Background: The information about the dynamics of the viral population and migration
events that affect the epidemic in different parts of the Russia is insufficient. Possibly, the huge size
of the country and limited transport accessibility to certain territories may determine unique traits of
the HIV-1 evolutionary history in different regions.
Objective: The aim of this study was to explore the genetic diversity of HIV-1 in the Krasnoyarsk
region and reconstruct spatial-temporal dynamics of the infection in the region.
Methods: The demographic and virologic data from 281 HIV-infected individuals in Krasnoyarsk
region collected during 2011-2016 were analyzed. The time to the most recent common ancestor,
evolutionary rates, population growth, and ancestral geographic movements was estimated using
Bayesian coalescent-based methods.
Results: The study revealed moderate diversity of the HIV-1 subtypes found in the region, which
included A6 (92.3%), CRF063_02A (4.3%), B (1.1%), and unique recombinants (2.5%). Phylogenetic
reconstruction revealed that the A6 subtype was introduced into Krasnoyarsk region by one viral
lineage, which arose around 1996.9 (1994.5-1999.5). The phylogeography analysis pointed to
Krasnoyarsk city as the geographical center of the epidemic, which further spread to central neighboring
districts of the region. At least two epidemic growth phases of subtype A6 were identified
which included exponential growth in early-2000s followed by the decline in the mid/late 2010s.
Conclusion: This study demonstrates a change in the genetic diversity of HIV-1 in the Krasnoyarsk
region. At the beginning of the epidemic, subtype A6 prevailed, subtypes B and CRF063_02A appeared
in the region later.