Molecular Epidemiology of HIV-1 in St Petersburg, Russia: Predominance of Subtype A, Former Soviet Union Variant, and Identification of Intrasubtype Subclusters

Abstract

The results of this study show a great predominance of AFSU viruses in St Petersburg and point to a few phylogenetically identifiable introductions as the origin of most current HIV-1 AFSU infections in the city.

Short Communication: Molecular Epidemiology, Phylogeny, and Phylodynamics of CRF63_02A1, a Recently Originated HIV-1 Circulating Recombinant Form Spreading in Siberia

“…Of the 20 samples in which at least one segment was of CRF63_02A1 and data on transmission route were available, 10 With regard to CRF63_02A1, analyses of a greater number of samples with epidemiological data would be required to examine the existence of transmission networks and their possible associations with different transmission routes. Antiretroviral (ARV) drug resistance-associated mutations were found in three samples, RU_8148, RU_8499, and RU_8516.…”

“…The rapid expansion of CRF63_02A1 is reminiscent of that reported for other HIV-1 genetic forms in established epidemics, 33,34 supporting the need for continued molecular epidemiological surveillance of HIV-1. Its propagation to distant areas of Russia and to Kazakhstan indicates that CRF63_02A1 should be taken into consideration in the design of vaccines adapted to HIV-1 strains circulating in Russia and other FSU countries, whose HIV-1 epidemics are becoming increasingly complex by the introduction of new genetic forms, phylogenetic diversification within the established strains, 10,[35][36][37] and recombination between cocirculating variants, with the generation of new circulating recombinant forms (CRFs). 17 Sequences were deposited in GenBank under accession numbers KJ197185-KJ197224.…”

“…[2][3][4] In 1995-1996 HIV-1 infections began to increase dramatically concomitantly with the expansion of a subtype A variant of Central African ancestry 5 that originated in Southern Ukraine 6,7 and spread to all countries of the former Soviet Union (FSU), in most of which it is the predominant HIV-1 genetic form 8,9 ; for this reason it is frequently designated A FSU variant. In addition to A FSU , other HIV-1 genetic forms circulating in FSU countries at lower prevalences include subtype B, predominant in men who have sex with men, [8][9][10] CRF03_AB, predominant in the Russian cities of Kaliningrad 11 and Cherepovets, 12 subtype F, circulating as a minor variant in St. Petersburg, Russia, 13 and a CRF02_AG variant (CRF02_AG FSU ), 14,15 which was first detected among injecting drug users (IDUs) in Tashkent, Uzbekistan, in 1999-2000, 14 and has subsequently been reported in Kazakhstan, new near full-length genome sequences of CRF63_02A1, reanalyzing its mosaic structure, and we estimate its epidemic history. For this study, 26 serum samples from HIV-1-infected individuals were collected in May and June 2013 at the Center for Prevention and Control of AIDS and Infectious Diseases, Koltsovo, Novosibirsk region, which is located 5 km from the city of Novosibirsk and attends all HIV-infected people of the Novosibirsk region.…”

The Analysis of Near Full-Length Genome Sequences of HIV Type 1 Subtype A Viruses from Russia Supports the Monophyly of Major Intrasubtype Clusters

“…2 The scarcity of available near full-length HIV-1 genome sequences from Russia was one of the main motivations of the current study. Another was an interest in analyzing near full-length genomes of two of the major A FSU monophyletic clusters in which this variant is subdivided, previously analyzed in partial sequences, one of them designated V77I PR , due the presence of the characteristic V77I substitution in protease, 8 widely circulating in Russia (nearly half of HIV-1 infections 2 ) and other FSU countries, and the other A SP1 , which represents approximately 56% of HIV-1 infections in St. Petersburg, 9 the second largest city in Russia and one of the cities most heavily affected by the HIV-1 epidemic. 10 Plasma samples used for this study were collected from 2002 through 2008 in different cities of Russia from individuals belonging to diverse risk categories.…”

“…Samples were selected for near full-length genome amplification and sequencing based on analyses of protease-reverse transcriptase (PR-RT) sequences showing their clustering in the V77I PR or A SP1 A FSU clusters. 2,9 Near full-length genomes were amplified from plasma RNA in four overlapping segments by RT-PCR and sequenced as previously described. 11,12 Electropherograms were assembled with SeqMan (DNASTAR, Madison, WI).…”