Identification and survey of a novel avian coronavirus in ducks

Abstract

The rapid discovery of novel viruses using next generation sequencing (NGS) technologies including DNA-Seq and RNA-Seq, has greatly expanded our understanding of viral diversity in recent years. The timely identification of novel viruses using NGS technologies is also important for us to control emerging infectious diseases caused by novel viruses. In this study, we identified a novel duck coronavirus (CoV), distinct with chicken infectious bronchitis virus (IBV), using RNA-Seq. The novel duck-specific CoV was a potential novel species within the genus Gammacoronavirus, as indicated by sequences of three regions in the viral 1b gene. We also performed a survey of CoVs in domestic fowls in China using reverse-transcription polymerase chain reaction (RT-PCR), targeting the viral nucleocapsid (N) gene. A total of 102 CoV positives were identified through the survey. Phylogenetic analysis of the viral N sequences suggested that CoVs in domestic fowls have diverged into several region-specific or host-specific clades or subclades in the world, and IBVs can infect ducks, geese and pigeons, although they mainly circulate in chickens. Moreover, this study provided novel data supporting the notion that some host-specific CoVs other than IBVs circulate in ducks, geese and pigeons, and indicated that the novel duck-specific CoV identified through RNA-Seq in this study is genetically closer to some CoVs circulating in wild water fowls. Taken together, this study shed new insight into the diversity, distribution, evolution and control of avian CoVs.

Figure 1. The genome structure of avian CoV and positions of the contigs and amplicons detected in this study.

Figure 2. Phylogenetic relationships of two duck CoVs and 13 IBVs based on the 1b1 (A), 1b2 (B) and 1b3 (C) regions in the viral 1b gene.

The GenBank accession numbers were given before the corresponding strain designations where CK, DK, CH were the abbreviations of chicken, duck and China. Two CoVs detected from ducks were marked in triangles and circles. Bootstrap values were given at the relevant nodes.

Figure 3. The percentage identities between two duck CoVs and 13 IBVs based on their amino acid sequences in the 1b1, 1b2 and 1b3 regions in the viral 1b gene.

Figure 4. Phylogenetic relationships of representative avian CoVs based on their N gene sequences.

The GenBank accession numbers were given before the corresponding strain designations where CK, DK, TK, GS, PN, CH were the abbreviations of chicken, duck, turkey, goose, pigeon and China. The CoVs reported by this study were marked with triangles, and the CoVs from birds other than chickens were marked with circles except for those reported by this study. Bootstrap values were given at the relevant nodes.

Figure 5. Phylogenetic relationships of some CoVs based on their 1b3 sequences.

Duck CoVs were marked with triangles. Bootstrap values were given at the relevant nodes.