Analysis of HIV-1 BF pr/rt recombinant strains from Rio de Janeiro/Brazil reveals multiple unrelated mosaic structures

Infection, Genetics and Evolution

Volumn 10, Issue 7, 2010, Pages 1094-1100

  Guimarães, Monick Lindenmeyer ^a   Couto Fernandez, José Carlos ^a   Eyer Silva, Walter de Araujo ^a   Teixeira, Sylvia Lopes Maia ^a   Chequer Fernandez, Saada Lima ^a   Morgado, Mariza Gonçalves ^a  

^a INSTITUTO OSWALDO CRUZ   (Brazil)

Author keywords

Brazil; CRF_BF1; HIV 1; Recombination; URF_BF1

Indexed keywords

INTEGRASE; PROTEINASE; RNA DIRECTED DNA POLYMERASE; VIRUS ENVELOPE PROTEIN;

ARTICLE; BRAZIL; CONTROLLED STUDY; GENE SEQUENCE; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR PHYLOGENY; MOSAICISM; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; VIRUS RECOMBINANT; VIRUS RECOMBINATION; VIRUS STRAIN;

BAYES THEOREM; BRAZIL; DNA, VIRAL; EVOLUTION, MOLECULAR; GENOME, VIRAL; HIV INFECTIONS; HIV-1; HUMANS; PHYLOGENY; REASSORTANT VIRUSES;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 77956266716     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2010.07.001     Document Type: Article

References (44)

