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

Abstract

The HIV-1 epidemic in Russia has been insufficiently studied, with only 11 complete genome sequences from this country currently available, only three of which are of the locally predominant genetic form, the former Soviet Union (FSU) subtype A variant (A_FSU). Here we analyze 10 newly derived A_FSU near full-length genome sequences from Russia. Samples were selected based on phylogenetic clustering in protease-reverse transcriptase in two of the major A_FSU clusters, V77I_PR (n=6), widely circulating in Russia and other FSU countries, and A_SP1 (n=4), predominant in St. Petersburg. The phylogenetic analysis shows that the V77I_PR genomes group in a monophyletic cluster together with 10 previously obtained A_FSU genome sequences from Uzbekistan, Kazakhstan, Russia, and Cyprus, all bearing the V77I substitution in protease. Similarly, the four A_SP1 genomes group in a monophyletic cluster. These results therefore show that the monophyly of V77I_PR and A_SP1 A_FSU clusters is supported in near complete genomes.

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