Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A

Abstract

Human immunodeficiency virus type 2 (HIV-2) emerged in West Africa and has spread further to countries that share socio-historical ties with this region. However, viral origins and dispersal patterns at a global scale remain poorly understood. Here, we adopt a Bayesian phylogeographic approach to investigate the spatial dynamics of HIV-2 group A (HIV-2A) using a collection of 320 partial pol and 248 partial env sequences sampled throughout 19 countries worldwide. We extend phylogenetic diffusion models that simultaneously draw information from multiple loci to estimate location states throughout distinct phylogenies and explicitly attempt to incorporate human migratory fluxes. Our study highlights that Guinea-Bissau, together with Côte d'Ivoire and Senegal, have acted as the main viral sources in the early stages of the epidemic. We show that convenience sampling can obfuscate the estimation of the spatial root of HIV-2A. We explicitly attempt to circumvent this by incorporating rate priors that reflect the ratio of human flow from and to West Africa. We recover four main routes of HIV-2A dispersal that are laid out along colonial ties: Guinea-Bissau and Cape Verde to Portugal, Côte d'Ivoire and Senegal to France. Within Europe, we find strong support for epidemiological linkage from Portugal to Luxembourg and to the UK. We demonstrate that probabilistic models can uncover global patterns of HIV-2A dispersal providing sampling bias is taken into account and we provide a scenario for the international spread of this virus.

Fig. 1.

The historical population dynamics of HIV-2A. Bayesian skyride analysis depicting the mean changes in effective population size (N_et) through time with 95 % BCI for the most informative dataset (global env).

Fig. 2.

Ancestral root state reconstructions for the global HIV-2A datasets. The analyses were performed separately (a and b) and together (c and d) for each locus and for the shared analyses (c and d).

Fig. 3.

MCC genealogies for the global HIV-2A datasets. The pol (n = 320) and env (n = 248) phylogenies shown in (a) and (b), respectively, were generated using a multilocus Bayesian Markov chain Montc Carlo (MCMC) analysis under the asymmetrical diffusion model using the 1000 : 1 rate prior setup. Branch lengths are shown in units of time and branch widths are proportional to location state probability. Each colour represents the most probable location state of the descendant node.

Fig. 4.

BF test for significant epidemiological non-zero rates. Epidemiological links with BF support greater than 15 were obtained by combining the results from three different prior specifications (1 : 10, 1 : 100 and 1 : 1000). The yellow–red gradient represents the relative strength by which the rates are supported. All locations involved in significant epidemiological linkage are depicted, except South Korea that was omitted for purpose of clarity (a KML interactive summary is available as Supplementary Fig. S2).