Genetic characterization of HIV-1 BC recombinants and evolutionary history of the CRF31_BC in Southern Brazil

Infection, Genetics and Evolution

Volumn 9, Issue 4, 2009, Pages 474-482

  Passaes, Caroline Pereira Bittencourt ^a   Bello, Gonzalo ^a   Lorete, Roberta S ^a   Matos Almeida, Sabrina E ^b   Junqueira, Dennis Maletich ^b   Veloso, Valdilea G ^c   Morgado, Mariza G ^a   Guimarães, Monick Lindenmeyer ^a  

^a INSTITUTO OSWALDO CRUZ   (Brazil)

^b Fundacao Estadual de Producao   (Brazil)

^c Funda??o Oswaldo Cruz   (Brazil)

Author keywords

Brazil; CRF31_BC; Evolutionary history; HIV 1; Second generation recombinants; Subtype C

Indexed keywords

INTEGRASE;

ARTICLE; BAYES THEOREM; CONTROLLED STUDY; GENE FREQUENCY; GENE LOCATION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC RECOMBINATION; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS; VIRAL GENETICS; VIRUS ISOLATION; VIRUS RECOMBINATION; VIRUS STRAIN;

BASE SEQUENCE; BAYES THEOREM; BRAZIL; EVOLUTION, MOLECULAR; HIV ENVELOPE PROTEIN GP120; HIV ENVELOPE PROTEIN GP41; HIV INFECTIONS; HIV-1; HUMANS; MARKOV CHAINS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; POL GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; RECOMBINATION, GENETIC; SEQUENCE ALIGNMENT;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 68649096601     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2009.01.008     Document Type: Article

References (49)

