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Volume 17
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10.3390/v17091189
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Article

Molecular Epidemiology of SARS-CoV-2 Detected from Different Areas of the Kandy District of Sri Lanka from November 2020–March 2022

by
Bushran N. Iqbal
1,
Sibra R. M. Shihab
1,
Tao Zhang
2,
Aadhil Ahamed
1,
Shiyamalee Arunasalam
1,
Samanthika Jagoda
3,
Leo L. M. Poon
2,
Malik Peiris
2 and
Faseeha Noordeen
1,*
1
Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya 20400, Sri Lanka
2
School of Public Health, Li KaShing, Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
3
Department of Veterinary Pathobiology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya 20400, Sri Lanka
*
Author to whom correspondence should be addressed.
Viruses 2025, 17(9), 1189; https://doi.org/10.3390/v17091189
Submission received: 14 July 2025 / Revised: 15 August 2025 / Accepted: 26 August 2025 / Published: 29 August 2025
(This article belongs to the Section Coronaviruses)
Versions Notes

Abstract

A comprehensive analysis of the molecular epidemiology of SARS-CoV-2 in the Kandy District of Sri Lanka from November 2020 to March 2022 was conducted to address the limited genomic surveillance data available across the country. The study investigated the circulating SARS-CoV-2 lineages, their temporal dynamics, and the associated mutational profiles in the study area. A total of 280 SARS-CoV-2-positive samples were selected, and 252 complete genomes were successfully sequenced using Oxford Nanopore Technology. Lineage classification was performed using the EPI2ME tool, while phylogenetic relationships were inferred through maximum likelihood and time-scaled phylogenetic trees using IQ-TREE2 and BEAST, respectively. Amino acid substitutions were analyzed to understand lineage-specific mutation patterns. Fifteen SARS-CoV-2 lineages were identified, and of those B.1.411 (36%) was the most prevalent, followed by Q.8 (21%), AY.28 (9.5%), and the Delta and Omicron variants. The lineage distribution showed a temporal shift from B.1.411 to Alpha, Delta, and finally the Omicron, mirroring the global trends. Time to the most recent common ancestor analyses provided estimates for the introduction of major variants, while mutation analysis revealed the widespread occurrence of D614G in the spike protein and lineage-specific mutations across structural, non-structural, and accessory proteins.Detection of the Epsilon variant (absent in other national-level studies) in November 2020, highlighted the regional heterogeneity viral spread. This study emphasizes the importance of localized genomic surveillance to capture the true diversity and evolution of SARS-CoV-2, to facilitate containment strategies in resource-limited settings.
Keywords: Sri Lanka; Kandy district; SARS-CoV-2 infection; mutation profile; phylogenetic analysis Sri Lanka; Kandy district; SARS-CoV-2 infection; mutation profile; phylogenetic analysis

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MDPI and ACS Style

Iqbal, B.N.; Shihab, S.R.M.; Zhang, T.; Ahamed, A.; Arunasalam, S.; Jagoda, S.; Poon, L.L.M.; Peiris, M.; Noordeen, F. Molecular Epidemiology of SARS-CoV-2 Detected from Different Areas of the Kandy District of Sri Lanka from November 2020–March 2022. Viruses 2025, 17, 1189. https://doi.org/10.3390/v17091189

AMA Style

Iqbal BN, Shihab SRM, Zhang T, Ahamed A, Arunasalam S, Jagoda S, Poon LLM, Peiris M, Noordeen F. Molecular Epidemiology of SARS-CoV-2 Detected from Different Areas of the Kandy District of Sri Lanka from November 2020–March 2022. Viruses. 2025; 17(9):1189. https://doi.org/10.3390/v17091189

Chicago/Turabian Style

Iqbal, Bushran N., Sibra R. M. Shihab, Tao Zhang, Aadhil Ahamed, Shiyamalee Arunasalam, Samanthika Jagoda, Leo L. M. Poon, Malik Peiris, and Faseeha Noordeen. 2025. "Molecular Epidemiology of SARS-CoV-2 Detected from Different Areas of the Kandy District of Sri Lanka from November 2020–March 2022" Viruses 17, no. 9: 1189. https://doi.org/10.3390/v17091189

APA Style

Iqbal, B. N., Shihab, S. R. M., Zhang, T., Ahamed, A., Arunasalam, S., Jagoda, S., Poon, L. L. M., Peiris, M., & Noordeen, F. (2025). Molecular Epidemiology of SARS-CoV-2 Detected from Different Areas of the Kandy District of Sri Lanka from November 2020–March 2022. Viruses, 17(9), 1189. https://doi.org/10.3390/v17091189

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