GENOME ANNOUNCEMENT
Complete Genome Sequence of a Novel Porcine Enterovirus Strain in China Wen Zhang,a Shixing Yang,b Quan Shen,a Liping Ren,c Tongling Shan,d Jianzhong Wei,e Li Cui,f and Xiuguo Huaf Department of Microbiology, School of Medical Science and Laboratory Medicine, Jiangsu University, Zhenjiang, People’s Republic of Chinaa; Translational Medicine Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of Chinab; School of Life Sciences, Fuyang Teacher’s College, Fuyang, People’s Republic of Chinac; Division of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of Chinad; College of Animal Science and Technology, Anhui Agricultural University, Hefei, People’s Republic of Chinae; and Zoonotic Diseases and Comparative Medicine Group, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai, People’s Republic of Chinaf
The porcine enteroviruses (PEVs) belong to the family Picornaviridae. We report a complete genome sequence of a novel PEV strain that is widely prevalent in pigs at least in central and eastern China. The complete genome consists of 7,390 nucleotides, excluding the 3= poly(A) tail, and has an open reading frame that maps between nucleotide positions 812 and 7318 and encodes a 2,168-amino-acid polyprotein. Phylogenetic analysis based on the 3CD and VP1 regions reveals that this PEV strain belongs to a species of PEV9 but may represent a novel sero-/genotype in CPE group III. We also report the major findings from bootscan analysis based on the whole genomes of PEVs in the present study and those available in GenBank.
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he porcine enteroviruses (PEVs) belong to the family Picornaviridae (3). PEVs are the causative agents of neurological disorders, fertility disorders, and dermal lesions of swine (6). Based on the results of cytopathic effect (CPE) and serological assays, the PEVs were divided into three groups, and based on genomic analysis, CPE group I was categorized into a novel genus, Teschovirus (2), CPE group II was renamed as Porcine sapelovirus and reclassified into a new picornavirus genus, Sapelovirus, and the members of CPE group III were determined to belong to the Enterovirus genus; the term “porcine enteroviruses” is used to identify the members of CPE group III (6). During our studies to detect human enterovirus in water specimens, as previously described (9), we obtained some unexpected sequences which showed sequence homology with PEVs in CPE group III. Further detection revealed that 8.3% (37/447) of the pigs in central and eastern China from 2007 to 2009 were positive for this virus, and the 37 313-nucleotide (nt) fragments showed ⬎98% identity with each other. Here, we report the complete genome of this virus from one swine fecal specimen using 10 sets of primers designed according to the PEV9 and PEV10 strains available in GenBank (Y14459, AF363453, and AF363455). The 3=-end fragment was determined by reverse transcription (RT)-PCR using 3= rapid amplification of cDNA ends (3= RACE). The 5=-end fragment was determined using a forward primer designed according to the most-5=-end sequences of PEV9 and PEV10 strains and a reverse primer designed according to the sequence we determined. RT-PCR-amplified DNA fragments of the expected sizes were sequenced in a DNA analyzer (Applied Biosystems 3730 DNA analyzer; Invitrogen, United States) and assembled using Phred software (5). The complete genome of this virus consists of 7,390 nucleotides, excluding the 3= poly(A) tail. Analysis of the sequence demonstrated the presence of an 811-nt 5= untranslated region (UTR), a 72-nt 3= UTR, and an open reading frame (ORF) that maps between positions 812 and 7318 and encodes a 2,168-amino-acid polyprotein. The genome organization of this virus is identical to that of previously published CPE group III strains (1, 6, 10). Over the whole genome, the virus in the present study shows the highest
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sequence homology, 82.4%, with PEV9 strains (GenBank nucleotide sequence accession no. Y14459). When compared with the genome of PEV10 (GenBank nucleotide sequence accession no. AF363455), it shows 77.5% sequence identity. Over the complete protein sequence, the virus shows 90% and 83% sequence identities with the above-mentioned PEV9 (GenBank accession no. Y14459) and PEV10 (GenBank accession no. AF363455) strain, respectively. In order to identify the sero-/genotype and species that this Chinese sequence belongs to, two phylogenetic trees based on the VP1 gene and the 3CD gene regions, respectively, were constructed (11, 12). The results indicated that though the Chinese PEV determined in the present study belongs to a species of PEV9 based on the phylogenetic tree of the P1 gene, based on the phylogenetic tree of 3CD genes, it may represent a new sero-/ genotype which is intermediate between PEV9 and PEV10. Bootscan analysis (7) based on the PEV strain in this study, the PEV9 strain (isolate UKG/410/73, GenBank sequence accession no. Y14459), the PEV10 strain (strain LP 54, GenBank sequence accession no. AF363455), and swine/K23/2008/HUN (GenBank nucleotide sequence accession no. HQ702854) indicates that the 5= UTR of LP54 shows a mosaic-like structure, suggesting that recombination may exist between different PEVs, which is a relatively common phenomenon in RNA viruses (4, 8, 13, 14). Nucleotide sequence accession number. The virus genome sequence was deposited in GenBank with strain name Ch-ah-f1 and GenBank accession no. HM131607. ACKNOWLEDGMENTS This work was partly supported by the Natural Science Foundation Research Project of the Anhui Provinces Education Commission under grant no. KJ2011Z295, the Research Project of Fuyang Teachers College,
Received 22 March 2012 Accepted 26 March 2012 Address correspondence to Li Cui,
[email protected]. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JVI.00711-12
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grant no. 2008LQ08, the Ph.D. Programs Foundation of the Ministry of Education of China, grant no. 20113227120008, the Professional Research Foundation for Advanced Talents of Jiangsu University under grant no. 12JDGXX, the Open Fund of the State Key Laboratory of Veterinary Etiological Biology, grant no. SKLVEB2010KFKT002, and the National Natural Science Foundation of China, grant no. 31070132. We thank Qinsheng Chen of the Pig Breeder’s Association of Anui Province, Junfeng Liu and Huibo Ning of Shanghai Jiaotong University, and Kezhang Fan of Fuyang Teacher’s College for their assistance with collecting swine fecal samples.
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