Co-mutation modules capture the evolution and transmission patterns of SARS-CoV-2

Area of Science:

• Genomics
• Virology
• Epidemiology

Background:

• The COVID-19 pandemic, caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), necessitates understanding viral genetic diversity.
• Mutation analysis reveals ongoing evolution, potentially altering infectivity and pathogenicity.
• Delineating SARS-CoV-2 genetic variants is crucial for tracking evolution and transmission.

Purpose of the Study:

• To identify and classify SARS-CoV-2 genetic variants based on nucleotide co-substitution patterns.
• To analyze the phylogenetic relationships and spatio-temporal distribution of these variants.
• To provide insights into viral evolution and transmission dynamics for pandemic control.

Main Methods:

• Identification of 42 co-mutation modules comprising co-substituted nucleotides in SARS-CoV-2 genomes.
• Classification of the viral population into 43 distinct groups based on these modules.
• Phylogenetic analysis using inconsistent co-mutation modules, validated with phylogenetic trees.
• Tracking spatio-temporal distribution and geographic specificity of identified viral groups.

Main Results:

• 42 co-mutation modules were identified, leading to the classification of SARS-CoV-2 into 43 groups.
• Phylogenetic relationships among groups were established.
• Spatio-temporal tracking revealed 11 geographic-specific groups.
• Distinct co-circulating groups were observed during different epidemic periods, with dominant groups exhibiting parallel evolution sub-groups.

Conclusions:

• The co-mutation module approach effectively captures SARS-CoV-2 evolution and transmission patterns.
• Understanding variant dynamics aids in guiding COVID-19 pandemic prevention and control strategies.
• An interactive website is available for genome grouping and spatio-temporal visualization.