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Reconstructing the Temporal Origin and the Transmission Dynamics of the HIV Subtype B Epidemic in St. Petersburg,Russia
Authors:Marina Siljic  Valentina Cirkovic  Luka Jovanovic  Anastasiia Antonova  Aleksey Lebedev  Ekaterina Ozhmegova  Anna Kuznetsova  Tatiyana Vinogradova  Aleksei Ermakov  Nikita Monakhov  Marina Bobkova  Maja Stanojevic
Affiliation:1.Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia;2.Institute for Oncology and Radiology of Serbia, 11000 Belgrade, Serbia;3.Laboratory of T-Lymphotropic Viruses, N.F. Gamaleya National Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia;4.St. Petersburg City AIDS Center, 190103 St. Petersburg, Russia
Abstract:The HIV/AIDS epidemic in Russia is among the fastest growing in the world. HIV epidemic burden is non-uniform in different Russian regions and diverse key populations. An explosive epidemic has been documented among people who inject drugs (PWID) starting from the mid-1990s, whereas presently, the majority of new infections are linked to sexual transmission. Nationwide, HIV sub-subtype A6 (previously called AFSU) predominates, with the increasing presence of other subtypes, namely subtype B and CRF063_02A. This study explores HIV subtype B sequences from St. Petersburg, collected from 2006 to 2020, in order to phylogenetically investigate and characterize transmission clusters, focusing on their evolutionary dynamics and potential for further growth, along with a socio-demographic analysis of the available metadata. In total, 54% (107/198) of analyzed subtype B sequences were found grouped in 17 clusters, with four transmission clusters with the number of sequences above 10. Using Bayesian MCMC inference, tMRCA of HIV-1 subtype B was estimated to be around 1986 (95% HPD 1984–1991), whereas the estimated temporal origin for the four large clusters was found to be more recent, between 2001 and 2005. The results of our study imply a complex pattern of the epidemic spread of HIV subtype B in St. Petersburg, Russia, still in the exponential growth phase, and in connection to the men who have sex with men (MSM) transmission, providing a useful insight needed for the design of public health priorities and interventions.
Keywords:St. Petersburg   Russia   HIV subtype B   transmission clusters   phylodynamics   latent class analysis
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