{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T01:57:31Z","timestamp":1774317451810,"version":"3.50.1"},"reference-count":29,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T00:00:00Z","timestamp":1761436800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"U.S. Department of Energy by Lawrence Livermore National Laboratory","award":["DE-AC52-07NA27344"],"award-info":[{"award-number":["DE-AC52-07NA27344"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Background: The early months of the COVID-19 pandemic were characterized by high transmission rates and mortality, compounded by the emergence of multiple SARS-CoV-2 lineages, including Variants of Concern (VOCs). This study investigates the phylodynamic and spatio-temporal trends of VOCs during the peak of the pandemic in Nigeria. Methods: Whole-genome sequencing (WGS) data from three major VOCs circulating in Nigeria, B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.529 (Omicron), were analyzed using tools such as Nextclade, R Studio v 4.2.3, and BEAST X v 10.5.0. The spatial distribution, evolutionary history, viral ancestral introductions, and geographic dispersal patterns were characterized. Results: Three major lineages following WHO nomenclature were identified: Alpha, Delta, and Omicron. The Delta variant exhibited the widest geographic spread, detected in 14 states, while the Alpha variant was the least distributed, identified in only eight states but present across most epidemiological weeks studied. Evolutionary rates varied slightly, with Alpha exhibiting the slowest rate (2.66 \u00d7 10\u22124 substitutions\/site\/year). Viral population analyses showed distinct patterns: Omicron sustained elevated population growth over time, while Delta declined after initial expansion. The earliest Times to Most Recent Common Ancestor (TMRCA) were consistent with the earliest outbreaks of SARS-CoV-2 globally. Geographic transmission analysis indicated a predominant coastal-to-inland spread for all variants, with Omicron showing the most diffuse dispersal, highlighting commercial routes as significant drivers of viral diffusion. Conclusion: The SARS-CoV-2 epidemic in Nigeria was characterized by multiple variant introductions and a dominant coastal-to-inland spread, emphasizing that despite lockdown measures, commercial trade routes played a critical role in viral dissemination. These findings provide insights into pandemic control strategies and future outbreak preparedness.<\/jats:p>","DOI":"10.3390\/pathogens14111091","type":"journal-article","created":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T00:51:42Z","timestamp":1761526302000},"page":"1091","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Phylodynamics of SARS-CoV-2 Lineages B.1.1.7, B.1.1.529 and B.1.617.2 in Nigeria Suggests Divergent Evolutionary Trajectories"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9933-8751","authenticated-orcid":false,"given":"Babatunde O.","family":"Motayo","sequence":"first","affiliation":[{"name":"Department of Medical Microbiology, Federal Medical Centre, Abeokuta 110222, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0647-498X","authenticated-orcid":false,"given":"Olukunle O.","family":"Oluwasemowo","sequence":"additional","affiliation":[{"name":"Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, P.O Box 808, L-452, Livermore, CA 94550, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anyebe B.","family":"Onoja","sequence":"additional","affiliation":[{"name":"Department of Virology, College of Medicine, University of Ibadan, Ibadan 211101, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0697-8176","authenticated-orcid":false,"given":"Paul A.","family":"Akinduti","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratory Science, Babcock University, Ilishan 121103, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adedayo O.","family":"Faneye","sequence":"additional","affiliation":[{"name":"Department of Virology, College of Medicine, University of Ibadan, Ibadan 211101, Nigeria"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,10,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in China","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1056\/NEJMoa2001017","article-title":"A Novel Coronavirus from Patients with Pneumonia in China 2019","volume":"382","author":"Zhu","year":"2020","journal-title":"N. 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