Genomic characterization and molecular evolutionary relationship of a recombinant porcine deltacoronavirus strain...

Since the porcine deltacoronavirus (PDCoV) was discovered and reported in 2012, it has spread to multiple countries. In this study, the complete genome sequence of a recombinant PDCoV strains (CH/XJYN/2016 strain) was obtained using a high-throughput sequencing method and its organization was characterized. The results of evolutionary relationship analysis based on complete genome sequences showed that the CH/XJYN/2016 strain clusters into a large clade with part of Chinese strains and Southeast Asian strains. The nucleotide homology analysis of CH/XJYN/2016 strain proved that the complete genome shared 97.3-97.9% homology; the E gene of CH/XJYN/2016 has the highest homology (99.2-100%) and the S gene has the lowest homology (95.6-97.7%) compared with its closed strains. In particular, there are multiple specific and common amino acid variations in S protein of CH/XJYN/2016 strain, and the potential high antigenic diversities of different proteins were clustered in antigenic space. Moreover, the major recombination of CH/XJYN/2016 strain from Thai PDCoV/Swine/Thailand/S5015L/2015 strain and minor recombination from Chinese strain were revealed. Together, the characterization and genetic analysis of a recombinant PDCoV strain provide important references for the epidemiological study of PDCoV.