The aim of the study. The comparison of genetic diversity of Rev protein in HIV-1 sub-subtype A6 in people living with HIV (PLHIV) with different stages of the disease.Materials and methods. 227 whole blood clinical samples received from PLHIV who have not had previously treatment and observed in Moscow Regional Center for the Prevention and Control of AIDS and Infectious Diseases were analyzed. The extraction of proviral DNA, the amplification of the first and the second rev exons with the followed sequencing was carried out. Subtyping was conducted by analyzing the rev second exon. Then the conservatism and amino acid substitutions in Rev sequences were compared in patients from different groups.Results and discussion. 220/227 (96.9%) samples contained HIV-1 sub-subtype A6. In patients with IV stage of the disease the conservation in Rev was significantly lower. There were found two substitutions (L13I, S113P) with a statistically significant difference in occurrence in PLHIV with different stages of HIV infection.Conclusion. The results obtained confirm the hypothesis of correlation between Rev structure and course of HIV infection and indicate the necessity for further research on this field.

The aim of the study: to compare the genetic diversity of the Vpu protein in HIV-1 in the people living with HIV (PLWH) with different stages of the disease.Materials and methods. An analysis was carried out of 259 clinical samples of whole blood from HIV-infected patients with no experience of taking antiretroviral therapy, who were observed at the Center for the Prevention and Control of AIDS and Infectious Diseases, Moscow, Russia. The analysis included the following stages: extraction of proviral DNA, amplification of the region of the virus genome containing the vpu gene, sequencing of amplification products, genotyping, comparison of conservation and amino acid substitutions in the Vpu protein sequences in PLWH with different stages of the disease.Results and discussion. In 255 out of 259 (98.4%) clinical samples, a sub-subtype A6 virus variant was identified. The consensus sequence of the Vpu sub-subtype A6 protein was obtained, which contained 81 amino acids. No significant differences in the conservation of Vpu protein sequences were found between HIV-1 variants obtained from patients with different stages of the disease. Amino acid substitution P3A was significantly more common in PLWH with the second stage of HIV infection.Conclusion. The results obtained highlight the issue of the influence of non-structural proteins of HIV-1 on the course of the disease and indicate directions for possible research in the future.

Introduction. The amino acid substitution A62V in reverse transcriptase was identified as a mutation correlated with virologic failure in patients on first-line therapy including tenofovir (TDF) and tenofovir alafenamide (TAF). A62V is a typically polymorphic mutation in HIV-1 sub-subtype A6, which is the most widespread virus variant in Russia. Materials and methods. The European EuResist (EIDB) database was queried to form two equivalent groups of patients: group 1 ‒ patients with A62V at baseline treated with TDF or TAF on the first-line therapy, group 2 ‒ patients without A62V at baseline treated with TDF or TAF on the first-line therapy. Each group included 23 patients. Results. There was no statistical difference between the two groups in virologic efficacy in 4, 12, and 24 weeks after the start of antiretroviral therapy (ART) and in the frequency of virologic failures. Conclusion. This study has some limitations, and the exact role of A62V in the efficacy of the first-line ART based on tenofovir deserves further investigation.

BACKGROUND:This study aimed to investigate mutations associated with, the causes of, and the conditions that contribute to HIV drug resistance (DR). This research provides crucial insights into the mechanisms through which HIV evades antiretroviral drugs and suggests strategies to counter this phenomenon. Our objective was to assess the prevalence and structure of DR in HIV-1 across various regions in Russia and identify the primary factors influencing the development of HIV DR. METHODS:The study used nucleotide sequences from the HIV-1 pol gene obtained from 1369 patients with a history of therapy and virological failure between 2005 and 2019 to analyze the frequency and structure of DR and the factors associated with it. RESULTS:The analysed HIV-1 genotypes included viruses resistant to nucleoside reverse transcriptase inhibitors (NRTIs; 11.8%), non-nucleoside reverse transcriptase inhibitors (NNRTIs; 6.4%), and NRTIs + NNRTIs (31.7%). The mutations M184V/I and G190A/S/E were the most prevalent, accounting for 54.5% and 26.6%, respectively. The dominance of multiple DR persisted throughout the entire observation period. The likelihood of encountering drug-resistant variants was increased among men, patients in the late stage of infection, and those with a viral load <30 000 RNA copies/mL. Injection drug use was not associated with DR. CONCLUSION:This study has yielded new insights into HIV DR in Russia, offering valuable information to identify clinical or programmatic events warranting closer attention and support.

