Whole Genome Sequence Analysis to Identify SARS-CoV-2 Variant in Nepal

Area of Science:

• Virology
• Genomics
• Public Health

Background:

• The global spread of SARS-CoV-2 (COVID-19) presents a significant public health challenge.
• Nepal is experiencing its second COVID-19 wave with limited data on circulating SARS-CoV-2 genomic variants.

Purpose of the Study:

• To perform whole-genome sequencing of SARS-CoV-2 in Nepal.
• To identify mutation profiles and phylogenetic lineages of circulating SARS-CoV-2 variants.
• To detect specific variants of concern within Nepal.

Main Methods:

• SARS-CoV-2 positive swab samples were collected.
• RNA extraction followed by real-time PCR and whole-genome sequencing was performed.
• Bioinformatics tools were used for consensus genome sequence analysis.

Main Results:

• Two SARS-CoV-2 genomes from patients without travel history belonged to lineage B.1.1.
• Four genomes from travelers returning from the UK included lineage B.1.36 (two samples) and lineage B.1.1.7 (Alpha Variant) (two samples).
• Detected mutations corresponded to the defining mutations of identified SARS-CoV-2 lineages.

Conclusions:

• The study confirmed the presence of the Alpha Variant (B.1.1.7) in Nepal.
• Genomic evidence for the spread of SARS-CoV-2 lineages B.1.1, B.1.36, and B.1.1.7 in Nepal was established.