Genetic Analysis of Hiv-1 in the Altai Kray: The Further Spread of the Crf63_02a1 Variant in Western Siberia

Abstract

IThe aim of this study was to characterize HIV-1 genetic strains currently circulating in Altay Kray (Western Siberia) and to analyze the HIV resistance on this territory.Materials and methods. Blood samples were collected, with informed consent, in 2017 from 82 HIV infected persons living in Altai Kray. Sequences of pol gene fragments coding protease and part of reverse transcriptase were obtained by in house system and Sanger sequencing. Genotyping, phylogenetic and recombinant analyses were carried out by HIVdbProgram: Sequence Analysis, COMET HIV-1, REGA HIV-1 Subtyping Tool (V 3.0), MEGA 5.05, RIP and jpHMM.Results and discussion. The results of genotype analysis revealed that the circulating recombinant form CRF63_02A1 dominated in Altay Kray (61%), subtype А was identified in 33%, the remaining subtypes, such as B, G, URF, accounted for 6%. According to phylogenetic analysis results, CRF63_02A1 sequences formed the common branch with nucleotide sequences of strains found in other regions of Siberia and Far East. All of HIV-1 variants belonging to subtype A clustered together with nucleotide sequences of A6 dominating in Russia. RIP analysis allowed to identify three unique recombinant forms (URFs), formed by CRF63_02A1 and A6. Drug resistance mutations were identified in 8 of 21 ART patients (8/21, 38%). The prevalence of drug resistance mutations in naïve patients equaled to 5,1%. Conclusion. Currently, the process of changing the dominant strain to CRF63_02A1 is ongoing in the Altai Kray, where 13 years ago the main variant was HIV sub-subtype A6 (IDU-A).

Spatiotemporal dynamics of HIV-1 CRF63_02A6 sub-epidemic

“…Several outbreaks of the CRF63_02A6 were detected in different Siberian regions between 2007 and 2014. This genetic variant has dominated in Siberia since that time ( Gashnikova et al, 2015 , 2017 ; Ulyanova et al, 2019 ; Kazennova et al, 2020 ; Maksimenko et al, 2020 ). The number of new HIV-1 cases has been gradually rising in Russia and has peaked in 2014, followed by the decline stage ( Figure 1 ).…”