Methods:In 2011, we received a total of 756 intestinal samples from 48 pig farms, located in the major pig-raising provinces across China. We performed PCR and viral culture assays (1) on all suitable samples. Positive PCR products corresponding to the full ORF3 and full M genes derived from Vero cell-cultured PED isolates were extracted from gels by commercial kits (Qiagen). The complete nucleotide sequence of ORF3 and M genes within these recombinant clones were then sequenced (both nucleotide strands) by a commercial service. The molecular relationships among the nucleotides of the ORF3 and M genes from our Chinese PED isolates were inferred using the Neighbour-joining method. The evolutionary distances were computed by the p-distance method involving nucleotide base (ORF3 gene) and amino acid (M gene) differences. Results: We detected PCR products consistent with PED virus in 426/756 intestinal samples (56%) derived in 2011 from 26/48 farms (54%) located across China, which had had clinical outbreaks resembling PED. We isolated and partially sequenced wild-type PED virus from nine of the PCR-positive samples. Phylogeny tree analyses based on the deduced amino acid sequences of the M gene and the nucleotide sequence of ORF3 gene of these recent isolates indicates that several isolates formed new clusters of distinct lineages, suggesting that the Chinese PED coronavirus strains show strong mutation and possible recombination potential. A total of 24 piglets were challenged orally (4 pigs per isolate) with 4 control sham-inoculation piglets. Three days after inoculation, all challenged piglets showed clinical, pathological and PCR reactions consistent with PED virus. Conclusion: The phylogeny tree analyses we conducted on both the M gene and ORF3 gene showed that several of the recent Chinese isolates appeared to form new clusters, particularly the Hebei and Guangxi origin isolates. These provinces are not connected by farming practices suggesting that the Chinese PED coronavirus strains show the strong mutation and possible recombination potential of other coronaviruses. This suggests that the recent PED isolates retain their strong pathogenicity in the field and challenge study situation, even though considerable shifts have occurred in major viral membrane protein genes.