Published online Jun 25, 2025. doi: 10.5501/wjv.v14.i2.106108
Revised: April 6, 2025
Accepted: April 24, 2025
Published online: June 25, 2025
Processing time: 126 Days and 16.7 Hours
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.
To investigate the genomic, clinical, and demographic characteristics of Omicron infections within the early outbreak cluster in western part of Sri Lanka.
We analyzed sequence data from January 2022 to April 2022 to understand variant dynamics, clinical presentation, and demographic associations.
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.
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.
Core Tip: This study investigates into the critical period of the early Omicron outbreak in Western Sri Lanka, providing valuable insights into the variant's genomic profile and its impact on the local population. The emergence of the Omicron variant, specifically B.1.1.529, triggered global alarm due to its high transmissibility. In this retrospective study, we aimed to characterize the genomic, clinical, and demographic features of Omicron infections during the initial outbreak phase in Western Sri Lanka, spanning from January to April 2022. Methodology involved analyzing sequence data from 85 nasopharyngeal and throat swab samples. Whole-genome sequencing, conducted using the Oxford Nanopore Midnight protocol and analyzed via the Epi2Me platform, revealed that 70 samples, representing 82.34% of the total, were Omicron variants. We utilized bioinformatic tools such as Mega 11, Nextstrain, and PangoLineage for in-depth phylogenetic and lineage analysis. Demographic and clinical data were extracted from patient request forms. Findings highlighted the dominance of the BA.2 sub-lineage, accounting for 57% of the Omicron cases, followed by BA.1.1 at 14.20%. The study population primarily consisted of individuals over 12 years of age, and a male predominance was observed. Phylogenetic analysis revealed distinct clustering into clades 21K, 21L, and 21M, suggesting multiple introductions and local transmission events. The prevalence of BA.2 aligns with global trends during that period, emphasizing its enhanced transmissibility and immune evasion. The demographic data, showing a higher incidence in adults and males, raised questions about vaccine effectiveness and potential gender-specific factors. The phylogenetic clustering indicates a complex transmission dynamic, highlighting the need for continuous genomic surveillance. In conclusion, this study underscores the importance of genomic surveillance and robust public health measures in managing the evolving severe acute respiratory syndrome coronavirus 2 landscape. The dominance of BA.2 and the observed demographic patterns offer crucial insights for targeted public health interventions. However, the retrospective design and limited sample size suggest the need for future research with larger, more diverse datasets to further elucidate the impact of Omicron and its sub-lineages.