HIVIntact

HIVIntact infers the genetic intactness of HIV-1 proviral genomes to identify potentially replication-competent integrated proviruses for characterization of the HIV-1 reservoir.

Key Features:

• Automated Characterization: Automates genetic characterization and annotation of near full-length (NFL) HIV-1 sequences, detecting insertions, deletions, and substitutions that disrupt coding regions.
• Integration into Pipelines: Integrates with deep-sequencing and next-generation sequencing pipelines to process large datasets derived from near full-length PCR and sequencing.
• Identification of Intact Genomes: Classifies proviral sequences as genetically intact or defective based on detected genomic defects, flagging sequences likely to be replication competent.
• Customizable Settings: Provides adjustable analytic parameters to tailor defect-calling and annotation criteria to specific study designs.

Scientific Applications:

• Reservoir Characterization: Quantifies and catalogs intact versus defective HIV-1 proviruses to inform studies of reservoir size and composition during antiretroviral therapy (ART).
• Cure Strategy Research: Supports evaluation of interventions aimed at eliminating or controlling the reservoir by identifying sequences likely capable of replication.

Methodology:

Processes near full-length PCR and sequencing data to annotate HIV-1 sequences, detect insertions/deletions/substitutions, assess whether proviruses carry defects, and classify sequences as intact or defective while integrating with deep-sequencing/next-generation sequencing pipelines.