Molecular epidemiology of HIV-1 in Oryol Oblast, Russia
Authors: Safina Ksenia R , Sidorina Yulia , Efendieva Natalya , Belonosova Elena , Saleeva Darya , Kirichenko Alina , Kireev Dmitry , Pokrovsky Vadim , Bazykin Georgii A. 
Published: October 2021

The HIV/AIDS epidemic in Russia is growing, with approximately 100,000 people infected annually. Molecular epidemiology can provide insight on the structure and dynamics of the epidemic. However, its applicability in Russia is limited by the weakness of genetic surveillance, as viral genetic data is only available for <1% of cases. Here, we provide a detailed description of the HIV-1 epidemic for one geographic region of Russia, Oryol Oblast, by collecting and sequencing viral samples from about a third of its HIV-positive population. We identify multiple introductions of HIV-1 into Oryol Oblast, resulting in 82 transmission lineages that together comprise 66% of the samples. Most introductions are of subtype A, the predominant HIV-1 subtype in Russia, followed by CRF63 and subtype B. Bayesian analysis estimates the effective reproduction number Re for subtype A at 2.8 [1.7-4.4], in line with a growing epidemic. The frequency of CRF63 has been growing more rapidly, with the median Re of 11.8 [4.6-28.7], in agreement with recent reports of this variant rising in frequency in some regions of Russia. In contrast to the patterns described previously in European and North American countries, we see no overrepresentation of males in transmission lineages; meanwhile, injecting drug users are overrepresented in transmission lineages. This likely reflects the structure of the HIV-1 epidemic in Russia dominated by heterosexual and, to smaller extent, IDU transmission. Samples attributed to MSM transmission are associated with subtype B and are less prevalent than expected from the male-to-female ratio for this subtype, suggesting underreporting of this transmission route. Together, our results provide a high-resolution description of the HIV-1 epidemic in Oryol Oblast, Russia, characterized by frequent interregional transmission, rapid growth of the epidemic and rapid displacement of subtype A with the recombinant CRF63 variant.

Author Summary

In 2017, Russia registered 138,843 new HIV-1 infections, which is nearly 5 times that of the second-highest European country. Meanwhile, genetic surveillance of HIV-1 in Russia is low, with only <1% of all HIV-positive samples sequenced. Here, we characterize the HIV-1 epidemic in Oryol Oblast, a region of Russia with an HIV-positive population of 2,157 as of 2019, by collecting viral genetic data covering a third of this population. We show that HIV-1 has been introduced into the region hundreds of times over the last 25 years, with many of the introductions resulting in sustained transmission within the region. By studying the branching patterns of the viral evolutionary trees, we reveal a persistently growing epidemic. A rapidly growing transmission cluster is associated with the CRF63 recombinant variant which has been spreading rapidly through the population of injecting drug users since its introduction around 2014. By analysing the subtype B which is characteristic of transmission between men who have sex with men (MSM), we show that the MSM transmission route is underreported. To our knowledge, this study is the most detailed description of the HIV-1 epidemic in a region of Russia.