Emerging and re-emerging coronaviruses in pigs

Abstract

Porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), and swine acute diarrhea syndrome-coronavirus (SADS-CoV) are emerging/reemerging coronaviruses (CoVs). They cause acute gastroenteritis in neonatal piglets. Sequence analyses suggest that PEDV and SADS-CoV may have originated from bat CoVs and PDCoV from a sparrow CoV, reaffirming the interspecies transmission of CoVs. The clinical signs and pathogenesis of the three viruses are similar. Necrosis of infected intestinal epithelial cells occurs, causing villous atrophy that results in malabsorptive diarrhea. The severe diarrhea and vomiting may lead to dehydration and death of piglets. Natural infection induces protective immunity, but there is no cross-protection among the three viruses. Besides strict biosecurity measures, individual vaccines are needed for each virus for disease prevention and control.

Graphical abstract

Figure 1

Genomic organization of alphacoronavirus porcine epidemic diarrhea virus (α-PEDV), swine acute diarrhea syndrome-coronavirus (α-SADS-CoV), and porcine deltacoronavirus (δ-PDCoV). Each genome is 5′capped and 3′ polyadenylated. Viral genomes are flanked by UTRs and are polycistronic encoding replicase ORFs1a and 1b followed by the genes encoding spike glycoprotein (S), envelope (E), membrane (M), and nucleocapsid (N) proteins. Among the structural protein genes, the genome also contains accessory genes: ORF3 of PEDV; NS3a, NS7a and NS7b of SADS-CoV; and NS6 and NS7 of PDCoV. Expression of ORF 1a and 1b yields 2 polyproteins (pp1a and pp1ab) through a -1 programmed ribosomal frameshift (-1RFS). The polyprotein is co-translationally or post-translationally processed into an estimated 14–16 nonstructural proteins (NSPs): PLpro, papain-like cysteine protease; 3CLpro, main 3C-like cysteine protease; RdRp, RNA-dependent RNA polymerase; Hel, helicase; ExoN, 3′-5′ exonuclease; NendoU, nidovirus uridylate-specific endoribonuclease; 2′OMT, ribose-2′-O-methyltransferase.

Figure 2

Phylogenetic comparison of the full-length genomes of PEDV, SADS-CoV, and PDCoV with other coronavirus species. Evolutionary history was inferred using the Maximum Likelihood method [112]. The tree with the highest log likelihood (−511751.49) is shown. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Joining and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 23 nucleotide sequences. There were a total of 32,538 positions in the final dataset. Evolutionary analyses were conducted in MEGA X [113].

Figure 3

Schematic diagram of S protein of emerging porcine coronaviruses. S1-NTD – S1 subunit N terminal domain is shown in purple; S1-CTD – S1 subunit C terminal domain is shown in red; RBD – PDCoV receptor binding domain is shown in yellow; TMD – trans-membrane domain is shown in orange.