Coronaviruses (Co. Vs) 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 Co. Vs dominant in birds other than chickens remain enigmatic. In our previous study, we proposed that the Co. Vs dominant (i.e. mainly circulating) in ducks (Dd. CoVs) should represent a novel species, which was different from the one represented by the Co. Vs dominant in chickens (Cd. CoVs). In this study, we conducted a large-scale surveillance of Co. Vs in chickens, ducks, geese, pigeons and other birds (quails, sparrows and partridges) using a conserved RT-PCR assay. The surveillance demonstrated that Cd. CoVs, Dd. CoVs and the Co. Vs dominant in pigeons (Pd. CoVs) 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 Pd. CoVs and found that the genetic distances in these domains between Pd. CoVs and Dd. CoVs or Cd. CoVs are large enough to separate Pd. CoVs into a novel species, which were different from the ones represented by Dd. CoVs or Cd. CoVs 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 Co. Vs.
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