1. Bello G., Eyer-Silva W.A., Couto-Fernandez J.C., Guimaraes M.L., Chequer-Fernandez S.L., Teixeira S.L., and Morgado M.G. Demographic history of HIV-1 subtypes B and F in Brazil. Infect. Genet. Evol. 7 (2007) 263-270
2. Bello G., Guimaraes M.L., and Morgado M.G. Evolutionary history of HIV-1 subtype B and F infections in Brazil. AIDS 20 (2006) 763-768
3. Bello G., Passaes C.P., Guimaraes M.L., Lorete R.S., Matos Almeida S.E., Medeiros R.M., Alencastro P.R., and Morgado M.G. Origin and evolutionary history of HIV-1 subtype C in Brazil. AIDS 22 (2008) 1993-2000
4. Bongertz V., Bou-Habib D.C., Brigido L.F., Caseiro M., Chequer P.J., Couto-Fernandez J.C., Ferreira P.C., Galvao-Castro B., Greco D., Guimaraes M.L., Linhares de Carvalho M.I., Morgado M.G., Oliveira C.A., Osmanov S., Ramos C.A., Rossini M., Sabino E., Tanuri A., and Ueda M. 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. 23 (2000) 184-193
5. Brigido L.F., Franco H.M., Custodio R.M., Oliveira C.A., Eira J.L.P.F.M., Bergel F., Araujo F., Carvalheiro J.R., and Rodrigues R. Molecular characteristics of HIV type 1 circulating in Sao Paulo, Brazil. AIDS Res. Hum. Retroviruses 21 (2005) 673-682
6. Brigido L.F., Nunes C.C., Oliveira C.M., Knoll R.K., Ferreira J.L., Freitas C.A., Alves M.A., Dias C., and Rodrigues R. HIV type 1 subtype C and CB Pol recombinants prevail at the cities with the highest AIDS prevalence rate in Brazil. AIDS Res. Hum. Retroviruses 23 (2007) 1579-1586
7. 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., and Tanuri A. Brazilian Network for HIV Drug Resistance Surveillance (HIV-BResNet): a survey of chronically infected individuals. AIDS 17 (2003) 1063-1069
8. Cabral V.P., Cunha C.B., Magalhaes E.F., Pinto-Neto L.F., Couto-Fernandez J.C., Dietze R., Morgado M.G., and Ribeiro-Rodrigues R. Human immunodeficiency virus type-1 subtypes of infected patients in Espirito Santo, Brazil. Mem. Inst. Oswaldo Cruz. 101 (2006) 881-885
9. Cavalcanti A.M., Lacerda H.R., Brito A.M., Pereira S., Medeiros D., and 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. 102 (2007) 785-792
10. Chin M.P., Chen J., Nikolaitchik O.A., and Hu W.S. Molecular determinants of HIV-1 intersubtype recombination potential. Virology 363 (2007) 437-446
11. Chin M.P., Lee S.K., Chen J., Nikolaitchik O.A., Powell D.A., Fivash Jr. M.J., and Hu W.S. Long-range recombination gradient between HIV-1 subtypes B and C variants caused by sequence differences in the dimerization initiation signal region. J. Mol. Biol. 377 (2008) 1324-1333
12. Chin M.P., Rhodes T.D., Chen J., Fu W., and Hu W.S. Identification of a major restriction in HIV-1 intersubtype recombination. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 9002-9007
13. Couto-Fernandez J.C., Morgado M.G., Bongertz V., Tanuri A., Andrade T., Brites C., and Galvao-Castro B. HIV-1 subtyping in Salvador, Bahia, Brazil: a city with African sociodemographic characteristics. J. Acquir. Immune Defic. Syndr. 22 (1999) 288-293
14. de Medeiros L.B., Lacerda H.R., Cavalcanti A.M., and de Albuquerque Mde F. Primary resistance of human immunodeficiency virus type 1 in a reference center in Recife, Pernambuco, Brazil. Mem. Inst. Oswaldo Cruz. 101 (2006) 845-849
15. De Sa Filho D.J., Sucupira M.C., Casiero M.M., Sabino E.C., Diaz R.S., and Janini L.M. Identification of two HIV type 1 circulating recombinant forms in Brazil. AIDS Res. Hum. Retroviruses 22 (2006) 1-13
16. Drummond A.J., Ho S.Y., Phillips M.J., and Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4 (2006) e88
17. Drummond A.J., Nicholls G.K., Rodrigo A.G., and Solomon W. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161 (2002) 1307-1320
18. Drummond A.J., and Rambaut A. BEAST: bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7 (2007) 214
19. Drummond A.J., Rambaut A., Shapiro B., and Pybus O.G. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22 (2005) 1185-1192
20. Gadelha S.R., Shindo N., Cruz J.N., Morgado M.G., and Galvao-Castro B. Molecular epidemiology of human immunodeficiency virus-1 in the state of Ceara, Northeast, Brazil. Mem. Inst. Oswaldo Cruz. 98 (2003) 461-463
21. Guimaraes M.L., dos Santos Moreira A., Loureiro R., Galvao-Castro B., and Morgado M.G. High frequency of recombinant genomes in HIV type 1 samples from Brazilian southeastern and southern regions. AIDS Res. Hum. Retroviruses 18 (2002) 1261-1269
22. Guimaraes M.L., Eyer-Silva W.A., Couto-Fernandez J.C., and Morgado M.G. Identification of two new CRF_BF in Rio de Janeiro State, Brazil. AIDS 22 (2008) 433-435
23. Hasegawa M., Kishino H., and Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22 (1985) 160-174
