MMMVI

MMMVI identifies SARS-CoV-2 Variants of Concern (VoCs) and Variants of Interest (VOIs) in metagenomic sequencing data by detecting and aggregating sequencing reads that contain multiple signature mutations to support wastewater-based genomic surveillance.

Key Features:

• Enhanced Biomarker Detection: Identifies and aggregates sequencing reads that contain multiple SARS-CoV-2 signature mutations to increase confidence in variant presence.
• Metagenomic Read Analysis: Processes metagenomic sequencing data from complex samples such as wastewater to detect SARS-CoV-2 genomes amidst mixed viral populations.
• Implementation: Implemented in Python and distributed under the MIT license.

Scientific Applications:

• Wastewater-based surveillance: Detects SARS-CoV-2 variants in community wastewater samples for early warning of VoC/VOI emergence.
• Public health monitoring: Provides evidence of variant presence to inform epidemiological and public health response efforts.

Methodology:

Analyzes metagenomic sequencing reads from wastewater to detect SARS-CoV-2 genomes and identifies reads containing multiple signature mutations characteristic of VoCs/VOIs.