Coronavirus infections cause diseases that range from mild to severe in mammals and birds. In this study, we detected coronavirus infections in 748 farmed wild animals of 23 species in Guangdong, southern China, by RT-PCR and metagenomic analysis. We identified four coronaviruses in these wild animals and analysed their evolutionary origins. Coronaviruses detected in Rhizomys sinensis were genetically grouped into canine and rodent coronaviruses, which were likely recombinants of canine and rodent coronaviruses. The coronavirus found in Phasianus colchicus was a recombinant pheasant coronavirus of turkey coronavirus and infectious bronchitis virus. The coronavirus in Paguma larvata had a high nucleotide identity (94.6–98.5 per cent) with a coronavirus of bottlenose dolphin (Tursiops truncates). These findings suggested that the wildlife coronaviruses may have experienced homologous recombination and/or crossed the species barrier, likely resulting in the emergence of new coronaviruses. It is necessary to reduce human–animal interactions by prohibiting the eating and raising of wild animals, which may contribute to preventing the emergence of the next coronavirus pandemic.

Hybrid wild boar husbandry is an important component of livestock production in Northeast China. However, the current disease situation of these animals is largely unknown due to a lack of disease surveillance. The present study was conducted to determine the prevalence of several important viral diseases in the hybrid wild boar population of Northeast China. Between September 2015 to December 2016, 169 blood and 61 tissue samples were collected from apparently healthy hybrid wild boars from farms in Jilin, Inner Mongolia and Heilongjiang provinces. ELISA detected serum antibodies against classical swine fever virus (CSFV), porcine reproductive and respiratory syndrome virus (PRRSV), pseudorabies virus (PRV), porcine circovirus type 2 (PCV2) and Japanese encephalitis virus (JEV), but not against African swine fever virus (ASFV), with PCV2 having the highest seropositive rate (87.2–100% in different farms). RT-PCR or PCR performed on the processed samples detected only PCV2, with 33.1% (56/169) of blood samples and 32.8% (20/61) of spleen samples being positive, respectively, indicating widespread PCV2 infection in hybrid wild boars. Phylogenetic analysis of 15 PCV2 ORF2 sequences showed that they belong to genotypes PCV2a, PCV2b and PCV2d, with nucleotide and deduced amino acid homologies of 88.5–100% and 88.1–100%, respectively.

Circoviruses are a group of small circular, single-stranded DNA viruses that belong to the family Circoviridae. They are known to infect a wide variety of animals. Rhizomys sinensis is a species of rodent that is the reservoir of many zoonotic pathogens. Our previous study identified many sequencing reads mapped to the genome of viruses in Circoviridae in R. sinensis. However, little is known about the circulation and genetic characterization of circoviruses in R. sinensis. This study identified three different circoviruses in samples from 195 R. sinensis. First, the bamboo rat circovirus is widely prevalent in R. sinensis in Guangdong Province, and all strains could be divided into three clades based on nucleotide substitutions at specific sites. Second, and more important, porcine circovirus 2 (PCV2) was isolated for the first time from R. sinensis, which expanded the host range of PCV2 and indicated extra procedures would be required to protect livestock from this virus. Finally, a novel circovirus phylogenetically close to the dromedary stool-associated circular ssDNA virus was detected in 86 (44.1) samples, which may represent a new circovirus species. These results not only expand our understanding of the circovirus diversity in rodents, particularly in R. sinensis, but also underscore the importance of continued surveillance of viruses in wildlife populations, particularly in rodents, to prevent and control the spread of zoonotic pathogens.