A Genomic Surveillance During the Evolution of SARS-CoV-2O micron Variants in Sri Lanka

Abstract

Objective: To illustrate the genomic evolution and mutation pattern of the SARS-CoV-2 Omicron variant and its sub-variants in Sri Lanka from December 2021 to March 2024, examine the association with the sample characteristics, and summarize the principle of the Oxford Nanopore Technology sequencing platform.

Methods: The study retrospectively analyzed 189 SARS-CoV-2 RNA-positive swab samples received at the sequencing laboratory from December 2021 to March 2024. SARS-CoV-2 positive samples sequenced as the Omicron variant was considered the major inclusion criteria. The viral RNA was extracted, and the DNA library was prepared according to the ONT protocol and subjected to the Nanopore sequencing. Consensus sequences were generated and analyzed.

Results: Of the total 189 Omicron cases, 8 major Omicron sub-lineages including BA.1(30.2%), BA.2(14.3%), BA.5(16.4%), BA.2.12.1(0.5%), BA.2.75(1.6%), CH.1.1(4.2%), XBB(16.9%), JN.1(15.9%) were identified, and the spike protein showed the highest number of mutations in all sub-lineages. The Omicron variant was circulated among all age groups, predominated in the 20 ≤ age <40 group and Western province reported the highest cases.

Conclusion: The present study examined the genomic evolution and mutation pattern of the SARS-CoV-2 Omicron variant locally and the principle and application of Oxford Nanopore Technology in the sequencing platform. Further, the study strongly convinced the importance of continuous surveillance systems and strengthened sequencing facilities in the country