Please use this identifier to cite or link to this item:http://hdl.handle.net/20.500.12105/8711
Molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1, a recently originated HIV-1 circulating recombinant form spreading in Siberia
Shcherbakova, Nadezhda S | Shalamova, Lyudmila A | Delgado, Elena ISCIII | Fernandez-Garcia, Aurora ISCIII | Vega Rocha, Yolanda ISCIII | Karpenko, Larissa I | Ilyichev, Alexander A | Sokolov, Yuri V | Shcherbakov, Dmitry N | Perez-Alvarez, Lucia ISCIII | Thomson, Michael M ISCIII
AIDS Res Hum Retroviruses. 2014 Sep;30(9):912-9. doi: 10.1089/AID.2014.0075. Epub 2014 Aug 14.
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.
Base Sequence | DNA Primers | Female | HIV-1 | Humans | Male | Molecular Sequence Data | Polymerase Chain Reaction | Recombination, Genetic | Siberia | Molecular Epidemiology | Phylogeny
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