The HIV-1 Rev protein expressed in the early stage of virus replication is involved in the nuclear export of some forms of virus RNA. Naturally occurring polymorphisms in the Rev protein could influence its activity. The association between the genetic features of different virus variants and HIV infection pathogenesis has been discussed for many years. In this study, Rev diversity among HIV-1 group M clades was analyzed to note the signatures that could influence Rev activity and, subsequently, clinical characteristics. From the Los Alamos HIV Sequence Database, 4962 Rev sequences were downloaded and 26 clades in HIV-1 group M were analyzed for amino acid changes, conservation in consensus sequences, and the presence of clade-specific amino acid substitutions (CSSs) and the Wu–Kabat protein variability coefficient (WK). Subtypes G, CRF 02_AG, B, and A1 showed the largest amino acid changes and diversity. The mean conservation of the Rev protein was 80.8%. In consensus sequences, signatures that could influence Rev activity were detected. In 15 out of 26 consensus sequences, an insertion associated with the reduced export activity of the Rev protein, 95QSQGTET96, was identified. A total of 32 CSSs were found in 16 clades, wherein A6 had the 41Q substitution in the functionally significant region of Rev. The high values of WK coefficient in sites 51 and 82, located on the Rev interaction surface, indicate the susceptibility of these positions to evolutionary replacements. Thus, the noted signatures require further investigation.

Tat, the trans-activator of transcription, is a multifunctional HIV-1 protein that can induce chronic inflammation and the development of somatic diseases in HIV-infected patients. Natural polymorphisms in Tat can impact the propagation of the inflammatory signal. Currently, Tat is considered an object for creating new therapeutic agents. Therefore, the identification of Tat protein features in various HIV-1 variants is a relevant task. The purpose of the study was to characterize the genetic variations of Tat-A6 in virus variants circulating in the Moscow Region. The authors analyzed 252 clinical samples from people living with HIV (PLWH) with different stages of HIV infection. Nested PCR for two fragments (tat1, tat2) with subsequent sequencing, subtyping, and statistical analysis was conducted. The authors received 252 sequences for tat1 and 189 for tat2. HIV-1 sub-subtype A6 was identified in 250 samples. The received results indicated the features of Tat1-A6 in variants of viruses circulating in the Moscow Region. In PLWH with different stages of HIV infection, C31S in Tat1-A6 was detected with different occurrence rates. It was demonstrated that Tat2-A6, instead of a functional significant 78RGD80 motif, had a 78QRD80 motif. Herewith, G79R in Tat2-A6 was defined as characteristic amino acid substitution for sub-subtype A6. Tat2-A6 in variants of viruses circulating in the Moscow Region demonstrated high conservatism.

Objective on creating a universal tool with Russian user interface (UI) to systematically collect and store epidemiological-demographic and clinical-laboratory data of patients with the possibility of their structured export for subsequent multifaceted analysis. Materials and methods. When creating an online tool, the solutions of European colleagues used to conduct a multicenter study of EuroSIDA, including a list, algorithms for collecting, storing and exchanging data, were used as a model. Research and discussion . A Russian UI online resource RuSIDA has been developed, hosted on the website http://hivgen.org/, designed to fulfill the tasks above. The tool requires authorized access and has been successfully tested on data collection from HIV-infected patients at several AIDS centers in the Russian Federation. Conclusion. The developed online resource RuSIDA can be used to maintain medical electronic records, intralaboratory databases, as well as to conduct epidemiological monitoring of various nosologies and multicenter scientific studies.

INTRODUCTION:The human immunodeficiency virus (HIV) protein p24 plays an important role in the life cycle of the virus, and also is a target for diagnostic tests and for new antiretroviral drugs and therapeutic vaccines. The most studied variant of HIV-1 in the world is subtype B. In Russia, the most common variant is A6, the spread of recombinant forms (CRF63_02A6, CRF03_A6B) is observed as well as circulation of G and CRF02_AG variants. However, a detailed study of the p24 protein in these variants has not yet been conducted. The aim was to study the features of the p24 protein in HIV-1 variants circulating in Russia and estimate the frequency of occurrence of pre-existing mutations associated with resistance to lenacapavir, the first antiretroviral drug in the class of capsid inhibitors.MATERIALS AND METHODS:The objects of the study were the nucleotide sequences obtained from the Los Alamos international database and clinical samples from HIV infected patients.RESULTS AND DISCUSSION:The features of HIV-1 variants circulating in Russia have been determined. V86A, H87Q, I91F are characteristic substitutions in A6 genome. It is shown that the presence of preexisting mutations associated with resistance to lenacapavir is unlikely.CONCLUSION:Features of the p24 protein in HIV-1 variants circulating in Russia allow them to be distinguished from others variants and among themselves. The prognosis for the use of lenacapavir in Russia is generally favorable. The results obtained could be taken into account in developing and using antiretroviral drugs and therapeutic vaccines.

