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HIV-2 diversity displays two clades within group A with distinct geographical distribution and evolution.

ABSTRACT: Genetic diversity of HIV-2 groups A and B has not yet been fully described, especially in a few Western Africa countries such as Ivory-Coast or Mali. We collected 444 pol, 152 vif, 129 env, and 74 LTR sequences from patients of the French ANRS CO5 HIV-2 cohort completed by 221 pol, 18 vif, 377 env, and 63 LTR unique sequences from public databases. We performed phylogenetic reconstructions and revealed two distinct lineages within HIV-2 group A, herein called A1 and A2, presenting non-negligible genetic distances and distinct geographic distributions as A1 is related to coastal Western African countries and A2 to inland Western countries. Estimated early diversification times for groups A and B in human populations were 1940 [95% higher probability densitiy: 1935-53] and 1961 [1952-70]. A1 experienced an early diversification in 1942 [1937-58] with two distinct early epidemics in Guinea-Bissau or Senegal, raising the possibility of group A emergence in those countries from an initial introduction from Ivory-Coast to Senegal, two former French colonies. Changes in effective population sizes over time revealed that A1 exponentially grew concomitantly to Guinea-Bissau independence war, but both A2 and B lineages experienced a latter growth, starting during the 80s economic crisis. This large HIV-2 genetic analysis provides the existence of two distinct subtypes within group A and new data about HIV-2 early spreading patterns and recent epidemiologic evolution for which data are scarce outside Guinea-Bissau.

SUBMITTER: Visseaux B

PROVIDER: S-EPMC8377049 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Since its first emergence in December 2019, the world has witnessed the eruption of mutations in the SARS-CoV-2 genome that have led to increased viral transmissibility and pathogenicity due to sustained local viral transmission. Zooanthroponotic and zoonotic transmissions have further raised concerns as they could result in the emergence of viral variants with a novel antigenicity and transmissibility that could jeopardize the vaccine efficacy. To understand the viral evolution during such transmissions, 1016 whole-genome sequences (deposited in GISAID as of March 7, 2022) (from 18 countries) corresponding to mink, cat, deer, dog, hyena, tiger, lion, gorilla, Syrian hamster, leopard cat, fishing cat, bear cat, coati, ferret, snow leopard and green monkey have been analysed here. Intriguingly, phyloproteome analysis indicate that Nsp2:R218C, Nsp2:D268-(deletion), Spike:D614G, Nsp12:P323L, Nsp2:A192V, ORF3a protein:Q57H, N protein:R203K and N protein:G204R/L, Spike:A222V, ORF10 protein:V30L and N protein:A220V are moderate or high recurring and clade decisive mutations, leading to 6 primary clades during the early stage of pandemic. Most interestingly, the human evolved delta variant having a combination of 26 (clade decisive) mutations defines the seventh clade and transmits to non-human hosts across the globe without exhibiting any country-specific mutation(s). Nonetheless, Spike:D614G and Nsp12:P323L together with (i)N protein:R203K,N protein:G204R/L,Spike:V70-, Spike:H69-, Nsp12:T739I, and Nsp1:M85-, (ii)Nsp2:A192V, Nsp3:D178Y, (iii)Nsp2:T85I, N protein:P67S and ORF3a protein:Q57H and (iv)Spike:A222V, ORF10 protein:V30L, N protein:A220V and Spike:F486I are specific to Denmark, Netherlands, USA and Latvia respectively and, (v)Nsp2:D268- and Nsp13:R292C that are devoid of Spike:D614G and Nsp12:P323L is specific to Netherlands. SARS-CoV-2 variants consisting of these mutations are also seen in the human SARS-CoV-2 sequences from the same country. Independent country-specific SARS-CoV-2 variant evolution further indicates distinct epidemiological dynamics during zooanthroponotic and zoonotic transmissions. Thus, the results presented here indicate the need for the surveillance of viral evolution in non-human hosts also during the future pandemic.

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HIV-2 diversity displays two clades within group A with distinct geographical distribution and evolution.

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