Genetic Profile of HIV-1 in the Vologda Region: Domination of CRF03_AB and Rapid Distribution of URFs

Abstract

The work was carried out molecular-epidemiological analysis of HIV-1 in the cities of the North-West Federal District — Vologda and Cherepovets. The study used a collection of peripheral blood mononuclear cells (PBMC) obtained from 80 HIVinfected patients: 52 samples were obtained from patients living in Cherepovets, and 28 samples — from Vologda. The distribution of the HIV-1 genetic variants in the studied cities was as follows: sub-subtype A6 — 51,25%; subtype B — 6,25%; the recombinant form of CRF_03AB — 32,5%; unique recombinant forms (URFs) — 6,25%, and 3,75% were represented by other subtypes: G and CRF63_02A1. A phylogenetic analysis confirmed the relationship of the sub-subtype A6 viruses with the A6 (IDU-A) variant predominating in Ukraine, Russia and other former Soviet Union (FSU) countries; the sequences of subtype B formed a common branch on the phylogram with reference strains characteristic of men who have sex with men; 32,5% of the nucleotide sequences formed a single cluster with the reference strain CRF03_AB. In addition to these subtypes, the presence of unique recombinant forms of HIV-1 containing segments of the sub-subtype A6 and IDU-B viruses were also found. The results of the molecular epidemiological analysis in the Vologda Oblast also showed significant differences in the genetic profile of HIV-1 in two nearby cities — Vologda and Cherepovets. Thus, the evolution of HIV-1 in the Vologda Oblast continues, with the main source of variability being the mutual penetration of viruses between risk groups and recombination processes.

Spatiotemporal dynamics of HIV-1 CRF63_02A6 sub-epidemic

“…Subtype B was identified among MSM population and presently accounts for up to 2–5% of all HIV-1 cases ( Gashnikova et al, 2015 ; Pasechnik and Blokh, 2018 ; Lebedev et al, 2019 ). Recombinant form of subtype B and sub-subtype A6 - CRF03_AB caused several outbreaks among PWID in the Northwestern Russia ( Lebedev et al, 2020 ) and predominates alongside with the sub-subtype A6 ( Ozhmegova et al, 2020 ). HIV-1 genetic diversity in the Russian Far East is different from the rest of the country.…”

“…Frontiers in Microbiology frontiersin.org (Ozhmegova et al, 2020). HIV-1 genetic diversity in the Russian Far East is different from the rest of the country.…”

“…This genetic variant predominates in most of the Russian territories ever since ( Bobkov et al, 2004 ; Thomson et al, 2009 ; Diez-Fuertes et al, 2015 ; Aibekova et al, 2018 ). In late-1990s, HIV-1 sub-epidemic among different high-risk groups was detected on the territories of the Russian Fast East ( Kazennova et al, 2014 ; Kotova et al, 2019 ) and European part of Russia ( Liitsola et al, 2000 ; Lebedev et al, 2020 ; Ozhmegova et al, 2020 ). Currently, along with the predominant sub-subtype A6, subtypes B, C, and CRF03_AB have been constantly identified ( Karamov et al, 2018 ; Pasechnik and Blokh, 2018 ; Kotova et al, 2019 ; Safina et al, 2022 ).…”

Features of Tat Protein in HIV-1 Sub-Subtype A6 Variants Circulating in the Moscow Region, Russia

“…The predominant HIV-1 variant in Russia now remains sub-subtype A6 [15,16], with the exception of in Siberia, Kaliningrad, and Vologda Regions, where CRF063_02A1 [17], CRF 03AB, and various unique recombinant forms (URFs) between subtypes A and B [18,19] are highly prevalent. Previously, we have identified characteristic features for Tat1-A6 by analyzing the sequences downloaded from the Los Alamos international database [20].…”