Display options
Cite
Ode H, Matsuda M, Matsuoka K, et al. Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq. Front Microbiol. 2015;6:1258doi: 10.3389/fmicb.2015.01258.
Ode, H., Matsuda, M., Matsuoka, K., Hachiya, A., Hattori, J., Kito, Y., Yokomaku, Y., Iwatani, Y., & Sugiura, W. (2015). Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq. Frontiers in microbiology, 61258. https://doi.org/10.3389/fmicb.2015.01258
Ode, Hirotaka, et al. "Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq." Frontiers in microbiology vol. 6 (2015): 1258. doi: https://doi.org/10.3389/fmicb.2015.01258
Ode H, Matsuda M, Matsuoka K, Hachiya A, Hattori J, Kito Y, Yokomaku Y, Iwatani Y, Sugiura W. Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq. Front Microbiol. 2015 Nov 12;6:1258. doi: 10.3389/fmicb.2015.01258. eCollection 2015. PMID: 26617593; PMCID: PMC4641896.
Copy Download .nbib Format: NLM
Share it on

Front Microbiol. 2015 Nov 12;6:1258. doi: 10.3389/fmicb.2015.01258. eCollection 2015.

Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq.

Frontiers in microbiology

Hirotaka Ode, Masakazu Matsuda, Kazuhiro Matsuoka, Atsuko Hachiya, Junko Hattori, Yumiko Kito, Yoshiyuki Yokomaku, Yasumasa Iwatani, Wataru Sugiura

Affiliations

  1. Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan.
  2. Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan ; Department of AIDS Research, Graduate School of Medicine, Nagoya University Nagoya, Japan.

PMID: 26617593 PMCID: PMC4641896 DOI: 10.3389/fmicb.2015.01258

Abstract

Human immunodeficiency virus type-1 (HIV-1) exhibits high between-host genetic diversity and within-host heterogeneity, recognized as quasispecies. Because HIV-1 quasispecies fluctuate in terms of multiple factors, such as antiretroviral exposure and host immunity, analyzing the HIV-1 genome is critical for selecting effective antiretroviral therapy and understanding within-host viral coevolution mechanisms. Here, to obtain HIV-1 genome sequence information that includes minority variants, we sought to develop a method for evaluating quasispecies throughout the HIV-1 near-full-length genome using the Illumina MiSeq benchtop deep sequencer. To ensure the reliability of minority mutation detection, we applied an analysis method of sequence read mapping onto a consensus sequence derived from de novo assembly followed by iterative mapping and subsequent unique error correction. Deep sequencing analyses of aHIV-1 clone showed that the analysis method reduced erroneous base prevalence below 1% in each sequence position and discarded only < 1% of all collected nucleotides, maximizing the usage of the collected genome sequences. Further, we designed primer sets to amplify the HIV-1 near-full-length genome from clinical plasma samples. Deep sequencing of 92 samples in combination with the primer sets and our analysis method provided sufficient coverage to identify >1%-frequency sequences throughout the genome. When we evaluated sequences of pol genes from 18 treatment-naïve patients' samples, the deep sequencing results were in agreement with Sanger sequencing and identified numerous additional minority mutations. The results suggest that our deep sequencing method would be suitable for identifying within-host viral population dynamics throughout the genome.

Keywords: HIV-1; consensus sequence estimation; deep sequencing; drug resistance; error correction; quasispecies

