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

Sri lanka Pandemic 2019-20 coronavirus outbreak
DOI: 10.3389/fmicb.2021.722838 Publication Date: 2021-09-16T04:56:25Z
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 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.
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