Co-detection of various viruses in SARS-CoV-2 in children with respiratory infections

The co-detection of SARS-CoV-2 variant with other respiratory virus has been extensively investigated. However, conclusive evidence remains elusive and conflicted. This study investigated the source- and age-dependent prevalence, incidence, and co-detection of multiple viral infections in children younger than 18 years old who presented with clinical symptoms indicative of respiratory infections during SARS-CoV-2 pandemic. We retrospectively obtained and analyzed pediatric patients admitted to the institution and underwent Film Array Respiratory Panel (BIOFIRE^® RP2.1) testing between January 2021 and December 2022. This encompassed pre-Delta, Delta and omicron periods, evaluating Film Array results for singular and co-detections. The overall detection rate was 84.2% (1670/1983) among 1,983 pediatric patients. Of these, 106 were SARS-CoV-2 positive. Notably, 45 patients (42%) harbored SARS-CoV-2 as the sole pathogen. Co-detection was significant; 32 cases (30.2%) involved Human Rhinovirus/Enterovirus, 29 (24.5%) involved parainfluenza 3, and 26 (24.5%) involved Respiratory syncytial virus. Peaks of co-detected parainfluenza 3 and Respiratory syncytial virus were evident in the winter of 2022 and absent in 2021. The top three viral strain for co-detection was HRV/EV, PIV-3, and RSV. The emergence order of co-detection strain was HRV/EV ◊PIV-3◊ RSV during the Omicron period in Taiwan. We identified characteristic patterns of SARS-CoV-2-associated co-detections, with a notable emphasis on the co-detection of HRV/EV, PIV3, and RSV alongside SARS-CoV-2. This association appears to hold heightened significance during the Omicron variant era compared to earlier SARS-CoV-2 variants, which contrast with previous studies. The simultaneous circulation of different variants may contribute to variations in viral co-detection, particularly in young children, warranting further investigation.