Analysis of HIV-1 pol sequences from Panama: Identification of phylogenetic clusters within subtype B and detection of antiretroviral drug resistance mutations

Infection, Genetics and Evolution

Volumn 9, Issue 5, 2009, Pages 933-940

  Ahumada Ruiz, Sara ^a,b   Flores Figueroa, Dario ^c   Toala González, Iván ^c   Thomson, Michael M ^a  

^a INSTITUTO DE SALUD CARLOS III   (Spain)

^b UNIVERSIDAD DE PANAMÁ   (Panama)

^c Departamento de Enfermedades Infecciosas   (Panama)

Author keywords

Antiretroviral drug resistance; HIV 1; Panama; Phylogeny; Subtype B

Indexed keywords

DIDANOSINE; EFAVIRENZ; INDINAVIR; LAMIVUDINE; NELFINAVIR; POL PROTEIN; STAVUDINE; ZIDOVUDINE;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; ANTIVIRAL RESISTANCE; ARTICLE; BAYES THEOREM; CLUSTER ANALYSIS; CONTROLLED STUDY; EPIDEMIC; FEMALE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; MAJOR CLINICAL STUDY; MALE; MOLECULAR PHYLOGENY; NONHUMAN; PANAMA; PRIORITY JOURNAL; SEQUENCE ANALYSIS; VIRUS MUTATION; VIRUS RECOMBINANT; VIRUS TRANSMISSION;

CERCOPITHECINE HERPESVIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 67749120011     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2009.06.013     Document Type: Article

References (37)