The aim of the study: assessment of genetic diversity and prevalence of recombinant forms of HIV-1 at the current stage of the epidemic in the Russian Federation. Materials and methods . The study used collections of blood and its components obtained from 3178 HIV-infected patients of federal and regional «Centers for the Prevention and Control of AIDS» in the period from 2011 to 2020. Next, the extraction of proviral DNA or HIV-1 viral RNA was carried out, followed by amplification of the pol gene region and sequencing of the ampli fication products. Then, the obtained nucleotide sequences were analyzed to determine their subtype and the prevalence of recombinant forms of the virus was estimated. Results and discussion . It was found that sub-subtype A6 remains the dominant (82.9%) genetic variant of HIV-1 at the current stage of the epidemic in the Russian Federation. The second most common was subtype B — 7.14%. The share of each of the recombinant forms of HIV-1 — CRF02_AG and CRF03_AB accounted for about 1% of all analyzed samples, CRF63_02A6 — about 3.59%. In addition to circulating recombinant forms of HIV-1, 87 unique recombinants (2.74%) were identified. A significant (p<0.001) increase in the frequency of occurrence of HIV-1 recombinant forms of over time was revealed. The largest proportion of recombinant forms of HIV-1 was detected in the Siberian (35.83%) and Northwestern (15.98%) federal districts, the smallest — in the Volga (1.99%) and Ural (2.36%) federal districts. Conclusion. The results obtained indicate the growing genetic diversity of HIV-1 in the Russian Federation, along with the spread of HIV infection beyond vulnerable groups, as well as an increase in the frequency of occurrence of recombinant forms of HIV-1 over time and their involvement in the epidemic process.

Currently, HIV-1 displays a substantial level of genetic diversity on a global scale, partly attributed to its recombinant variants. This study seeks to identify and analyze HIV-1 recombinants in Russia during the last decade of the epidemic. A comprehensive examination was conducted, encompassing 3178 partial pol sequences. Subtyping was achieved through various programs including COMET, the Stanford Database, REGA, jpHMM, RIP, and RDP4 for recombination analysis. The study also involved phylogenetic analysis to trace the origins of the identified recombinants. Primary resistance (PrimDR) prevalence and Drug Resistance Mutations (DRMs) were assessed. The study uncovered an overall proportion of recombinants at 8.7%, with a statistically significant increase in their frequency observed over time (p < 0.001). The Northwestern (18.5%) and Siberian (15.0%) Federal Districts exhibited a high prevalence of recombinants, while the Volga (1.9%) and Ural (2.8%) Federal Districts had a lower prevalence. Among HIV-1 recombinants, a PrimDR prevalence of 11.4% was identified. Notably, significant differences in DRMs were observed, with a higher prevalence of M184V in sub-subtype A6 (p = 0.018) and K103N in CRF63_02A6 (p = 0.002). These findings underscore the increasing HIV-1 genetic diversity and highlight a substantial prevalence of PrimDR among its recombinant forms, emphasizing the necessity for ongoing systematic monitoring.

The CRF02_AG and sub-subtype A6 are currently the predominant HIV-1 variants in the Republic of Uzbekistan, but little is known about their time-spatial clustering patterns in high-risk populations. We have applied molecular evolution methods and network analyses to better understand the transmission patterns of these subtypes by analyzing 316 pol sequences obtained during the surveillance study of HIV drug resistance. Network analysis showed that about one third of the HIV infected persons were organized into clusters, including large clusters with more than 35 members. These clusters were composed mostly of injecting drug users and/or heterosexuals, with women having mainly high centrality within networks identified in both subtypes. Phylogenetic analyses of the ‘Uzbek’ sequences, including those publicly available, show that Russia and Ukraine played a role as the main sources of the current subtype A6 epidemic in the Republic. At the same time, Uzbekistan has been a local center of the CRF02_AG epidemic spread in the former USSR since the early 2000s. Both of these HIV-1 variants continue to spread in Uzbekistan, highlighting the importance of identifying transmission networks and transmission clusters to prevent further HIV spread, and the need for HIV prevention and education campaigns in high-risk groups.

