Bayesian phylogeographic analyses clarify the origin of the HIV-1 subtype A variant circulating in former Soviet Union’s countries

Abstract

The HIV-1 subtype A variant dominating the HIV-1 epidemics in former Soviet Union (FSU) countries (A(FSU)) represents one of the major clades of the HIV-1 pandemic. This variant was reported to have begun spreading among injecting drug users (IDUs) in the Ukrainian city of Odessa in late 1994. Two competing hypotheses have been proposed on the ancestral origin of the A(FSU) variant, locating it either in the Democratic Republic of Congo (DRC) or in the Republic of Guinea (RG). The studies supporting these hypotheses employed phylogenetic analyses to identify HIV-1 sequences collected outside FSU countries ancestrally related to A(FSU). A different approach, based on Bayesian phylogenetic inference and coalescent-based population genetics, has been employed here to elucidate the ancestry of this HIV-1 variant and to improve our knowledge on its spread in FSU countries. The analyses were carried out using env (C2-V3-C3) and p24(gag) fragments of the HIV-1 genome. The inferred migration for the HIV-1 A(FSU) variant revealed only one significantly supported migration pathway from Africa to Eastern Europe, supporting the hypothesis of its origin in the DRC and estimating the upper limit of the migration of the ancestral virus from Africa around 1970. The support for an origin in the RG was negligible. The results supported the main role of Odessa as the epicenter of the A(FSU) epidemic, dating the tMRCA of the A(FSU) variant around 1984, ten years before its explosive expansion among IDUs. The estimated origin of the AFSU subcluster responsible for the IDU outbreak was also located in Odessa, with the estimated tMRCA around 1993. Statistically supported migration routes from Odessa to other cities of Ukraine, Russia, Kazakhstan, Uzbekistan and Belarus were also inferred by the Bayesian phylogeographic analysis. These results shed new light on the origin and spread of the HIV-1 A(FSU) variant.

Molecular epidemiology of HIV-1 infection in Europe: An overview

“…In the mid-1990s Ukraine experienced the begging of a large epidemic in the PWID communities which subsequently spread into the Russian Federation, Belarus, Moldova, Lithuania, Latvia, Kazakhstan, Kyrgyzstan, Turkmenistan, Georgia, Azerbaijan and Armenia (Bobkov et al, 1998;Bobkova, 2013;Saad et al, 2006b). The geographic origin of the A FSU PWID-epidemic was in Odessa and the tMRCA was approximately in 1993 (Diez-Fuertes et al, 2015). Moreover, the origin of the A FSU PWID-epidemic strain has been recently identified in Democratic Republic of Congo (DRC), and the upper limit of the dispersal time for the ancestral strain in 1970 (Diez-Fuertes et al, 2015).…”

“…The geographic origin of the A FSU PWID-epidemic was in Odessa and the tMRCA was approximately in 1993 (Diez-Fuertes et al, 2015). Moreover, the origin of the A FSU PWID-epidemic strain has been recently identified in Democratic Republic of Congo (DRC), and the upper limit of the dispersal time for the ancestral strain in 1970 (Diez-Fuertes et al, 2015). Besides the A FSU that dominates in FSU countries, subtype B transmissions have been described at low prevalence and are mainly associated with MSM, probably associated with the Western European epidemic (Bobkova, 2013).…”

Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia

“…A FSU that originated in Africa (Thomson et al, 2007), appeared in Odessa, a major seaport and transportation hub in Southern Ukraine, in 1994-1995 (Novitsky et al, 1998). Research suggests that A FSU originated in the Democratic Republic of the Congo and dates the most recent common ancestor (tMRCA) of A FSU in Odessa in 1984 (Díez-Fuertes et al, 2015). The tMRCA of the sub-cluster of A FSU that caused the PWID-related epidemic was probably also present in Odessa in 1993, a few years before the huge explosion of HIV in PWID (Díez-Fuertes et al, 2015).…”

Immunological Characteristic of Synthetic Peptides Similar to Actual Hiv Antigen Determinants

“…Желательно, чтобы полу-ченные в результате иммунизации антитела мог-ли нейтрализовать различные изоляты ВИЧ, от-носящиеся к различным субтипам. Известно, что на территории РФ преимущественно циркулиру-ет ВИЧ1, принадлежащий к субтипу А1 (IDU-A) [5]. В наших исследованиях мы использовали молекулярные клоны, копирующие оболочечные белки вирусов двух субтипов А и С: CAP 45.2.00.…”