Molecular epidemiology of HIV-1 infection in a small Brazilian county: Usefulness of envelope and polymerase sequences to epidemiologic studies

Journal of Acquired Immune Deficiency Syndromes

Volumn 41, Issue 5, 2006, Pages 664-670

  Eyer Silva, Walter A ^a,b,c   Morgado, Mariza G ^a  

^a INSTITUTO OSWALDO CRUZ   (Brazil)

^b HOSPITAL UNIVERSITÁRIO GAFFRÉE E GUINLE   (Brazil)

^c Programa Municipal de HIV/Aids de Miracema   (Brazil)

Author keywords

Brazil; HIV 1; Molecular epidemiology; Pol gene; Small counties; Transmission networks

Indexed keywords

ACQUIRED IMMUNODEFICIENCY SYNDROME; ADOLESCENT; ADULT; BRAZIL; CD4 LYMPHOCYTE COUNT; COHORT STUDIES; EPIDEMIOLOGY, MOLECULAR; HIV INFECTIONS; HIV-1; HUMANS; MIDDLE AGED; PHYLOGENY;

EID: 33646796019     PISSN: 15254135     EISSN: None     Source Type: Journal    
DOI: 10.1097/01.qai.0000194736.66322.02     Document Type: Article

References (35)

1. Szwarcwald CL, Bastos FI, Esteves MA, et al. The spread of the AIDS epidemic in Brazil from 1987 to 1996: a spatial analysis. Cad Saude Publica. 2000;16:7-19.
2. Kuiken C, Thakallapalli R, Esklid A, et al. Genetic analysis reveals epidemiologic patterns in the spread of human immunodeficiency virus. Am J Epidemiol. 2000;152:814-822.
3. Albert J, Wahlberg J, Leitner T, et al. Analysis of a rape case by direct sequencing of the human immunodeficiency virus type 1 pol and gag genes. J Virol. 1994;68:5918-5924.
4. Ou CY, Ciesielski CA, Myers G, et al. Molecular epidemiology of HIV transmission in a dental practice. Science. 1992;256:1165-1171.
5. Leitner T, Escanilla D, Franzen C, et al. Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis. Proc Natl Acad Sci USA. 1996;93:10864-10869.
6. Yu XF, Liu W, Chen J, et al. Rapid dissemination of a novel B/C recombinant HIV-1 among injection drug users in southern China. AIDS. 2001;15:523-525.
7. Ou CY, Takebe Y, Weniger BG, et al. Independent introduction of two major HIV-1 genotypes into distinct high-risk populations in Thailand. Lancet. 1993;341:1171-1174.
8. Oelrichs RB, Shrestha IL, Anderson DA, et al. The explosive human immunodeficiency virus type 1 epidemic among injecting drug users of Kathmandu, Nepal, is caused by a subtype C virus of restricted genetic diversity. J Virol. 2000;74:1149-1157.
9. Nguyen L, Hu DJ, Choopanya K, et al. Genetic analysis of incident HIV-1 strains among injection drug users in Bangkok: evidence for multiple transmission clusters during a period of high incidence. J Acquir Immune Defic Syndr. 2002;30:248-256.
10. Vidal N, Peeters M, Mulanga-Kabeya C, et al. Unprecedented degree of human immunodeficiency virus type 1 (HIV-1) group M genetic diversity in the Democratic Republic of Congo suggests that the HIV-1 pandemic originated in Central Africa. J Virol. 2000;74:10498-10507.
11. Trask SA, Derdeyn CA, Fideli U, et al. Molecular epidemiology of human immunodeficiency virus type 1 transmission in a heterosexual cohort of discordant couples in Zambia. J Virol. 2002;76:397-405.
12. Eyer-Silva WA, Basílio-de-Oliveira CA, Morgado MG. HIV-1 infection and AIDS in a small municipality in Southeast Brazil. Rev Saude Publica. 2005;39:950-955.
13. Instituto Brasileiro de Geografia e Estatística (IBGE). Censo Demográfico de 2000. IBGE, 2001, Rio de Janiero, Brazil.
14. Centers for Disease Control and Prevention. 1993 Revised classification system for HIV infection and expanded surveillance case definition for AIDS among adolescents and adults. MMWR Recomm Rep. 1992;41:961-962.
15. Burland TG. DNASTAR's Lasergene sequence analysis software. Methods Mol Biol. 2000;132:71-91.
16. Thompson JD, Gibson TJ, Plewniak F, et al. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25:4876-4882.
17. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406-425.
18. PAUP*: Phylogenetic analysis using parsimony (*and other methods) [computer program]. Version 4.0b10. Saunderland, MA: Sinauer Associates; 1999.
19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39:783-791.
20. Salminen MO, Carr JK, Burke DS, et al. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res Hum Retroviruses. 1995;11:1423-1425.
21. Felsenstein J. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am J Hum Genet. 1973;25:471-492.
22. Brindeiro PA, Brindeiro RM, Mortensen C, et al. Testing genotypic and phenotypic resistance in human immunodeficiency virus type 1 isolates of clade B and other clades from children failing antiretroviral therapy. J Clin Microbiol. 2002;40:4512-4519.
23. Posada D, Crandall KA. MODELTEST: testing the model of DNA substitution. Bioinformatics. 1998;14:817-818.
24. Xia X, Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J Hered. 2001;92:371-373.
25. Ihaka R, Gentleman RR. A language for data analysis and graphics. J Comput Graph Stat. 1996;5:299-314.
26. Posada D, Crandall KA. Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1). Mol Biol Evol. 2001;18:897-906.
27. Goujon CP, Schneider VM, Grofti J, et al. Phylogenetic analyses indicate an atypical nurse-to-patient transmission of human immunodeficiency virus type 1. J Virol. 2000;74:2525-2532.
28. Metzker ML, Mindell DP, Liu XM, et al. Molecular evidence of HIV-1 transmission in a criminal case. Proc Natl Acad Sci USA. 2002;99:14292-14297.
29. Hue S, Clewley JP, Cane PA, et al. HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy. AIDS. 2004;18:719-728.
30. Palmer S, Vuitton D, Gonzales MJ, et al. Reverse transcriptase and protease sequence evolution in two HIV-1-infected couples. J Acquir Immune Defic Syndr. 2002;31:285-290.
31. Sturmer M, Preiser W, Gute P, et al. Phylogenetic analysis of HIV-1 transmission: pol gene sequences are insufficient to clarify true relationships between patient isolates. AIDS. 2004;18:2109-2113.
32. Jenwitheesuk E, Liu T. Single phylogenetic reconstruction method is insufficient to clarify relationships between patient isolates in HIV-1 transmission case. AIDS. 2005;19:743-744.
33. Lemey P, Derdelinckx I, Rambaut A, et al. Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain. J Virol. 2005;79:11981-11989.
34. Song JZ, Wang B, Ge YC, et al. Significance of plasma and peripheral blood mononuclear cell derived HIV-1 sequences in establishing epidemiologic linkage between two individuals multiply exposed to HIV-1. Microb Pathog. 1999;26:287-298.
35. Guimaraes ML, dos Santos Moreira A, Loureiro R, et al. High frequency of recombinant genomes in HIV type 1 samples from Brazilian southeastern and southern regions. AIDS Res Hum Retroviruses. 2002;18:1261-1269.