ORF3a deletion in field strains of porcine-transmissible gastroenteritis virus in China: A hint of association with porcine respiratory coronavirus. 2017

X Zhang, and Y Zhu, and X Zhu, and J Chen, and H Shi, and D Shi, and H Dong, and L Feng
State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China.

Porcine-transmissible gastroenteritis virus (TGEV) is a pathogenic coronavirus responsible for high diarrhoea-associated morbidity and mortality in suckling piglets. We analysed the TGEV ORF3 gene using nested polymerase chain reaction and identified an ORF3a deletion in three field strains of TGEV collected from piglets in China in 2015. Eight TGEV ORF3 sequences were obtained in this study. Phylogenetic tree analysis of ORF3 showed that the eight TGEV ORF3 genes all belonged to the Miller cluster. CH-LNCT and CH-MZL were closely correlated with Miller M6, while CH-SH was correlated with Miller M60. These results thus indicate that the existence of Miller, as well as the Purdue cluster, in Chinese field strains of TGEV. Furthermore, we found the first evidence for a large deletion in ORF3 resulting in the loss of ORF3a, previously reported in porcine respiratory coronavirus, in three field strains (CH-LNCT, CH-MZL, and CH-SH) of TGEV. The results of the present study thus provide important information regarding the underlying evolution mechanisms of coronaviruses.

UI MeSH Term Description Entries
D010802 Phylogeny The relationships of groups of organisms as reflected by their genetic makeup. Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D002681 China A country spanning from central Asia to the Pacific Ocean. Inner Mongolia,Manchuria,People's Republic of China,Sinkiang,Mainland China
D005760 Transmissible gastroenteritis virus A species of CORONAVIRUS causing a fatal disease to pigs under 3 weeks old. Gastroenteritis Virus of Swine,Gastroenteritis Virus, Porcine Transmissible,Porcine Transmissible Gastroenteritis Virus,TGE Virus,Transmissible Gastroenteritis Virus, Swine,Swine Gastroenteritis Virus,Swine Gastroenteritis Viruses,TGE Viruses
D005761 Gastroenteritis, Transmissible, of Swine A condition of chronic gastroenteritis in adult pigs and fatal gastroenteritis in piglets caused by a CORONAVIRUS. Gastroenteritis, Transmissible, Porcine,Porcine Gastroenteritis, Transmissible,Swine Transmissible Gastroenteritis,Transmissible Gastroenteritis of Swine,Porcine Transmissible Gastroenteritis,Gastroenteritides, Porcine Transmissible,Gastroenteritides, Swine Transmissible,Gastroenteritides, Transmissible Porcine,Gastroenteritis, Porcine Transmissible,Gastroenteritis, Swine Transmissible,Gastroenteritis, Transmissible Porcine,Porcine Gastroenteritides, Transmissible,Porcine Transmissible Gastroenteritides,Swine Transmissible Gastroenteritides,Transmissible Gastroenteritides, Porcine,Transmissible Gastroenteritides, Swine,Transmissible Gastroenteritis, Porcine,Transmissible Gastroenteritis, Swine,Transmissible Porcine Gastroenteritides,Transmissible Porcine Gastroenteritis
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D013552 Swine Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA). Phacochoerus,Pigs,Suidae,Warthogs,Wart Hogs,Hog, Wart,Hogs, Wart,Wart Hog
D016133 Polymerase Chain Reaction In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships. Anchored PCR,Inverse PCR,Nested PCR,PCR,Anchored Polymerase Chain Reaction,Inverse Polymerase Chain Reaction,Nested Polymerase Chain Reaction,PCR, Anchored,PCR, Inverse,PCR, Nested,Polymerase Chain Reactions,Reaction, Polymerase Chain,Reactions, Polymerase Chain
D045722 Porcine Respiratory Coronavirus A mutant strain of TRANSMISSIBLE GASTROENTERITIS VIRUS causing mild or subclinical respiratory infections in young SWINE. It may also play a role in post-weaning porcine respiratory disease complex, especially when combined with other respiratory agents. Coronavirus, Porcine Respiratory,Respiratory Coronavirus, Porcine
D018352 Coronavirus Infections Virus diseases caused by the CORONAVIRUS genus. Some specifics include transmissible enteritis of turkeys (ENTERITIS, TRANSMISSIBLE, OF TURKEYS); FELINE INFECTIOUS PERITONITIS; and transmissible gastroenteritis of swine (GASTROENTERITIS, TRANSMISSIBLE, OF SWINE). Infections, Coronavirus,MERS (Middle East Respiratory Syndrome),Middle East Respiratory Syndrome,Coronavirus Infection,Infection, Coronavirus

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