The detection of in vivo and in vitro HIV type 1 B/F profiles in Brazil using a real-time PCR assay for five HIV type 1 genomic regions

AIDS Research and Human Retroviruses

Volumn 26, Issue 9, 2010, Pages 981-990

  Teixeira, Daniela ^a   Munerato, Patricia ^a   Komninakis, Shirley Cavalcante Vasconcelos ^a   Fusuma, Erika Etsuko ^a   Janini, Luiz Mario ^a   Sucupira, Maria Cecilia Araripe ^a   Diaz, Ricardo Sobhie ^a  

^a FEDERAL UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BRAZIL; CIRCULATING RECOMBINANT FORM; GENETIC RECOMBINATION; GENOMICS; GEOGRAPHY; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 B; HUMAN IMMUNODEFICIENCY VIRUS 1 F; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; VIRUS DETECTION; VIRUS STRAIN; CELL LINE; GENETICS; HIV INFECTIONS; HUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; VIRUS GENOME;

VIRUS RNA;

BRAZIL; CELL LINE; GENOME, VIRAL; HIV INFECTIONS; HIV-1; HUMANS; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, VIRAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, RNA;

EID: 77956382944     PISSN: 08892229     EISSN: None     Source Type: Journal    
DOI: 10.1089/aid.2010.0023     Document Type: Article

References (41)

