Phylodynamics of SARSCoV-2 Lineages B.1.1.7, B.1.1.52 and B.1.617.2 in Nigeria suggests divergent Evolutionary trajectories
Abstract
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, and BEAST v2.5 The spatial distribution, evolutionary history, viral ancestral introductions, and geographic dispersal patterns were characterized.
Results
The Delta variant exhibited the widest geographic spread, detected in 14 states, while the Alpha variant was 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 × 10^-4 substitutions/site/year). Effective viral population analyses showed distinct patterns: Omicron sustained elevated population growth over time, while Delta experienced a decline after initial expansion. The Time to Most Recent Common Ancestor (TMRCA) analysis suggested that some variants circulated earlier than previously reported, with the earliest introduction dating back to October 2019.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.
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