{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:41:37Z","timestamp":1760060497910,"version":"build-2065373602"},"reference-count":27,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T00:00:00Z","timestamp":1756425600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"University of Peradeniya","award":["URG-CG-2021\/22\/56\/M","T11-705\/21-N"],"award-info":[{"award-number":["URG-CG-2021\/22\/56\/M","T11-705\/21-N"]}]},{"name":"Peradeniya Medical School Alumni Association-UK (PeMSAA-UK)","award":["URG-CG-2021\/22\/56\/M","T11-705\/21-N"],"award-info":[{"award-number":["URG-CG-2021\/22\/56\/M","T11-705\/21-N"]}]},{"name":"University of Hong Kong and Theme-Based Research Scheme","award":["URG-CG-2021\/22\/56\/M","T11-705\/21-N"],"award-info":[{"award-number":["URG-CG-2021\/22\/56\/M","T11-705\/21-N"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/v17091189","type":"journal-article","created":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T16:18:15Z","timestamp":1756484295000},"page":"1189","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Molecular Epidemiology of SARS-CoV-2 Detected from Different Areas of the Kandy District of Sri Lanka from November 2020\u2013March 2022"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6299-9556","authenticated-orcid":false,"given":"Bushran N.","family":"Iqbal","sequence":"first","affiliation":[{"name":"Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya 20400, Sri Lanka"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sibra R. M.","family":"Shihab","sequence":"additional","affiliation":[{"name":"Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya 20400, Sri Lanka"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tao","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Public Health, Li KaShing, Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-3437-2202","authenticated-orcid":false,"given":"Aadhil","family":"Ahamed","sequence":"additional","affiliation":[{"name":"Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya 20400, Sri Lanka"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2410-8844","authenticated-orcid":false,"given":"Shiyamalee","family":"Arunasalam","sequence":"additional","affiliation":[{"name":"Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya 20400, Sri Lanka"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samanthika","family":"Jagoda","sequence":"additional","affiliation":[{"name":"Department of Veterinary Pathobiology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya 20400, Sri Lanka"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leo L. M.","family":"Poon","sequence":"additional","affiliation":[{"name":"School of Public Health, Li KaShing, Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Malik","family":"Peiris","sequence":"additional","affiliation":[{"name":"School of Public Health, Li KaShing, Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2018-0606","authenticated-orcid":false,"given":"Faseeha","family":"Noordeen","sequence":"additional","affiliation":[{"name":"Diagnostic and Research Virology Laboratory, Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya 20400, Sri Lanka"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,8,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"109968","DOI":"10.1016\/j.intimp.2023.109968","article-title":"Update on the effectiveness of COVID-19 vaccines on different variants of SARS-CoV-2","volume":"117","author":"Firouzabadi","year":"2023","journal-title":"Int. Immunopharmacol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1001\/jama.2020.13719","article-title":"Presence of Genetic Variants among Young Men with Severe COVID-19","volume":"324","author":"Simons","year":"2020","journal-title":"JAMA-J. Am. Med. Assoc."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Kumar, R., Srivastava, Y., Muthuramalingam, P., Singh, S.K., Verma, G., Tiwari, S., Tandel, N., Beura, S.K., Panigrahi, A.R., and Maji, S. (2023). Understanding Mutations in Human SARS-CoV-2 Spike Glycoprotein: A Systematic Review & Meta-Analysis. Viruses, 15.","DOI":"10.3390\/v15040856"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"106121","DOI":"10.1016\/j.jinf.2024.106121","article-title":"Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein","volume":"88","author":"Yao","year":"2024","journal-title":"J. Infect."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Jeewandara, C., Jayathilaka, D., Ranasinghe, D., Hsu, N.S., Ariyaratne, D., Jayadas, T.T., Panambara Arachchige, D.M., Lindsey, B.B., Gomes, L., and Parker, M.D. (2021). Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.722838"},{"key":"ref_6","first-page":"OP4-A27","article-title":"Surveillance of SARS-CoV-2 variants targeting SARS-CoV-2 spike protein mutations associated with variants of concern and variants of interest in the Central Province of Sri Lanka from November 2020 to November 2021","volume":"13","author":"Iqbal","year":"2023","journal-title":"Sri Lankan J. Infect. Dis."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"114374","DOI":"10.1016\/j.jviromet.2021.114374","article-title":"Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR","volume":"300","author":"Gomes","year":"2022","journal-title":"J. Virol. Methods"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Ranasinghe, D., Jayathilaka, D., Jeewandara, C., Gunasinghe, D., Ariyaratne, D., Jayadas, T.T.P., Kuruppu, H., Wijesinghe, A., Bary, F.F., and Madhusanka, D. (2022). Molecular Epidemiology of AY.28 and AY.104 Delta Sub-lineages in Sri Lanka. Front. Public Health, 10.","DOI":"10.3389\/fpubh.2022.873633"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"313","DOI":"10.4103\/1995-7645.380720","article-title":"Surveillance of emerging SARS-CoV-2 variants by nanopore technology-based genome sequencing","volume":"16","author":"Abeynayake","year":"2023","journal-title":"Asian Pac. J. Trop. Med."