A SARS-CoV-2 variant of C-36 lineage with L452R mutation infects a family in Sri Lanka, but has limited spread – A Case Series

We report a family cluster of six members who tested positive for SARS-CoV-2 infection in April 2021 at University Hospital, Kotelawala Defence University, Sri Lanka. Samples from three members were subjected to Next Generation Sequencing (NGS) and all were identified as SARS-CoV-2 variant of pangolin lineage C.36, containing the L452R mutation which is associated with high infectivity. All patients recovered with mild symptoms and no complications. This is the first report identifying a new variant of the C.36 lineage containing the L452R mutation from Sri Lanka followed by detection of the same lineage from Northern Sri Lanka in June 2021 and no reported cases hereafter. At that time, it was relatively rare for a whole family to get infected, and the concern was that this strain would spread rapidly. Due to unknown circumstances it never spread to be detected by the national surveillance programme. Other variants, B.1.411 and B.1.1.7, more dominant and infectious, were already in circulation and presumably outcompeted this strain.