Indels in SARS-CoV-2 occur at template-switching hotspots

Area of Science:

• Virology
• Molecular Biology
• Evolutionary Biology

Background:

• The COVID-19 pandemic highlighted the need to understand SARS-CoV-2 evolutionary dynamics.
• Previous analyses primarily focused on single nucleotide polymorphisms, neglecting insertions and deletions (indels) and recombination.
• Indels and recombination are crucial but understudied aspects of SARS-CoV-2 evolution.

Purpose of the Study:

• To catalogue insertions and deletions (indels) in SARS-CoV-2 consensus sequences.
• To investigate the role of imperfect homologous recombination in generating these indels.
• To explore the relationship between RNA secondary structure, indels, and template-switching in SARS-CoV-2.

Main Methods:

• Analysis of SARS-CoV-2 sequences from the GISAID database.
• Cataloguing over 100 insertions and deletions in consensus sequences.
• Examination of indel distribution, correlation with transcription regulatory site (TRS) independent transcriptome breakpoints, and intra-host sequence heterogeneity.

Main Results:

• Over 100 insertions and deletions (indels) were identified in SARS-CoV-2 consensus sequences.
• Indels are clustered in specific genomic regions associated with RNA-dependent RNA polymerase (RdRp) template-switching.
• Evidence suggests indels arise from imperfect homologous recombination and are influenced by RNA secondary structures.

Conclusions:

• Indels are significant structural variations in SARS-CoV-2 evolution, driven by RdRp template-switching and recombination.
• Understanding indel formation improves reconstructions of SARS-CoV-2 evolutionary history.
• RNA secondary structure may play a role in facilitating template-switching events in coronaviruses.