Early functional maturation of anti-Spike antibodies predicts SARS-CoV-2 RNA clearance in mild infection

SARS-CoV-2 infection exhibits heterogeneous viral clearance kinetics even in individuals with mild disease. The immunological determinants underlying rapid versus prolonged viral RNA detection remain incompletely defined. Here, we performed a three-year longitudinal analysis of 77 healthcare professionals infected with the ancestral Wuhan strain. Participants were stratified according to viral RNA clearance kinetics into non-persistent ([≤]21 days) and persistent (>21 days) groups. Non-persistent individuals exhibited accelerated seroconversion to Spike and receptor-binding domain (RBD) antigens during the first 11 days after symptom onset. Early antibody responses were characterized by higher functional activity, including significantly greater neutralizing activity against the ancestral strain. In contrast, persistent individuals displayed delayed seroconversion, prolonged IgM responses, and weaker coordination among IgG subclasses, with less synchronized subclass responses, during early infection. Importantly, total immunoglobulin levels did not distinguish the groups. Cross-variant antibody recognition during acute infection was limited and largely strain-focused in both groups. During convalescence, durable anti-Spike IgG responses were maintained independently of persistence status, without significant differences in cross-variant breadth. Vaccination robustly amplified antibody titers, enhanced variant recognition, and sustained high-affinity responses in both groups. Together, our findings demonstrate that the timing and functional quality of early humoral maturation, reflected by neutralizing antibody activity, rather than antibody magnitude or breadth, are key determinants of SARS-CoV-2 RNA clearance in mild infection. These results highlight the importance of early neutralizing antibody generation in shaping acute viral control and the long-term immune architecture.