title: MinVar: A rapid and versatile tool for HIV-1 drug resistance genotyping by deep sequencing.
abstract: Genotypic monitoring of drug-resistance mutations (DRMs) in HIV-1 infected individuals is strongly recommended to guide selection of the initial antiretroviral therapy (ART) and changes of drug regimens. Traditionally, mutations conferring drug resistance are detected by population sequencing of the reverse transcribed viral RNA encoding the HIV-1 enzymes target by ART, followed by manual analysis and interpretation of Sanger sequencing traces. This process is labor intensive, relies on subjective interpretation from the operator, and offers limited sensitivity as only mutations above 20% frequency can be reliably detected. Here we present MinVar, a pipeline for the analysis of deep sequencing data, which allows reliable and automated detection of DRMs down to 5%. We evaluated MinVar with data from amplicon sequencing of defined mixtures of molecular virus clones with known DRM and plasma samples of viremic HIV-1 infected individuals and we compared it to VirVarSeq, another virus variant detection tool exclusively working on Illumina deep sequencing data. MinVar was designed to be compatible with a diverse range of sequencing platforms and allows the detection of DRMs and insertions/deletions from deep sequencing data without the need to perform additional bioinformatics analysis, a prerequisite to a widespread implementation of HIV-1 genotyping using deep sequencing in routine diagnostic settings.
authors.affiliation: Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
authors.forename: Michael
authors.initials: M
authors.lastname: Huber
authors.affiliation: Institute of Medical Virology, University of Zurich, Zurich, Switzerland; Division of Infectious Diseases and Hospital Epidemiology, University of Zurich, Zurich, Switzerland.
authors.forename: Karin J
authors.initials: KJ
authors.lastname: Metzner
authors.affiliation: Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
authors.forename: Fabienne D
authors.initials: FD
authors.lastname: Geissberger
authors.affiliation: Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
authors.forename: Cyril
authors.initials: C
authors.lastname: Shah
authors.affiliation: Institute of Medical Virology, University of Zurich, Zurich, Switzerland; Division of Infectious Diseases and Hospital Epidemiology, University of Zurich, Zurich, Switzerland.
authors.forename: Christine
authors.initials: C
authors.lastname: Leemann
authors.affiliation: Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Klimkait
authors.affiliation: Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
authors.forename: Jürg
authors.initials: J
authors.lastname: Böni
authors.affiliation: Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Trkola
authors.affiliation: Institute of Medical Virology, University of Zurich, Zurich, Switzerland. Electronic address: zagordi.osvaldo@virology.uzh.ch.
authors.forename: Osvaldo
authors.initials: O
authors.lastname: Zagordi
mesh_terms: D019380:Anti-HIV Agents / Q000494:pharmacology*; D024882:Drug Resistance, Viral / Q000235:genetics*; D005838:Genotype; D015658:HIV Infections / Q000821:virology; D015497:HIV-1 / Q000145:classification / Q000187:drug effects* / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D054643:INDEL Mutation; D008826:Microbial Sensitivity Tests; D009154:Mutation; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D019380:Anti-HIV Agents
keywords: Bioinformatics; Deep sequencing; Drug resistance mutations; Genotyping; HIV-1; Minority variants