lineagespot

lineagespot identifies SARS-CoV-2 lineages and tracks variant-associated mutations using next-generation sequencing (NGS) data from wastewater for community-level surveillance.

Key Features:

• Wastewater Surveillance: Detects SARS-CoV-2 RNA in wastewater to monitor community-level virus prevalence.
• Next-Generation Sequencing (NGS) Integration: Analyzes NGS-derived sequencing data to detect mutations and infer viral lineages.
• Variant Detection and Tracking: Records temporal dynamics of SARS-CoV-2 variants, including detection of the Alpha variant (B.1.1.7), across samples.
• Correlation with Clinical Data: Compares mutations detected in wastewater with those observed in clinical samples from the same geographic area and time period.
• Implementation in R: The analytical framework and lineage-assignment procedures are implemented in R.

Scientific Applications:

• Wastewater-based epidemiology: Validated on NGS data from 14 wastewater samples collected over six months in Thessaloniki, Greece, to identify SARS-CoV-2 variants and characterize lineage composition for epidemiological surveillance.

Methodology:

Implemented in R; analyzes NGS-derived SARS-CoV-2 wastewater sequencing to detect mutations and assign viral lineages.