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NanoHIV: A Bioinformatics Pipeline for Producing Accurate, Near Full-Length HIV Proviral Genomes Sequenced Using the Oxford Nanopore Technology

  1. Author:
    Wright, Imogen A.
    Delaney, Kayla E.
    Katusiime, Mary Grace K.
    Botha, Johannes C.
    Engelbrecht, Susan
    Kearney,Mary
    van Zyl, Gert U.

  2. Author Address

    Stellenbosch Univ, Div Med Virol, ZA-7505 Cape Town, South Africa.NHLS Tygerberg, ZA-7505 Cape Town, South Africa.Natl Canc Inst Frederick, HIV Dynam & Replicat Program, Ctr Canc Res, 1050 Boyles St,Bldg 535,Room 109, Frederick, MD 21702 USA.
    1. Year: 2021
    2. Date: Sep 28
  2. Journal: Cells
  3. MDPI
    1. 10
    2. 10
  5. Type of Article: Article
  6. Article Number: ARTN 2577
  7. ISSN: 2073-4409
  1. Abstract:

    HIV-1 proviral single-genome sequencing by limiting-dilution polymerase chain reaction (PCR) amplification is important for differentiating the sequence-intact from defective proviruses that persist during antiretroviral therapy (ART). Intact proviruses may rebound if ART is interrupted and are the barrier to an HIV cure. Oxford Nanopore Technologies (ONT) sequencing offers a promising, cost-effective approach to the sequencing of long amplicons such as near full-length HIV-1 proviruses, but the high diversity of HIV-1 and the ONT sequencing error render analysis of the generated data difficult. NanoHIV is a new tool that uses an iterative consensus generation approach to construct accurate, near full-length HIV-1 proviral single-genome sequences from ONT data. To validate the approach, single-genome sequences generated using NanoHIV consensus building were compared to Illumina(R) consensus building of the same nine single-genome near full-length amplicons and an average agreement of 99.4% was found between the two sequencing approaches.

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External Sources

  1. View Full Text
  2. DOI: 10.3390/cells10102577
  3. PMID: 34685559
  4. PMCID: PMC8534097
  5. View record in Web of Science®
  6. WOS: 000711765800001

Library Notes

  1. Fiscal Year: FY2021-2022
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