Direct whole-genome sequencing of HIV-1 for clinical drug-resistance analysis and public health surveillance.
J Clin Virol
; 174: 105709, 2024 10.
Article
in En
| MEDLINE
| ID: mdl-38924832
ABSTRACT
BACKGROUND:
Human Immunodeficiency virus type 1 (HIV-1) remains a significant global health threat partly due to its ability to develop resistance to anti-retroviral therapies. HIV-1 genotype and drug resistance analysis of the polymerase (pol) sequence is a mainstay of its clinical and public health management. However, as new treatments and resistances evolve, analysis methods must change accordingly. In this study, we outline the development and implementation of a direct whole-genome sequencing approach (dWGS) using probe-capture target-enrichment for HIV-1 genotype and drug resistance analysis.METHODS:
We implemented dWGS and performed parallel pol Sanger sequencing for clinical samples, followed by comparative genotype and drug-resistance analysis. These HIV-1 WGS sequences were also utilised for a novel partitioned phylogenetic analysis.RESULTS:
Optimised nucleic acid extraction and DNAse I treatment significantly increased HIV-1 whole-genome coverage and depth, and improved recovery of high-quality genomes from low viral load clinical samples, enabling routine sequencing of viral loads as low as 1000 copies/mL. Overall, dWGS was robust, accurate and more sensitive for detecting low-frequency variants at drug-resistance sites compared to Sanger sequencing. Analysis of multiple sequence regions improved phylogenetic reconstruction for recombinant HIV-1 sequences compared to analysis of pol sequence alone.CONCLUSIONS:
These findings demonstrate dWGS enhances HIV-1 drug-resistance analysis by quantitative variant detection and improves reconstruction of HIV-1 phylogenies compared to traditional pol sequencing. This work supports that HIV-1 dWGS is a viable option to replace Sanger sequencing for clinical and public health applications.Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Phylogeny
/
HIV Infections
/
HIV-1
/
Genome, Viral
/
Drug Resistance, Viral
/
Whole Genome Sequencing
/
Genotype
Limits:
Humans
Language:
En
Journal:
J Clin Virol
Journal subject:
VIROLOGIA
Year:
2024
Document type:
Article
Country of publication: