rhinotypeR

rhinotypeR automates genotype assignment of rhinoviruses by comparing VP4/2 sequence data against prototype strains using standardized pairwise distance thresholds within the Bioconductor ecosystem.

Key Features:

• Automated Genotype Assignment: Compares sequence data against prototype strains using predefined pairwise distance thresholds.
• Standardized Thresholds: Applies species-specific distance thresholds of 10.5% for HRV-A/C and 9.5% for HRV-B.
• Integrated Analytical Workflow: Consolidates alignment, distance calculation, genotype assignment, and visualization in a single framework.
• SNP and Amino Acid Substitution Analysis: Supports comprehensive visualization and analysis of single nucleotide polymorphisms and amino acid substitutions.
• Reproducible Distance Calculation: Reproduces pairwise genetic distances with Mantel correlation (r = 1.000, p = 0.001) and negligible numerical deviation compared to ape and MEGA X.

Scientific Applications:

• Rhinovirus Molecular Surveillance: Enables efficient epidemiological surveillance and scalable, transparent molecular characterization of rhinoviruses.
• Genetic and Evolutionary Studies: Facilitates in-depth analysis of rhinovirus genetic diversity and evolutionary patterns through SNP and substitution analysis.
• Public Health Genotyping: Supports routine public health applications by standardizing genotype assignment across studies and analysts.

Methodology:

The package performs sequence alignment, pairwise distance calculation, and genotype assignment by comparison against prototype strains using standardized thresholds, implemented as a scriptable workflow within the Bioconductor ecosystem.