With a possible origin from bats, the alphacoronavirus Porcine epidemic diarrhea virus (PEDV) causes significant hazards and widespread epidemics in the swine population. However, the ecology, evolution, and spread of PEDV are still unclear. Here, from 149,869 fecal and intestinal tissue samples of pigs collected in an 11-year survey, we identified PEDV as the most dominant virus in diarrheal animals. Global whole genomic and evolutionary analyses of 672 PEDV strains revealed the fast-evolving PEDV genotype 2 (G2) strains as the main epidemic viruses worldwide, which seems to correlate with the use of G2-targeting vaccines. The evolving pattern of the G2 viruses presents geographic bias as they evolve tachytely in South Korea but undergo the highest recombination in China. Therefore, we clustered six PEDV haplotypes in China, whereas South Korea held five haplotypes, including a unique haplotype G. In addition, an assessment of the spatiotemporal spread route of PEDV indicates Germany and Japan as the primary hubs for PEDV dissemination in Europe and Asia, respectively. Overall, our findings provide novel insights into the epidemiology, evolution, and transmission of PEDV, and thus may lay a foundation for the prevention and control of PEDV and other coronaviruses.

A B S T R A C TIn China, variants of infectious bronchitis virus (IBV) evolve continually and diverse recombinant strains have been reported. Here, an IBV strain, designated as ck/CH/LJX/2017/07 (referred as JX17) was isolated from chicken vaccinated with H120 and 4/91 in Jiangxi, China, in 2017. Sequence analysis reveals of the S1 gene of JX17 the highest nucleotide identity of 98.15% with that of GI-7 genotype TW2575/98 strain. Furthermore, whole genome analysis among JX17 and other 18 IBV strains demonstrates that JX17 has the highest nucleotide identity of 95.94% with GI-19 genotype YX10 strain. Among all genes of JX17 except the S1 gene, the N gene and 3' UTR have the highest identity to GI-13 genotype 4/91 strain and the rest genes are the most identical to GI-19 genotype YX10 strain. Analyzed by the RDP and SimPlot, the recombination of JX17 strain was shown to occur in regions which include 5'-terminal S1 gene (20,344 to 22,447 nt), most N gene and 3' UTR (26,163 to 27,648 nt). The pathogenicity study shows that JX17 is a natural low virulent IBV variant which caused respiratory symptoms but no death. Taken together, these results indicate that IBV strains continue to evolve through genetic recombination and three prevalent genotypes in China including QX, TW and 4/91 have started to recombine.

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A B S T R A C TPorcine enteric alphacoronavirus (PEAV) is a newly identified swine enteropathogenic coronavirus that causes watery diarrhea in newborn piglets. In this study, an original, highly virulent PEAV strain GDS04 was serially passaged in Vero cells. The virus titers and sizes of syncytia increased gradually with the cell passages. Newborn piglets were orally inoculated with PEAV P15, P67 and P100. Compared with P15 and P67, P100 resulted in only mild clinical signs and intestinal lesions in piglets. The virus shedding in feces and viral antigens in intestinal tract were markedly reduced in P100-inoculated piglets. Importantly, all P100-inoculated newborn piglets survived, indicating that P100 was an attenuated variant. Sequence analysis revealed that the virulent strain GDS04 had four, one, six and eleven amino acid differences in membrane, nucleocapsid, spike and ORF1ab proteins, respectively, from P100. Furthermore, more differences in the predicted three-dimensional structure of S protein between GDS04 and P100 were observed, indicating that these differences might be associated with the pathogenicity of PEAV. Collectively, our research successfully prepared a PEAV attenuated variant which might serve as a live attenuated vaccine candidate against PEAV infection.

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