Introduction. Tat protein is a major factor of HIV (human immunodeficiency virus) transcription regulation and has other activities. Tat is characterized by high variability, with some amino acid substitutions, including subtypespecific ones, being able to influence on its functionality. HIV type 1 (HIV-1) sub-subtype A6 is the most widespread in Russia. Previous studies of the polymorphisms in structural regions of the A6 variant have shown numerous characteristic features; however, Tat polymorphism in A6 has not been studied.Goals and tasks. The main goal of the work was to analyze the characteristics of Tat protein in HIV-1 A6 variant, that is, to identify substitutions characteristic for A6 and A1 variants, as well as to compare the frequency of mutations in functionally significant domains in sub-subtype A6 and subtype B.Material and methods. The nucleotide sequences of HIV-1 sub-subtypes A6, A1, A2, A3, A4, subtype B and the reference nucleotide sequence were obtained from the Los Alamos international database.Results and discussion. Q54H and Q60H were identified as characteristic substitutions. Essential differences in natural polymorphisms between sub-subtypes A6 and A1 have been demonstrated. In the CPP-region, there were detected mutations (R53K, Q54H, Q54P, R57G) which were more common in sub-subtype A6 than in subtype B.Conclusion. Tat protein of sub-subtype A6 have some characteristics that make it possible to reliably distinguish it from other HIV-1 variants. Mutations identified in the CPP region could potentially alter the activity of Tat. The data obtained could form the basis for the drugs and vaccines development.

General consensus suggests that even singleton E138A mutations in HIV reverse transcriptase at baseline are associated with resistance to rilpivirine (RPV). We detected 11 pre-existing E138A carriers treated with RPV in the pan European EuResist database. However, all 11 patients presented with full virological efficacy for first-line RPV-based ART regimens.

[This corrects the article DOI: 10.1371/journal.pone.0241269.].

Introduction It was previously shown that the presence of the E138A mutation is associated with resistance to rilpivirine (RPV). Detection of this mutation is considered as contraindication for RPV use within the first-line ART. It is a lack of knowledge regarding efficacy of first-line RPV-based ART in patients bearing HIV with E138A mutation. In absence of HIV genotyping in naïve patients it may influence the clinical decisions. Methods We have collected all available patients unconventionally treated with RPV and carefully analyzed the ART efficacy in E138A carriers from the EuResist database. The viral load data in patients with E138A mutation at baseline was extracted from the database. Due to uniqueness of these cases only 11 HIV infected patients were found. The virologic outcome was analyzed according to the national and international ART guidelines. Results The full virologic efficacy of the first-line RPV-based ART regimen was demonstrated in 11 out of 11 patients according to all guidelines. Conclusions Our data suggest that the influence of the pre-existing E138A mutation on the sensitivity to RPV is very low or insignificant. The results support importance of investigation of polymorphic pre-existing HIV drug mutations for ART efficacy.

To evaluate the national prevalence of antiretroviral therapy (ART)-resistant HIV-1 viruses among both ART-initiators (pretreatment drug resistance, PDR) and ART-failure HIV patients in Uzbekistan. A nation-wide, cross-sectional active HIV-1 PDR surveillance was conducted in Uzbekistan from 2015 to 2016. In total, 713 blood plasma samples from adults were collected, including samples from ART-naive patients initiating ART and ART-failure HIV patients. HIV-1 genome polregion viral sequences were obtained from 309 patients, of those 106 on ART and 203 on ART-initiators. Analysis of HIV-1 subtypes and drug resistance mutations (DRMs) to HIV protease and reverse transcriptase inhibitors was performed. Among all the viruses studied, HIV-1 CRF 02_AG recombinant was the most common-57% (176/309). The second major group was represented by A1-40.5% (125/309). Two viruses were found to be recombinants formed by subtypes A1 and CRF02_AG sequences. ART-naive cohort I (PDR) included six samples that contained at least one surveillance drug resistance mutation (SDRM) (2.96%), with the most common being K103N mutation (4/6). In ART-experienced patients, cohort II, 77.4% (82/106) of viruses contained at least one mutation against PIs, NRTIs, or NNRTIs, with the most common mutations of M184V/I (49.1%; 52/106), K65R (18.9%; 20/106), K103N (23.6%; 25/106), and G190S (22.6%; 24/106). The significant difference in frequency of mutations was found between two dominant subtypes, A1 and CRF02_AG. The molecular epidemiological profile of HIV infection in Uzbekistan has changed toward a predominance of CRF02_AG viruses. In the first national-scale study of the PDR prevalence, it was found to be relatively low (2.96%). The DR mutations in failure patients correspond to the main therapy regimens (NRTI/NNRTI) adopted in the country. The observations provide new evidence for differences in ART efficacy and resistance profiles for different subtypes.

ITheaimof 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.Materialsandmethods.Blood samples were collected, with informed consent, in 2017 from 82 HIV infected persons living in Altai Kray. Sequences ofpolgene 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.Resultsanddiscussion.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).

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.

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.