Special Issue "Next Generation Sequencing for HIV Drug Resistance Testing"

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Antivirals & Vaccines".

Deadline for manuscript submissions: closed (31 May 2020).

Special Issue Editor

Dr. Rami Kantor
Website
Guest Editor
Brown University; Providence, RI, USA
Interests: HIV drug resistance; treatment monitoring and transmission

Special Issue Information

Dear Colleagues,

Drug resistance remains a global challenge in the fight against the HIV pandemic, as recognized by the World Health Organization and the United Nations. Where feasible, guidelines recommend testing for drug resistance before and during antiretroviral therapy to guide regimen selection. Where less available, such testing is used only in specific populations, and where even less accessible, it is used for public health surveillance. Sanger sequencing, available since the 1970s, has conventionally been used for HIV drug resistance testing in clinical care and research. More recently developed next-generation sequencing (NGS) methods are increasingly used in diverse circumstances, including for HIV drug resistance testing. Whether these technologies can and should replace Sanger sequencing for HIV drug resistance testing is unclear, mostly due to associated financial, infrastructure, and logistical challenges. This topic was recently discussed at the International Symposium on External Quality Assurance Strategies for NGS-based HIV drug resistance testing, convened in Winnipeg, Canada in September 2019. In this Special Issue, I invite Symposium participants to highlight related opportunities and challenges that were discussed in the Symposium. I also invite other experts and interested individuals to contribute to this discussion. Deliberations will emphasize logistical and implementation needs and considerations in incorporation of NGS for HIV drug resistance testing, towards clarifying this existing gap and helping clinical, public health and programmatic resolutions.

Dr. Rami Kantor
Guest Editor

Manuscript Submission Information

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Keywords

  • HIV drug resistance
  • Next-generation sequencing

Published Papers (3 papers)

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Open AccessCommentary
Are We Ready for NGS HIV Drug Resistance Testing? The Second “Winnipeg Consensus” Symposium
Viruses 2020, 12(6), 586; https://doi.org/10.3390/v12060586 - 27 May 2020
Abstract
HIV drug resistance is a major global challenge to successful and sustainable antiretroviral therapy. Next-generation sequencing (NGS)-based HIV drug resistance (HIVDR) assays enable more sensitive and quantitative detection of drug-resistance-associated mutations (DRMs) and outperform Sanger sequencing approaches in detecting lower abundance resistance mutations. [...] Read more.
HIV drug resistance is a major global challenge to successful and sustainable antiretroviral therapy. Next-generation sequencing (NGS)-based HIV drug resistance (HIVDR) assays enable more sensitive and quantitative detection of drug-resistance-associated mutations (DRMs) and outperform Sanger sequencing approaches in detecting lower abundance resistance mutations. While NGS is likely to become the new standard for routine HIVDR testing, many technical and knowledge gaps remain to be resolved before its generalized adoption in regular clinical care, public health, and research. Recognizing this, we conceived and launched an international symposium series on NGS HIVDR, to bring together leading experts in the field to address these issues through in-depth discussions and brainstorming. Following the first symposium in 2018 (Winnipeg, MB Canada, 21–22 February, 2018), a second “Winnipeg Consensus” symposium was held in September 2019 in Winnipeg, Canada, and was focused on external quality assurance strategies for NGS HIVDR assays. In this paper, we summarize this second symposium’s goals and highlights. Full article
(This article belongs to the Special Issue Next Generation Sequencing for HIV Drug Resistance Testing)
Open AccessOpinion
External Quality Assessment Program for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Logistical Considerations
Viruses 2020, 12(5), 556; https://doi.org/10.3390/v12050556 - 18 May 2020
Abstract
Next-generation sequencing (NGS) is likely to become the new standard method for HIV drug resistance (HIVDR) genotyping. Despite the significant advances in the development of wet-lab protocols and bioinformatic data processing pipelines, one often-missing critical component of an NGS HIVDR assay for clinical [...] Read more.
Next-generation sequencing (NGS) is likely to become the new standard method for HIV drug resistance (HIVDR) genotyping. Despite the significant advances in the development of wet-lab protocols and bioinformatic data processing pipelines, one often-missing critical component of an NGS HIVDR assay for clinical use is external quality assessment (EQA). EQA is essential for ensuring assay consistency and laboratory competency in performing routine biomedical assays, and the rollout of NGS HIVDR tests in clinical practice will require an EQA. In September 2019, the 2nd International Symposium on NGS HIVDR was held in Winnipeg, Canada. It convened a multidisciplinary panel of experts, including research scientists, clinicians, bioinformaticians, laboratory biologists, biostatisticians, and EQA experts. A themed discussion was conducted on EQA strategies towards such assays during the symposium. This article describes the logistical challenges identified and summarizes the opinions and recommendations derived from these discussions, which may inform the development of an inaugural EQA program for NGS HIVDR in the near future. Full article
(This article belongs to the Special Issue Next Generation Sequencing for HIV Drug Resistance Testing)
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Open AccessCommentary
External Quality Assessment for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Unique Requirements and Challenges
Viruses 2020, 12(5), 550; https://doi.org/10.3390/v12050550 - 16 May 2020
Cited by 1
Abstract
Over the past decade, there has been an increase in the adoption of next generation sequencing (NGS) technologies for HIV drug resistance (HIVDR) testing. NGS far outweighs conventional Sanger sequencing as it has much higher throughput, lower cost when samples are batched and, [...] Read more.
Over the past decade, there has been an increase in the adoption of next generation sequencing (NGS) technologies for HIV drug resistance (HIVDR) testing. NGS far outweighs conventional Sanger sequencing as it has much higher throughput, lower cost when samples are batched and, most importantly, significantly higher sensitivities for variants present at low frequencies, which may have significant clinical implications. Despite the advantages of NGS, Sanger sequencing remains the gold standard for HIVDR testing, largely due to the lack of standardization of NGS-based HIVDR testing. One important aspect of standardization includes external quality assessment (EQA) strategies and programs. Current EQA for Sanger-based HIVDR testing includes proficiency testing where samples are sent to labs and the performance of the lab conducting such assays is evaluated. The current methods for Sanger-based EQA may not apply to NGS-based tests because of the fundamental differences in their technologies and outputs. Sanger-based genotyping reports drug resistance mutations (DRMs) data as dichotomous, whereas NGS-based HIVDR genotyping also reports DRMs as numerical data (percent abundance). Here we present an overview of the need to develop EQA for NGS-based HIVDR testing and some unique challenges that may be encountered. Full article
(This article belongs to the Special Issue Next Generation Sequencing for HIV Drug Resistance Testing)
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