Characterization of Partial and Near Full-Length Genomes of HIV-1 Strains Sampled from Recently Infected Individuals in Sao Paulo, Brazil

Imagem de Miniatura
Arquivos
art_SANABANI_Characterization_of_Partial_and_Near_FullLength_Genomes_of_2011.PDF (1013.35 KB)
Citações na Scopus
31
Tipo de produção
article
Data de publicação
2011
Editora
PUBLIC LIBRARY SCIENCE
DOI
Indexadores
Scopus
Web of Science
PubMed
Título da Revista
ISSN da Revista
Título do Volume
Autores
PASTENA, Evelyn Regina de Souza
MARTINEZ, Vanessa Pouza
KLEINE-NETO, Walter
SAUER, Mariana Melillo
BASSICHETTO, Katia Cristina
OLIVEIRA, Solange Maria Santos
TOMIYAMA, Helena Tomoko Iwashita
Autor de Grupo de pesquisa
Editores
Coordenadores
Organizadores
Citação
PLOS ONE, v.6, n.10, article ID e25869, 11p, 2011
Projetos de Pesquisa
Unidades Organizacionais
Fascículo
Resumo
Background: Genetic variability is a major feature of human immunodeficiency virus type 1 (HIV-1) and is considered the key factor frustrating efforts to halt the HIV epidemic. A proper understanding of HIV-1 genomic diversity is a fundamental prerequisite for proper epidemiology, genetic diagnosis, and successful drugs and vaccines design. Here, we report on the partial and near full-length genomic (NFLG) variability of HIV-1 isolates from a well-characterized cohort of recently infected patients in Sao Paul, Brazil. Methodology: HIV-1 proviral DNA was extracted from the peripheral blood mononuclear cells of 113 participants. The NFLG and partial fragments were determined by overlapping nested PCR and direct sequencing. The data were phylogenetically analyzed. Results: Of the 113 samples (90.3% male; median age 31 years; 79.6% homosexual men) studied, 77 (68.1%) NFLGs and 32 (29.3%) partial fragments were successfully subtyped. Of the successfully subtyped sequences, 88 (80.7%) were subtype B sequences, 12 (11%) BF1 recombinants, 3 (2.8%) subtype C sequences, 2 (1.8%) BC recombinants and subclade F1 each, 1 (0.9%) CRF02 AG, and 1 (0.9%) CRF31 BC. Primary drug resistance mutations were observed in 14/101 (13.9%) of samples, with 5.9% being resistant to protease inhibitors and nucleoside reverse transcriptase inhibitors (NRTI) and 4.9% resistant to non-NRTIs. Predictions of viral tropism were determined for 86 individuals. X4 or X4 dual or mixed-tropic viruses (X4/DM) were seen in 26 (30.2%) of subjects. The proportion of X4 viruses in homosexuals was detected in 19/69 (27.5%). Conclusions: Our results confirm the existence of various HIV-1 subtypes circulating in Sao Paulo, and indicate that subtype B account for the majority of infections. Antiretroviral (ARV) drug resistance is relatively common among recently infected patients. The proportion of X4 viruses in homosexuals was significantly higher than the proportion seen in other study populations.
Palavras-chave
URI
https://observatorio.fm.usp.br/handle/OPI/23084
Referências
  1. Thompson JD, 1997, NUCLEIC ACIDS RES, V25, P4876, DOI 10.1093/nar/25.24.4876
  2. Gao F, 1998, J VIROL, V72, P5680
  3. Brennan CA, 2006, J MED VIROL, V78, pS24, DOI 10.1002/jmv.20603
  4. de Mendoza C, 2007, J ANTIMICROB CHEMOTH, V59, P698, DOI 10.1093/jac/dkm012
  5. Brindeiro RM, 2003, AIDS, V17, P1063, DOI 10.1097/01.aids.0000060345.12269.d7
  6. Schultz AK, 2006, BMC BIOINFORMATICS, V7, DOI 10.1186/1471-2105-7-265
  7. Nye TMW, 2006, BIOINFORMATICS, V22, P117, DOI 10.1093/bioinformatics/bti720
  8. Raymond S, 2008, AIDS, V22, pF11, DOI 10.1097/QAD.0b013e32830ebcd4
  9. Soares EAJM, 2003, JAIDS-J ACQ IMM DEF, V34, P520, DOI 10.1097/00126334-200312150-00012
  10. Plantier JC, 2009, NAT MED, V15, P871, DOI 10.1038/nm.2016
  11. Kuiken C, 2000, AM J EPIDEMIOL, V152, P814, DOI 10.1093/aje/152.9.814
