title: Short communication: Molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1, a recently originated HIV-1 circulating recombinant form spreading in Siberia.
abstract: The HIV-1 epidemic in Russia is dominated by the former Soviet Union subtype A (A(FSU)) variant, but other genetic forms are circulating in the country. One is the recently described CRF63_02A1, derived from recombination between a CRF02_AG variant circulating in Central Asia and A(FSU), which has spread in the Novosibirsk region, Siberia. Here we phylogenetically analyze pol and env segments from 24 HIV-1 samples from the Novosibirsk region collected in 2013, with characterization of three new near full-length genome CRF63_02A1 sequences, and estimate the time of the most recent common ancestor (tMRCA) and the demographic growth of CRF63_02A1 using a Bayesian method. The analyses revealed that CRF63_02A1 is highly predominant in the Novosibirsk region (81.2% in pol sequences) and is transmitted both among injecting drug users and by heterosexual contact. Similarity searches with database sequences combined with phylogenetic analyses show that CRF63_02A1 is circulating in East Kazakhstan and the Eastern area of Russia bordering China. The analyses of near full-length genome sequences show that its mosaic structure is more complex than reported, with 18 breakpoints. The tMRCA of CRF63_02A1 was estimated around 2006, with exponential growth in 2008-2009 and subsequent stabilization. These results provide new insights into the molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1.
authors: 1 Department of Bioengineering, State Research Center of Virology and Biotechnology "Vector," Koltsovo, Novosibirsk, Russia .
authors: Nadezhda S
authors: NS
authors: Shcherbakova
authors: Lyudmila A
authors: LA
authors: Shalamova
authors: Elena
authors: E
authors: Delgado
authors: Aurora
authors: A
authors: Fernández-García
authors: Yolanda
authors: Y
authors: Vega
authors: Larissa I
authors: LI
authors: Karpenko
authors: Alexander A
authors: AA
authors: Ilyichev
authors: Yuri V
authors: YV
authors: Sokolov
authors: Dmitry N
authors: DN
authors: Shcherbakov
authors: Lucía
authors: L
authors: Pérez-Álvarez
authors: Michael M
authors: MM
authors: Thomson
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D005260:Female; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008297:Male; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011995:Recombination, Genetic; D012800:Siberia
chemical_list: D017931:DNA Primers