Genomic analysis of SARS-CoV-2 Circulating during Second and Third Wave of COVID-19 in Nepal

  • Dipesh Tamrakar Department of Community Medicine, Kathmandu University School of Medical Science
  • Nishan Katuwal Molecular and Genomic Sequencing Research Lab, Dhulikhel Hospital, Kathmandu University Hospital
  • Navin Adhikari Department of Zoology and Physiology, University of Wyoming
  • Surendra Kumar Madhup Department of Microbiology, Kathmandu University School of Medical Sciences
  • Meghnath Dhimal Nepal Health Research Council, Ramshahpath, Kathmandu, Nepal
  • Rajeev Shrestha Molecular and Genomic Sequencing Research Lab and Center for infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University Hospital
DOI: https://doi.org/10.33314/jnhrc.v21i1.4489

Abstract

Background: In Nepal, since the first detection of COVID-19 case in January 2020, the total cases have rose to almost a million with more than 12,000 deaths. Till now, WHO has classified 5 variants of SARS-Cov2 as variant of concerns at different time points causing many waves in different countries and regions at different time points. Nepal had also faced three distinct waves of COVID-19 caused by different variant of COVID 19. The objective of this study was to perform whole-genome sequencing of SARS-CoV-2 circulating in different waves of COVID-19 in Nepal and investigate its variant or lineage.
Methods: In this study, samples from 49 SARS-CoV-2 infected subjects from May 2021 to January 2022, were investigated. The methodology followed RNA extraction, real-time PCR for confirmation and whole-genome sequencing. The consensus genomes were interpreted with appropriate bioinformatics tools and databases.
Results: Sequence analysis of 49 genomes revealed to be of Delta (n=27) and Omicron Variant (n=22). The mutations in the consensus genomes contained the defining mutations of the respective lineages/variants. There were 20 genomes of Omicron sub-lineage BA.2, 1 of BA.1.1 and 1 of B.1.1.529.
Conclusions: This study provides concise genomic evidence of presence of Delta and Omicron variant of COVID-19 in Nepal. Delta and Omicron variants were driving the second wave and the third wave of COVID-19 respectively in Nepal. Therefore, the genomic surveillance must be increased to clearly map out the pandemic and strategize vaccination approaches in the country.
Keywords: COVID-19; delta, omicron; Nepal;SARS-CoV-2; whole-genome sequencing

Published
2023-09-08
How to Cite
TamrakarD., KatuwalN., AdhikariN., MadhupS. K., DhimalM., & ShresthaR. (2023). Genomic analysis of SARS-CoV-2 Circulating during Second and Third Wave of COVID-19 in Nepal. Journal of Nepal Health Research Council, 21(1), 57-62. https://doi.org/10.33314/jnhrc.v21i1.4489
Issue
Vol. 21 No. 1 (2023): Issue 58 Jan-March, 2023
Section
Original Article

Copyright (c) 2023 Dipesh Tamrakar, Nishan Katuwal, Navin Adhikari, Surendra Kumar Madhup, Meghnath Dhimal, Rajeev Shrestha

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