Human Immunodeficiency Virus-1 Diversity in the Moscow Region, Russia: Phylodynamics of the Most Common Subtypes

Bobkov, 2001, An HIV type 1 subtype A strain of low genetic diversity continues to spread among injecting drug users in Russia: study of the new local outbreaks in Moscow and Irkutsk, AIDS Res. Hum. Retroviruses, 17, 257, 10.1089/088922201750063188

Bobkov, 1998, A sudden epidemic of HIV type 1 among injecting drug users in the former Soviet Union: identification of subtype A, subtype B, and novel gagA/envB recombinants, AIDS Res. Hum. Retroviruses, 14, 669, 10.1089/aid.1998.14.669

Bobkova, 2013, Current status of HIV-1 diversity and drug resistance monitoring in the former USSR, AIDS Rev., 15, 204

Darriba, 2012, jModelTest 2: more models, new heuristics and parallel computing, Nat. Methods, 9, 772, 10.1038/nmeth.2109

Diez-Fuertes, 2015, Bayesian phylogeographic analyses clarify the origin of the HIV-1 subtype A variant circulating in former Soviet Union's countries, Infect. Genet. Evol., 33, 197, 10.1016/j.meegid.2015.05.003

Dukhovlinova, 2015, Two independent HIV epidemics in Saint Petersburg, Russia revealed by molecular epidemiology, AIDS Res. Hum. Retroviruses, 31, 608, 10.1089/aid.2014.0150

Report on the Russian HIV/AIDS Epidemic2010

Foley, 2016, Primate immunodeficiency virus classification and nomenclature: review, Infect. Genet. Evol., 46, 150, 10.1016/j.meegid.2016.10.018

Gashnikova, 2015, A rapid expansion of HIV-1 CRF63_02A1 among newly diagnosed HIV-infected individuals in the Tomsk Region, Russia, AIDS Res. Hum. Retroviruses, 31, 456, 10.1089/aid.2014.0375

Gashnikova, 2011, Properties of CRF02_AG HIV-1 isolates circulating in Novosibirsk region, Zh. Mikrobiol. Epidemiol. Immunobiol., 38

Gashnikova, 2017, Predominance of CRF63_02A1 and multiple patterns of unique recombinant forms of CRF63_A1 among individuals with newly diagnosed HIV-1 infection in Kemerovo Oblast, Russia, Arch. Virol., 162, 379, 10.1007/s00705-016-3120-4

Giliazova, 2010, Molecular epidemiology of HIV-1 strains in the Moscow Region, Vopr. Virusol., 55, 25

Hemelaar, 2011, Global trends in molecular epidemiology of HIV-1 during 2000-2007, AIDS, 25, 679, 10.1097/QAD.0b013e328342ff93

Johnson, 2011, 2011 update of the drug resistance mutations in HIV-1, Top. Antivir. Med., 19, 156

Katoh, 2017, MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization, Brief. Bioinform, 10.1093/bib/bbx108

Kazennova, 2017, Genetic variants of HIV type 1 in men who have sex with men in Russia, AIDS Res. Hum. Retroviruses, 33, 1061, 10.1089/aid.2017.0078

Kazennova, 2011, Molecular and epidemiology studies of HIV-1 prevalence in the Republic of Sakha (Yakutia), Vopr Virusol, 56, 30

Kostaki, 2018, Spatiotemporal characteristics of the HIV-1 CRF02_AG/CRF63_02A1 epidemic in Russia and Central Asia, AIDS Res. Hum. Retroviruses, 34, 415, 10.1089/aid.2017.0233

Lapovok, 2014, Short communication: molecular epidemiology of HIV type 1 infection in Kazakhstan: CRF02_AG prevalence is increasing in the southeastern provinces, AIDS Res. Hum. Retroviruses, 30, 769, 10.1089/aid.2013.0291

Lapovok, 2017, Molecular epidemiological analysis of HIV-1 variants circulating in Russia in 1987-2015, Ter. Arkh., 89, 44, 10.17116/terarkh2017891144-49

Maljkovic Berry, 2007, Unequal evolutionary rates in the human immunodeficiency virus type 1 (HIV-1) pandemic: the evolutionary rate of HIV-1 slows down when the epidemic rate increases, J. Virol., 81, 10625, 10.1128/JVI.00985-07

Nabatov, 2002, Simultaneous introduction of HIV type 1 subtype A and B viruses into injecting drug users in southern Ukraine at the beginning of the epidemic in the former Soviet Union, AIDS Res. Hum. Retroviruses, 18, 891, 10.1089/08892220260190380

Nguyen, 2015, IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol. Biol. Evol., 32, 268, 10.1093/molbev/msu300

Pineda-Pena, 2013, Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools, Infect. Genet. Evol., 19, 337, 10.1016/j.meegid.2013.04.032

Rambaut, 2016, Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen), Virus Evol., 2, vew007, 10.1093/ve/vew007

Schultz, 2012, jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus, Nucleic Acids Res., 40, W193, 10.1093/nar/gks414

Struck, 2014, COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification, Nucleic Acids Res., 42, e144, 10.1093/nar/gku739

Suchard, 2018, Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10, Virus Evol., 4, vey016, 10.1093/ve/vey016

Thomson, 2009, Molecular epidemiology of HIV-1 in St Petersburg, Russia: predominance of subtype A, former Soviet Union variant, and identification of intrasubtype subclusters, J. Acquir. Immune Defic. Syndr., 51, 332, 10.1097/QAI.0b013e31819c1757