Genomic and epidemiological analysis of SARS-CoV-2 viruses in Sri Lanka

Abstract

Background: In order to understand the molecular epidemiology of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Sri Lanka, since March 2020, we carried out genomic sequencing overlaid on available epidemiological data until April 2021.

Methods: Whole genome sequencing was carried out on diagnostic sputum or nasopharyngeal swabs from 373 patients with COVID-19. Molecular clock phylogenetic analysis was undertaken to further explore dominant lineages.

Results: The B.1.411 lineage was most prevalent, which was established in Sri Lanka and caused outbreaks throughout the country until March 2021. The estimated time of the most recent common ancestor (tMRCA) of this lineage was June 1, 2020 (with 95% lower and upper bounds March 30 to July 27) suggesting cryptic transmission may have occurred, prior to a large epidemic starting in October 2020. Returning travellers were identified with infections caused by lineage B.1.258, as well as the more transmissible B.1.1.7 lineage, which has replaced B.1.411 to fuel the ongoing large outbreak in the country.

Conclusions: The large outbreak that started in early October, is due to spread of a single virus lineage, B.1.411 until the end of March 2021, when B.1.1.7 emerged and became the dominant lineage.

Metadata

Authors/Creators:	Jeewandara, C. Jayathilaka, D. Ranasinghe, D. Hsu, N.S. Ariyaratne, D. Jayadas, T.T. Panambara Arachchige, D.M. Lindsey, B.B. https://orcid.org/0000-0003-4227-2592 Gomes, L. Parker, M.D. Wijewickrama, A. Karunaratne, M. Ogg, G.S. de Silva, T.I. https://orcid.org/0000-0002-6498-9212 Malavige, G.N.
Copyright, Publisher and Additional Information:	© 2021 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Keywords:	SARS-CoV-2; genomic sequencing; pangolin lineages; B.1.411; B.1.1.7; molecular epidemiology
Dates:	Accepted: 24 August 2021 Published (online): 16 September 2021 Published: 16 September 2021
Institution:	The University of Sheffield
Academic Units:	The University of Sheffield > Faculty of Medicine, Dentistry and Health (Sheffield)
Depositing User:	Symplectic Sheffield
Date Deposited:	07 Oct 2021 15:04
Last Modified:	07 Oct 2021 15:04
Status:	Published
Publisher:	Frontiers Media SA
Refereed:	Yes
Identification Number:	https://doi.org/10.3389/fmicb.2021.722838
Related URLs:	Dataset