IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v10y2019i1d10.1038_s41467-019-10659-2.html
   My bibliography  Save this article

HIV-1 DNA sequence diversity and evolution during acute subtype C infection

Author

Listed:
  • Guinevere Q. Lee

    (Ragon Institute of MGH, MIT and Harvard
    Brigham and Women’s Hospital
    Harvard Medical School)

  • Kavidha Reddy

    (University of KwaZulu-Natal
    Africa Health Research Institute)

  • Kevin B. Einkauf

    (Ragon Institute of MGH, MIT and Harvard
    Brigham and Women’s Hospital)

  • Kamini Gounder

    (University of KwaZulu-Natal
    Africa Health Research Institute)

  • Joshua M. Chevalier

    (Ragon Institute of MGH, MIT and Harvard)

  • Krista L. Dong

    (Ragon Institute of MGH, MIT and Harvard
    Harvard Medical School)

  • Bruce D. Walker

    (Ragon Institute of MGH, MIT and Harvard
    Brigham and Women’s Hospital
    Harvard Medical School
    University of KwaZulu-Natal)

  • Xu G. Yu

    (Ragon Institute of MGH, MIT and Harvard
    Brigham and Women’s Hospital
    Harvard Medical School
    Broad Institute of MIT and Harvard)

  • Thumbi Ndung’u

    (Ragon Institute of MGH, MIT and Harvard
    University of KwaZulu-Natal
    Africa Health Research Institute
    Max Planck Institute for Infection Biology)

  • Mathias Lichterfeld

    (Ragon Institute of MGH, MIT and Harvard
    Brigham and Women’s Hospital
    Harvard Medical School
    Broad Institute of MIT and Harvard)

Abstract

Little is known about the genotypic make-up of HIV-1 DNA genomes during the earliest stages of HIV-1 infection. Here, we use near-full-length, single genome next-generation sequencing to longitudinally genotype and quantify subtype C HIV-1 DNA in four women identified during acute HIV-1 infection in Durban, South Africa, through twice-weekly screening of high-risk participants. In contrast to chronically HIV-1-infected patients, we found that at the earliest phases of infection in these four participants, the majority of viral DNA genomes are intact, lack APOBEC-3G/F-associated hypermutations, have limited genome truncations, and over one year show little indication of cytotoxic T cell-driven immune selections. Viral sequence divergence during acute infection is predominantly fueled by single-base substitutions and is limited by treatment initiation during the earliest stages of disease. Our observations provide rare longitudinal insights of HIV-1 DNA sequence profiles during the first year of infection to inform future HIV cure research.

Suggested Citation

  • Guinevere Q. Lee & Kavidha Reddy & Kevin B. Einkauf & Kamini Gounder & Joshua M. Chevalier & Krista L. Dong & Bruce D. Walker & Xu G. Yu & Thumbi Ndung’u & Mathias Lichterfeld, 2019. "HIV-1 DNA sequence diversity and evolution during acute subtype C infection," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10659-2
    DOI: 10.1038/s41467-019-10659-2
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-019-10659-2
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-019-10659-2?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Guinevere Q. Lee & Pragya Khadka & Sarah N. Gowanlock & Dennis C. Copertino & Maggie C. Duncan & F. Harrison Omondi & Natalie N. Kinloch & Jingo Kasule & Taddeo Kityamuweesi & Paul Buule & Samiri Jami, 2024. "HIV-1 subtype A1, D, and recombinant proviral genome landscapes during long-term suppressive therapy," Nature Communications, Nature, vol. 15(1), pages 1-10, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10659-2. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.