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Viruses
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Next Generation Sequencing for HIV Drug Resistance Testing, 2nd Edition
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Next Generation Sequencing for HIV Drug Resistance Testing, 2nd Edition

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

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 938

Special Issue Editor

Dr. Guinevere Q. Lee

E-Mail Website
Guest Editor
Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
Interests: HIV reservoir and cure; viral genomics; viral diversity; molecular epidemiology; drug resistance; viral bioinformatics

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. Wherever feasible, guidelines recommend to particularly test for drug resistance before and during antiretroviral therapy to guide regimen selection. In circumstances where it is less viable, such testing is used only in specific populations, and where it is entirely unattainable, testing is generally 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. In recent times, the newly developed next-generation sequencing (NGS) methods are being increasingly used in diverse circumstances, including HIV drug-resistance testing. However, due to several financial, infrastructural, and logistical challenges, it has not yet been determined how feasible it would be to replace Sanger sequencing with NGS for HIV drug-resistance testing. Thus, the logistics of resistance testing involving newly FDA-approved antiretroviral drugs, resistance patterns in different HIV subtypes, and their archival patterns in the viral reservoir are research priorities.

For this Special Issue, we cordially invite researchers working in the field of HIV drug resistance to submit their valuable manuscripts that report on their latest findings, summarize the status of the field, and highlight the related opportunities and challenges.

Dr. Guinevere Q. Lee
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • NGS
  • HIV drug resistance
  • HIV genetic diversity
  • HIV subtypes

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Published Papers (1 paper)

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Research

10 pages, 1043 KiB  
Article
A Sensitivity and Consistency Comparison Between Next-Generation Sequencing and Sanger Sequencing in HIV-1 Pretreatment Drug Resistance Testing
by Ying Zhou, Fei Ouyang, Xiaoyan Liu, Jing Lu, Haiyang Hu, Qi Sun and Haitao Yang
Viruses 2024, 16(11), 1713; https://doi.org/10.3390/v16111713 - 31 Oct 2024
Viewed by 620
Abstract
Next-generation sequencing (NGS) for HIV drug resistance (DR) testing has an increasing number of applications for the detection of low-abundance drug-resistant variants (LA-DRVs) in regard to its features as a quasi-species. However, there is less information on its detection performance in DR detection [...] Read more.
Next-generation sequencing (NGS) for HIV drug resistance (DR) testing has an increasing number of applications for the detection of low-abundance drug-resistant variants (LA-DRVs) in regard to its features as a quasi-species. However, there is less information on its detection performance in DR detection with NGS. To determine the feasibility of using NGS technology in LA-DRV detection for HIV-1 pretreatment drug resistance, 80 HIV-infected individuals who had never undergone antiretroviral therapy were subjected to both NGS and Sanger sequencing (SS) in HIV-1 drug resistance testing. The results reported in this study show that NGS exhibits higher sensitivity for drug resistance identification than SS at a 5% detection threshold. NGS showed a better consistency compared with that of SS for both protease inhibitors (PIs) and integrase inhibitors (INSTIs), with a figure amounting to more than 90%, but worse consistency in nucleotide reverse transcriptase inhibitors (NRTIs), with a consistency ranging from only 61.25% to 87.50%. The consistency of non-nucleotide reverse transcriptase inhibitors (NNRTIs) between NGS and SS was around 85%. NGS showed the highest sensitivity of 87.0% at a 5% threshold. The application of NGS technology in HIV-1 genotype resistance detection in different populations infected with HIV requires further documentation and validation. Full article
(This article belongs to the Special Issue Next Generation Sequencing for HIV Drug Resistance Testing, 2nd Edition)
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