HIV-DRLink

HIV-DRLink detects and analyzes linked drug resistance mutations in HIV-1 from next-generation sequencing (NGS) data to characterize mutation frequencies and linkage relevant to combination antiretroviral therapy (cART) outcomes.

Key Features:

• Detection of linked mutations: Identifies dual-class drug resistance mutations that are linked on the same viral genomes, preserving associations detectable by single-genome approaches.
• Compatibility with NGS and uSGS/SGS: Processes datasets produced by next-generation sequencing (NGS), including Ultrasensitive Single-Genome Sequencing (uSGS) and Single-Genome Sequencing (SGS).
• Handling large datasets: Scales to analyze large sequencing datasets that are impractical to assess manually at the single-sequence level.
• Mutation frequency and linkage reporting: Calculates and reports frequencies of individual mutations and their linkage to other mutations conferring resistance to the same or different drug classes.
• PCR artifact avoidance: Operates using data from sequencing methods that eliminate PCR recombination artifacts to ensure accurate detection of linked mutations.

Scientific Applications:

• Mechanisms of treatment failure: Enables investigation of how linked drug resistance mutations, including dual-class linkages identified by uSGS, correlate with treatment failure.
• Epidemiological surveillance: Supports large-scale analyses to track the emergence and spread of drug-resistant HIV-1 strains in populations under cART.
• Resistance evolution studies: Facilitates study of intra-host viral population dynamics and the co-occurrence of resistance mutations across drug classes.

Methodology:

Analyzes datasets generated by sequencing methods that avoid PCR bias and recombination (SGS, uSGS), calculates mutation frequencies, and identifies linkages between mutations across different drug classes.