1. Barreto C.C., Nishyia A., Araujo L.V., Ferreira J.E., Busch M.P., Sabino E.C. Trends in antiretroviral drug resistance and clade distributions among HIV-1--infected blood donors in Sao Paulo, Brazil. J. Acquir. Immune Defic. Syndr. 2006, 41:338-341.
2. Bello G., Eyer-Silva W.A., Couto-Fernandez J.C., Guimaraes M.L., Chequer-Fernandez S.L., Teixeira S.L., Morgado M.G. Demographic history of HIV-1 subtypes B and F in Brazil. Infect. Genet. Evol. 2007, 7:263-270.
3. Bello G., Guimaraes M.L., Morgado M.G. Evolutionary history of HIV-1 subtype B and F infections in Brazil. AIDS 2006, 20:763-768.
4. Brennan C.A., Brites C., Bodelle P., Golden A., Hackett J., Holzmayer V., Swanson P., Vallari A., Yamaguchi J., Devare S., Pedroso C., Ramos A., Badaro R. HIV-1 strains identified in Brazilian blood donors: significant prevalence of B/F1 recombinants. AIDS Res. Hum. Retroviruses 2007, 23:1434-1441.
5. Brindeiro R.M., Diaz R.S., Sabino E.C., Morgado M.G., Pires I.L., Brigido L., Dantas M.C., Barreira D., Teixeira P.R., Tanuri A. Brazilian network for HIV drug resistance surveillance (HIV-BResNet): a survey of chronically infected individuals. AIDS 2003, 17:1063-1069.
6. Cabral V.P., Cunha C.B., Magalhaes E.F., Pinto-Neto L.F., Couto-Fernandez J.C., Dietze R., Morgado M.G., Ribeiro-Rodrigues R. Human immunodeficiency virus type-1 subtypes of infected patients in Espirito Santo, Brazil. Mem. Inst. Oswaldo Cruz 2006, 101:881-885.
7. Cardoso L.P., Queiroz B.B., Stefani M.M. HIV-1 pol phylogenetic diversity and antiretroviral resistance mutations in treatment naive patients from Central West Brazil. J. Clin. Virol. 2009, 46:134-139.
8. Cardoso L.P., Stefani M.M. High level of multidrug resistance mutations in HIV type 1 pol gene and resistance-associated mutations to enfuvirtide (T-20) among antiretroviral-experienced patients from central Brazil. AIDS Res. Hum. Retroviruses 2009, 25:943-950.
9. Cavalcanti A.M., Lacerda H.R., Brito A.M., Pereira S., Medeiros D., Oliveira S. Antiretroviral resistance in individuals presenting therapeutic failure and subtypes of the human immunodeficiency virus type 1 in the Northeast Region of Brazil. Mem. Inst. Oswaldo Cruz 2007, 102:785-792.
10. Couto-Fernandez J.C., Silva-de-Jesus C., Veloso V.G., Rachid M., Gracie R.S., Chequer-Fernandez S.L., Oliveira S.M., Arakaki-Sanchez D., Chequer P.J., Morgado M.G. Human immunodeficiency virus type 1 (HIV-1) genotyping in Rio de Janeiro. Brazil: assessing subtype and drug-resistance associated mutations in HIV-1 infected individuals failing highly active antiretroviral therapy. Mem. Inst. Oswaldo Cruz 2005, 100:73-78.
11. de Sa-Filho D.J., Soares Mda S., Candido V., Gagliani L.H., Cavaliere E., Diaz R.S., Caseiro M.M. HIV type 1 pol gene diversity and antiretroviral drug resistance mutations in Santos, Brazil. AIDS Res. Hum. Retroviruses 2008, 24:347-353.
12. De Sá Filho D.J., Sucupira M.C., Caseiro M.M., Sabino E.C., Diaz R.S., Janini L.M. Identification of two HIV type 1 circulating recombinant forms in Brazil. AIDS Res. Hum. Retroviruses 2006, 22:1-13.
13. de Souza A.C., de Oliveira C.M., Rodrigues C.L., Silva S.A., Levi J.E. Short communication: molecular characterization of HIV type 1 BF pol recombinants from Sao Paulo, Brazil. AIDS Res. Hum. Retroviruses 2008, 24:1521-1525.
14. Dilernia D.A., Gomez A.M., Lourtau L., Marone R., Losso M.H., Salomón H., Gómez-Carrillo M. HIV type 1 genetic diversity surveillance among newly diagnosed individuals from 2003 to 2005 in Buenos Aires, Argentina. AIDS Res. Hum. Retroviruses 2007, 23:1201-1207.
15. Eyer-Silva W.A., Bello G., Morgado M.G. Molecular evidence that human immunodeficiency virus type 1 dissemination in a small Brazilian city was already taking place in the early 1990s. Mem. Inst. Oswaldo Cruz 2007, 102:647-649.
16. Eyer-Silva W.A., Couto-Fernandez J.C., Morgado M.G. Molecular epidemiology of HIV type 1 in inner Rio De Janeiro State, Brazil. AIDS Res. Hum. Retroviruses 2007, 23:303-308.
17. Gonsalez C.R., Alcalde R., Nishiya A., Barreto C.C., Silva F.E., de Almeida A., Mendonca M., Ferreira F., Fernandes S.S., Casseb J., Duarte A.J. Drug resistance among chronic HIV-1-infected patients naive for use of anti-retroviral therapy in Sao Paulo city. Virus Res. 2007, 129:87-90.
18. Guimarães M.L., dos Santos Moreira A., Loureiro R., Galvao-Castro B., Morgado M.G. High frequency of recombinant genomes in HIV type 1 samples from Brazilian southeastern and southern regions. AIDS Res. Hum. Retroviruses 2002, 18:1261-1269.
19. Guimarães M.L., Eyer-Silva W.A., Couto-Fernandez J.C., Morgado M.G. Identification of two new CRF_BF in Rio de Janeiro State, Brazil. AIDS 2008, 22:433-435.
20. Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006, 23:254-267.
21. Magiorkinis G., Paraskevis D., Vandamme A.M., Magiorkinis E., Sypsa V., Hatzakis A. In vivo characteristics of human immunodeficiency virus type 1 intersubtype recombination: determination of hot spots and correlation with sequence similarity. J. Gen. Virol. 2003, 84:2715-2722.
