Patient and Immunological Factors Associated With Delayed Clearance of Mucosal Severe Acute Respiratory Syndrome Coronavirus 2 RNA and Symptom Persistence

Serial blood and mucosal samples were characterized for 102 participants enrolled a median of 7.0 days after coronavirus disease 2019 diagnosis. Mucosal RNA was detectable for a median of 31.5 (95% confidence interval [CI], 20.5-63.5) days, with persistence >= 1 month associated with obesity (body mass index [BMI] >= 30 kg/m2; odds ratio [OR], 3.9 [95% CI, 1.2-13.8]) but not age, sex, or chronic conditions. Fifteen participants had likely reinfection; lower serum anti-spike IgG levels were associated with reinfection risk. Nearly half of participants (47%) reported symptoms lasting >= 2-3 months; persistence >= 3 months was associated with BMI >= 30 kg/m2 (OR, 4.2 [95% CI, 1.1-12.8]) and peak anti-spike and anti-nucleocapsid antibody levels. Elevated body mass index is associated with mucosal viral persistence and prolonged symptoms after SARS-CoV-2 infection. Low serum anti-S IgG levels were associated with reinfection risk, and higher peak anti-S and anti-NC antibody levels were associated with persistent symptoms.