Detection of HIV-1 Resistance Mutations to Antiretroviral Therapy and Cell Tropism in Russian Patients Using Next-Generation Sequencing

Background: Use of ART as the only effective way to control HIV infection results in HIV drug resistance. NGS became the common method for identifying drug-resistant variants and reducing analysis costs. The aim of the study was to develop the NGS based protocol for identifying resistance mutations and cell tropism of HIV-1 in adult patients with and without treatment experience in Russia in 2024–2025. Methods: Plasma samples from adult HIV-infected patients from Russia were analyzed. Consensus nucleotide sequences of pol and env genes were obtained using Illumina NextSeq NGS. HIV-1 drug resistance analysis was conducted using Stanford University HIVdb database. CXCR4 cell tropism was predicted using empirical rule classifier. Results: The protocol for NGS of HIV-1 pol and env genes was developed. The most common HIV-1 surveillance mutations were in the reverse transcriptase. In treatment-experienced patients, high levels of resistance were observed to NNRTIs and NRTIs, and in treatment-naive— to NNRTIs. Low levels of resistance were observed to protease and integrase inhibitors. CXCR4 cell tropism was extremely rare. Conclusion: NGS allows for the simultaneous processing of large data sets during epidemiological studies. The introduction of NGS based protocols allows performing ART efficiency and tropism monitoring at scale.