Tracking SARS-CoV-2 variants by entire S-gene analysis using long-range RT-PCR and Sanger sequencing

Area of Science:

• Virology
• Genomics
• Molecular Epidemiology

Background:

• Genomic surveillance is crucial for tracking SARS-CoV-2 transmissibility, disease severity, and vaccine effectiveness.
• The large SARS-CoV-2 genome necessitates targeted sequencing approaches.
• The S-gene is a key target for analyzing viral mutations.

Purpose of the Study:

• To analyze the mutational dynamics of the SARS-CoV-2 S-gene.
• To assess the utility of S-gene sequencing for molecular surveillance of SARS-CoV-2 variants.

Main Methods:

• Long-range RT-PCR was used to amplify the 4kb S-gene region.
• Sanger sequencing determined the entire S-gene sequence.
• Amino acid mutations were identified by comparison to the reference genome.

Main Results:

• The S:D614G mutation was present in all samples.
• SARS-CoV-2 variants R.1, Alpha, Delta, and Omicron emerged sequentially.
• Observed mutational dynamics mirrored national trends in Japan.

Conclusions:

• Analysis of the entire S-gene effectively identified the emergence of variants of concern (VOCs).
• Unique mutational patterns within the S-gene facilitate molecular surveillance.
• S-gene analysis is a valuable tool for clinical laboratories monitoring SARS-CoV-2.