Respiratory viral co-detection in paediatric SARS-CoV-2 infection: associations with viral co-circulation and clinical phenotypes

BACKGROUND Respiratory viral infections in children are characterised by the co-circulation of multiple viral pathogens, but the relevance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-detection with other respiratory viruses remains unclear. OBJECTIVES To evaluate the clinical and epidemiological implications of respiratory viral co-detection and the impact of viral diversity in paediatric SARS-CoV-2 infection. METHODS We conducted a retrospective-prospective molecular epidemiology study including children (0-11 years) with reverse transcription-polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2 infection in Natal, northeast Brazil, between 2021 and 2024. Samples were analysed by multiplex RT-PCR for ten respiratory viruses. Associations between co-detection, the number of co-detected viruses, and clinical manifestations were assessed using multivariable logistic regression. FINDINGS Among 545 cases, 13.2% showed viral co-detection. Co-detection was associated with dyspnoea, respiratory distress, low oxygen saturation, and diarrhoea, and inversely associated with cough. An increasing number of co-detected viruses was linked to more severe manifestations. Distinct viral combinations were associated with different clinical profiles. SARS-CoV-2 viral load and variants were not associated with co-detection. MAIN CONCLUSIONS Respiratory viral co-detection is associated with distinct clinical and epidemiological profiles influenced by the number of co-detected viruses and viral combinations. These findings highlight the role of viral co-circulation and suggest interactions among respiratory viruses in the clinical expression of disease in children.