Enhanced detection of viral diversity using partial and near full-length genomes of human immunodeficiency virus Type 1 provirus deep sequencing data from recently infected donors at four blood centers in Brazil

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art_PESSOA_Enhanced_detection_of_viral_diversity_using_partial_and_2015.PDF (443.17 KB)
Citações na Scopus
12
Tipo de produção
article
Data de publicação
2015
DOI
Scopus
Web of Science
PubMed
Título da Revista
ISSN da Revista
Título do Volume
Editora
WILEY-BLACKWELL
Autores
CALABRIA, Paula
LOUREIRO, Paula
LOPES, Maria Esther
PROETTI, Anna Barbara
BUSCH, Michael P.
Citação
TRANSFUSION, v.55, n.5, p.980-990, 2015
Projetos de Pesquisa
Unidades Organizacionais
Fascículo
Resumo
BackgroundHere, we report application of high-throughput near full-length genome (NFLG) and partial human immunodeficiency virus Type 1 (HIV-1) proviral genome deep sequencing to characterize HIV in recently infected blood donors at four major blood centers in Brazil. Study Design and MethodsFrom 2007 to 2011, a total of 341 HIV+ blood donors from four blood centers were recruited to participate in a case-control study to identify HIV risk factors and motivations to donate. Forty-seven (17 from SAo Paulo, eight from Minas Gerais, 11 from Pernambuco, and 11 from Rio de Janeiro) were classified as recently infected based on testing by less-sensitive enzyme immunoassays. Five overlapping amplicons spanning the HIV genome were polymerase chain reaction amplified from peripheral blood mononuclear cells. The amplicons were molecularly barcoded, pooled, and sequenced by a paired-end protocol (Illumina). ResultsOf the 47 recently infected donor samples studied, 39 (82.9%) NFLGs and six (12.7%) partial fragments were de novo assembled into contiguous sequences and successfully subtyped. Subtype B was the only nonrecombinant virus identified in this study and accounted for 62.2% (28/45) of samples. The remaining 37.8% (17/45) of samples showed various patterns of subtype discordance in different regions of HIV-1 genomes, indicating two to four circulating recombinant subtypes derived from Clades B, F, and C. Fourteen samples (31.1%) from this study harbored drug resistance mutations, indicating higher rate of drug resistance among Brazilian blood donors. ConclusionOur findings revealed a high proportion of HIV-1 recombinants among recently infected blood donors in Brazil, which has implications for future blood screening, diagnosis, therapy, and vaccine development.
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https://observatorio.fm.usp.br/handle/OPI/9789
Referências
  1. Alencar CS, 2013, JAIDS-J ACQ IMM DEF, V63, P387, DOI 10.1097/QAI.0b013e31828ff979
  2. Arien KK, 2007, NAT REV MICROBIOL, V5, P141, DOI 10.1038/nrmicro1594
  3. Bansode V, 2013, BMC INFECT DIS, V13, DOI 10.1186/1471-2334-13-52
  4. Bello G, 2007, INFECT GENET EVOL, V7, P263, DOI 10.1016/j.meegid.2006.11.002
  5. Blackard JT, 2004, SEX TRANSM DIS, V31, P201, DOI 10.1097/01.OLQ.0000118082.45312.1F
  6. Bon I, 2007, NEW MICROBIOL, V30, P313
  7. Brennan CA, 2007, AIDS RES HUM RETROV, V23, P1434, DOI 10.1089/aid.2007.0121
  8. Carr JK, 2001, AIDS, V15, pF41, DOI 10.1097/00002030-200110190-00002
  9. Cohen OJ, 1998, NEW ENGL J MED, V339, P341, DOI 10.1056/NEJM199807303390511
