Origin, Evolution, and Virulence of Porcine Deltacoronaviruses in the United States

Ma, Yuanmei; Zhang, Yu; Liang, Xueya; Lou, Fangfei; Oglesbee, Michael; Krakowka, Steven; Li, Jianrong

Phylogenetic analysis. Phylogenetic trees were constructed by the neighbor-joining method in the MEGA 6 program using 11 U.S. PdCV strains, two Hong Kong PdCV strains, one South Korean PdCV strain, and nine avian deltacoronavirus strains. Sequence BLAST found that CoVs from Asian leopard cats and Chinese ferret-badgers also belongs to the genus Deltacoronavirus, for which partial genomic sequences encoded by the 3CLpro, RdRp, Hel, S, and N genes are available (23) . Thus, known viral protein genes of Asian leopard cat and Chinese ferret-badger CoVs were included in the phylogenetic analysis. All U.S. PdCV strains, together with two Hong Kong strains, HKU15-44 and HKU15-155, and one Korean strain, fell into one cluster, forming the PdCV group ( Fig. 2A ). PdCV shares a closer relationship with other mammal deltacoronaviruses (i.e., Asian leopard cat and Chinese ferret-badger CoVs) than with avian deltacoronaviruses. This suggests that porcine, feline, and avian deltacoronaviruses may have a common ancestor ( Fig. 2A) . Similarly, PdCV shares higher homology with Asian leopard cat CoVs than with avian deltacoronaviruses in the phylogenetic tree analysis when the N, M, E, and NS6 protein gene sequences are used (data not shown). In addition, the phylogenetic tree of the NS7 protein gene showed that PdCV Ohio CVM1 is more closely related to HKU15-44 and HKU15-155 than to other U.S. PdCV strains (Fig. 2B) .