Surveillance of emerging SARS-CoV-2 variants by nanopore technology-based genome sequencing

Abstract

Objective: To surveill emerging variants by nanopore technology-based genome sequencing in different COVID-19 waves in Sri Lanka and to examine the association with the sample characteristics, and vaccination status. Methods: The study analyzed 207 RNA positive swab samples received to sequence laboratory during different waves. The N gene cut-off threshold of less than 30 was considered as the major inclusion criteria. Viral RNA was extracted, and elutes were subjected to nanopore sequencing. All the sequencing data were uploaded in the publicly accessible database, GISAID. Results: The Omicron, Delta and Alpha variants accounted for 58%, 22% and 4% of the variants throughout the period. Less than 1% were Kappa variant and 16% of the study samples 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 of 10-15 while only 45% assigned Ct value over 25. Conclusions: The present study examined the emergence, prevalence, and distribution of SARS-CoV-2 variants locally and has shown that nanopore technology-based genome sequencing enables whole genome sequencing in a low resource setting country.

Keywords

• emerging sars-cov-2 variants; laboratory surveillance; nanopore technology; genome sequencing; bioinformatics analysis and phylogeny; sociodemographic and sample cutoff (ct) threshold; global sharing of genomic data/gisaid