Publication: Genomic analysis of SARS-CoV-2 Circulating during Second and Third Wave of COVID-19 in Nepal
Date
2023
Journal Title
Journal ISSN
Volume Title
Publisher
Nepal Health Research Council
Abstract
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
Description
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