2020
DOI: 10.3390/v12060617
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Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations

Abstract: Higher accessibility and decreasing costs of next generation sequencing (NGS), availability of commercial kits, and development of dedicated analysis pipelines, have allowed an increasing number of laboratories to adopt this technology for HIV drug resistance (HIVDR) genotyping. Conventional HIVDR genotyping is traditionally carried out using population-based Sanger sequencing, which has a limited capacity for reliable detection of variants present at intra-host frequencies below a threshold of approximately 2… Show more

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Cited by 60 publications
(48 citation statements)
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“…This is because Sanger sequencing has been available long enough for use in HIVDR genotyping, producing high quality sequence data, with short turnaround times, and relatively simple workflows and data interpretation [14]. However, in addition to the inability of Sanger sequencing to reliably detect LA-DRVs [19,52], it has limited data throughput [53].…”
Section: Advantages and Disadvantages Of Sequencing Methods For Hivdr Genotypingmentioning
confidence: 99%
See 1 more Smart Citation
“…This is because Sanger sequencing has been available long enough for use in HIVDR genotyping, producing high quality sequence data, with short turnaround times, and relatively simple workflows and data interpretation [14]. However, in addition to the inability of Sanger sequencing to reliably detect LA-DRVs [19,52], it has limited data throughput [53].…”
Section: Advantages and Disadvantages Of Sequencing Methods For Hivdr Genotypingmentioning
confidence: 99%
“…It can sequence fragments up to 900 bp in a single read and can process 96 reactions simultaneously and continuously for several sequencing plates at a time [17]. However, its throughput is nowhere comparable to NGS, which can produce millions of reads from a single sequencing run [18,19]. Moreover, NGS has several sequencing platforms from different manufacturers such as Illumina (Illumina, CA, USA), Thermo Fisher (Thermo Fisher Scientific, Waltham, MA, USA), Pacific Biosciences (PacBio) (PacBio, CA, USA) and Oxford Nanopore Technologies (ONT) (ONT, Oxford, UK).…”
Section: Overview Of Sanger Sequencing and Ngs Platformsmentioning
confidence: 99%
“…Leprohon et al have reviewed all critical information relevant to drug resistance and to resistance mechanism(s) in Leishmania infections generated from NGS analysis [211]. Furthermore, NGS has been successfully used for testing for HIV-1 drug resistance, although such studies are yet to be standardized [212][213][214][215][216]. Likewise, NGS and pyrosequencing have been used to investigate resistance of the Influenta A virus to baloxavir [217].…”
Section: Drug Resistance and Ngsmentioning
confidence: 99%
“…Drug resistance testing (DRT) methods for HIV-1 are continually evolving as exemplified by NGS technology, which is gradually replacing Sanger chemistry in clinical diagnostics [1,2]. NGS has the capability to generate high-quality genotypic data at a low cost when a large volume of samples is available, with a relatively shorter turn-around time and higher sensitivity compared to traditional Sanger methods.…”
Section: Introductionmentioning
confidence: 99%