The HIV epidemic in Eastern Europe and Russia is large and not well-controlled. To describe the more recent molecular epidemiology of HIV-1, transmitted drug resistance, and the relationship between the epidemics in this region, we sequenced the protease and reverse transcriptase genes of HIV-1 from 812 people living with HIV from Ukraine (n = 191), Georgia (n = 201), and Russia (n = 420) before the initiation of antiretroviral therapy. In 190 Ukrainian patients, the integrase gene sequence was also determined. The most reported route of transmission was heterosexual contact, followed by intravenous drug use, and men having sex with men (MSM). Several pre-existing drug resistance mutations were found against non-nucleoside reverse transcriptase inhibitors (RTIs) (n = 103), protease inhibitors (n = 11), and nucleoside analogue RTIs (n = 12), mostly polymorphic mutations or revertants. In the integrase gene, four strains with accessory integrase strand transfer inhibitor mutations were identified. Sub-subtype A6 caused most of the infections (713/812; 87.8%) in all three countries, including in MSM. In contrast to earlier studies, no clear clusters related to the route of transmission were identified, indicating that, within the region, the exchange of viruses among the different risk groups may occur more often than earlier reported.

Background HIV-1 circulating recombinant forms (CRFs) infections has been increasing in Former Soviet Union (FSU) countries in the recent decade. One is the CRF03_AB, which circulated in the region since late 1990s and probably became widespread in northwestern FSU countries. However, there is not much information provided about the dissemination of this recombinant. Here, we examine the prevalence, evolutionary dynamics and dispersion pattern of HIV-1 CRF03_AB recombinant. Methods We analyzed 32 independent studies and 151 HIV-1 CRF03_AB pol sequences isolated from different FSU countries over a period of 22 years. Pooled prevalence was estimated using a random effects model. Bayesian coalescent-based method was used to estimate the evolutionary, phylogeographic and demographic parameters. Results Our meta-analysis showed that the pooled prevalence of CRF03_AB infection in northwestern FSU region was 5.9% [95%CI: 4.1–7.8]. Lithuania (11.6%), Russia (5.9%) and Belarus (2.9%) were the most affected by CRF03_AB. We found that early region wide spread of HIV-1 CRF03_AB originated from one viral clade that arose in the city of Kaliningrad in 1992 [95%HPD: 1990–1995]. Fourteen migration route of this variant were found. The city of Kaliningrad is involved in most of these, confirming its leading role in CRF03_AB spread within FSU. Demographic reconstruction point to this is that CRF03_AB clade seems to have experienced an exponential growth until the mid-2000s and a decrease in recent years. Conclusion These data provide new insights into the molecular epidemiology of CRF03_AB as well as contributing to the fundamental understanding of HIV epidemic in FSU.

Background: The information about the dynamics of the viral population and migration events that affect the epidemic in different parts of the Russia is insufficient. Possibly, the huge size of the country and limited transport accessibility to certain territories may determine unique traits of the HIV-1 evolutionary history in different regions. Objective: The aim of this study was to explore the genetic diversity of HIV-1 in the Krasnoyarsk region and reconstruct spatial-temporal dynamics of the infection in the region. Methods: The demographic and virologic data from 281 HIV-infected individuals in Krasnoyarsk region collected during 2011-2016 were analyzed. The time to the most recent common ancestor, evolutionary rates, population growth, and ancestral geographic movements was estimated using Bayesian coalescent-based methods. Results: The study revealed moderate diversity of the HIV-1 subtypes found in the region, which included A6 (92.3%), CRF063_02A (4.3%), B (1.1%), and unique recombinants (2.5%). Phylogenetic reconstruction revealed that the A6 subtype was introduced into Krasnoyarsk region by one viral lineage, which arose around 1996.9 (1994.5-1999.5). The phylogeography analysis pointed to Krasnoyarsk city as the geographical center of the epidemic, which further spread to central neighboring districts of the region. At least two epidemic growth phases of subtype A6 were identified which included exponential growth in early-2000s followed by the decline in the mid/late 2010s. Conclusion: This study demonstrates a change in the genetic diversity of HIV-1 in the Krasnoyarsk region. At the beginning of the epidemic, subtype A6 prevailed, subtypes B and CRF063_02A appeared in the region later.

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.

Objective. Molecular genetic analysis of AIDS-1, having spread in the territory of Krasnodar region over the 2014 to 2019, including analysis of drug resistance mutationMaterials and methods. The study used the collection of samples, obtained from 478 HIV-infected people, living in the territory of Krasnodar region over the 2014 to 2019; out of them 155 received antiretroviral therapy (ART). Genotyping of the obtained samples was carried out with the further phylogenetic analysis, including detailed analysis of identified unique recombinant forms of HIV-1.Results. It is shown that HIV-1 sub-subtype A6 (80,5%) continues dominating in the territory of Krasnodar region, genetic variant B (9,2%) is the second most common one. Also 11 unique recombinant forms (URFs) were discovered, 10 out of which are the result of A6 and B genetic variants recombination. Drug resistance mutations were registered with 114 patients, received ART (73,6%); primary mutations — M184V and A62V. Provisional indicator of transmissible drug resistance in the population of naïve patients is 4,6% (15/323); primary mutations — K103N и G190S. Conclusion. The analysis of genetic profile and HIV-1 drug resistance mutation is carried out in the territory of Krasnodar region over the 2014 to 2019.