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.
Highlights
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has emerged as the leading cause of mortality in several countries in the world
Presence of ORF1ab gene and N gene of SARS-CoV-2 was detected with Novel Coronavirus (2019-Ncov) Nucleic Acid Diagnostic Kit (Sansure Biotech) and S gene was detected by Taqpath COVID-19 RT PCR kit (Applied Biosystems) by real time RT PCR in ABI 7500 real time PCR system (Applied Biosystems, United States)
During early April, SARS-CoV-2 spread within closed community clusters in the Colombo Municipality region (CMC) region
Summary
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has emerged as the leading cause of mortality in several countries in the world. There was a surge in the number of cases with discovery of a new cluster in early October 2020 in a clothing factory in the district adjacent to Colombo (Gampaha) This was followed by rapid spread of SARS-CoV-2 within the Colombo Municipality region (CMC), fish markets and subsequently to the whole country. This outbreak continued to evolve, with infections being reported in all regions of the country, but the numbers gradually declined by end of March 2021, with the number of daily cases been reported falling to 200–300 cases per day (Ministry of Health, 2021a). 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
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