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

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creativeworkseries.issn1812-2027
dc.contributor.authorShrestha, R
dc.contributor.authorKatuwal, N
dc.contributor.authorAdhikari, N
dc.contributor.authorVanaerschot, M
dc.contributor.authorTamrakar, D
dc.contributor.authorDhimal, M
dc.contributor.authorGyanwali, P
dc.contributor.authorBhattarai, S
dc.contributor.authorMadhup, SK
dc.contributor.authorDevkota, B
dc.date.accessioned2025-12-14T06:55:43Z
dc.date.available2025-12-14T06:55:43Z
dc.date.issued2021
dc.descriptionShrestha 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
dc.description.abstractABSTRACT 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
dc.identifier.urihttps://hdl.handle.net/20.500.14572/3617
dc.language.isoen_US
dc.publisherKathmandu University
dc.subjectCOVID-19
dc.subjectNepal
dc.subjectSARS-CoV-2
dc.subjectVariant of concern
dc.subjectWhole genome sequencing
dc.titleWhole Genome Sequence Analysis to Identify SARS-CoV-2 Variant in Nepal
dc.typeArticle
dspace.entity.typePublication
local.article.typeOriginal Article
oaire.citation.endPage242
oaire.citation.startPage237
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relation.isJournalIssueOfPublication.latestForDiscovery4c8a2c01-809d-4901-9318-1bc7ee5426a3
relation.isJournalOfPublicationa782b7ff-cf89-4178-ad1c-11ed89cfe1bd

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