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

• DOI: 10.3389/fmicb.2021.722838
• Publication Date: 2021-09-16T04:56:25Z
• Authors: Chandima Jeewandara; Deshni Jayathilaka; Diyanath Ranasinghe; Nienyun Sharon Hsu; Dinuka Ariyaratne; Tibutius Thanesh ...; Deshan Madhusanka...; Benjamin B. Lindsey; Laksiri Gomes; Matthew D. Parker; Ananda Wijewickrama; Malika Karunaratne; Graham S. Ogg; Thushan I. de Silva; Gathsaurie Neelik...
• Keywords: Sri lanka; Pandemic; 2019-20 coronavirus outbreak

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 was diagnostic sputum or nasopharyngeal swabs from 373 patients with COVID-19. Molecular clock phylogenetic analysis undertaken further explore dominant lineages. Results: The B.1.411 lineage most prevalent, which established Lanka and caused outbreaks throughout country estimated time recent common ancestor (tMRCA) this June 1, 2020 (with 95% lower upper bounds 30 July 27) suggesting cryptic transmission may have occurred, prior a large epidemic starting October 2020. Returning travellers were identified infections by B.1.258, as well more transmissible B.1.1.7 lineage, has replaced fuel ongoing outbreak country. Conclusions: that started early October, is due spread single virus end 2021, when emerged became lineage.