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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes
Journal of Clinical Microbiology, Volume 50, No. 12, Year 2012
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Description
Whole HIV-1 genome sequences are pivotal for large-scale studies of inter-and intrahost evolution, including the acquisition of drug resistance mutations. The ability to rapidly and cost-effectively generate large numbers of HIV-1 genome sequences from different populations and geographical locations and determine the effect of minority genetic variants is, however, a limiting factor. Next-generation sequencing promises to bridge this gap but is hindered by the lack of methods for the enrichment of virus genomes across the phylogenetic breadth of HIV-1 and methods for the robust assembly of the virus genomes from shortread data. Here we report a method for the amplification, next-generation sequencing, and unbiased de novo assembly of HIV-1 genomes of groups M, N, and O, as well as recombinants, that does not require prior knowledge of the sequence or subtype. A sensitivity of at least 3,000 copies/ml was determined by using plasma virus samples of known copy numbers. We applied our novel method to compare the genome diversities of HIV-1 groups, subtypes, and genes. The highest level of diversity was found in the env, nef, vpr, tat, and rev genes and parts of the gag gene. Furthermore, we used our method to investigate mutations associated with HIV-1 drug resistance in clinical samples at the level of the complete genome. Drug resistance mutations were detected as both major variant and minor species. In conclusion, we demonstrate the feasibility of our method for large-scale HIV-1 genome sequencing. This will enable the phylogenetic and phylodynamic resolution of the ongoing pandemic and efficient monitoring of complex HIV-1 drug resistance genotypes. Copyright © 2012, American Society for Microbiology. All Rights Reserved.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC3502977/bin/supp_50_12_3838__index.html
https://efashare.b-cdn.net/share/pmc/articles/PMC3502977/bin/JCM.01516-12_zjm999092079so1.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3502977/bin/JCM.01516-12_zjm999092079so2.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3502977/bin/JCM.01516-12_zjm999092079so3.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3502977/bin/JCM.01516-12_zjm999092079so4.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3502977/bin/JCM.01516-12_zjm999092079so5.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3502977/bin/JCM.01516-12_zjm999092079so6.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3502977/bin/JCM.01516-12_zjm999092079so7.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3502977/bin/JCM.01516-12_zjm999092079so8.pdf
Authors & Co-Authors
Gall, Astrid
United Kingdom, Hinxton
Wellcome Sanger Institute
Ferns, Bridget
United Kingdom, London
University College London
Watson, Simon James
United Kingdom, Hinxton
Wellcome Sanger Institute
Cotten, Matt
United Kingdom, Hinxton
Wellcome Sanger Institute
Robinson, Mark James
United Kingdom, London
Imperial College London
Berry, Neil J.
United Kingdom, London
Public Health England
Morris, Lynn G.
United Kingdom, London
University College London
Kellam, P.
United Kingdom, Hinxton
Wellcome Sanger Institute
Statistics
Citations: 124
Authors: 8
Affiliations: 4
Identifiers
Doi:
10.1128/JCM.01516-12
ISSN:
1098660X
Research Areas
Genetics And Genomics
Infectious Diseases