Short Communication: HIV-DRLink: A Tool for Reporting Linked HIV-1 Drug Resistance Mutations in Large Single-Genome Data Sets Using the Stanford HIV Database

• Published in: AIDS research and human retroviruses Vol. 36; no. 11; p. 942
• Main Authors: Shao, Wei, Boltz, Valerie F, Hattori, Junko, Bale, Michael J, Maldarelli, Frank, Coffin, John M, Kearney, Mary F
• Format: Journal Article
• Language: English
• Published: United States 01.11.2020
• Subjects: linked drug resistance mutations; Stanford HIVdb; HIV-DRLink; HIV; uSGS; next-generation sequencing
• ISSN: 1931-8405
• DOI: 10.1089/aid.2020.0109

The prevalence of HIV-1 drug resistance is increasing worldwide and monitoring its emergence is important for the successful management of populations receiving combination antiretroviral therapy. It is likely that pre-existing drug resistance mutations linked on the same viral genomes are predictive of treatment failure. Because of the large number of sequences generated by ultrasensitive single-genome sequencing (uSGS) and other similar next-generation sequencing methods, it is difficult to assess each sequence individually for linked drug resistance mutations. Several software/programs exist to report the frequencies of individual mutations in large data sets, but they provide no information on linkage of resistance mutations. In this study, we report the HIV-DRLink program, a research tool that provides resistance mutation frequencies as well as their genetic linkage by parsing and summarizing the Sierra output from the Stanford HIV Database. The HIV-DRLink program should only be used on data sets generated by methods that eliminate artifacts due to polymerase chain reaction recombination, for example, standard single-genome sequencing or uSGS. HIV-DRLink is exclusively a research tool and is not intended to inform clinical decisions.