Paradoxical G-quadruplex distribution in coronavirus genomes reveals functional constraints and antiviral therapeutic opportunities

We computationally characterized G-quadruplex (G4) distributions across 31 coronavirus genomes to identify conserved structural features as potential antiviral therapeutic targets. Through an integrated approach combining consensus G4 detection, dinucleotide-preserving null models, and pooled Poisson rate ratios, we identified a paradoxical G4 distribution pattern: genome-wide depletion (mean fold change = 0.56) coupled with strong regional enrichment in Spike (S) protein (incidence rate ratio [IRR] = 17.9; 95% CI: 11.7-27.6) and Nucleocapsid (N) protein (IRR = 15.2; 95% CI: 8.7-26.6), while untranslated regions (UTRs) showed complete G4 absence. Thermodynamic stability assessment identified 38 stable G4 candidates (ΔG < -5 kcal/mol), with 52.6% concentrated in Nucleocapsid protein regions, suggesting candidates for structure-based antiviral drug development awaiting experimental confirmation. This paradoxical distribution pattern-genome-wide depletion coupled with strong regional enrichment in functionally critical proteins (Spike and Nucleocapsid)-provides a mechanistic framework for developing betacoronavirus-targeted therapeutics based on conserved G4 structures.