| ISSN |
2220-3249 (online) |
| Open Access |
This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: https://creativecommons.org/Licenses/by-nc/4.0/ |
| Copyright |
© The Author(s) 2025. Published by Baishideng Publishing Group Inc. All rights reserved. |
| Article Reprints |
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| Permissions |
For details, please visit: http://www.wjgnet.com/bpg/gerinfo/207
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| Publisher |
Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA |
| Website |
http://www.wjgnet.com |
| Category |
Virology |
| Manuscript Type |
Retrospective Study |
| Article Title |
Genomic and demographic characterization of SARS-CoV-2 infections within early Omicron cluster, Western Sri Lanka
|
| Manuscript Source |
Invited Manuscript |
| All Author List |
Nipuni Arachchige, Ramesha Dharmasiri, Achini Weerathunga, Shehan Senanayake, Nadeeka Janage and Rohitha Muthugala |
| ORCID |
|
| Funding Agency and Grant Number |
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| Corresponding Author |
Rohitha Muthugala, Head, MD, Department of Molecular Biology, Medical Research Institute, No. 527 Dr. Danister De Silva Mawatha, Colombo 00800, Western, Sri Lanka. rohithavm@yahoo.com |
| Key Words |
SARS-CoV-2; COVID-19; Omicron variant; Genomic characterization; Western Sri Lanka |
| 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. |
| Publish Date |
2025-06-23 07:18 |
| Citation |
<p>Arachchige N, Dharmasiri R, Weerathunga A, Senanayake S, Janage N, Muthugala R. Genomic and demographic characterization of SARS-CoV-2 infections within early Omicron cluster, Western Sri Lanka. <i>World J Virol</i> 2025; 14(2): 106108</p> |
| URL |
https://www.wjgnet.com/2220-3249/full/v14/i2/106108.htm |
| DOI |
https://dx.doi.org/10.5501/wjv.v14.i2.106108 |
