Neutral Impact of SARS-CoV-2 Coinfection on the Recombination-Driven Evolution of Endemic HCoV-OC43

Knowledge gaps exist on whether SARS-CoV-2 co-infection alters recombination frequency or induces phylogenetic incongruities in endemic β-coronaviruses (HCoV-OC43, HCoV-HKU1), limiting our understanding of cross-species evolution. Among 7213 COVID-19 and 1590 non-COVID-19 acute respiratory cases (2021–2022) screened via multiplex PCR, β-coronavirus co-infections (SARS-CoV-2 + HCoV-OC43/HKU1) and single HCoV-OC43/HKU1 infections were identified. Whole-genome sequencing (Illumina NovaSeq) was performed. Phylogenies were reconstructed using Bayesian inference (MrBayes). Recombination was assessed via Bootscan analysis (SimPlot). Co-infection prevalence was low (0.51%, mainly HCoV-HKU1: 0.28%, HCoV-OC43: 0.11%). HCoV-OC43 diverged into lineage 1 (genotype K) and a novel recombinant lineage 2 (genotypes F/J/G/I segments), exhibiting accelerated evolution. HCoV-HKU1 remained genetically stable (genotype B). Co-infection status did not influence evolutionary outcomes. While SARS-CoV-2 co-infection may favor transmission of endemic HCoVs, their evolution appears driven by population-level selection, not co-infection. HCoV-OC43 underwent recombination-driven diversification, contrasting sharply with HCoV-HKU1’s stasis, highlighting distinct evolutionary strategies. Integrated genomic and clinical surveillance is critical for tracking coronavirus adaptation.