Improved HIV-1 Subtyping Accuracy Using near Full-Length Sequencing: A Comparison of Common Tools.

ABSTRACT: The extensive genetic diversity of HIV-1, also represented by the circulation of multiple subtypes and circulating recombinant forms (CRFs), poses significant challenges for accurate subtype classification, especially when sequencing is limited to partial genomic regions. This study evaluated the performance of four commonly used automated subtyping tools (Stanford HIVdb, COMET, REGA, and Geno2pheno) by comparing their outputs with molecular phylogenetic analysis (Mphy), considered the gold standard, using three NGS-derived sequence data sets: protease-reverse transcriptase (PR-RT), pol, and near full-length (NFL). One hundred plasma samples were processed to generate sequences of increasing length, which were analyzed to assess concordance, sensitivity, and specificity. NFL-based M

SUBMITTER: Smoquina F 

PROVIDER: S-EPMC12691708 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature