The Molecular Epidemiology of HIV-1 in Russia, 1987–2023: Subtypes, Transmission Networks and Phylogenetic Story
Aleksey Lebedev, Dmitry Kireev, Alina Kirichenko, Ekaterina Ozhmegova, Anastasiia Antonova, Vyacheslav Bobkov, Ilya Lapovok, Anastasia V. Shlykova, Alexey Lopatukhin, Andrey Shemshura, Valery Kulagin, Aleksei Kovelenov, Alexandra Cherdantseva, Natalia Filoniuk, Galina Turbina, А. И. Ермаков, N. E. Monakhov, M. V. Piterskiy, А. В. Семенов, S. V. Shtrek, Aleksej Sannikov, Natalia Zaytseva, O.Yu. Peksheva, Aleksandr Suladze, Dmitry Kolpakov, В. О. Котова, Е. А. Базыкина, В. Г. Акимкин, Bobkova Mr
Abstract
Regional HIV-1 epidemics are evolving with distinct patterns in transmission routes, subtype distribution, and molecular transmission cluster (MTCs) characteristics. We analyzed 9500 HIV-1 cases diagnosed over 30 years using phylogenetic and network methods, integrating molecular, epidemiological, demographic, and behavioral data. Subtype A6 remains dominant nationally (80.6%), followed by 63_02A6 (7.9%), subtype B (5.6%), 02_AGFSU (1.2%), 03_A6B (0.7%), and 14/73_BG (0.6%). Non-A6 infections were more common among males (OR 1.51) and men who have sex with men (OR 7.33). Network analysis identified 421 MTCs, with 256 active clusters. Clustering was more likely among young individuals (OR: 1.31), those not receiving antiretroviral therapy (OR: 2.70), and injecting drug users (OR: 1.28). Non-A6 subtypes showed a higher likelihood of clustering. Phylogenetic analysis revealed that local clusters of the major subtypes originated between the late 1970s (subtype B) and the mid-2000s (63_02A6) with links to populations in Eastern Europe, Central Asia (subtypes A6, 63_02A6, 02_AGFSU, 03_A6B), and Western Europe and the Americas (subtype B, 14/73_BG). These findings indicate a complex, evolving regional epidemic transitioning from subtype A6 dominance to a more diverse mix of subtypes. The ability of non-A6 subtypes to form active MTCs suggests their establishment in the local population.