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

We previously reported that nasal SARS-CoV-2 viral loads (VLs) peaked around the fourth day of symptoms in highly immune adults sampled April 2022 to April 2023, while influenza A VLs 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.

Participants with symptomatic upper respiratory infection were recruited at testing centers in Georgia 14 April 2023 to 11 April 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 cycle threshold (Ct) values recorded.

552 adults (aged ≥16 years) and 60 children (aged <16 years) were SARS-CoV-2 positive; lowest median Ct values (highest VL) were observed on the second symptomatic day. Adults vaccinated within 12 months (n = 106) had peak VL on the third day, and those vaccinated ≥12 months prior (n = 334), on the second. In influenza A-positive adults (n = 181) and children (n = 147), median VL peaked on the first symptomatic day, vs the fourth day in 157 influenza B-positive participants.

In 2023-2025, median SARS-CoV-2 VL peaked earlier relative to symptom onset compared to a highly immune 2022-2023 cohort. More recent vaccination correlated with delayed peak VL, suggesting that more robust immunity correlates with earlier symptom onset relative to peak. Median influenza A VLs were highest at symptom onset, vs 4 days into symptoms for influenza B. These findings can inform use of multiplexed antigen tests amidst changing immunity and viral circulation patterns.