Polymorphism of the Genome Region Coding for Protease and Reverse Transcriptase in HIV Type 1 Subtype A Variants Prevailing in CIS Countries

Efficacy of first-line ART regimens based on tenofovir in HIV-infected patients with pre-existing A62V mutation in reverse transcriptase

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.

High-Level Drug-Resistant Mutations among HIV-1 Subtype A6 and CRF02_AG in Kazakhstan

HIV incidence in Kazakhstan increased by 73% between 2010 and 2020, with an estimated 35,000 people living with HIV (PLHIV) in 2020. The development of antiretroviral drug resistance is a major threat to effective antiretroviral therapy (ART), yet studies on the prevalence of drug resistance in Kazakhstan are sparse. In this study on the molecular epidemiology of HIV in Kazakhstan, we analyzed 968 partial HIV-1 pol sequences that were collected between 2017 and 2020 from PLHIV across all regions of Kazakhstan, covering almost 3% of PLHIV in 2020. Sequences predominantly represented subtypes A6 (57%) and CRF02_AG (41%), with 32% of sequences exhibiting high-level drug resistance. We further identified distinct drug-resistant mutations (DRMs) in the two subtypes: subtype A6 showed a propensity for DRMs A62V, G190S, K101E, and D67N, while CRF02_AG showed a propensity for K103N and V179E. Codon usage analysis revealed that different mutational pathways for the two subtypes may explain the difference in G190S and V179E frequencies. Phylogenetic analysis highlighted differences in the timing and geographic spread of both subtypes within the country, with A62V-harboring subtype A6 sequences clustering on the phylogeny, indicative of sustained transmission of the mutation. Our findings suggest an HIV epidemic characterized by high levels of drug resistance and differential DRM frequencies between subtypes. This emphasizes the importance of drug resistance monitoring within Kazakhstan, together with DRM and subtype screening at diagnosis, to tailor drug regimens and provide effective, virally suppressive ART.

Prevalence of Antiretroviral Drug Resistance Mutations Among Pretreatment and Antiretroviral Therapy-Failure HIV Patients in Uzbekistan

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.

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

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.

Isolation, characterization, and sequence analysis of a novel HIV type 1 subtype A1 strain from Russia

A new syncytia-inducing human immunodeficiency virus type 1 (HIV-1) strain designated PokA79 was first isolated from a peripheral blood mononuclear cells (PBMC) pool from 24 HIV-1-infected patients from Russia and adapted to growth in MT2, MT4, and U937 cell cultures. The full-length genome of this isolate was amplified by RT-two-round PCR and sequenced. The obtained sequence belongs to the A1 subtype and clustered with other A1 former Soviet Union (FSU) strains. Full-length genome analysis showed that some of the PokA79 genes contain insertions and frame shifts, and the gp120 V3 loop has the three amino acid insertion inside its apex, which is rare for subtype A1 sequences. Nonidentical insertions of the same size are also present in the V3 apex region of several HIV-1 sequences from Central Africa.

Low prevalence of transmitted drug resistance among newly diagnosed HIV-1 patients in Latvia

Transmitted drug resistance (TDR) is a concern because it may reduce the efficacy of antiretroviral treatment. Plasma samples of 119 HIV-1-infected patients who were newly diagnosed at the Infectology Center of Latvia in 2005 and 2006 were analyzed by an in-house genotypic resistance assay to determine the prevalence of TDR in Latvia. TDR was identified using the WHO 2009 list of mutations for surveillance of TDR as implemented in the Stanford Calibrated Population Resistance tool. Neighbor-joining phylogenetic analyses were used to determine genetic subtype and investigate the relatedness of the sequences. Resistance testing was successful in 117 of 119 patients. The study population represented ∼20% of all patients that were diagnosed in Latvia in 2005 and 2006 and was well distributed between gender, transmission routes, and areas of residence. Four patients showed evidence of TDR, which represents a prevalence of TDR of 3.4% (95% CI: 0.9-8.5%). All four patients displayed single, but different resistance mutations (M46I, F53L, M41L, and G190A). All patients, except one, were predicted to respond well to standard first-line therapy in Latvia. The prevalence of TDR in Latvia was low, which partly may be due to the low proportion of HIV-1 patients who receive antiretroviral therapy. The results indicate that routine resistance testing in Latvia currently should be focused on patients who display treatment failure, rather than treatment naive patients.

Epidemiological networks and drug resistance of HIV type 1 in Krasnoyarsk region, Russia

To study the molecular epidemiology of HIV-1 in Krasnoyarsk region, Russia, where HIV-1 has spread rapidly since 2000, we obtained pol sequences from individuals living in this region (n = 67) as well as in the geographically closely related Altay region (n = 13). In both regions, subtype A viruses specific for the former Soviet Union (IDU-A strains) were dominant (92.5%). Virus sequences clustered according to the geographic origin of the infected individuals rather than to their risk group, demonstrating the role of geographically defined epidemiological networks in the propagation of the HIV-1 epidemic in the region. Six viruses belonged to subtype B. Three of them were phylogenetically (and therefore epidemiologically) closely related to each other, demonstrating that even though IDU-A viruses dominate the epidemic, the spread of other virus strains does occur. Most viruses (75%) had an A62V mutation in reverse transcriptase, specific for HIV-1 strains in Russia. Remarkably, 26 of 47 (55%) patients under HAART with detectable virus loads did not have any known drug-resistant mutation, indicating the need to increase compliance to therapy.