HIITE

HIITE estimates HIV-1 incidence and individual time since infection from envelope gene sequences to inform epidemiological and clinical analyses.

Key Features:

• Envelope gene sequence processing: Processes HIV-1 envelope gene sequences as the primary molecular input for analysis.
• Genomic assay for cross-sectional surveys: Estimates epidemiological metrics from a single cross-sectional survey sample set.
• Hierarchical clustering algorithms: Uses hierarchical clustering algorithms to analyze sequence relationships and inform infection-stage classification.
• Dual metric estimation from single time point: Simultaneously infers population incidence and individual time since infection from a single sequence sample at one point in time.
• Validation on global cohorts: Validated on 585 incident and 305 chronic specimens from global cohorts, including HIV-1 vaccine trial participants.
• Classification accuracy: Correctly identified chronically infected individuals with an error rate of less than 1% and classified 94% of recently infected individuals as incident.
• Time-since-infection prediction: Estimates time since infection using a mixed-effect model based on single-lineage diversity with a prediction error of 14%.

Scientific Applications:

• Epidemiological monitoring: Provides incidence estimates and infection timing to support HIV-1 epidemic surveillance.
• Prevention strategy optimization: Identifies populations contributing to transmission to inform targeted prevention programs.
• Clinical management: Supplies estimated onset times of infection to aid clinical decision-making for recently infected individuals.
• Transmission chain analysis: Infers transmission relationships to investigate individual-level transmission events and inform public health interventions.

Methodology:

Processes envelope gene sequences, employs hierarchical clustering algorithms to classify incident versus chronic infections, and uses a mixed-effect model applied to single-lineage diversity to estimate time since infection.