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

Archives of Virology

Volumn 157, Issue 12, 2012, Pages 2335-2341

  Baryshev, P B ^a   Bogachev, V V ^a   Gashnikova, N M ^a  

^a STATE RESEARCH CENTER OF VIROLOGY AND BIOTECHNOLOGY VECTOR   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; EPIDEMIC; GENETIC REASSORTMENT; GENETIC VARIABILITY; GENETICS; GENOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MALE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; RISK FACTOR; RUSSIAN FEDERATION; UZBEKISTAN; VIROLOGY; VIRUS GENOME;

ADULT; BASE SEQUENCE; EPIDEMICS; GENETIC VARIATION; GENOME, VIRAL; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; MALE; MOLECULAR SEQUENCE DATA; PHYLOGENY; REASSORTANT VIRUSES; RISK FACTORS; SIBERIA; UZBEKISTAN;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84870294141     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-012-1442-4     Document Type: Article

References (30)

1. Temin HM (1993) Retrovirus variation and reverse transcription: abnormal strand transfers result in retrovirus genetic variation. Proc Natl Acad Sci USA 90: 6900-6903.
2. Hu WS, Temin HM (1990) Retroviral recombination and reverse transcription. Science 250: 1227-1233.
3. 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.
4. 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.
5. Peeters M, Sharp PM (2000) Genetic diversity of HIV-1: the moving target. AIDS 14(Suppl 3): S129-S140.
6. 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.
7. 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.
8. McCutchan FE (2000) Understanding the genetic diversity of HIV-1. AIDS 14(Suppl 3): S31-S44.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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.
16. Gashnikova NM, Safronov PF, Nikonorova YV, Unagaeva NV, Lapteva TA, Bogachev VV, Baryshev PB, Totmenin AV, Bukin EK, Bocharov EF, Chernousova NIa, Stavskiǐ EA (2011) Properties of CRF02_AG HIV-1 isolates circulating in Novosibirsk region. Zh Mikrobiol Epidemiol Immunobiol 3: 38-43.
17. 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.
18. 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.
19. 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.
20. 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.
21. 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.
22. 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.
23. 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.
24. 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.
25. Luk KC, Holzmayer V, Yamaguchi J, Swanson P, Brennan CA, Ngansop C, Mbanya D, Gayum H, Djuidje MN, Ndembi N, Kamdem D, Kaptuer L, GuIo{cyrillic} 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.
26. 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.
27. 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.
28. 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.
29. Russia 2010 Country Progress Report. http://www. unaids. org/en/dataanalysis/monitoringcountryprogress/2010progressreportssubmittedbycountries/russia_2010_country_progress_report_en. pdf.
30. 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.