seropositive gorillas appear in bold). The number of fecal samples for each gorilla sampled at a given collection location and date are noted. Putative group F1 is linked with group F3 and group F2 by two independent gorillas, i.e., ID2 and ID36, respectively (highlighted by vertical arrows). These three putative groups may be a single group, but they were analyzed separately because of the lack of certainty. Cluster 64, collected in 2011, is linked with group C by ID10, and cluster 61, collected in 2011, is linked with putative group F2 by ID35. These two individuals could have emigrated from their original groups, or clusters 64 and 61 may in fact be groups C and F2, respectively. Data from the collections carried out in 2011 are shown in the dotted area, since genotyping data were available only for positive samples.

Fig 2

Inferred minimum home ranges for gorilla groups of interest, with overlapping ranges shown. From April 2004 to November 2011, an area of approximately 200 km² was covered during successive field missions in the Campo Ma'an National Park (CP). (Inset) Map of Cameroon (adapted from The World Factbook, https://www.cia.gov/library/publications/the-world-factbook/geos/cm.html). The arrow indicates the CP field site. Minimum home ranges inferred from collection sites (small circles) are delineated by solid-line ellipses for identified social groups and for the three putative social groups (F1, F2, and F3) (Table 1; Fig. 1). The positive individuals and years of collection are given for each gorilla group. The hypothetical home ranges of the possible groups (group C?, group F2?, and group F??) with linked individuals are highlighted by dashed-line ellipses, and the corresponding linked IDs are noted (Fig. 1).

Fig 3

SIVgor-infected gorilla capture and recapture (via sampling) in the Campo Ma'an study area. From April 2004 to November 2011, an area of approximately 200 km² was covered during successive field missions in the Campo Ma'an National Park. The 11 SIVgor-positive individuals that were captured and recaptured (via sampling) in at least two different collection missions (Table 2) were plotted and are identified by ID numbers, with a positive sign for those found to be SIV seropositive and a negative sign for those that were first found to be SIV negative (ID32 and ID36).

Fig 4

Phylogenetic analyses of partial env (gp41) (263 bp [A] and 195 bp [B]) nucleotide sequences of SIVgor strains. The trees were inferred by maximum likelihood phylogeny (PhyML) with previously characterized SIVcpzPtt/SIVgor/HIV-1 strains (in black). Stars represent support values above 800 (A) or 700 (B) for 1,000 maximum likelihood bootstraps. Bar, 0.1 substitution per site. Sample numbers and collection dates (i.e., 11-CP6466 is sample CP6466, collected in 2011), individual identification numbers (IDs), clusters (i.e., 20, 61, and 64 [in gray]), and social groups (A, C, G, E, and F1/2/3 [in color]) are noted and are used in Table 1. The color code for social groups is conserved in Fig. 2 to 4 and in Fig. S1 in the supplemental material. Solid brackets highlight individuals from the same group/cluster that were infected with closely related strains (very short genetic distance), whereas dashed links indicate individuals from the same group/cluster that were infected with divergent strains.

Fig 5

Amino acid evolution of the SIVgorID1 Env hypervariable region between April 2004 (SIVgor-04CP684) and December 2008 (SIVgor-08CP3425). The hypervariable loops V1, V2, V3, and V4 and the C2 and C3 regions were analyzed. The SIVgor-04CP684 sequence (the 20 clones found for SIVgor-04CP684 were 100% similar), indicated at the top (684 clones), was compared with the consensus of all clonal sequences from SIVgor-08CP3425 (3,425 clones). Dots stand for gaps, and dashes stand for the same amino acids as those in the sequence above. The putative N-linked glycosylation consensus motifs (NXT/S) are highlighted in gray, important cysteines are shown in bold, and the V3 crown is shown in a dashed rectangle, stressing the switch from GPL to GPM.