London Calling 2023: Coinfection in endemic influenza A virus-infected herds using nanopore metagenomic sequencing of tracheobronchial swabs

Respiratory disease in swine results in lowered animal health, welfare, and economic losses. Influenza A plays an important role in respiratory infections, but the problem is multifactorial. To date, there are no complete diagnostics available to study these complexes. Hence, practitioners rely on targeted diagnostics, including RT-qPCR, antigen detection, and serology. This hampers effective preventive and therapeutic actions. A metagenomic diagnostic platform was applied to study respiratory disease across four age groups on 25 German farms. The detection of swine influenza A virus (swIAV) was assessed using RT-qPCR on tracheobronchial swabs, along with metagenomic characterization. This revealed the age-dependent interplay of known viral and bacterial agents. Also, some lesser-known microbes were identified. The effect of swIAV detection and associated clinical symptoms could also be studied. In conclusion, nanopore metagenomics was shown as promising tool to facilitate more complete routine diagnostics. The results contribute to the understanding of pathogen dynamics within the disease complex.