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

Core Tip

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.