AUTHOR=Jeewandara Chandima , Jayathilaka Deshni , Ranasinghe Diyanath , Hsu Nienyun Sharon , Ariyaratne Dinuka , Jayadas Tibutius Thanesh , Panambara Arachchige Deshan Madhusanka , Lindsey Benjamin B. , Gomes Laksiri , Parker Matthew D. , Wijewickrama Ananda , Karunaratne Malika , Ogg Graham S. , de Silva Thushan I. , Malavige Gathsaurie Neelika 

TITLE=Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.722838

DOI=10.3389/fmicb.2021.722838

ISSN=1664-302X

ABSTRACT=<p><bold>Background:</bold> 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.</p><p><bold>Methods:</bold> 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.</p><p><bold>Results:</bold> 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.</p><p><bold>Conclusions:</bold> 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.</p>