Genetic Diversity of HIV-1 in Krasnoyarsk Krai: Area with High Levels of HIV-1 Recombination in Russia

Abstract

More than a quarter of HIV-infected individuals registered in Russia live in Siberia. Unlike Central Russia where HIV-1 subtype A6 is predominant, in most Siberian regions since 2012, a new HIV-1 CRF63_02A1 genetic variant has spread, with the share of this variant attaining 75–85% among newly identified HIV cases. Krasnoyarsk Krai is considered to be a high-risk territory according to morbidity rate and HIV infection incidence among the population. The current paper aims to study the molecular epidemiologic characteristics of HIV-1 spreading in Krasnoyarsk Krai. Phylogenetic and recombination analyses of pol (PR-RT, IN) and env regions of the virus were used for genotyping 159 HIV-1 isolated in Krasnoyarsk Krai. 57.2% of the isolates belonged to subtype A (A6) specific to Russia, 12.6% to CRF63_02A1, and 0.6% to CRF02_AGСА, and in 29.6% HIV-1 URFs were detected, including URF63/А (23.9%), URFА/В (4.4%), and URF02/А (1.3%). In 6 of 7, HIV-1 URFА/В identical recombination model was detected; the origin of 38 URF63/А was proven to be the result of individual recombination events. Since 2015, a share of the population with newly diagnosed HIV who were infected with HIV-1 URF reached an exceptionally high rate of 38.6%. As distinct from adjacent Siberian regions, the HIV-1 CRF63_02A1 prevalence rate in Krasnoyarsk Krai is within 16%; however, the increased contribution of new HIV-1 into the regional epidemic development was observed due to the recombination of viruses of subtypes А, В, and CRF63_02A1. The difference between the described molecular epidemiologic picture in Krasnoyarsk Krai and in adjacent areas is likely caused by differences in predominant routes of HIV transmission and by more recent HIV-1 CRF63_02A1 transmission in the PWID group, which had a high prevalence of HIV-1 subtype A by the time of the new virus transmission, resulting in increased possibility of coinfection with various HIV-1 genetic variants.

Characterization of HIV-1 Epidemic in Kyrgyzstan

“…RNA/DNA was used for the amplification of HIV-1 partial pol gene region coding protease and reverse transcriptase (HXB2 #K03455 reference strain coordinates: 2249-3420). Amplification of the pol gene fragments and sequencing analysis were performed as previously described (Maksimenko et al, 2020). phylogenetic method using FastTree v2.1.9 (Price et al, 2010) with HIV-1 subtype references from Los Alamos National Laboratory (LANL) HIV Sequence Database, 2020 4 .…”

Spatiotemporal dynamics of HIV-1 CRF63_02A6 sub-epidemic

“…This study uses HIV-1partial pol gene sequences (1,047 base pairs, HXB2 #K03455 positions 2,252–3,299, n = 587) from our previous surveillance studies ( Baryshev et al, 2012 ; Gashnikova et al, 2015 , 2017 ; Ulyanova et al, 2019 ; Maksimenko et al, 2020 ; Sivay et al, 2021 ). Blood samples were collected from 2009 to 2020 from PWLH, both ART-naïve and therapy experienced, and were used for routine antiretroviral drug resistance testing.…”

“…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(Gashnikova et al, , 2017Ulyanova 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 1 http://www.hivrussia.info/wp-content/uploads/2022/03/Spravka-VICHv-Rossii-na-31.12.2021-g.pdf (Figure 1).…”

The Blood of the HIV-Infected Patients Contains κ-IgG, λ-IgG, and Bispecific κλ-IgG, Which Possess DNase and Amylolytic Activity

“…The isolation of IgG using affinity chromatography on protein-G-Sepharose was performed according to our previously published protocols [13,39,40]. The absence of virus RNA in the obtained IgG preparations was confirmed by real-time RT-PCR, as in [41,42].…”