Pairwise Respiratory Viral Co-Detection Patterns Before, During, and After the COVID-19 Pandemic: An 18-Year Multiplex PCR Surveillance Study

The coronavirus disease pandemic impacted respiratory virus circulation and seasonality, but its effect on viral co-detection patterns remains unclear. We examined temporal changes in co-detection burden and dominant pairwise patterns across pandemic periods. We analyzed 23,284 respiratory virus multiplex PCR tests performed at a tertiary care center in the Republic of Korea from 2007 to 2024. Co-detection was defined as detection of ≥2 viruses in a single episode. To address temporal panel changes, we used crude full-panel, restricted 12-target, and recent-period sensitivity analyses based on a stable respiratory virus target set. Co-detection burden showed discordant trends across analytical approaches. In the crude analysis, co-detection among positive episodes was the highest during the pandemic. In the restricted analysis, co-detection decreased from 20.5% before to 14.8% during and 12.2% after the pandemic. Pairwise co-detection patterns also shifted: adenovirus–rhinovirus predominated before the pandemic, whereas rhinovirus-containing pairs involving parainfluenza virus type 3 or respiratory syncytial virus B accounted for relatively larger shares during and, to a lesser extent, after the pandemic. These findings suggest that post-pandemic respiratory virus surveillance should consider not only single-virus positivity or overall co-detection frequency, but also the composition of dominant pairwise viral combinations captured by multiplex PCR.