The incidence of
long COVID is substantial, even in people who did not require hospitalization for acute
COVID-19. The pathobiological mechanisms of
long COVID and the role of early viral kinetics in its development are largely unknown. Seventy-three non-hospitalized adult participants were enrolled within approximately 48 hours of their first positive SARS-CoV-2 RT-PCR test, and mid-turbinate nasal and saliva samples were collected up to 9 times within the first 45 days after enrollment. Samples were assayed for SARS-CoV-2 using RT-PCR and additional test results were abstracted from the clinical record. Each participant indicated the presence and severity of 49
long- COVID symptoms at 1-, 3-, 6-, 12-, and 18-months post-COVID-19 diagnosis. Time from acute
COVID-19 illness onset to SARS-CoV-2
RNA clearance greater or less than 28 days was tested for association with the presence or absence of each of 49
long COVID symptoms at 90+ days from acute
COVID-19 symptom onset.
Brain fog and
muscle pain at 90+ days after acute
COVID-19 onset were negatively associated with
viral RNA clearance within 28 days of acute
COVID-19 onset with adjustment for age, sex, BMI ≥ 25, and COVID vaccination status prior to
COVID-19 (
brain fog: aRR 0.46, 95% CI 0.22-0.95;
muscle pain: aRR 0.28, 95% CI 0.08-0.94). This work indicates that at least two
long COVID symptoms -
brain fog and
muscle pain - at 90+ days from acute
COVID-19 onset are specifically associated with longer time to clearance of SARS-CoV-2
RNA from the upper respiratory tract.