Genetic characterization of an isolate of HIV type 1 AG recombinant form circulating in Siberia, Russia

Archives of Virology - Tập 157 - Trang 2335-2341 - 2012
P. B. Baryshev1, V. V. Bogachev1, N. M. Gashnikova1
1State Research Center of Virology and Biotechnology « Vector », Novosibirsk, Russia

Tóm tắt

Before 2008, HIV-1 subtype A was the predominant genetic variant in the Novosibirsk oblast of Russia as well as in most parts of this country. However, a rapid spread of the recombinant HIV-1 02_AG form has been reported in Novosibirsk since 2009. We have analyzed the genome of the 10.RU.6637 isolate, a HIV-1 02_AG recombinant form, which represents a monophyletic cluster of the HIV-1 variants widespread in this region. Phylogenetic analysis has shown that the Siberian 10.RU.6637 isolate displays the highest sequence identity to the HIV-1 subtype AG forms circulating in Uzbekistan. However, recombination analysis of 10.RU.6637 has demonstrated that this isolate is a recombinant form between HIV-1 subtype A and CRF02_AG, differing in its genetic structure from both the CRF02_AG reference sequences and the Central Asian variants of HIV-1 02_AG.

Tài liệu tham khảo

Temin HM (1993) Retrovirus variation and reverse transcription: abnormal strand transfers result in retrovirus genetic variation. Proc Natl Acad Sci USA 90:6900–6903 Hu WS, Temin HM (1990) Retroviral recombination and reverse transcription. Science 250:1227–1233 Moutouh L, Corbeil J, Richman DD (1996) Recombination leads to the rapid emergence of HIV-1 dually resistant mutants under selective drug pressure. Proc Natl Acad Sci USA 93:6106–6111 Nora T, Charpentier C, Tenaillon O, Hoede C, Clavel F, Hance AJ (2007) Contribution of recombination to the evolution of human immunodeficiency viruses expressing resistance to antiretroviral treatment. J Virol 81:7620–7628 Peeters M, Sharp PM (2000) Genetic diversity of HIV-1: the moving target. AIDS 14(Suppl 3):S129–S140 Hemelaar J, Gouws E, Ghys PD, Osmanov S (2006) Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004. AIDS 20:W13–W23 Robertson DL, Anderson JP, Bradac JA, Carr JK, Foley B, Funkhouser RK, Gao F, Hahn BH, Kalish ML, Kuiken C, Learn GH, Leitner T, McCutchan F, Osmanov S, Peeters M, Pieniazek D, Salminen M, Sharp PM, Wolinsky S, Korber B (2000) HIV-1 nomenclature proposal. Science 288:55–56 McCutchan FE (2000) Understanding the genetic diversity of HIV-1. AIDS 14(Suppl 3):S31–S44 Hemelaar J, Gouws E, Ghys PD, Osmanov S (2006) Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004. AIDS 20:W13–W23 Howard TM, Olaylele DO, Rasheed S (1994) Sequence analysis of the glycoprotein 120 coding region of a new HIV type 1 subtype A strain (HIV-1IbNg) from Nigeria. AIDS Res Hum Retroviruses 10:1755–1757 Carr JK, Torimiro JN, Wolfe ND, Eitel MN, Kim B, Sanders-Buell E, Jagodzinski LL, Gotte D, Burke DS, Birx DL, McCutchan FE (2001) The AG recombinant IbNG and novel strains of group M HIV-1 are common in Cameroon. Virology 286:168–181 Kurbanov F, Kondo M, Tanaka Y et al (2003) Human immunodeficiency virus in Uzbekistan: epidemiological and genetic analyses. AIDS Res Hum Retroviruses 19:731–738 Eyzaguirre L, Erasilova I, Nadai Y et al (2007) Genetic characterization of HIV-1 strains circulating in Kazakhstan. J Acquir Immune Defic Syndr 46(1):19–23 Bobkov A, Kazennova E, Selimova L et al (2004) Temporal trends in the HIV-1 epidemic in