Viral Metagenomic Sequencing Reveals Viral Codetection Patterns in Children with Respiratory Syncytial Virus Infection

Respiratory syncytial virus (RSV) is a leading cause of pediatric respiratory infections, yet the frequency and composition of viral codetections in affected children have not been extensively profiled using unbiased sequencing approaches. Here, we performed viral metagenomic sequencing on nasopharyngeal swabs collected from 42 pediatric patients with confirmed RSV infection to characterize the codetection landscape. RSV was detected and genotyped in all specimens. Beyond RSV, we identified nine additional human respiratory viruses coexisting across the cohort; several of these fall outside the scope of routine diagnostic panels, although their clinical significance remains uncertain. Codetections were the rule rather than the exception: 30 of 42 samples harbored at least three viruses, with up to seven distinct viruses detected in a single case. These findings underscore the taxonomic breadth and polymicrobial complexity of respiratory infections in children. Our results describe the viral codetection landscape in RSV-infected children, revealing a broader spectrum of co-occurring viruses than typically captured by targeted diagnostics, although the clinical significance of most codetections remains uncertain. These findings highlight the polymicrobial complexity of RSV infections and underscore the need for prospective studies to determine which codetections are clinically meaningful.