},{"key":"ref_10","first-page":"2","article-title":"A Genomic Surveillance During the Evolution of SARS-CoV-2 Omicron Variants in Sri Lanka","volume":"168","author":"Chathuranga","year":"2024","journal-title":"J. Virol. Res. Rep."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Nguyen, T.T., Pham, T.N., Van, T.D., Nguyen, T.T., Ngoc Nguyen, D.T., Minh Le, H.N., Eden, J.S., Rockett, R.J., Hong Nguyen, T.T., and Ngoc Vu, B.T. (2020). Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0242537"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Jeewandara, C., Guruge, D., Abyrathna, I.S., Danasekara, S., Gunasekera, B., Pushpakumara, P.D., Madhusanka, D., Jayathilaka, D., Ranasinghe, T., and Somathilake, G. (2021). Seroprevalence of SARS-CoV-2 Infection in the Colombo Municipality Region, Sri Lanka. Front. Public Health, 9.","DOI":"10.3389\/fpubh.2021.724398"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"vew007","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"Rambaut","year":"2016","journal-title":"Virus Evol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"vey016","DOI":"10.1093\/ve\/vey016","article-title":"Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10","volume":"4","author":"Suchard","year":"2018","journal-title":"Virus Evol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Syst. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2910","DOI":"10.1016\/j.bpj.2022.11.025","article-title":"Structural effects of spike protein D614G mutation in SARS-CoV-2","volume":"122","author":"Dokainish","year":"2023","journal-title":"Biophys. J."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Tsuchiya, K., Yamamoto, N., Hosaka, Y., Wakita, M., Hiki, M., Matsushita, Y., Mori, H., Hori, S., Misawa, S., and Miida, T. (2022). Molecular characterization of SARS-CoV-2 detected in Tokyo, Japan during five waves: Identification of the amino acid substitutions associated with transmissibility and severity. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.912061"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1186\/s12985-022-01951-7","article-title":"Mutations in SARS-CoV-2 structural proteins: A global analysis","volume":"19","author":"Abavisani","year":"2022","journal-title":"Virol. J."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Johnson, B.A., Zhou, Y., Lokugamage, K.G., Vu, M.N., Bopp, N., Crocquet-Valdes, P.A., Kalveram, B., Schindewolf, C., Liu, Y., and Scharton, D. (2022). Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. PLoS Pathog., 18.","DOI":"10.1371\/journal.ppat.1010627"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Chatterjee, S., Bhattacharya, M., Nag, S., Dhama, K., and Chakraborty, C. (2023). A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies. Viruses, 15.","DOI":"10.3390\/v15010167"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Goldswain, H., Dong, X., Penrice-Randal, R., Alruwaili, M., Shawli, G.T., Prince, T., Williamson, M.K., Raghwani, J., Randle, N., and Jones, B. (2023). The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection. Genome Biol., 24.","DOI":"10.1186\/s13059-023-02881-5"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/s12985-024-02342-w","article-title":"SARS-CoV-2 outbreak: Role of viral proteins and genomic diversity in virus infection and COVID-19 progression","volume":"21","author":"Hussein","year":"2024","journal-title":"Virol. J."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Hassan, S.S., Choudhury, P.P., Dayhoff, G.W., Aljabali, A.A.A., Uhal, B.D., Lundstrom, K., Rezaei, N., Pizzol, D., Adadi, P., and Lal, A. (2022). The importance of accessory protein variants in the pathogenicity of SARS-CoV-2. Arch. Biochem. Biophys., 717.","DOI":"10.1016\/j.abb.2022.109124"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"331","DOI":"10.12688\/f1000research.146123.1","article-title":"SARS-CoV-2-ORF3a variant Q57H reduces its pro-apoptotic activity in host cells","volume":"13","author":"Landherr","year":"2024","journal-title":"F1000Research"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e262","DOI":"10.1017\/S0950268820002599","article-title":"ORF3a mutation associated with higher mortality rate in SARS-CoV-2 infection","volume":"148","author":"Majumdar","year":"2020","journal-title":"Epidemiol. Infect."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"10","DOI":"10.5501\/wjv.v14.i2.106108","article-title":"Genomic and demographic characterization of SARS-CoV-2 infections within early Omicron cluster, Western Sri Lanka","volume":"14","author":"Arachchige","year":"2025","journal-title":"World J. Virol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/9\/1189\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:35:48Z","timestamp":1760034948000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/9\/1189"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,29]]},"references-count":27,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2025,9]]}},"alternative-id":["v17091189"],"URL":"https:\/\/doi.org\/10.3390\/v17091189","relation":{},"ISSN":["1999-4915"],"issn-type":[{"type":"electronic","value":"1999-4915"}],"subject":[],"published":{"date-parts":[[2025,8,29]]}}}