CovidPhy

CovidPhy analyzes SARS-CoV-2 genome sequences to classify them phylogenetically, detect sequencing variations and Variants of Concern (VOCs), provide phylogeographic and lineage/haplogroup frequency information, and identify outbreak candidate genomes using FASTA inputs or GISAID/GenBank identifiers against a reference sequence and a repository of over 1.49 million GISAID genomes.

Key Features:

• Input formats: Accepts plain FASTA sequences or identity codes from GISAID and GenBank.
• Genome repository integration: Integrates a repository of over 1.49 million SARS-CoV-2 genomes from GISAID for comparative analyses.
• Reference alignment: Aligns input sequences against a reference sequence for comparative analysis.
• Phylogenetic classification: Automatically classifies genome sequences into a pre-computed phylogeny to determine evolutionary relationships.
• Phylogeographic information: Provides phylogeographic data to trace the geographic distribution of viral strains.
• Lineage and haplogroup frequencies: Reports haplogroup and lineage frequencies to track prevalence across time and space.
• Variant analysis: Identifies sequencing variations within genomes and highlights known Variants of Concern (VOCs).
• Custom variant and haplotype searches: Enables searches for specific variants or haplotypes.
• Outbreak candidate identification: Identifies genomes likely responsible for significant outbreaks, provides potential geographic epicenters, and assesses relative impact based on GISAID data.

Scientific Applications:

• Phylogenetic analysis: Determining evolutionary relationships and lineage diversification of SARS-CoV-2 genomes.
• Variant surveillance: Monitoring and identifying sequencing variations and known VOCs relevant to public health.
• Phylogeography: Tracing geographic spread and migration patterns of viral strains.
• Epidemiological investigation: Identifying candidate genomes linked to outbreaks and potential superspreading events.
• Frequency monitoring: Tracking haplogroup and lineage prevalence over time and across regions.

Methodology:

Processes input FASTA sequences or GISAID/GenBank identifiers, integrates >1.49 million GISAID genomes, aligns sequences against a reference sequence, classifies sequences into a pre-computed phylogeny, identifies sequencing variations and highlights known VOCs, supports searches for specific variants or haplotypes, and identifies outbreak candidate genomes with potential geographic epicenters and relative impact assessment based on GISAID data.