Evolutionary and genomic analysis of four SARS-CoV-2 isolates circulating in March 2020 in Sri Lanka; Additional evidence on multiple introduction and further transmission

Abstract The molecular epidemiology of the virus, and mapping help to understand the evolution of the epidemics and apply quick control measures. The study genomic evidence of multiple SARS-CoV-2 introductions into Sri Lanka and virus evolution during circulation. Whole-genome sequences of four SARS-CoV-2 strains obtained from COVID-19 positive patients reported in Sri Lanka during March 2020 were compared with sequences from Europe and elsewhere. The phylogenetic analysis revealed that the sequence of the sample of first local patient collected on 10th March, who contacted tourists from Italy, was clustered with SARS-CoV-2 strains collected from Italy, Germany, France and Mexico. Subsequently, the sequence of the isolate obtained on 19th March also clustered in the same group with the samples collected in March and April from Belgium, France, India, and South Africa. The other two strains of SARS-CoV-2 were segregated from the main cluster, and the sample collected from 16th March clustered with England and the sample collected on 30th March showed the highest genetic divergent to the isolate of Wuhan, China. Here we report the first molecular epidemiological study conducted on circulating SARS-CoV-2 in Sri Lanka. The finding provides the robustness of molecular epidemiological tools and its application in tracing possible exposure in disease transmission during the pandemic.