Metagenomic sequencing of avian coronavirus positive clinical chicken samples

Avian coronavirus (Igacovirus, Gammacoronavirus genus, Orthocoronavirinae subfamily) or infectious bronchitis virus (IBV)causes the economically important highly contagious disease infectious bronchitis in chicken (Gallus gallus). The present study used random primed RNA sequencing to determine the complete genome of IBV directly from a realtime RT-PCR positive pooled cloacal swab sample of chickens sampled in 2019 in Belgium, as well as from a pooled respiratory/intestinal tissue sample realtime RT-PCR positive for both IBV and Newcastle disease virus (NDV) from a chicken sampled in Belgium in 2020. In addition, the IBV isolated in ovo from the later sample was included for comparison. A rich RNA virome containing known avian viruses was present in the clinical samples