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

Abstract

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. 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. 552 adults (≥16 years) and 60 children (<16y) were SARS-CoV-2-positive; lowest median Ct values (highest VL) were observed on the 2nd symptomatic day. Adults vaccinated within 12M (n=106) had peak VL on the 3rd day, and those vaccinated >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. 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.