24. Hue S., Pillay D., Clewley J.P., and Pybus O.G. Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 4425-4429
25. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16 (1980) 111-120
26. Locateli D., Stoco P.H., de Queiroz A.T., Alcantara L.C., Ferreira L.G., Zanetti C.R., Rodrigues R., Grisard E.C., and Pinto A.R. Molecular epidemiology of HIV-1 in Santa Catarina State confirms increases of subtype C in Southern Brazil. J. Med. Virol. 79 (2007) 1455-1463
27. Magiorkinis G., Paraskevis D., Vandamme A.M., Magiorkinis E., Sypsa V., and 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. 84 (2003) 2715-2722
28. Paraskevis D., Magiorkinis E., Magiorkinis G., Sypsa V., Paparizos V., Lazanas M., Gargalianos P., Antoniadou A., Panos G., Chrysos G., Sambatakou H., Karafoulidou A., Skoutelis A., Kordossis T., Koratzanis G., Theodoridou M., Daikos G.L., Nikolopoulos G., Pybus O.G., and Hatzakis A. Increasing prevalence of HIV-1 subtype A in Greece: estimating epidemic history and origin. J. Infect. Dis. 196 (2007) 1167-1176
29. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
30. Rambaut A., Drummond A, 2007. Tracer v1.4. Available from http://beast.bio.ed.ac.uk/Tracer.
31. Ramos A., Tanuri A., Schechter M., Rayfield M.A., Hu D.J., Cabral M.C., Bandea C.I., Baggs J., and Pieniazek D. Dual and recombinant infections: an integral part of the HIV-1 epidemic in Brazil. Emerg. Infect. Dis. 5 (1999) 65-74
32. Ray S., 2009. Simplot v3.5.1. Available from: http://www.med.jhu.edu/deptmed/sray/download/.
33. Ronquist F., and Huelsenbeck J.P. MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
34. Sa Filho D.J., Sanabani S., Diaz R.S., Munerato P., Brunstein A., Fusuma E., Sabino E.C., and 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 21 (2005) 145-151
35. Salemi M., de Oliveira T., Ciccozzi M., Rezza G., and Goodenow M.M. High-Resolution Molecular Epidemiology and Evolutionary History of HIV-1 Subtypes in Albania. PLoS ONE 3 (2008) e1390
36. Sanabani S., Neto W.K., Kalmar E.M., Diaz R.S., Janini L.M., and Sabino E.C. Analysis of the near full length genomes of HIV-1 subtypes B, F and BF recombinant from a cohort of 14 patients in Sao Paulo, Brazil. Infect. Genet. Evol. (2006)
37. Santos A.F., Schrago C.G., Martinez A.M., Mendoza-Sassi R., Silveira J., Sousa T.M., Lengruber R.B., Soares E.A., Sprinz E., and Soares M.A. Epidemiologic and evolutionary trends of HIV-1 CRF31_BC-related strains in southern Brazil. J. Acquir. Immune Defic. Syndr. 45 (2007) 328-333
38. Santos A.F., Sousa T.M., Soares E.A., Sanabani S., Martinez A.M., Sprinz E., Silveira J., Sabino E.C., Tanuri A., and Soares M.A. Characterization of a new circulating recombinant form comprising HIV-1 subtypes C and B in southern Brazil. AIDS 20 (2006) 2011-2019
39. 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., and 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. 5 (2005) 209-217
40. Soares E.A., Santos R.P., Pellegrini J.A., Sprinz E., Tanuri A., and Soares M.A. Epidemiologic and molecular characterization of human immunodeficiency virus type 1 in southern Brazil. J. Acquir. Immune Defic. Syndr. 34 (2003) 520-526
41. Soares M.A., De Oliveira T., Brindeiro R.M., Diaz R.S., Sabino E.C., Brigido L., Pires I.L., Morgado M.G., Dantas M.C., Barreira D., Teixeira P.R., Cassol S., and Tanuri A. A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil. AIDS 17 (2003) 11-21
42. Stefani M.M., Pereira G.A., Martelli C.M., Shindo N., and Galvao-Castro B. Evidence of HIV-1 genetic diversity among pregnant women with AIDS or infected with HIV-1 in Central Brazil. J. Acquir. Immune Defic. Syndr. 23 (2000) 205-207
43. Suchard M.A., Weiss R.E., and Sinsheimer J.S. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 18 (2001) 1001-1013
44. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. In: Miura R.M. (Ed). Some Mathematical Questions in Biology-DNA Sequence Analysis (1986), American Mathematical Society, Providence (RI) 57-86
45. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
46. Thomson M.M., Sierra M., Tanuri A., May S., Casado G., Manjon N., and 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 20 (2004) 1126-1133
47. Veras N.M., Veras V.S., Ramalho E.D., Kyaw C., Silva R.R., Brigido M.M., and Martins C.R. HIV type 1 genetic variability in central Brazil. AIDS Res. Hum. Retroviruses 23 (2007) 1481-1490
48. Vicente A.C., Otsuki K., Silva N.B., Castilho M.C., Barros F.S., Pieniazek D., Hu D., Rayfield M.A., Bretas G., and 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. 23 (2000) 327-331
49. Xia X., and Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 92 (2001) 371-373