Sri Lanka is currently experiencing a massive and interconnected cluster. The initial cluster was reported on the 4th of October 2020 in an apparel industry factory in Minuwangoda, Gampaha. Subsequently, linked clusters were identified in Peliyagoda at a location commonly referred to as a fish market and in the Colombo Municipality Council area (CMC). Scientists at the Department of Immunology and Molecular Medicine and Allergy, Immunology and Cell Biology Unit, University of the Sri Jayewardenepura, conducted a whole genomic sequencing of the SARS-CoV2 virus with support from the Australian Government through WHO Sri Lanka.
Whole genome sequencing is the process of determining the complete DNA sequence of an organism’s genome, or all of the genetic material of an organism, at a single time. Whole genome sequencing has many applications as a research tool. In this case, genomic sequencing allowed scientists to determine the strain or strains of the virus responsible for the current outbreak. It also allowed them to assess whether there are any mutations and, if so, the implications of these mutations. Finally, it enabled them to investigate the relationship between the currently circulating virus strains and previously circulating strains in Sri Lanka.
Sixteen virus strains from patients of the three current clusters were sequenced. Results indicated that the virus strains circulating in all the three clusters are of a common origin . Fifteen of the sixteen strains also had the D614G mutation, which is associated with high viral loads and higher rates of transmissibility.
Thus the scientists conclude that, unlike the COVID-19 outbreak in March-April in Sri Lanka, which was due to several SARS-CoV2 virus strains, the current outbreak is caused by one strain. It has B.1.42 lineage, which means it is similar to strains seen in Europe (Denmark/Sweden).
The information garnered from the whole genomse sequencing will inform risk communication and community engagement work. Since the strain associated with the new cluster has the property of high transmissibility, upcoming communication materials will place additional emphasis on the importance of practicing prevention measures to protect onself and our communities. Generated data will also be shared with WHO headquarters and will be included in the global data base for further studies.