Genomic characterization and pathogenicity analysis of a porcine deltacoronavirus strain isolated in western China

Abstract

Porcine deltacoronavirus (PDCoV) is an enteric virus that was first identified in 2012. Although PDCoV has been detected worldwide, there is little information about its circulation in western China. In this study, fecal samples were collected from piglets with watery diarrhea in western China between 2015 and 2018 for the detection of PDCoV. The positive rate was 29.9%. A PDCoV strain (CHN/CQ/BN23/2016, BN23) was isolated and selected for further investigation. Phylogenetic analysis showed that this strain formed an individual cluster between the early Chinese lineage and the Chinese lineage. RDP4 and SimPlot analysis demonstrated that strain BN23 is a recombinant of Thailand/S5015L/2015 and CHN-AH-2004. The pathogenicity of BN23 was evaluated in 3-day-old piglets. Challenged piglets developed serious clinical signs and died at 3 days post-inoculation. Our data show that PDCoV is prevalent in western China and that strain BN23 is highly pathogenic to newborn piglets. Therefore, more attention should be paid to emerging PDCoV strains in western China. Supplementary Information The online version contains supplementary material available at 10.1007/s00705-022-05549-w.

Phylogenetically evolutionary analysis provides insights into the genetic diversity and adaptive evolution of porcine deltacoronavirus

“…As shown in Table 3 and Fig. 5, all the reported recombinant PDCoV strains were summarized and analyzed [14,[16][17][18][19][20][21][22]. The data displayed that the recombinant events often occurred in Nsp2 (5 times) and Nsp3 (4 times), followed by S gene (3 times), Nsp12 (2 times), Nsp13 (2 times), M gene (2 times), 5′ UTR (1 time), Nsp4 (1time), Nsp15 (1 time), and NS6 (1 time).…”