Peak Nasal SARS-CoV-2 and Influenza Viral Loads Relative to Symptom Onset, 2022–2025: Impact of Vaccination and Implications for Multiplexed Testing

BACKGROUND: We previously reported that nasal SARS-CoV-2 viral loads (VL) peaked around the fourth day of symptoms in highly immune adults sampled April 2022 - April 2023, while influenza A VL peaked soon after symptom onset. We hypothesized that SARS-CoV-2 kinetics may have changed due to reduced COVID-19 incidence and altered vaccination patterns. Understanding how viral kinetics evolve over time is essential to inform testing strategies. METHODS: Participants with symptomatic upper respiratory infection were recruited at testing centers in Georgia April 14, 2023-April 11, 2025. Participants reported date of symptom onset and vaccination history. A nasal swab was tested on the Xpert® Xpress CoV-2/Flu/RSV-Plus assay and Ct values recorded. RESULTS: 552 adults (≥16 years) and 60 children (12M prior (n=334), on the 2nd. In influenza A-positive adults (n=181) and children (n=147), median VL peaked on the 1st symptomatic day, versus the 4th day in 157 influenza B-positive participants. CONCLUSIONS: In 2023-25, median SARS-CoV-2 VL peaked earlier relative to symptom onset compared to a highly immune 2022-23 cohort. More recent vaccination correlated with delayed peak VL, suggesting more robust immunity correlates with earlier symptom onset relative to peak. Median influenza A VL were highest at symptom onset, versus 4 days into symptoms for influenza B. These findings can inform use of multiplexed antigen tests amidst changing immunity and viral circulation patterns.