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A comprehensive genomics solution for HIV surveillance and clinical monitoring in low-income settings

Title: A comprehensive genomics solution for HIV surveillance and clinical monitoring in low-income settings
Authors: Bonsall, D
Golubchik, T
De Cesare, M
Limbada, M
Kosloff, B
MacIntyre-Cockett, G
Hall, M
Wymant, C
Ansari, MA
Abeler-Dorner, L
Schaap, A
Brown, A
Barnes, E
Piwowar-Manning, E
Eshleman, S
Wilson, E
Emel, L
Hayes, R
Fidler, S
Ayles, H
Bowden, R
Fraser, C
Item Type: Journal Article
Abstract: Viral genetic sequencing can be used to monitor the spread of HIV drug resistance, identify appropriate antiretroviral regimes, and characterize transmission dynamics. Despite decreasing costs, next-generation sequencing (NGS) is still prohibitively costly for routine use in generalized HIV epidemics in low- and middle-income countries. Here, we present veSEQ-HIV, a high-throughput, cost-effective NGS sequencing method and computational pipeline tailored specifically to HIV, which can be performed using leftover blood drawn for routine CD4 cell count testing. This method overcomes several major technical challenges that have prevented HIV sequencing from being used routinely in public health efforts; it is fast, robust, and cost-efficient, and generates full genomic sequences of diverse strains of HIV without bias. The complete veSEQ-HIV pipeline provides viral load estimates and quantitative summaries of drug resistance mutations; it also exploits information on within-host viral diversity to construct directed transmission networks. We evaluated the method’s performance using 1,620 plasma samples collected from individuals attending 10 large urban clinics in Zambia as part of the HPTN 071-2 study (PopART Phylogenetics). Whole HIV genomes were recovered from 91% of samples with a viral load of >1,000 copies/ml. The cost of the assay (30 GBP per sample) compares favorably with existing VL and HIV genotyping tests, proving an affordable option for combining HIV clinical monitoring with molecular epidemiology and drug resistance surveillance in low-income settings.
Issue Date: 22-Sep-2020
Date of Acceptance: 10-Jul-2020
URI: http://hdl.handle.net/10044/1/87411
DOI: 10.1128/JCM.00382-20
ISSN: 0095-1137
Publisher: American Society for Microbiology
Start Page: 1
End Page: 13
Journal / Book Title: Journal of Clinical Microbiology
Volume: 58
Issue: 10
Copyright Statement: © 2020 Bonsall et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
Keywords: Science & Technology
Life Sciences & Biomedicine
Microbiology
HIV
NGS
viral genomics
public health
sub-Saharan Africa
viral sequencing
bait capture
short-read sequencing
Illumina
SMARTer
HPTN
PopART
HPTN 071
phylogenetics
viral evolution
drug resistance
antiretroviral therapy
RNA virus
antiretroviral resistance
drug resistance evolution
gene sequencing
human immunodeficiency virus
phylogenetic analysis
surveillance studies
REVERSE-TRANSCRIPTASE
TRANSMISSION
EPIDEMICS
HIV
HPTN
HPTN 071
Illumina
NGS
PopART
RNA virus
SMARTer
antiretroviral resistance
antiretroviral therapy
bait capture
drug resistance
drug resistance evolution
gene sequencing
human immunodeficiency virus
phylogenetic analysis
phylogenetics
public health
short-read sequencing
sub-Saharan Africa
surveillance studies
viral evolution
viral genomics
viral sequencing
HPTN 071 (PopART) Team
Science & Technology
Life Sciences & Biomedicine
Microbiology
HIV
NGS
viral genomics
public health
sub-Saharan Africa
viral sequencing
bait capture
short-read sequencing
Illumina
SMARTer
HPTN
PopART
HPTN 071
phylogenetics
viral evolution
drug resistance
antiretroviral therapy
RNA virus
antiretroviral resistance
drug resistance evolution
gene sequencing
human immunodeficiency virus
phylogenetic analysis
surveillance studies
REVERSE-TRANSCRIPTASE
TRANSMISSION
EPIDEMICS
Microbiology
06 Biological Sciences
07 Agricultural and Veterinary Sciences
11 Medical and Health Sciences
Publication Status: Published
Article Number: ARTN e00382-20
Online Publication Date: 2020-09-22
Appears in Collections:Department of Infectious Diseases



This item is licensed under a Creative Commons License Creative Commons