Variability in HIV-1 partial genomic sequences in Costa Rican patients: Analysis with different bioinformatics tools

Revista Panamericana de Salud Publica/Pan American Journal of Public Health

Volumn 27, Issue 1, 2010, Pages 23-31

  Taylor Castillo, Lizeth ^a   León Bratti, María Paz ^a   Solano Chinchilla, Antonio ^b   Herrera Martínez, Gisela ^b   Boza Cordero, Ricardo ^a   León, Bernal ^c   Luftig, Ronald B ^c   Visoná, Kirsten ^c  

^a UNIVERSIDAD DE COSTA RICA   (Costa Rica)

^b Hospital Calderon Guardia   (Costa Rica)

^c Louisiana State University   (Costa Rica)

Author keywords

Costa Rica; Genetic variation; HIV 1; Recombination, genetic; Sequence analysis; Software

Indexed keywords

BIOINFORMATICS; GENETIC VARIATION; GENOMICS; GENOTYPE; HUMAN IMMUNODEFICIENCY VIRUS; PHYLOGENETICS; POLYMORPHISM; RECOMBINATION; SOFTWARE;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 77949349444     PISSN: 10204989     EISSN: 16805348     Source Type: Journal    
DOI: 10.1590/S1020-49892010000100004     Document Type: Article

References (36)

