MyCoV

MyCoV classifies coronaviruses into subgenera using partial RNA-dependent RNA polymerase (RdRp) sequences to enable subgenus-level taxonomic attribution.

Key Features:

• Subgenus Classification: Predicts coronavirus subgenera from partial RdRp sequences for subgenus-level taxonomic assignment.
• Phylogenetic Analysis: Uses Bayesian phylogenies inferred from over 7,000 publicly available coronavirus sequences to establish clade groupings relative to holotype sequences.
• Distance Measures: Employs pairwise distance measures to form discrete clusters and define threshold boundaries for subgenus delineation.
• Unclassified Sequences: Identifies sequences that fall outside defined subgenus clusters, indicating likely unclassified subgenera.
• Reliability Assessment: Evaluates the reliability of subgenus attributions to provide a measure of taxonomic confidence.

Scientific Applications:

• Molecular Epidemiology: Supports epidemiological studies requiring precise subgenus-level lineage identification.
• Public Health Research: Aids standardization of virus classification relevant to Coronaviridae taxonomic updates and public health surveillance.
• PCR Amplicon Analysis: Classifies PCR amplicons from biological samples when sequences diverge from type strains.

Methodology:

Operates as a wrapper script for nucleotide BLAST+ and requires a local installation of BLAST+ in a Linux environment; utilizes partial RdRp sequence data to infer phylogenetic relationships using Bayesian phylogenies and applies distance-based clustering methods to delineate subgenera.