While gammacoronaviruses mainly comprise infectious bronchitis virus (IBV) and its closely related bird coronaviruses (Co. Vs), the only mammalian gammacoronavirus was discovered from a white beluga whale (beluga whale CoV [BWCoV] SW1) in 2008. In this study, we discovered a novel gammacoronavirus from fecal samples from three Indo-Pacific bottlenose dolphins (Tursiops aduncus), which we named bottlenose dolphin CoV (Bd. CoV) HKU22. All the three Bd. CoV HKU22-positive samples were collected on the same date, suggesting a cluster of infection, with viral loads of 1×103 to 1×105 copies per ml. Clearance of virus was associated with a specific antibody response against the nucleocapsid of Bd. CoV HKU22. Complete genome sequencing and comparative genome analysis showed that Bd. CoV HKU22 and BWCoV SW1 have similar genome characteristics and structures. Their genome size is about 32,000 nucleotides, the largest among all Co. Vs, as a result of multiple unique open reading frames (NS5a, NS5b, NS5c, NS6, NS7, NS8, NS9, and NS10) between their membrane (M) and nucleocapsid (N) protein genes. Although comparative genome analysis showed that Bd. CoV HKU22 and BWCoV SW1 should belong to the same species, a major difference was observed in the proteins encoded by their spike (S) genes, which showed only 74.3 to 74.7% amino acid identities. The high ratios of the number of synonymous substitutions per synonymous site (Ks) to the number of nonsynonymous substitutions per nonsynonymous site (Ka) in multiple regions of the genome, especially the S gene (Ka/Ks ratio, 2.5), indicated that Bd. CoV HKU22 may be evolving rapidly, supporting a recent transmission event to the bottlenose dolphins. We propose a distinct species, Cetacean coronavirus, in Gammacoronavirus, to include Bd. CoV HKU22 and BWCoV SW1, whereas IBV and its closely related bird Co. Vs represent another species, Avian coronavirus, in Gammacoronavirus. © 2014, American Society for Microbiology.
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