Genomic and demographic characterization of SARS-CoV-2 infections within early Omicron cluster, Western Sri Lanka.

Abstract

Background: The emergence of the Omicron variant (B.1.1.529) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) raised global concerns with its highly transmissible nature.

Aim: To investigate the genomic, clinical, and demographic characteristics of Omicron infections within the early outbreak cluster in western part of Sri Lanka.

Methods: We analyzed sequence data from January 2022 to April 2022 to understand variant dynamics, clinical presentation, and demographic associations.

Results: Whole-genome sequencing of 85 nasopharyngeal and throat swab samples collected in western part of Sri Lanka between January and April 2022 identified 70 (82.34%) of it as Omicron variants. BA.2 was the most prevalent sub-lineage (57%), followed by BA.1.1 (14.20%) and majority of them were from > 12 years old individuals. Phylogenetic analysis revealed clustering into four distinct clades (21I, 21K, 21L, and 21M), suggesting potential differences in transmission chains or evolutionary pressures.

Conclusion: This study found BA.2 to be the predominant Omicron sub-lineage in the western part of Sri Lanka during the first quarter of 2022, aligning with global trends. Phylogenetic analysis revealed diverse introductions and local transmission. Continued genomic surveillance and robust public health measures remain crucial for managing the evolving SARS-CoV-2 landscape.