The early spread of HIV-2 in Western Africa has not been explored yet for group B and subtype A2 recently described using the French ANRS CO5 HIV-2 cohort datasets. In this study we performed the first phylogeographic study describing the early spreading patterns of HIV-2 subtypes A1, A2 and group B in the human population.
All publicly available HIV-2 pol sequences including both time of sampling and patient’s country of birth (n=49 and 8 sequences for groups A and B, respectively) were added to 125 (group A) and 68 (group B) sequences from the ANRS cohort, sampled between 1994 and 2014. Phylogeographic reconstructions were performed under the best fitting combination of evolutionary, demographic and molecular clock models, using BEAST 1.8. The trees were assessed with maximum likelihood trees obtained using RAxML. Because of the large number of sequences sampled in France in the dataset, the patient’s country of birth was used to model the geographical dispersion instead of the sampling country.
The estimated time of the most common ancestors (tMRCA) of group A was 1945 [95% HPD 1935-53]. Subtype A1, mainly present in patient born Senegal, Gambia, Guinea-Bissau and Guinea, presents an early diversification in 1946 [1936-54] with two distinct epidemics in Guinea-Bissau and Senegal. Several later transmission events from Guinea-Bissau to Senegal are also observed. Subtype A2, mainly present in patients born in Ivory Coast and Mali, spreads latter than subtype A1 (1956 [1947-63]). Subtype A2 initially spreads initially in Ivory Coast and presents two introduction events in Mali in 1963 [1957-69] and 1967 [1960-74]. Group B was originally introduced in Ivory Coast in 1962 [1953-13].
This phylogeographic study is the first to reconstruct the early subtype A2 and group B dispersal and allows a better understanding of HIV-2 early epidemic in West Africa. These two HIV-2 clades rose at similar time but diversified latter than subtype A1. Both A2 and B clades originated in Ivory Coast, suggesting that a local historical or socio-demographic event may have triggered the dispersal of these viral strains. An early fonder effect for subtype A1 in Senegal occurred before the Guinea-Bissau independence war, suggesting that HIV-2 group A was already circulating in these countries before the war that contributed to further dispersal of HIV-2 within and outside West Africa.