22. Maia Teixeira S.L., Bastos F.I., Hacker M.A., Guimaraes M.L., Morgado M.G. Trends in drug resistance mutations in antiretroviral-naive intravenous drug users of Rio de Janeiro. J. Med. Virol. 2006, 78:764-769.
23. McCutchan F.E. Understanding the genetic diversity of HIV-1. AIDS 2000, 14(Suppl. 3):S31-44.
24. Morgado M.G., Sabino E.C., Shpaer E.G., Bongertz V., Brigido L., Guimaraes M.D., Castilho E.A., Galvao-Castro B., Mullins J.I., Hendry R.M., et al. V3 region polymorphisms in HIV-1 from Brazil: prevalence of subtype B strains divergent from North American/European prototype and detection of subtype F. AIDS Res. Hum. Retroviruses 1994, 10:569-576.
25. Passaes C.P., Bello G., Lorete R.S., Matos Almeida S.E., Junqueira D.M., Veloso V.G., Morgado M.G., Guimaraes M.L. Genetic characterization of HIV-1 BC recombinants and evolutionary history of the CRF31_BC in Southern Brazil. Infect. Genet. Evol. 2009, 9:474-482.
26. Quarleri J.F., Rubio A., Carobene M., Turk G., Vignoles M., Harrigan R.P., Montaner J.S., Salomon H., Gomez-Carrillo M. HIV type 1 BF recombinant strains exhibit different pol gene mosaic patterns: descriptive analysis from 284 patients under treatment failure. AIDS Res. Hum. Retroviruses 2004, 20:1100-1107.
27. Rios M., Delgado E., Perez-Alvarez L., Fernandez J., Galvez P., de Parga E.V., Yung V., Thomson M.M., Najera R. Antiretroviral drug resistance and phylogenetic diversity of HIV-1 in Chile. J. Med. Virol. 2007, 79:647-656.
28. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
29. Ruchansky D., Casado C., Russi J.C., Arbiza J.R., Lopez-Galindez C. Identification of a new HIV Type 1 circulating recombinant form (CRF38_BF1) in Uruguay. AIDS Res. Hum. Retroviruses 2009, 25:351-356.
30. Sá-Ferreira J.A., Brindeiro P.A., Chequer-Fernandez S., Tanuri A., Morgado M.G. Human immunodeficiency virus-1 subtypes and antiretroviral drug resistance profiles among drug-naïve Brazilian blood donors. Transfusion 2007, 47:97-102.
31. Sa Filho D.J., Sanabani S., Diaz R.S., Munerato P., Brunstein A., Fusuma E., Sabino E.C., Janini L.M. Analysis of full-length human immunodeficiency virus type 1 genome reveals a variable spectrum of subtypes B and f recombinants in Sao Paulo, Brazil. AIDS Res. Hum. Retroviruses 2005, 21:145-151.
32. Sabino E.C., Shpaer E.G., Morgado M.G., Korber B.T., Diaz R.S., Bongertz V., Cavalcante S., Galvao-Castro B., Mullins J.I., Mayer A. 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.
33. Salminen M.O., Carr J.K., Burke D.S., McCutchan F.E. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res. Hum. Retroviruses 1995, 11:1423-1425.
34. Sierra M., Thomson M.M., Rios M., Casado G., Castro R.O., Delgado E., Echevarria G., Munoz M., Colomina J., Carmona R., Vega Y., Parga E.V., Medrano L., Perez-Alvarez L., Contreras G., Najera R. The analysis of near full-length genome sequences of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Chile. Venezuela and Spain reveals their relationship to diverse lineages of recombinant viruses related to CRF12_BF. Infect. Genet. Evol. 2005, 5:209-217.
35. Stefani M.M.A., Pereira G.A.S., Lins J.A.B., Alcantara K.C., Silveira A.A., Viegas A.A., Maya N.C., Mussi A.H. Molecular screening shows extensive HIV-1 genetic diversity in Central West Brazil. J. Clin. Virol. 2007, 39:205-209.
36. Swofford, D.L., 2003. PAUP: phylogenetic analysis using parsimony (M and other methods), version 4.0b 10. Sinauer Associates, Sunderland, MA.
37. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
38. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Some Mathematical Questions in Biology-DNA Sequence Analysis 1986, 57-86. American Mathematical Society, Providence (RI). R.M. Miura (Ed.).
39. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882.
40. Thomson M.M., Najera R. Molecular epidemiology of HIV-1 variants in the global AIDS pandemic: an update. AIDS Rev. 2005, 7:210-224.
41. Thomson M.M., Sierra M., Tanuri A., May S., Casado G., Manjon N., Najera R. 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.
42. Veras N.M., Veras V.S., Ramalho E.D., Kyaw C., Silva R.R., Brigido M.M., Martins C.R. HIV type 1 genetic variability in central Brazil. AIDS Res. Hum. Retroviruses 2007, 23:1481-1490.
43. Vicente A.C., Otsuki K., Silva N.B., Castilho M.C., Barros F.S., Pieniazek D., Hu D., Rayfield M.A., Bretas G., Tanuri A. The HIV epidemic in the Amazon Basin is driven by prototypic and recombinant HIV-1 subtypes B and F. J. Acquir. Immune Defic. Syndr. 2000, 23:327-331.
44. Waleria-Aleixo A., Martins A.N., Arruda M.B., Brindeiro R.M., Da-Silva R.M., Nobre F.F., Greco D.B., Tanuri A. Drug resistance mutation profile and accumulation kinetics in human immunodeficiency virus-positive individuals infected with subtypes B and F failing highly active antiretroviral therapy are influenced by different viral codon usage patterns. Antimicrob. Agents Chemother. 2008, 52:4497-4502.