Next Generation Sequencing for HIV-1 Drug Resistance Testing—A Special Issue Walkthrough

Kantor, Rami

doi:10.3390/v13020340

Cited by 3 publications

(2 citation statements)

References 24 publications

(23 reference statements)

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“…In our data, clusters vary in their profile-sampled support, and consensus approaches can fail to detect clusters supported by deep-sequenced data, as in the case of the largest cluster, which was detected by profile sampling , not by consensus approaches. As data acquisition increasingly shifts to NGS approaches ( Kantor, 2021 ), it is important to compare results of larger datasets from new methods to the more common conventional Sanger pol consensus sequences.…”

Section: Discussionmentioning

confidence: 99%

Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses

et al. 2022

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BackgroundPhylogenetic analyses of HIV sequences are used to detect clusters and inform public health interventions. Conventional approaches summarize within-host HIV diversity with a single consensus sequence per host of the pol gene, obtained from Sanger or next-generation sequencing (NGS). There is growing recognition that this approach discards potentially important information about within-host sequence variation, which can impact phylogenetic inference. However, whether alternative summary methods that incorporate intra-host variation impact phylogenetic inference of transmission network features is unknown.MethodsWe introduce profile sampling, a method to incorporate within-host NGS sequence diversity into phylogenetic HIV cluster inference. We compare this approach to Sanger- and NGS-derived pol and near-whole-genome consensus sequences and evaluate its potential benefits in identifying molecular clusters among all newly-HIV-diagnosed individuals over six months at the largest HIV center in Rhode Island.ResultsProfile sampling cluster inference demonstrated that within-host viral diversity impacts phylogenetic inference across individuals, and that consensus sequence approaches can obscure both magnitude and effect of these impacts. Clustering differed between Sanger- and NGS-derived consensus and profile sampling sequences, and across gene regions.DiscussionProfile sampling can incorporate within-host HIV diversity captured by NGS into phylogenetic analyses. This additional information can improve robustness of cluster detection.

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Section: Discussionmentioning

confidence: 99%

Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses

et al. 2022

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“…The use of unique molecular identifiers (UMIs, also known as “primer IDs”) in addition to the sample barcodes at the reverse-transcription step allows for the accurate quantification of the proportion of each individual variant [ 30 ]. Several publicly available and web-based bioinformatics pipelines specifically designed for the analysis of HIVDR have been described, and a special journal supplement was recently dedicated to discussing these methods [ 31 ].…”

Section: Methods Of Testing For Hiv Drug Resistancementioning

confidence: 99%

Need assessment for HIV drug resistance testing and landscape of current and future technologies in low- and middle-income countries

Parkin,

Harrigan,

Inzaule

et al. 2023

PLOS Glob Public Health

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Resistance to antiretroviral drugs used to treat HIV is an important and evolving concern, particularly in low- and middle-income countries (LMICs) which have been impacted to the greatest extent by the HIV pandemic. Efforts to monitor the emergence and transmission of resistance over the past decade have shown that drug resistance–especially to the nucleoside analogue and non-nucleoside reverse transcriptase inhibitors–can (and have) increased to levels that can jeopardize the efficacy of available treatment options at the population level. The global shift to integrase-based regimens as the preferred first-line therapy as well as technological advancements in the methods for detecting resistance have had an impact in broadening and diversifying the landscape of and use case for HIV drug resistance testing. This review estimates the potential demand for HIV drug resistance tests, and surveys current testing methodologies, with a focus on their application in LMICs.

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Roadmap for Achieving Universal Antiretroviral Treatment

Sokhela

Lalla-Edward

Siedner

et al. 2023

Annu. Rev. Pharmacol. Toxicol.

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Modern antiretroviral therapy safely, potently, and durably suppresses human immunodeficiency virus (HIV) that, if left untreated, predictably causes acquired immunodeficiency syndrome (AIDS), which has been responsible for tens of millions of deaths globally since it was described in 1981. In one of the most extraordinary medical success stories in modern times, a combination of pioneering basic science, innovative drug development, and ambitious public health programming resulted in access to lifesaving, safe drugs, taken as an oral tablet daily, for most of the world. However, substantial challenges remain in the fields of prevention, timely access to diagnosis, and treatment, especially in pediatric and adolescent patients. As HIV-positive adults age, treating their comorbidities will require understanding the course of different chronic diseases complicated by HIV-related and antiretroviral toxicities and finding potential treatments. Finally, new long-acting antiretrovirals on the horizon promise exciting new options in both the prevention and treatment fields.

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Next Generation Sequencing for HIV-1 Drug Resistance Testing—A Special Issue Walkthrough

Abstract: Drug resistance remains a global challenge in the fight against the HIV pandemic [...]

Cited by 3 publications

References 24 publications

Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses

Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses

Need assessment for HIV drug resistance testing and landscape of current and future technologies in low- and middle-income countries

Roadmap for Achieving Universal Antiretroviral Treatment

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