1. Ahumada-Ruiz S., Casado C., Toala-González I., Flores-Figueroa D., Rodríguez-French A., and López-Galíndez C. High divergence of HIV-1 subtype B viruses from Panama. AIDS Res. Hum. Retroviruses 24 (2008) 1461-1466
2. Carrión G., Hierholzer J., Montano S., Alava A., Pérez J., Guevara A., Laguna-Torres V., Mosquera C., Russell K., Cruz C., Chauca G., Kochel T., Birx D.L., Sanchez J.L., and Carr J.K. Circulating recombinant form CRF02_AG in South America. AIDS Res. Hum. Retroviruses 19 (2003) 329-332
3. Carr J.K., Ávila M., Gómez Carrillo M., Salomon H., Hierholzer J., Watanaveeradej V., Pando M.A., Negrete M., Russell K.L., Sanchez J., Birx D.L., Andrade R., Vinoles J., and McCutchan F.E. Diverse BF recombinants have spreads widely since the introduction of HIV-1 into South America. AIDS 14 (2001) 41-47
4. Delgado E., León-Ponte M., Villahermosa M.L., Cuevas M.T., Deibis L., Echevarría G., Thomson M., Pérez-Álvarez L., Osmanov S., and Nájera R. Analysis of HIV type 1 protease and reverse transcriptase sequences from Venezuela for drug resistance-associated mutations and subtype classification: a UNAIDS study. AIDS Res. Hum. Retroviruses 17 (2001) 753-758
5. Delgado E., Ampofo W., Sierra M., Torpey K., Pérez-Álvarez L., Bonney E., Mukadi Y., Lartey M., Nyarko C., Amenyah R., Thomson M., and Nájera R. High prevalence of unique recombinant forms of HIV-1 in Ghana: molecular epidemiology from antiretroviral resistance study. J. Acquir. Immune Defic. Syndr. 48 (2008) 599-606
6. Drummond A.J., and Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7 (2007) 214
7. Eyer-Silva W.A., and Morgado M.G. Autochthonous horizontal transmission of a CRF02_AG strain revealed by a human immunodeficiency virus type 1 diversity survey in a small city in inner state of Rio de Janeiro, Southeast Brazil. Mem. Inst. Oswaldo Cruz 102 (2007) 809-815
8. Eyzaguirre L., Bautista C.T., Ayala C., Acosta J., Negrete M., Sateren W., Montano S., Sánchez J., and Carr J. First case of HIV Type 1 subtype F among men who have sex with men in Colombia. AIDS Res. Hum. Retroviruses 22 (2006) 808-811
9. Goudsmit J., De Ronde A., Ho D.D., and Perelson A.S. Human immunodeficiency virus fitness in vivo: calculations based on a single zidovudine resistance mutation at codon 215 of reverse transcriptase. J. Virol. 70 (1996) 5662-5664
10. Hué S., Pillay D., Clewley J.P., and Pybus O. 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
11. Huelsenbeck J.P., and Ronquist F. Bioinformatics 17 (2001) 754-755
12. Kijak G., and McCutchan F. HIV diversity, molecular epidemiology, and the role of recombination. Curr. Inf. Dis. Rep. 7 (2005) 480-488
13. Kumar S., Tamura K., and Nei M. MEGA 3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5 (2004) 150-163
14. Lama J., Sanchez J., Suarez L., Caballero P., Laguna A., Sánchez J., Whittington W., Celum C., Grant R., and for the Peruvian HIV sentinel surveillance working group. Linking HIV and antiretroviral drug resistance surveillance in Peru: a model for a third generation HIV sentinel surveillance. J. Acquir. Immune Defic. Syndr. 42 (2006) 501-505
15. Lole K.S., Bollinger R.C., Paranjape R.S., Gadkaeri D., Kulkarni S.S., Novak N.G., Ingersoll R., Sheppard H.W., and Ray S.C. Full length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 73 (1999) 152-160
16. Los Alamos HIV Sequence Database. Available at: http://hiv-web.lanl.gov.
17. Lloyd B., O'Conell R., Michael N., Aviles R., Palou E., Hernández R., Cooley J., and Jagodzinski L. Prevalence of resistance mutations in HIV-1 infected Hondurans at the beginning of the national antiretroviral therapy program. AIDS Res. Hum. Retroviruses 24 (2008) 529-535
18. Meloni S.T., Kim B., Sankalé J.L., Hamel D., Tovanabutra S., Mboup S., McCutchan F., and Kanki P. Distinct human immunodeficiency virus type 1 subtype A virus circulating in West Africa: sub-subtype A3. J. Virol. 78 (2004) 12438-12445
19. Ministry of Health, STD/HIV/AIDS National Program, 2002. Guide to Care for People Living with HIV and AIDS. Panama.
20. Ministry of Health, National Program on HIV and AIDS, and UNAIDS, 2008. National Report on the Progress Made in the Implementation of UNGASS-Panama. Available at: http://data.unaids.org/pub/Report/2008/panama_2008_country_progress_repo rt_sp_es.pdf.
