Damond et al. 2000 showed that HIV-2 group A can be divided in two distinct genotypes. We analysed all the HIV-2 pol, env and vif sequences available in France to better characterise genetic variations between these two genotypes, analyse their relative prevalence in France and to explore a potential link with patient’s country of birth.
Maximum likelihood phylogenetic trees were reconstructed from 446 HIV-2 partial pol (PR and RT; 1350 nt), 155 vif (655 nt) and 154 partial env (525 nt) sequences sampled from 386 patients followed up in France, using FastTree 2.1 under the GTR evolutionary model. Publically available sequences sampled outside of France were included for pol and vif fragments (207 and 22 sequences, respectively). Recombination analyses were conducted with the RDP4 software. Patients’ country of birth was retrieved for the patients included in the French ANRS CO5 HIV-2 cohort (n=272).
The group A formed two distinct and strongly supported clusters, herein called A1 and A2, in all trees (cf. Figure 1), suggestive of a past founder effect. Overall, 72% and 28% of the group A sequences belonged to cluster A1 and A2 respectively, with 20% of the latter being sampled in France. Among the 193 HIV-2 A sequences obtained from public databases 19 (10%) belong to clade A2. Inter-cluster median genetic distances were 0.12 [IQR=0.11-0.14], 0.12 [0.11-0.13] and 0.15 [0.12-0.18] substitutions/site for pol, vif and env, respectively. For the 163 viruses with more than one genetic region available, 17 (10%) presented inconsistent clade assignments across trees, suggesting potential recombination events. A1 viruses were most prevalent amongst patients born in coastal Western African countries (i.e. Senegal, Gambia, Guinea Bissau and Guinea) with 40 A1- and 8 A2-infected patients. Inversely, A2 strains were predominantly found among patients originating from inland Western countries such as Mali and Burkina Faso with 8 A1- and 29 A2-infected patients, suggesting distinct origins of the two clades. Sequences issued from patients born in Ivory-coast displayed a balanced prevalence of these clades with 13 A1- and 16 A2-infected patients).
This study provides an enhanced understanding of the geographical and genetic diversity of HIV-2 group A. It highlights the co-circulation of two distinct clades in France that likely appeared from an ancient divergent event, followed by a founder effect explaining the distinct geographical patterns in Western Africa.