1. Boulerice F, Li XG, Lvovich A, and Wainberg MA: Recovery of infectious human immunodeficiency virus type 1 after fusion of defectively infected clones of U-937 cells. J Virol 1991;65:5589-5592.
2. Temin HM: Sex and recombination in retroviruses. Trends Genet 1991;7:71-74.
3. Diaz RS, Sabino ES, Mayer A, Mosley J, Busch MP, and The Transfusion Safety Study Group: Evidence of dual HIV-1 infection and recombination in a dually-exposed transfused recipient. J Virol 1995;69:3273-3281.
4. Tumas KM, Poszgay JM, Avidan N, Ksiazek SJ, Overmoyer B, Blank KJ, et al.: Loss of antigenic epitopes as the result of env gene recombination in retrovirus-induced leukemia in immunocompetent mice. Virology 1993;192: 587-595.
5. Kellam P and Larder BA: Retroviral recombination can lead to linkage of reverse transcriptase mutations that confer increased zidovudine resistance. J Virol 1995;69:669-674.
6. Moutouh L, Corbeil J, and Richman DD: Recombination leads to the rapid emergence of HIV-1 dually resistant mutants under selective drug pressure. Proc Natl Acad Sci USA 1996;93:6106-6111.
7. Costa LJ, Mayer AJ, Busch MP, and Diaz RS: Evidence for selection of more adapted human immunodeficiency virus type 1 recombinant strains in a dually infected transfusion recipient. Virus Genes 2004;28:259-272.
8. Najera R, Delgado E, Perez-Alvarez L, and Thomson MM: Genetic recombination and its role in the development of the HIV-1 pandemic. AIDS 2002;16(Suppl 4):3-16.
9. McCutchan FE: Understanding the genetic diversity of HIV-1. AIDS 2000;14(Suppl 3):31-44.
10. Carr JK, Salminen MO, Albert J, Sanders-Buell E, Gotte D, Birx DL, et al.: Full genome sequences of human immunodeficiency virus type 1 subtypes G and A/G intersubtype recombinants. Virology 1998;247:22-31.
11. HIV Sequence Database [database online]: Los Alamos National Laboratory HIV Database, 2009 (http://hiv-web .lanl.org). Updated September 10, 2009.
12. De Sa Filho DJ, Sucupira MC, Caseiro MM, Sabino EC, Diaz RS, and Janini LM: Identification of two HIV type 1 circulating recombinant forms in Brazil. AIDS Res Hum Retroviruses 2006;22:1-13.
13. Cohen MS, Hellmann N, Levy JA, Decock K, and Lange J: The spread, treatment, and prevention of HIV-1: Evolution of a global pandemic. J Clin Invest 2008;118:1244-1254.
14. Unaids-Report on the global AIDS epidemic-2007. Available at http://www.unaids.org.
15. Bongertz V, Bou-Habib DC, Brigido LF, Caseiro M, Chequer PJ, Couto-Fernandez JC, et al.: HIV-1 diversity in Brazil: Genetic, biologic, and immunologic characterization of HIV-1 strains in three potential HIV vaccine evaluation sites. Brazilian Network for HIV Isolation and Characterization. J Acquir Immune Defic Syndr 2000;23:184-193.
16. Morgado MG, Guimaraes ML, and alvao-Castro B: HIV-1 polymorphism: A challenge for vaccine development-a review. Mem Inst Oswaldo Cruz 2002;97:143-150.
17. Sabino EC, Shpaer EG, Morgado MG, Korber BT, Diaz RS, Bongertz V, et al.: Identification of human immunodeficiency virus type 1 envelope genes recombinant between subtypes B and F in two epidemiologically linked individuals from Brazil. J Virol 1994;68:6340-6346.
18. Janini LM, Pieniazek D, Peralta JM, Schechter M, Tanuri A, Vicente AC, et al.: Identification of single and dual infections with distinct subtypes of human immunodeficiency virus type 1 by using restriction fragment length polymorphism analysis. Virus Genes 1996;13:69-81.
19. Janini LM, Tanuri A, Schechter M, Peralta JM, Vicente AC, Dela Torre N, et al.: Horizontal and vertical transmission of human immunodeficiency virus type 1 dual infections caused by viruses of subtypes B and C. J Infect Dis 1998; 177:227-231.
20. Guimarães ML, Eyer-Silva WA, Couto-Fernandez JC, and Morgado MG: Identification of two new CRF-BF in Rio de Janeiro State, Brazil. AIDS 2008;22:433-435.
21. Santos AF, Sousa TM, Soares EA, Sanabani S, Martinez AM, Sprinz E, et al.: Characterization of a new circulating recombinant form comprising HIV-1 subtypes C and B in southern Brazil. AIDS 2006;20:2011-2019.
22. Leal E, Janini LM, and Diaz RS: Evolutionary dynamics of HIV-1 BF and CB recombinants and its parental counterparts in South America. Retrovirol Res Treat 2008;1:1-14
23. Sanabani S, Kleine-Neto W, Kalmar EM, Diaz RS, Janini LM, and Sabino EC: Analysis of the near full length genomes of HIV-1 subtype B, F and BF recombinant from a cohort of 14 patients in Sao Paulo, Brazil. Infect Genet Evol 2006;6:368-377.
24. Kozal MJ, Shah N, Shen N, Yang R, Fucini R, Merigan TC, et al.: Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat Med 1996;2:753-759.
25. Lima M: Aná lise de correlação entre eventos de hipermuta̧ão e carga viral em pacientes infectados pelo v́rus da imunodeficiencia humana tipo 1 (HIV-1). Disciplina de Infectologia- Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, 2009, p. 110.
26. Thomson MM, Delgado E, Herrero I, Villahermosa ML, Vázquez-de- Parga E, Cuevas MT, et al.: Diversity of mosaic structures and common ancestry of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Argentina revealed by analysis of near full-length genome sequences. J Gen Virol 2002;83:107-119.
27. Delwart EL, Shpaer EG, Louwagie J, McCutchan FE, Grez M, Rübsamen-Waigmann H, et al.: Genetic relationships determined by a DNA heteroduplex mobility assay: Analysis of HIV-1 env genes. Science 1993;262:1257-1261.
28. Simmonds P, Balfe P, Ludlam CA, Bishop JO, Brown AJ, et al.: Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1. J Virol 1990;64:5840-5850.
29. Saitou N and Nei M: The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406-425.
30. Rodenburg CM, Li Y, Trask SA, Chen Y, Decker J, Robertson DL, et al.: Near full-length clones and reference sequences for subtype C isolates of HIV type 1 from three different continents. AIDS Res Hum Retrovirus 2001;17:161-168.
31. Gao F, Robertson DL, Carruthers CD, Morrison SG, Jian B, Chen Y, et al.: A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1. J Virol 1998;72:5680-5698.
32. Thomson MM, Sierra M, Tanuri A, May S, Casado G, Manjon N, et al.: Analysis of near full-length genome sequences of HIV type 1 BF intersubtype recombinant viruses from Brazil reveals their independent origins and their lack of relationship to CRF12-BF. AIDS Res Hum Retroviruses 2004;20:1126-1133.
33. Costa LJ, Munerato P, Diaz RS, and Tanuri A: Generation of intersubtype human immunodeficiency virus type 1 recombinants in env gene in vitro. Virology 2000;268:440-451.
34. De Sa Filho DJ, Soares MS, Candido V, Gagliani LH, Cavaliere E, Diaz RS, et al.: HIV type 1 pol gene diversity and antiretroviral drug resistance mutations in Santos, Brazil. AIDS Res Hum Retroviruses 2008;24:347-353.
35. Gonzalez LM, Brindeiro RM, Tarin M, Calazans A, Soares MA, Cassol S, et al.: In vitro hypersusceptibility of human immunodeficiency virus type 1 subtype C protease to lopinavir. Antimicrob Agents Chemother 2003;47:2817-2822.
36. Calazans A, Brindeiro R, Brindeiro P, Verli H, Arruda MB, Gonzalez LM, et al.: Low accumulation of L90M in protease from subtype F HIV-1 with resistance to protease inhibitors is caused by the L89M polymorphism. J Infect Dis 2005;191: 1961-1970.
37. Sucupira MC, Caseiro MM, Alves K, Tescarollo G, Janini LM, Sabino EC, et al.: High levels of primary antiretroviral resistance genotypic mutations and B/F recombinants in Santos, Brazil. AIDS Patient Care STDs 2007;21:116-128.
38. Rerks-Ngarm S, Pitisuttithum P, Nitayaphan S, Kaewkungwal J, Chiu J, Paris R, et al.: Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand. N Engl J Med 2009;361:2209-2220.
39. Bibollet-Ruche F, Gao F, Bailes E, Saragosti S, Delaporte E, Peeters M, et al.: Complete genome analysis of one of the earliest SIVcpzPtt strains from Gabon (SIVcpzGAB2). AIDS Res Hum Retrovirus 2004;20:1377-1381.
40. Hierholzer J, Montano S, Hoelscher M, Negrete M, Hierholzer M, Avila MM, et al.: Molecular epidemiology of HIV Type 1 in Ecuador, Peru, Bolivia, Uruguay, and Argentina. AIDS Res Hum Retroviruses 2002;18:1339-1350.
41. Brown BK, Darden JM, Tovanabutra S, Oblander T, Frost J, Sanders-Buell E, et al.: Biologic and genetic characterization of a panel of 60 human immunodeficiency virus type 1 isolates, representing clades A, B, C, D, CRF01-AE, and CRF02-AG, for the development and assessment of candidate vaccines. J Virol 2005;79:6089-6101.