  10. desAlmeida-Neto C, 2013, VOX SANG, V105, P91
  11. desCastro CA, 2010, BMC INFECT DIS, V10, P224
  12. DIAZ RS, 1995, J VIROL, V69, P3273
  13. Ferreira AS, 2011, J MED VIROL, V83, P1301, DOI 10.1002/jmv.22128
  14. Gao F, 1999, NATURE, V397, P436, DOI 10.1038/17130
  15. Guindon S, 2010, SYST BIOL, V59, P307, DOI 10.1093/sysbio/syq010
  16. Gunthard HF, 1998, AIDS RES HUM RETROV, V14, P869, DOI 10.1089/aid.1998.14.869
  17. Huson DH, 2006, MOL BIOL EVOL, V23, P254, DOI 10.1093/molbev/msj030
  18. Jakobsen MR, 2010, CLIN INFECT DIS, V50, P566, DOI 10.1086/650001
  19. Katoh K, 2002, NUCLEIC ACIDS RES, V30, P3059, DOI 10.1093/nar/gkf436
  20. Lole KS, 1999, J VIROL, V73, P152
  21. Niama FR, 2009, AIDS RES HUM RETROV, V25, P1345, DOI 10.1089/aid.2009.0169
  22. Nye TMW, 2006, BIOINFORMATICS, V22, P117, DOI 10.1093/bioinformatics/bti720
  23. Perelson AS, 1996, SCIENCE, V271, P1582, DOI 10.1126/science.271.5255.1582
  24. Pessoa R, 2014, GENOME ANNOUNC, V2
  25. Pessoa R, 2014, GENOME ANNOUNC, V2
  26. Pessoa R, 2014, PLOS ONE, V9, DOI 10.1371/journal.pone.0093374
  27. Pilotto JH, 2013, AIDS RES HUM RETROV, V29, P681, DOI [10.1089/AID.2011.0333, 10.1089/aid.2011.0333]
  28. Plantier JC, 2009, NAT MED, V15, P871, DOI 10.1038/nm.2016
  29. Quail MA, 2012, BMC GENOMICS, V13, DOI 10.1186/1471-2164-13-341
  30. Ramos A, 1999, EMERG INFECT DIS, V5, P65
  31. Rawal BD, 2003, JAIDS-J ACQ IMM DEF, V33, P349
  32. Robertson DL, 2000, SCIENCE, V288, P55
  33. Sabino EC, 2012, TRANSFUSION, V52, P870, DOI 10.1111/j.1537-2995.2011.03344.x
  34. SALMINEN MO, 1995, AIDS RES HUM RETROV, V11, P1423, DOI 10.1089/aid.1995.11.1423
  35. Cavalcanti Ana Maria Salustiano, 2007, Mem Inst Oswaldo Cruz, V102, P785, DOI 10.1590/S0074-02762007005000109
  36. Sanabani S, 2006, INFECT GENET EVOL, V6, P368, DOI 10.1016/j.meegid.2006.01.003
  37. Sanabani S, 2006, AIDS RES HUM RETROV, V22, P171, DOI 10.1089/aid.2006.22.171
  38. Sanabani SS, 2011, PLOS ONE, V6, DOI 10.1371/journal.pone.0025869
  39. Sanabani SS, 2009, VIROL J, V6, DOI 10.1186/1743-422X-6-78
  40. Sanabani SS, 2013, PLOS ONE, V8, DOI 10.1371/journal.pone.0062552
  41. Schultz AK, 2006, BMC BIOINFORMATICS, V7, DOI 10.1186/1471-2105-7-265
  42. Shafer RW, 2007, AIDS, V21, P215, DOI 10.1097/QAD.0b013e328011e691
  43. de Oliveira ACS, 2012, VIROL J, V9, DOI 10.1186/1743-422X-9-223
  44. Soares EAJM, 2003, JAIDS-J ACQ IMM DEF, V34, P520, DOI 10.1097/00126334-200312150-00012
  45. Soares EAJM, 2005, AIDS, V19, pS81, DOI 10.1097/01.aids.0000191497.00928.e4
  46. Stefani MMA, 2007, J CLIN VIROL, V39, P205, DOI 10.1016/j.jcv.2007.04.012
  47. Sucupira MCA, 2007, AIDS PATIENT CARE ST, V21, P116, DOI 10.1089/apc.2006.0079
  48. Tebit DM, 2007, AIDS REV, V9, P75
  49. Thomson MM, 2002, LANCET INFECT DIS, V2, P461, DOI 10.1016/S1473-3099(02)00343-2
  50. Van Laethem K, 1999, J ACQ IMMUN DEF SYND, V22, P107
  51. Worobey M, 2001, MOL BIOL EVOL, V18, P254

Coleções
Artigos e Materiais de Revistas Científicas - FM/MIP
Artigos e Materiais de Revistas Científicas - HC/ICESP
Artigos e Materiais de Revistas Científicas - HC/ICHC
Artigos e Materiais de Revistas Científicas - LIM/03
Artigos e Materiais de Revistas Científicas - LIM/46
Artigos e Materiais de Revistas Científicas - LIM/52
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