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Volume 15
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10.3390/pathogens15020144
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Article

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

by
Artem Fadeev
1,
Veronika Eder
1,
Maria Pisareva
1,
Valery Tsvetkov
1,
Alexey Masharskiy
1,
Kseniya Komissarova
1,
Anna Ivanova
1,
Nikita Yolshin
1,
Andrey Komissarov
1,*,
Alexey Mazus
2 and
Dmitry Lioznov
1
1
Smorodintsev Research Institute of Influenza, Prof. Popova Str., 15/17, 197376 Saint Petersburg, Russia
2
Moscow City Center for AIDS Prevention and Control, 8th Sokolina Gora Str., 15, 105275 Moscow, Russia
*
Author to whom correspondence should be addressed.
Pathogens 2026, 15(2), 144; https://doi.org/10.3390/pathogens15020144
Submission received: 31 December 2025 / Revised: 23 January 2026 / Accepted: 26 January 2026 / Published: 28 January 2026
(This article belongs to the Section Epidemiology of Infectious Diseases)
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Abstract

The use of antiretroviral therapy (ART) as the only effective way to control human immunodeficiency virus (HIV) infection results in HIV drug resistance. Next-generation sequencing (NGS) has become a common method for identifying drug-resistant variants and reducing analysis costs. The aim of this study was to develop an 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. Plasma samples from adult HIV-infected patients from Russia were analyzed. Consensus nucleotide sequences of pol and env genes were obtained using NGS. HIV-1 drug resistance analysis was conducted using the Stanford University HIVdb database. CXCR4 cell tropism was predicted using an empirical rule classifier. A protocol for NGS of HIV-1 pol and env genes was developed. The most common HIV-1 surveillance mutations were in the reverse transcriptase. High levels of resistance were observed to non-nucleoside reverse transcriptase inhibitors (NNRTIs) and nucleoside reverse transcriptase inhibitors (NRTIs) in treatment-experienced patients and to NNRTIs in treatment-naïve patients. Low levels of resistance were observed to protease and integrase strand transfer inhibitors (INSTIs). CXCR4 cell tropism was extremely rare. NGS allows for the simultaneous processing of large data sets during epidemiological studies. The introduction of NGS-based protocols allows for performing ART efficiency and tropism monitoring at scale.
Keywords: human immunodeficiency virus; antiretroviral therapy; drug resistance mutations; next generation sequencing human immunodeficiency virus; antiretroviral therapy; drug resistance mutations; next generation sequencing

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MDPI and ACS Style

Fadeev, A.; Eder, V.; Pisareva, M.; Tsvetkov, V.; Masharskiy, A.; Komissarova, K.; Ivanova, A.; Yolshin, N.; Komissarov, A.; Mazus, A.; et al. Detection of HIV-1 Resistance Mutations to Antiretroviral Therapy and Cell Tropism in Russian Patients Using Next-Generation Sequencing. Pathogens 2026, 15, 144. https://doi.org/10.3390/pathogens15020144

AMA Style

Fadeev A, Eder V, Pisareva M, Tsvetkov V, Masharskiy A, Komissarova K, Ivanova A, Yolshin N, Komissarov A, Mazus A, et al. Detection of HIV-1 Resistance Mutations to Antiretroviral Therapy and Cell Tropism in Russian Patients Using Next-Generation Sequencing. Pathogens. 2026; 15(2):144. https://doi.org/10.3390/pathogens15020144

Chicago/Turabian Style

Fadeev, Artem, Veronika Eder, Maria Pisareva, Valery Tsvetkov, Alexey Masharskiy, Kseniya Komissarova, Anna Ivanova, Nikita Yolshin, Andrey Komissarov, Alexey Mazus, and et al. 2026. "Detection of HIV-1 Resistance Mutations to Antiretroviral Therapy and Cell Tropism in Russian Patients Using Next-Generation Sequencing" Pathogens 15, no. 2: 144. https://doi.org/10.3390/pathogens15020144

APA Style

Fadeev, A., Eder, V., Pisareva, M., Tsvetkov, V., Masharskiy, A., Komissarova, K., Ivanova, A., Yolshin, N., Komissarov, A., Mazus, A., & Lioznov, D. (2026). Detection of HIV-1 Resistance Mutations to Antiretroviral Therapy and Cell Tropism in Russian Patients Using Next-Generation Sequencing. Pathogens, 15(2), 144. https://doi.org/10.3390/pathogens15020144

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