Russia: predominance of subtype A. J Med Virol 74:191–196 Thomson M., Vázquez de Parga E., Vinogradova A. et al. (2007) New insights into the origin of the HIV type 1 subtype A epidemic in Former Soviet Union’s countries derived from sequence analyses of preepidemically transmitted viruses. AIDS Res Hum Retroviruses 23(12): 1599–1604 Gashnikova NM, Safronov PF, Nikonorova YV, Unagaeva NV, Lapteva TA, Bogachev VV, Baryshev PB, Totmenin AV, Bukin EK, Bocharov EF, Chernousova NIa, Stavskiĭ EA (2011) Properties of CRF02_AG HIV-1 isolates circulating in Novosibirsk region. Zh Mikrobiol Epidemiol Immunobiol 3:38–43 Nadai Y, Eyzaguirre LM, Constantine NT, Sill AM, Cleghorn F, et al. (2008) Protocol for Nearly Full-Length Sequencing of HIV-1 RNA from Plasma. PLoS ONE 3(1):e1420 A Hall T (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98 Schultz A-K, Zhang M, Bulla I, Leitner T, Korber B, Morgenstern B, Stanke M (2009) jpHMM: Improving the reliability of recombination prediction in HIV-1. Nucleic Acids Res 37:W647–W651 Schultz A-K, Zhang M, Leitner T, Kuiken C, Korber B, Morgenstern B, Stanke M (2006) A jumping profile hidden Markov model and applications to recombination sites in HIV and HCV genomes. BMC Bioinformatics 7:265 Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC (1999) Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination. J Virol 73(1):152–160 Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59(3):307–321 Carr J, Nadai Y, Eyzaguirre L et al (2005) Outbreak of a West African recombinant of HIV-1 in Tashkent, Uzbekistan. J Acquir Immune Defic Syndr 39(5):570–575 Kalish M, Robbins K, Pieniazek D, Schaefer A, Nzilambi N, Quinn T, Louis M, Youngpairoj A, Phillips J, Jaffe H, Folks T (2004) Recombinant viruses and early global HIV-1 epidemic. Emerg Infect Dis 10(7):1227–1234 Luk KC, Holzmayer V, Yamaguchi J, Swanson P, Brennan CA, Ngansop C, Mbanya D, Gayum H, Djuidje MN, Ndembi N, Kamdem D, Kaptuer L, GuЁ rtler L, Devare SG, Hackett J, (2007) Near full-length genome characterization of three additional HIV Type 1 CRF13_cpx strains from Cameroon. AIDS Res Hum Retroviruses 23(2):297–392 Niama FR, Toure-Kane C, Vidal N, Obengui P, Bikandou B, Ndoundou Nkodia MY, Montavon C, Diop-Ndiaye H, Mombouli JV, Mokondzimobe E, Diallo AG, Delaporte E, Parra HJ, Peeters M, Mboup S (2006) HIV-1 subtypes and recombinants in the Republic of Congo. Infect Genet Evol 6(5):337–343 Roudinskii NI, Sukhanova AL, Kazennova EV, Weber JN, Pokrovsky VV, Mikhailovich VM, Bobkov AF (2004) Diversity of human immunodeficiency virus type 1 subtype A and CRF03_AB protease in Eastern Europe: selection of the V77I variant and its rapid spread in injecting drug user populations. J Virol 78(20):11276–11287 Bobkov A, Cheingsong-Popov R, Selimova L, Ladnaya N, Kazennova E, Kravchenko A, Fedotov E, Saukhat S, Zverev S, Pokrovsky V, Weber J (1997) An HIV type 1 epidemic among injecting drug users in the former Soviet Union caused by a homogeneous subtype A strain. AIDS Res Hum Retroviruses 13(14):1195–1201 Russia 2010 Country Progress Report. http://www.unaids.org/en/dataanalysis/monitoringcountryprogress/2010progressreportssubmittedbycountries/russia_2010_country_progress_report_en.pdf Viktor Ivanov (2011) Consolidation of Russia’s and Europe’ efforts against global drug flows. http://fskn.gov.ru/includes/periodics/mainnews_gakeng/2011/0822/213215906/detail.shtml