Surveillance and taxonomic analysis of the coronavirus dominant in pigeons in China

Abstract

Coronaviruses (CoVs) are found in humans and a wide variety of wild and domestic animals, and of substantial impact on human and animal health. In poultry, the genetic diversity, evolution, distribution and taxonomy of CoVs dominant in birds other than chickens remain enigmatic. In our previous study, we proposed that the CoVs dominant (i.e. mainly circulating) in ducks (DdCoVs) should represent a novel species, which was different from the one represented by the CoVs dominant in chickens (CdCoVs). In this study, we conducted a large-scale surveillance of CoVs in chickens, ducks, geese, pigeons and other birds (quails, sparrows and partridges) using a conserved RT-PCR assay. The surveillance demonstrated that CdCoVs, DdCoVs and the CoVs dominant in pigeons (PdCoVs) belong to different lineages, and they are all prevalent in live poultry markets and the backyard flocks in some regions of China. We further sequenced seven Coronaviridae-wide conserved domains in their replicase polyprotein pp1ab of seven PdCoVs and found that the genetic distances in these domains between PdCoVs and DdCoVs or CdCoVs are large enough to separate PdCoVs into a novel species, which were different from the ones represented by DdCoVs or CdCoVs within the genus Gammacoronavirus, per the species demarcation criterion of International Committee on Taxonomy of Viruses. This report shed novel insight into the genetic diversity, distribution, evolution and taxonomy of avian CoVs.

Keywords: coronavirus; genetic distance; lineage; pigeon; sequence; species; surveillance; taxonomy.

FIGURE 1

Phylogenetic relationships among some CoVs identified through this study based on the sequences in the replicase gene amplified by the conserved RT‐PCR. Six reference sequences were marked with asterisks, and many sequence names were hided due to space limitation

FIGURE 2

The positive rates of PdCoVs, CdCoVs, DdCoVs and GdCoVs in pigeon, chicken, duck and goose samples

FIGURE 3

Alignment of partial sequences of the Nsp12 domain of some PdCoVs, CdCoVs and DdCoVs. The sites were numbered as per the first sequence, and those sites conserved in two lineages were marked with asterisks

FIGURE 4

Phylogenetic relationships of 22 CoVs based on the sequences of seven conserved domains. The first phylogenetic tree was based on the sequences of the seven domains combined together, and the remaining trees were based on the sequences of each domain. The longest branches were shortened for space saving