  12. Carr JK, 2001, AIDS, V15, pF41, DOI 10.1097/00002030-200110190-00002
  13. Mansky LM, 1996, VIROLOGY, V222, P391, DOI 10.1006/viro.1996.0436
  14. Pilcher CD, 2004, J CLIN INVEST, V113, P937, DOI 10.1172/JCI200421540
  15. SALMINEN MO, 1995, AIDS RES HUM RETROV, V11, P1423, DOI 10.1089/aid.1995.11.1423
  16. Bello G, 2007, INFECT GENET EVOL, V7, P263, DOI 10.1016/j.meegid.2006.11.002
  17. ROBERTSON DL, 1995, J MOL EVOL, V40, P249, DOI 10.1007/BF00163230
  18. Anisimova M, 2006, SYST BIOL, V55, P539, DOI 10.1080/10635150600755453
  19. Zhong P, 2007, AIDS RES HUM RETROV, V23, P847, DOI 10.1089/aid.2006.0196
  20. Perelson AS, 1996, SCIENCE, V271, P1582, DOI 10.1126/science.271.5255.1582
  21. Soares EAJM, 2005, AIDS, V19, pS81, DOI 10.1097/01.aids.0000191497.00928.e4
  22. Robertson DL, 2000, SCIENCE, V288, P55
  23. Brown BK, 2005, J VIROL, V79, P6089, DOI 10.1128/JVI.79.10.6089-6101.2005
  24. Essex M, 1999, ADV VIRUS RES, V53, P71, DOI 10.1016/S0065-3527(08)60343-7
  25. Eshleman SH, 2007, AIDS, V21, P1165, DOI 10.1097/QAD.0b013e32810fd72e
  26. Lole KS, 1999, J VIROL, V73, P152
  27. Frange P, 2009, J ANTIMICROB CHEMOTH, V64, P135, DOI 10.1093/jac/dkp151
  28. Koopman JS, 1997, J ACQ IMMUN DEF SYND, V14, P249
  29. Brumme ZL, 2005, J INFECT DIS, V192, P466, DOI 10.1086/431519
  30. Batista MD, 2009, PLOS ONE, V4, DOI 10.1371/journal.pone.0005613
  31. Brennan CA, 2007, AIDS RES HUM RETROV, V23, P1434, DOI 10.1089/aid.2007.0121
  32. Brigido LFM, 2005, AIDS RES HUM RETROV, V21, P673, DOI 10.1089/aid.2005.21.673
  33. Chueca N, 2009, J MED VIROL, V81, P763, DOI 10.1002/jmv.21425
  34. Cohen OJ, 1998, NEW ENGL J MED, V339, P341, DOI 10.1056/NEJM199807303390511
  35. de Castro CAV, 2010, BMC INFECT DIS, V10, DOI 10.1186/1471-2334-10-224
  36. de Souza ACMF, 2008, AIDS RES HUM RETROV, V24, P1521, DOI 10.1089/aid.2008.0089
  37. Fernandez-Garcia A, 2009, AIDS RES HUM RETROV, V25, P93, DOI 10.1089/aid.2008.0174
  38. Hall T.A., 1999, NUCL ACIDS S SER, V41, P95, DOI 10.1111/J.1469-8137.2009.02874.X
  39. Han MV, 2009, BMC BIOINFORMATICS, V10, DOI 10.1186/1471-2105-10-356
  40. Hunt PW, 2006, J INFECT DIS, V194, P926, DOI 10.1086/507312
  41. Kandathil AJ, 2005, INDIAN J MED RES, V121, P333
  42. Kato S, 2003, AIDS RES HUM RETROV, V19, P1057, DOI 10.1089/088922203322588431
  43. Lehmann C, 2006, J CLIN VIROL, V37, P300, DOI 10.1016/j.jcv.2006.08.008
  44. McGovern RA, 2010, AIDS, V24, P2512, DOI 10.1097/QAD.0b013e32833e6cfb
  45. Nicastri E, 2003, J MED VIROL, V69, P1, DOI 10.1002/jmv.10269
  46. Passaes CPB, 2009, AIDS RES HUM RETROV, V25, P1339, DOI 10.1089/aid.2009.0167
  47. Sa-Ferreira JA, 2007, TRANSFUSION, V47, P97, DOI 10.1111/j.1537-2995.2007.01069.x
  48. Cavalcanti Ana Maria Salustiano, 2007, Mem Inst Oswaldo Cruz, V102, P785, DOI 10.1590/S0074-02762007005000109
  49. Sanabani S, 2006, INFECT GENET EVOL, V6, P368, DOI 10.1016/j.meegid.2006.01.003
  50. Sanabani S, 2006, AIDS RES HUM RETROV, V22, P171, DOI 10.1089/aid.2006.22.171
  51. Sanabani SS, 2009, VIROL J, V6, DOI 10.1186/1743-422X-6-78
  52. Saracino A, 2009, J MED VIROL, V81, P2036, DOI 10.1002/jmv.21598
  53. Skrabal K, 2007, J CLIN MICROBIOL, V45, P279, DOI 10.1128/JCM.01118-06
  54. Stefani MMA, 2007, J CLIN VIROL, V39, P205, DOI 10.1016/j.jcv.2007.04.012
  55. Worobey M, 2001, MOL BIOL EVOL, V18, P254

Coleções
Artigos e Materiais de Revistas Científicas - FM/MIP
Artigos e Materiais de Revistas Científicas - FM/MCM
Artigos e Materiais de Revistas Científicas - HC/ICHC
Artigos e Materiais de Revistas Científicas - LIM/03
Artigos e Materiais de Revistas Científicas - LIM/52
Artigos e Materiais de Revistas Científicas - LIM/60