References

  1. J Acquir Immune Defic Syndr. 2009 Dec;52(5):569-73 - PubMed
  2. Bioinformatics. 2015 Jan 1;31(1):94-101 - PubMed
  3. J Virol. 2008 Apr;82(7):3261-70 - PubMed
  4. BMC Genomics. 2012 Sep 13;13:475 - PubMed
  5. PLoS One. 2009;4(3):e4724 - PubMed
  6. Clin Infect Dis. 2002 Apr 15;34(8):1108-14 - PubMed
  7. Nucleic Acids Res. 1996 Sep 15;24(18):3546-51 - PubMed
  8. Nature. 1995 Mar 9;374(6518):124-6 - PubMed
  9. Top Antivir Med. 2014 Jun-Jul;22(3):642-50 - PubMed
  10. Antiviral Res. 2010 Oct;88(1):72-9 - PubMed
  11. Bioinformatics. 2015 Mar 15;31(6):886-96 - PubMed
  12. Antimicrob Agents Chemother. 2014;58(4):2167-85 - PubMed
  13. Clin Infect Dis. 2010 Feb 15;50(4):566-73 - PubMed
  14. Nat Biotechnol. 2012 May;30(5):434-9 - PubMed
  15. J Clin Microbiol. 2012 Dec;50(12):3838-44 - PubMed
  16. Retrovirology. 2012 Aug 06;9:63 - PubMed
  17. Curr Opin Infect Dis. 2014 Dec;27(6):566-72 - PubMed
  18. Virus Res. 2011 Dec;162(1-2):203-15 - PubMed
  19. J Virol. 1996 Aug;70(8):5572-81 - PubMed
  20. Mol Biol Int. 2012;2012:256982 - PubMed
  21. Science. 1996 Mar 15;271(5255):1582-6 - PubMed
  22. PLoS One. 2010 Oct 22;5(10):e13564 - PubMed
  23. Microb Inform Exp. 2014 Jan 15;4(1):1 - PubMed
  24. J Infect Dis. 2010 Mar;201(5):662-71 - PubMed
  25. AIDS Rev. 2008 Apr-Jun;10(2):67-84 - PubMed
  26. Nucleic Acids Res. 2011 Jul;39(13):e90 - PubMed
  27. Nucleic Acids Res. 2014 Aug;42(14):e115 - PubMed
  28. Bioinformatics. 2010 Mar 1;26(5):589-95 - PubMed
  29. AIDS. 2011 Mar 13;25(5):679-89 - PubMed
  30. J Clin Microbiol. 2005 Jan;43(1):406-13 - PubMed
  31. PLoS One. 2014 Jul 15;9(7):e102633 - PubMed
  32. J Infect Dis. 2010 Apr 1;201(7):1063-71 - PubMed
  33. PLoS One. 2011;6(12):e28952 - PubMed
  34. Nucleic Acids Res. 2013 Jan 7;41(1):e13 - PubMed
  35. AIDS. 2008 Jul 31;22(12):1417-23 - PubMed
  36. Sci Rep. 2013 Oct 03;3:2837 - PubMed
  37. N Engl J Med. 2008 Apr 10;358(15):1590-602 - PubMed
  38. Brief Bioinform. 2014 May;15(3):431-42 - PubMed
  39. PLoS One. 2014 Nov 17;9(11):e112674 - PubMed
  40. PLoS Pathog. 2012;8(3):e1002529 - PubMed
  41. J Virol. 2014 Mar;88(5):2977-90 - PubMed
  42. Lancet Infect Dis. 2002 Aug;2(8):461-71 - PubMed
  43. J Clin Virol. 2009 May;45(1):34-8 - PubMed
  44. Nat Biotechnol. 2013 Apr;31(4):294-6 - PubMed
  45. J Virol. 2008 Jan;82(2):764-74 - PubMed
  46. Br Med Bull. 2001;58:19-42 - PubMed
  47. PLoS Med. 2008 Jul 29;5(7):e158 - PubMed
  48. Clin Infect Dis. 2009 Jan 15;48(2):239-47 - PubMed
  49. PLoS One. 2010 Jun 07;5(6):e10992 - PubMed
  50. Curr Opin Virol. 2011 Nov;1(5):413-8 - PubMed
  51. Nucleic Acids Res. 2015 Mar 31;43(6):e37 - PubMed
  52. Cell. 2002 Feb 8;108(3):305-12 - PubMed
  53. PLoS One. 2012;7(5):e36494 - PubMed
  54. Bioinformatics. 2009 Jul 15;25(14):1754-60 - PubMed
  55. PLoS One. 2013 Sep 18;8(9):e74249 - PubMed
  56. Antiviral Res. 2007 Jul;75(1):75-82 - PubMed
  57. Front Microbiol. 2012 Sep 11;3:329 - PubMed
  58. Nucleic Acids Res. 2012 Jan;40(1):e2 - PubMed
  59. Nat Rev Genet. 2004 Jun;5(6):467-75 - PubMed
  60. Nature. 2003 Dec 18;426(6968):789-96 - PubMed
  61. J Infect Dis. 2009 Mar 1;199(5):693-701 - PubMed
  62. Cold Spring Harb Perspect Med. 2011 Sep;1(1):a006841 - PubMed
  63. J Clin Invest. 2013 Sep;123(9):3848-60 - PubMed

Publication Types