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

A unique feature of PdCV Ohio CVM1. Sequence analysis showed that the nucleotide sequences of the N and NS7 genes of PdCV Ohio CVM1 share higher homology with those of Hong Kong strain HKU15-44 than all other U.S. strains. Four continuous nucleotides (405C, 534C, 558A, and 564A) in the N gene are unique to Hong Kong strain HKU15-44 and the Ohio CVM1 strain (see Fig. S1 in the supplemental material). The corresponding nucleotides in all other U.S. strains are 405T, 534A, 558G, and 564G, all of which are silent mutations for N protein. However, the first three nucleotide changes result in 3 amino acid substitutions in the protein encoded by the NS7 gene, which overlaps with the N gene (see Fig. S1 ). Specifically, the shared amino acids in the predicted NS7 protein sequence of the Ohio CVM1 and Hong Kong strains are P104, P147, and N155, whereas all other U.S. strains at the same positions have L, Q, and S, respectively. Importantly, all other viral protein genes of Ohio CVM1 share higher homology with genes of other U.S. strains than with genes of the Hong Kong strain. This finding suggests that Ohio CVM1 may represent a recombinant strain in which the NS7 gene is derived from Hong Kong strains and the rest of the genome is derived from the U.S. strains. In addition, PdCV Ohio CVM1 has six other unique amino acid changes across the genome. M5309 and R5354 were unique for ORF1ab, I553 and K642 were unique for S protein, and S24 was unique for N protein.