Tracing the origin and history of the HIV-2 epidemic

Abstract

In this study we date the introduction of HIV-2 into the human population and estimate the epidemic history of HIV-2 subtype A in Guinea-Bissau, the putative geographic origin of HIV-2. The evolutionary history of the simian immunodeficiency virussooty mangabey/HIV-2 lineage was reconstructed by using available database sequences with known sampling dates, and a timescale for this history was calculated by using maximum likelihood methods. The date of the most recent common ancestor of HIV-2 subtype A strains was estimated to be 1940 +/- 16 and that of B strains was estimated to be 1945 +/- 14. In addition we used coalescent theory to estimate the past population dynamics of HIV-2 subtype A in a rural population of Guinea-Bissau. Parametric and nonparametric estimates of the effective number of infections through time were obtained for an equal sample of gag, pol, and env sequences. Our estimates of the epidemic history of HIV-2 subtype A in Guinea-Bissau show a transition from constant size to rapid exponential growth around 1955-1970. Our analysis provides evidence for a zoonotic transfer of HIV-2 during the first half of the 20th century and an epidemic initiation in Guinea-Bissau that coincides with the independence war (1963-1974), suggesting that war-related changes in sociocultural patterns had a major impact on the HIV-2 epidemic.

Fig. 1.

Timescale for the SIV_SM/HIV-2 lineage. HIV-2 subtypes and sooty mangabey and macaque strains are indicated at the tips of the reconstructed phylogeny. Branch lengths were estimated under the SRDT model, which allowed us to impose the estimated timescale under the phylogenetic tree (19). Numbers at the nodes indicate the percentage of bootstrap samples (of 1,000) in which the right cluster is supported (only values >80% are shown).

Fig. 2.

Demographic history of HIV-2 subtype A in a rural population situated near the regional center of Canchungo. (a) Map of Guinea-Bissau pinpointing the location of the study population (26, 28). (b–d) Coalescent results for the env (b), pol (c), and gag (d) genes. The skyline plots, representing nonparametric estimates, are indicated by a gray line, whereas the parametric estimates under the piecewise expansion model are indicated by a superimposed black line. Both nonparametric and parametric results show the change in the effective number of infections on a natural timescale (23).