Wild birds are natural hosts of multiple microbial agents, including a wide diversity of coronaviruses. Here we describe a pan-Coronavirus detection RT-PCR method to identify those viruses regardless of the coronavirus genus or nature of the specimen. We also describe a protocol using high-throughput sequencing technologies to obtain their entire genome, which overcomes the inherent difficulties of wild bird coronavirus sequencing, that is, their genetic diversity and the lack of virus isolation methods.
Keywords: Deltacoronavirus; Gammacoronavirus; Illumina MiSeq; Next-generation sequencing; Pan-Coronavirus; RT-PCR; Sample collection; Wild birds.