CalmBelt

CalmBelt enables on-site Nanopore-based whole-genome characterization of SARS-CoV-2 for rapid outbreak tracking.

Key Features:

• On-site Nanopore sequencing and assembly: Uses Nanopore sequencing to construct draft SARS-CoV-2 genomes from multiple samples with a reported ~12-hour turnaround.
• Integration of genomic and epidemiological metadata: Combines whole-genome sequence data with collection dates and predefined potential clusters from epidemiological investigations.
• Nomenclature assignment and relatedness visualization: Assigns sequences to GISAID clades and PANGO lineages and visualizes sample relatedness alongside these classifications.
• Rapid cluster identification: Performs rapid analysis of SARS-CoV-2 genomes to identify potential COVID-19 clusters for infection-control decision-making.

Scientific Applications:

• Hospital transmission investigation: Detects and characterizes potential transmissions within healthcare settings by comparing relatedness of SARS-CoV-2 genomes.
• Outbreak transmission mining: Maps transmission patterns during large outbreaks by integrating genomic data with collection dates and cluster definitions.
• Surveillance for diagnostic escape variants: Monitors sequence data to identify variants that may affect diagnostic assays.
• Rapid infection-control support in clinical labs: Provides timely genomic information to support immediate infection-control measures and identification of variants of concern.

Methodology:

Performs Nanopore sequencing and rapid genome assembly to generate draft SARS-CoV-2 genomes and assigns sequences to GISAID clades and PANGO lineages for downstream relatedness analysis.