Genomic surveillance of SARS-CoV-2 in Nepal

Binod Khadka; Rajindra Napit; Kathie A Mihindukulasuriya; Smita Shrestha; Ramanuj Rauniyar; Eans T Tuladhar; Lindsay Droit; Anne M Paredes; Runa Jha; Roji Raut; Bimalesh K Jha; Scott A Handley; Annie Elong-Ngono; Sujan Shresta; David Wang; Krishna D Manandhar

doi:10.1128/mra.00789-24

Genomic surveillance of SARS-CoV-2 in Nepal

Microbiol Resour Announc. 2024 Dec 12;13(12):e0078924. doi: 10.1128/mra.00789-24. Epub 2024 Nov 12.

Authors

Binod Khadka¹, Rajindra Napit^{1

2}, Kathie A Mihindukulasuriya^{3

4

5}, Smita Shrestha¹, Ramanuj Rauniyar¹, Eans T Tuladhar^{1

6}, Lindsay Droit^{3

4}, Anne M Paredes⁴, Runa Jha⁷, Roji Raut^{1

2}, Bimalesh K Jha⁷, Scott A Handley^{4

5}, Annie Elong-Ngono⁸, Sujan Shresta⁸, David Wang³, Krishna D Manandhar¹

Affiliations

¹ Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal.
² Nirvana Biotech, Lalitpur, Nepal.
³ Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.
⁴ Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
⁵ The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA.
⁶ Maharajgunj Medical Campus, Tribhuvan University, Kathmandu, Nepal.
⁷ National Public Health Laboratory, Teku, Kathmandu, Nepal.
⁸ Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, California, USA.

Abstract

During the COVID-19 pandemic, Nepal, like other countries, faced emerging SARS-CoV-2 variants. To evaluate the circulating variants, 278 samples collected between September 2021 and March 2022 were sequenced in the country. From these, 229 high-quality genomes were obtained (82.97% Omicron and 17.03% Delta) highlighting the genomic diversity of SARS-CoV-2 in Nepal.

Keywords: COVID-19; Illumina; coronavirus; whole-genome sequencing.

Abstract

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