21. Nájera R., Delgado E., Pérez-Álvarez L., and Thomson M. Genetic recombination and its role in the development of the HIV-1 pandemic. AIDS 16 Suppl. 4 (2002) S3-S16
22. Pérez L., Thomson M., Bleda M., Aragonés C., González Z., Pérez J., Sierra M., Casado G., Delgado E., and Nájera R. HIV type 1 molecular epidemiology in Cuba: high genetic diversity, frequent mosaicism, and recent expansion of BG intersubtype recombinants form. AIDS Res. Hum. Retroviruses 22 (2006) 724-733
23. Pérez L., Pérez-Álvarez L., Carmona R., Aragonés C., Delgado E., Thomson M., González Z., Contreras G., Pérez J., and Nájera R. Genotypic resistance to antiretroviral drugs in patients infected with several HIV type 1 genetic forms in Cuba. AIDS Res. Hum. Retroviruses 23 (2007) 407-414
24. Pires I., Soares M., Speranza F., Ishii S., Vieira M., Gouvea M., Guimaraes M., Oliveira F., Magnanini M., Brindeiro R., and Tanuri A. Prevalence of human immunodeficiency virus drug resistance mutations and subtypes in drug-naïve, infected individuals in the army health service of Rio de Janeiro, Brazil. J. Clin. Microbiol. 42 (2004) 426-430
25. Rhee S.Y., Gonzales M.J., Kantor R., Betts B.J., Ravela J., and Shafer R.W. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucl. Acids Res. 31 (2003) 298-303
26. Ríos M., Delgado E., Pérez-Álvarez A., Fernández J., Gálvez P., Vázquez de Parga E., Yung V., Thomson M., and Nájera R. Antiretroviral drug resistance and phylogenetic diversity of HIV-1 in Chile. J. Med. Virol. 79 (2007) 647-656
27. Rivera-Morales L.G., Novitsky V.A., Trujillo J.R., Lavalle-Montalvo C., Cano-Domínguez C., Ramos-Jiménez J., Jiménez-Ríos E., Flores-Flores L., López-Guillén P., Gilbert P., Vannberg F., Tamez-Guerra R., Rodríguez-Padilla C., and Essex M. The molecular epidemiology of HIV Type-1 of men in Mexico. AIDS Res. Hum. Retroviruses 17 (2001) 87-92
28. Teixeira S., Bastos F., Hacker M., Lindenmeyer Guimaraes M., and Gonclaves Morgado M. Trends in drug resistance mutations in antiretroviral-naïve intravenous drugs users of Rio de Janeiro. J. Med. Virol. 78 (2006) 764-769
29. Thomson M., and Nájera R. Travel and the introduction of human immunodeficiency virus type 1 non-B subtype genetics forms into western countries. Clin. Infect. Dis. 32 (2001) 1732-1737
30. Thomson M., and Nájera R. Molecular epidemiology of HIV-1 variants in the global AIDS pandemic: an update. AIDS Rev. 7 (2005) 210-224
31. Thomson M., Villahermosa M.L., Vázquez de Parga E., Cuevas M.T., Delgado E., Manjón N., Medrano L., Pérez-Álvarez L., Contreras G., Carrillo M.G., Salomón H., and Nájera R. Widespread circulation of a B/F intersubtype recombinant form among HIV-1 infected individuals in Buenos Aires, Argentina. AIDS 14 (2000) 897-899
32. Thomson M., Pérez-Álvarez L., and Nájera R. Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy. Lancet Infect. Dis. 2 (2002) 461-471
33. Thomson M., Delgado E., Herrero I., Villahermosa M.L., Vázquez de Parga E., Cuevas M.T., Carmona R., Medrano L., Pérez-Álvarez L., Cuevas L., and Nájera R. 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. 83 (2002) 107-119
34. Thomson M., Vinogradova A., Delgado E., Rakhmanova A., Yakovlev A., Cuevas M.T., Muñoz M., Pinilla M., Vega Y., Pérez-Álvarez L., Osmanov S., and Nájera R. Molecular epidemiology of HIV-1 in St. Petersburg, Russia: predominance of subtype A, former Soviet Union variant, and identification of intrasubtype subclusters. J. Acquir. Immune Defic. Syndr. 51 (2009) 332-339
35. UNAIDS, 2009. AIDS Epidemic Update. Available at: http://www.unaids.org/en/CountryResponses/Countries/default.asp.
36. Vasehus Madsen T., Lohse N., Stilling Jensen E., Obel N., Ladefoged K., Gerstoft J., Petersen A., Nielsen A., and Jorgensen L. High prevalence of drug resistant human immunodeficiency virus type 1 in treatment naïve patients in Greenland. AIDS Res. Hum. Retroviruses 24 (2008) 1073-1077
37. Villahermosa M.L., Thomson M., Vázquez de Parga E., Cuevas M.T., Contreras G., Pérez-Álvarez L., Delgado E., Manjón N., Medrano L., and Nájera R. Improved conditions for extraction and amplification of human immunodeficiency virus type 1 RNA from plasma samples with low viral load. J. Hum. Virol. 3 (2000) 27-34