Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants.
HIV-1 group M subtype-independent approach
Near full genome amplification and sequencing
bulk sequencing and cloning
rational primer design
single-genome amplification (SGA)
third-generation sequencing (TGS)
Journal
Viruses
ISSN: 1999-4915
Titre abrégé: Viruses
Pays: Switzerland
ID NLM: 101509722
Informations de publication
Date de publication:
01 04 2019
01 04 2019
Historique:
received:
05
03
2019
revised:
26
03
2019
accepted:
27
03
2019
entrez:
4
4
2019
pubmed:
4
4
2019
medline:
30
4
2020
Statut:
epublish
Résumé
Near full genome sequencing (NFGS) of HIV-1 is required to assess the genetic composition of HIV-1 strains comprehensively. Population-wide, it enables a determination of the heterogeneity of HIV-1 and the emergence of novel/recombinant strains, while for each individual it constitutes a diagnostic instrument to assist targeted therapeutic measures against viral components. There is still a lack of robust and adaptable techniques for efficient NFGS from miscellaneous HIV-1 subtypes. Using rational primer design, a broad primer set was developed for the amplification and sequencing of diverse HIV-1 group M variants from plasma. Using pure subtypes as well as diverse, unique recombinant forms (URF), variable amplicon approaches were developed for NFGS comprising all functional genes. Twenty-three different genomes composed of subtypes A (A1), B, F (F2), G, CRF01_AE, CRF02_AG, and CRF22_01A1 were successfully determined. The NFGS approach was robust irrespective of viral loads (≥306 copies/mL) and amplification method. Third-generation sequencing (TGS), single genome amplification (SGA), cloning, and bulk sequencing yielded similar outcomes concerning subtype composition and recombinant breakpoint patterns. The introduction of a simple and versatile near full genome amplification, sequencing, and cloning method enables broad application in phylogenetic studies of diverse HIV-1 subtypes and can contribute to personalized HIV therapy and diagnosis.
Identifiants
pubmed: 30939815
pii: v11040317
doi: 10.3390/v11040317
pmc: PMC6520859
pii:
doi:
Substances chimiques
DNA Primers
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : FIC NIH HHS
ID : D43 TW009604
Pays : United States
Organisme : Wellcome Trust
ID : 107752/Z/15/Z
Pays : United Kingdom
Déclaration de conflit d'intérêts
The authors declare no conflict of interest.
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