SARS-CoV-2 intra-host recombination promotes epistatic spike interactions and temperature-dependent adaptation

Prolonged infections in immunocompromized individuals are associated with accumulation of unexpected combinations of mutations, as exemplified by the Omicron variant. Here, we show that intra-host evolution during a chronic SARS-CoV-2 infection in the pre-Omicron era was associated with mutations that modulate antibody evasion, cell entry efficiency, spike processing, and fusogenicity. Single spike N-terminal mutations S13I and W64G exerted deleterious impacts on S1/S2 cleavage, syncytia formation, and cell entry but combined through an inferred recombination event with P330S to restore function. The single mutants were never detected individually in respiratory samples, but mediated temperature-dependent evasion from neutralizing antibodies and altered reliance on TMPRSS2-mediated membrane fusion, possibly explaining their transient selection. Molecular dynamics simulations revealed that W64G induces local N-terminal domain destabilization with distal effects at the S1/S2 cleavage loop, linking structural perturbation to functional defects and immune evasion. Together, these findings demonstrate how intra-host recombination contributes to viral adaptation.