Publication: Whole Genome Sequence Analysis to Identify SARS-CoV-2 Variant in Nepal
Date
2021
Journal Title
Journal ISSN
Volume Title
Publisher
Kathmandu University
Abstract
ABSTRACT
Background
The spread of SARS-CoV-2 has become a global public health crisis. Nepal is facing the
second wave of COVID-19 pandemic but, there is still a limited data on the genomic
sequence of SARS-CoV-2 variants circulating in Nepal.
Objective
The objective of this study is to sequence the whole genome of SARS-CoV-2 in Nepal
to detect possible mutation profiles and phylogenetic lineages of circulating SARS-
CoV-2 variants.
Method
In this study, swab samples tested positive for SARS-CoV-2 were investigated. After
RNA extraction, the investigation was performed through real-time PCR followed by
whole genome sequencing. The consensus genome sequences were, then, analyzed
with appropriate bioinformatics tools.
Result
Sequence analysis of two SARS-CoV-2 genomes from patient without travel history
(Patient A1 and A2) were found to be of lineage B.1.1. Similarly, among other four
samples from subjects returning from the United Kingdom, genomes of two samples
were of lineage B.1.36, and the other two were of lineage B.1.1.7 (Alpha Variant).
The mutations in the consensus genomes contained the defining mutations of the
respective lineages of SARS-CoV-2.
Conclusion
We confirmed two genomic sequences of variant of concern VOC-202012/01 in
Nepal. Our study provides the concise genomic evidence for spread of different
lineages of SARS-CoV-2 – B.1.1, B.1.36 and B.1.1.7 of SARS-CoV-2 in Nepal.
KEY WORDS
COVID-19, Nepal, SARS-CoV-2, Variant of concern, Whole genome sequencing
Description
Shrestha R,1,2,3† Katuwal N,2,3† Adhikari N,2,3† Vanaerschot M,4 Tamrakar D,2,5 Dhimal M,6 Gyanwali P,6 Bhattarai S,6 Madhup SK,7 Devkota B8
1Department of Pharmacology,
Kathmandu University School of Medical Sciences,
Dhulikhel, Kavre, Nepal.
2Research and Development Division,
Dhulikhel Hospital, Kathmandu University Hospital,
Dhulikhel, Kavre, Nepal.
3Genomic Research Lab,
Dhulikhel Hospital, Kathmandu University Hospital,
Dhulikhel, Kavre, Nepal.
4Chan Zuckerberg Biohub,
San Francisco, USA.
5Department of Community Medicine,
Kathmandu University School of Medical Sciences,
Dhulikhel, Kavre, Nepal.
6Nepal Health Research Council, Ramshah Path,
Kathmandu, Nepal.
7Department of Microbiology,
Dhulikhel Hospital, Kathmandu University Hospital,
Dhulikhel, Kavre, Nepal.
8Ministry of Health and Population,
Kathmandu, Nepal
Keywords
COVID-19, Nepal, SARS-CoV-2, Variant of concern, Whole genome sequencing