Molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1, a recently originated HIV-1 circulating recombinant form spreading in Siberia
| Autor: | Shcherbakova, Nadezhda S, Shalamova, Lyudmila A, Delgado, Elena, Fernandez-Garcia, Aurora, Vega Rocha, Yolanda, Karpenko, Larissa I, Ilyichev, Alexander A, Sokolov, Yuri V, Shcherbakov, Dmitry N, Perez-Alvarez, Lucia, Thomson, Michael M |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: | |
| Zdroj: | Repisalud Instituto de Salud Carlos III (ISCIII) |
| Popis: | 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. We thank the personnel at the Genomic Unit of Instituto de Salud Carlos III, Majadahonda, Madrid, Spain, for technical assistance in sequencing, and Bonnie Mathieson, from the Office of AIDS Research, National Institutes of Health, Bethesda, Maryland for her support of this study. This work was funded by Office of AIDS Research, National Institutes of Health, through the training program “Molecular Epidemiology of HIV-1 in Eastern Europe and Its Significance for Vaccine Development.” Sí |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|