Variant emergence, not vaccine deployment, drives episodic positive selection on the SARS-CoV-2 spike at provincial scale in Canada

Mass immunization against SARS-CoV-2 created a heterogeneous landscape of antibody-mediated immune pressure, yet whether this pressure measurably altered episodic positive selection on spike remains unresolved. Using Canadian genomic surveillance data spanning the five major variants of concern (Alpha, Beta, Gamma, Delta, and Omicron), we inferred time-resolved phylogenies from spike-coding sequences and applied site- and branch-level episodic selection models to identify when and where adaptive change occurred. To evaluate whether vaccination intensity was associated with selection, we integrated these phylogenetic analyses with provincial vaccination time series using cross-correlation and lagged panel regression models that accounted for province and time effects, lineage prevalence, and sampling heterogeneity. Episodic positive selection was concentrated at a limited number of spike codons, especially within the N-terminal domain, receptor-binding domain, and furin cleavage region. However, these signals were dominated by substitutions associated with variant emergence, particularly during the Alpha-to-Delta transition, rather than by vaccination rollout. Whole-gene tests provided no evidence that vaccine intensity was associated with elevated episodic selection, and residualized vaccination trajectories did not predict selection at biologically plausible lags. Across provinces, the timing and distribution of selection events were inconsistent with a vaccine-driven escape model. Together, these results indicate that, at provincial resolution in Canada, episodic positive selection on SARS-CoV-2 spike was driven primarily by variant turnover rather than vaccine deployment. More broadly, this study provides a quantitative, VOC-resolved assessment of spike evolution in a structured epidemic and suggests that population-level vaccination intensity was not a detectable determinant of spike adaptation in the period examined.