Genetic characterization of an isolate of HIV type 1 AG recombinant form circulating in Siberia, Russia

P B Baryshev, V V Bogachev, N M Gashnikova, P B Baryshev, V V Bogachev, N M Gashnikova

Abstract

Before 2008, HIV-1 subtype A was the predominant genetic variant in the Novosibirsk oblast of Russia as well as in most parts of this country. However, a rapid spread of the recombinant HIV-1 02_AG form has been reported in Novosibirsk since 2009. We have analyzed the genome of the 10.RU.6637 isolate, a HIV-1 02_AG recombinant form, which represents a monophyletic cluster of the HIV-1 variants widespread in this region. Phylogenetic analysis has shown that the Siberian 10.RU.6637 isolate displays the highest sequence identity to the HIV-1 subtype AG forms circulating in Uzbekistan. However, recombination analysis of 10.RU.6637 has demonstrated that this isolate is a recombinant form between HIV-1 subtype A and CRF02_AG, differing in its genetic structure from both the CRF02_AG reference sequences and the Central Asian variants of HIV-1 02_AG.

Figures

Fig. 1
Fig. 1
Phylogenetic tree of HIV-1 full genome sequences. The tree was constructed using the maximum-likelihood approach, using the genome sequences of the main HIV-1 subtypes from the Los Alamos database as well as CRF01_AE and CRF02_AG sequences. The monophyletic branches containing sequences of one subtype were collapsed to facilitate phylogenetic analysis. The number of genome sequences belonging to a given clade is shown in square brackets to the left. The studied HIV-1 genome (10.RU.6637 isolate) and the genome of HIV-1 from Uzbekistan (02.UZ.AY829214 isolate), which is nearest in the branch, are marked with square brackets
Fig. 2
Fig. 2
Scheme of breakpoints in the 10.RU.6637 genome. a Comparison of the breakpoints in 10.RU.6637 (bottom) and 02.UZ.AY829214 (top) genome sequences determined by jpHMM. The regions between the breakpoints are numbered from I to X. Region V is divided into two subregions, V-I and V-II. Arrows point to the differences in breakpoint positions of the compared HIV-1 genomes (regions II/III and IV/V-I). b SimPlot diagram. The sample of HIV-1 genome sequences used for analysis contained the sequences of different subtypes, including the circulating HIV-1 recombinant forms 02_AG and 01_AE
Fig. 3
Fig. 3
Phylogenetic trees for the nucleotide sequences of regions III, V-I, V-II, and IX. These trees were constructed using the maximum-likelihood approach with a bootstrap value of 100. Regions III and IX are similar to those of HIV-1 subtype A. The V-I region of the 10.RU.6637 genome is in the same branch with HIV subtype A variants, whereas the V-II region has retained similarity to that of HIV-1 CRF02_AG

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Source: PubMed

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