Population genomics of intrapatient HIV-1 evolution

Abstract

Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolved and genome wide data including rare variants are essential. We performed whole-genome deep sequencing of HIV-1 populations in 9 untreated patients, with 6-12 longitudinal samples per patient spanning 5-8 years of infection. The data can be accessed and explored via an interactive web application. We show that patterns of minor diversity are reproducible between patients and mirror global HIV-1 diversity, suggesting a universal landscape of fitness costs that control diversity. Reversions towards the ancestral HIV-1 sequence are observed throughout infection and account for almost one third of all sequence changes. Reversion rates depend strongly on conservation. Frequent recombination limits linkage disequilibrium to about 100bp in most of the genome, but strong hitch-hiking due to short range linkage limits diversity.

Full text

Its licence does not allow us to show the full text. Read it at PubMed Central:

References 87

1. 1.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

2. 2.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

3. 3.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

4. 4.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

5. 5.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

6. 6.
   Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape · 2012

   No notice
7. 7.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

8. 8.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

9. 9.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

10. 10.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

11. 11.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

12. 12.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

13. 13.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

14. 14.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

15. 15.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

16. 16.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

17. 17.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

18. 18.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

19. 19.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

20. 20.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

21. 21.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

22. 22.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

23. 23.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

24. 24.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

25. 25.
    SeqAn An efficient, generic C++ library for sequence analysis · 2008

    No notice
26. 26.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

27. 27.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

28. 28.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

29. 29.
    The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing · 2014

    No notice
30. 30.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

31. 31.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

32. 32.
    Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing · 2010

    No notice
33. 33.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

34. 34.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

35. 35.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

36. 36.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

37. 37.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

38. 38.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

39. 39.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

40. 40.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

41. 41.
    Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method · 2005

    No notice
42. 42.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

43. 43.
    Quantitative Deep Sequencing Reveals Dynamic HIV-1 Escape and Large Population Shifts during CCR5 Antagonist Therapy In Vivo · 2009

    No notice
44. 44.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

45. 45.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

46. 46.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

47. 47.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

48. 48.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

49. 49.
    Recombination Rate and Selection Strength in HIV Intra-patient Evolution · 2010

    No notice
50. 50.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

51. 51.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

52. 52.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

53. 53.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

54. 54.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

55. 55.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

56. 56.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

57. 57.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

58. 58.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

59. 59.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

60. 60.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

61. 61.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

62. 62.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

63. 63.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

64. 64.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

65. 65.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

66. 66.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

67. 67.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

68. 68.
    Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection · 2012

    No notice
69. 69.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

70. 70.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

71. 71.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

72. 72.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

73. 73.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

74. 74.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

75. 75.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

76. 76.
    An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit · 2014

    No notice
77. 77.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

78. 78.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

79. 79.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

80. 80.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

81. 81.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

82. 82.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

83. 83.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

84. 84.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

85. 85.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

86. 86.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

87. 87.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

Cited by papers we hold 8

• An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar · 2019
  No notice
• Evolutionary dynamics of bacteria in the gut microbiome within and across hosts · 2019
  No notice
• A majority of HIV persistence during antiretroviral therapy is due to infected cell proliferation · 2018
  No notice
• Parallel evolution of influenza across multiple spatiotemporal scales · 2017
  No notice
• PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity · 2017
  No notice
• Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable · 2016
  Not checked
• Adaptation in protein fitness landscapes is facilitated by indirect paths · 2016
  No notice
• Establishment and stability of the latent HIV-1 DNA reservoir · 2016
  No notice

Questions about this paper

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.