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

Since identification of the first Sri Lankan individual with the SARS-CoV-2 in early March 2020, small clusters that occurred were largely contained until the current extensive outbreak that started in early October 2020. In order to understand the molecular epidemiology of SARS-CoV-2 in Sri Lanka, we carried out genomic sequencing overlaid on available epidemiological data. The B.1.411 lineage was most prevalent, which was established in Sri Lanka and caused outbreaks throughout the country. The estimated time of the most recent common ancestor of this lineage was 10th August 2020 (95% lower and upper bounds 6th July to 7th September), 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. Ongoing genomic surveillance in Sri Lanka is vital as vaccine roll-out increases. Article summary lineFollowing repeated successful control of small outbreaks early in the pandemic caused by multiple lineages, the subsequent spread of a single lineage established in Sri Lanka (B.1.411) appears to be the cause of the large outbreak that started in early October 2020.