Surveillance of Emerging SARS-CoV-2 Variants by Nanopore Technology based Genome Sequencing

Background: Detection of emerging variants of severe acute respiratory syndrome coronavirus-2, genome sequencing in all countries at least 1% of their infections is recommended. Nanopore technology platform was setup at the Reference laboratory during pandemic and sequencing is continued to understand the circulated variants in the country. Objectives: This study was to describe the surveillance of emerging variants by nanopore technology-based genome sequencing in different COVID-19 waves in Sri Lanka and to demonstrate the association with the sample characteristics, and vaccination status. Methodology: The study analyzed 207 RNA positive swab samples received to sequence laboratory during different waves. The N gene cut-off threshold <30 considered as the major inclusion criteria. Viral RNA was extracted, elutes were subjected to nanopore sequencing according to the manufacturer’s instructions using the SQK-RBK110.96 rapid barcoding kit. All the sequencing data were uploaded in the publicly accessible database, GISAID. Results: Analysis revealed variants distributed throughout the period were 58% Omicron, 22% Delta, 4% Alpha, and only less than 1% of Kappa variant. 16% study samples were remained unassigned. Omicron variant was circulated among all age groups and in all the provinces. Ct value and variants assigned percentage was 100% in Ct values 10-15 while only 45% assigned Ct value over 25. Conclusion: The present study declared the emergence, prevalence, and distribution of SARS-CoV-2 variants locally and summarized the establishment of Nanopore Technology by enabling whole genome sequencing in a low resource setting country.