Insertion and deletion mutations preserved in SARS-CoV-2 variants.

Area of Science:

• Virology
• Genomics
• Molecular Evolution

Background:

• SARS-CoV-2 evolution is driven by various mutations, including insertions/deletions (indels).
• Understanding indel profiles across different SARS-CoV-2 lineages, particularly Omicron, is crucial for tracking viral evolution and relationships.

Purpose of the Study:

• To compare whole-genome indel mutation profiles across diverse SARS-CoV-2 lineages.
• To infer ancestral relationships between variants using preserved indel patterns.
• To identify indel signatures specific to Omicron and other major variants.

Main Methods:

• Whole-genome sequencing data from multiple SARS-CoV-2 lineages were analyzed.
• Preserved indel patterns at specific genomic sites were identified and compared.
• Phylogenetic proximity was inferred based on shared indel profiles.

Main Results:

• Thirteen distinct indel patterns were identified across twelve genomic sites in SARS-CoV-2 sequences.
• Six of these indel sites were located in the spike gene's N-terminal domain.
• Seven indel patterns were specific to Omicron variants, with four unique to BA.1.
• Omicron shared some indels with Alpha and Gamma, but not Delta, suggesting a closer phylogenetic relationship to Alpha.

Conclusions:

• Distinct indel profiles characterize SARS-CoV-2 variants and sublineages.
• Preserved indels are valuable markers for understanding SARS-CoV-2 evolution and lineage relationships.
• The findings highlight the significance of indels in the ongoing evolution of SARS-CoV-2.