1. United Nations Programme on HIV/AIDS; World Health Organization. 2007 AIDS epidemic update [Internet]. Geneva: UNAIDS; 2007. Available from: http://www.unaids.org/en/KnowledgeCentre/HIVData/EpiUpdate/EpiUpdArchive/2007/ default.asp Accessed 19 April 2008.
2. El Salvador, Ministerio de Salud Pública y Asistencia Social, Programa Nacional de ITS/VIH-sida. Situación del VIH en El Salvador, 1984-2008 [Internet]. El Salvador: Ministerio de Salud Pública y Asistencia Social. Available from: http://www.mspas.gob.sv/pdf/SIDA-DOC/ Situacion-VIH-SIDA-El-Salvador-Abril2009.pdf. Accessed 19 April 2009.
3. Nicaragua, Ministerio de Salud, Biblioteca Nacional de Salud. Documentos a textos completos [HIV/AIDS Full Text Documents] [Internet]. Available from: http://www.minsa.gob.ni/bns/sida/doc.html. Accessed 18 September 2008.
4. Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the use of antiretroviral agents in HIV-1-infected adults and adolescents. Department of Health and Human Services. December 1, 2009; 1-161 [Internet]. Available from: http://aidsinfo.nih.gov/contentfiles/AdultandAdolescentGL.pdf. Accessed April 2008.
5. Wood E, Montaner JSG. When to initiate HIV antiretroviral therapy: do benefits other than survival deserve greater attention? J Acquir Immune Defic Syndr. 2007;45:131-2.
6. Iglesias-Sánchez MJ, López-Galíndez C. Each genomic RNA in HIV-1 heterozygous virus generates new virions. Virology. 2005;333: 316-23.
7. Holguín A, Lospitao E, López M, de Arellano ER, Pena MJ, del Romero J, et al. Genetic characterization of complex inter-recombinant HIV-1 strains circulating in Spain and reliability of distinct rapid subtyping tools. J Med Virol. 2008;80:383-91.
8. Schroeder TL, Burger H, Weiser B, Bengualid V, Kimani J, Anzala AO, et al. Characterization of intersubtype recombinant HIV type 1 genomes using a nonradioactive heteroduplex tracking assay. AIDS Res Hum Retroviruses. 2005;21:314-8.
9. Casado G, Thomson MM, Sierra M, Nájera R. Identification of a novel HIV-1 circulating ADG intersubtype recombinant form (CRF19-cpx) in Cuba. J Acquir Immune Defic Syndr. 2005;40:532-7.
10. Grant RM, Kuritzkes DR, Johnson VA, Mellors JW, Sullivan JL, Swanstrom R, et al. Accuracy of TRUGENE HIV-1 genotyping kit. J Clin Microbiol. 2003;41:1586-93.
11. Hirigoyen DL, Cartwrigth CP. Use of sequence data generated in the Bayer TruGene genotyping assay to recognize and characterize non-subtype-B human immunodeficiency virus type1 strains. J Clin Microbiol. 2005;43: 5263-71.
12. Taylor-Castillo L, Herrera-Martínez G, León-Bratti MP, Boza R, León-Rodríguez B, Luftig RB, et al. Study of antiretroviral mutants in HIV patients with treatment failures and the effect of risk factors in the virological failures. Rev Inst Med Trop Sao Paulo. 2005;47:327-31.
13. Cuevas MT, Ruibal I, Villahermosa MT, Díaz H, Delgado T, Vázquez de Parga E, et al. High HIV-1 genetic diversity in Cuba. AIDS. 2002; 16:1643-53.
14. Posada D. Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol Biol Evol. 2002;19:708-17.
15. Rozanov M, Plikat U, Chappey C, Kochergin A, Tatusosa T. A web-based genotyping resource for viral sequences. Nucleic Acids Res. 2004;32:654-9.
16. Eyer-Silva W, Morgado MG. Molecular epidemiology of HIV-1 infection in small Brazilian county usefulness of envelope and polymerase sequences to epidemiologic studies. J Acquir Immune Defic Syndr. 2006;41:664-70.
17. Levy DN, Adrovandi GM, Kutsh O, Shaw GM. Dynamics of HIV-1 recombination in its natural target cells. Proc Natl Acad Sci. 2004; 101:4204-9.
18. Bacharov G, Ford NJ, Edwards J, Breining T, Wain-Jobson S, Meyerhans A. A geneticalgorithm approach to simulating human immunodeficiency virus evolution reveals the strong impact of multiply infected cells and recombination. J Gen Virol. 2005;86:3109-18.
19. Aulicino PC, Kopra J, Rocco C, Mangano A, Sen L. Sequence analysis of a South American HIV type 1 BC recombinant. AIDS Res Hum Retroviruses. 2005;21:894-6.
20. Chin MPS, Rhodes TD, Chen J, Fu W, Hu W-Sh. Identification of a major restriction in HIV-1 intersubtype recombination. Proc Natl Acad Sci. 2005;102:9002-7.
21. HIV sequence database. The circulating recombinant form (CRFs) [Internet]. Available from: http://www.hiv.lanl.gov/content/sequence/HIV/CRFs/ CRFs.html. Accessed 15 July 2009.
22. Couto-Fernandez JC, Silva-de-Jesus C, Veloso VG, Rachid M, Gracie RSG, Chequer-Fernandez SL, et al. 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 mailing highly active antiretroviral therapy. Mem Inst Oswaldo Cruz. 2005;100: 73-8.
23. Thomson MM, Delgado E, Herrero I, Villahermosa RL, Vazquez de Parga E, Cuevas MT, et al. Diversity of mosaic structures and common ancestry of human immunodeficiency virus type 1BF intersubtypes recombinant viruses from Argentina revealed by analysis of near full-length genome sequences. J Gen Virol. 2002;83:107-19.
24. NCBI genotyping tool [Internet]. Available from: http://www.ncbi.nlm.nih. gov/projects/genotyping/formpage.cgi. Accessed 18 September 2008.
25. de Oliveira T, Deforche K, Cassol S, Salminen M, Paraskevis D, Sebregts C, et al. An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics. 2005;21:3797-800.
26. Stanford University HIV drug resistance database [Internet]. Available from: http://hivdb.stanford.edu/Accessed 19 April 2008.
27. HIV sequence databases. Recombinant Identification Program (RIP 3.0) [Internet]. Available from: http://www.hiv.lanl.gov/content/sequence/RIP/RIP. html. Accessed 17 July 2009.
28. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95-8.
29. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596-9. Available from: http://www.kumarlab.net/publications.
30. HIV sequence database. PhyML interface [Internet]. Available from: http://www.hiv.lanl.gov/content/sequence/PHYML/interface.html Accessed 17 July 2009.
31. Hoekstra CE, Riedijk M, Matute AJ, Hak E, Delgado E, Alonso RE, et al. Prevalence of HIV and syphilis in pregnant women in León, Nicaragua. Am J Trop Med Hyg. 2006;75:522-5.
32. Lara C, Sällberg M, Johansson B, de Rivera IL, Sönnerborg A. The Honduran human immunodeficiency virus type 1 (HIV-1) epidemic is dominated by HIV-1 subtype B as determined by V3 domain sero- and genotyping. J Clin Microbiol. 1997;35:783-4.
33. Keiffer TL, Finucane MM, Nettles RE, Quinn TC, Bromann KW, Ray SC, et al. Genotypic analysis of HIV-1 drug resistance at the limit of detection: virus production without evolution in treated adults with undetectable HIV loads. J Infect Dis. 2004;189:1452-65.
34. Ying L, Eran E, Ivet B. Sequence analysis. Analysis of correlated mutations in HIV-1 protease using spectral clustering. Bioinformatics. 2008;24:1243-50.
35. Freedberg K, Hirschhorn L, Schackman B, Wolf LL, Martin LA, Weinstein MC, et al. Cost-effectiveness of an intervention to improve adherence to antiretroviral therapy in HIV-infected patients. J Acquir Immune Defic Syndr. 2006;43:S113-8.
36. Gordon ChM. Commentary on meta-analysis of randomized controlled trials for HIV treatment adherence interventions research directions and implications for practice. J Acquir Immune Defic Syndr. 2006;43:S36-40.