key: cord-0712805-czh0jilm authors: Li, Kai; Song, Deping; Zhang, Fanfan; Gong, Wang; Guo, Nannan; Li, Anqi; Zhou, Xingrong; Huang, Dongyan; Ye, Yu; Tang, Yuxin title: Complete Genome Sequence of a Recombinant Porcine Epidemic Diarrhea Virus Strain, CH/JXJA/2017, Isolated in Jiangxi, China, in 2017 date: 2018-02-08 journal: Genome Announc DOI: 10.1128/genomea.01590-17 sha: a4c0d3619ba273adce8a9d0df51eca6adaaf2f23 doc_id: 712805 cord_uid: czh0jilm The full-length genome sequence of a variant of porcine epidemic diarrhea virus (PEDV), that of strain CH/JXJA/2017, was highly homologous to CH/ZMDZY/11, a highly virulent Chinese PEDV strain. CH/JXJA/2017 had a distant relationship with the attenuated CV777 vaccine strain, but the insertion sites of the S1 gene were similar to those of the recombinant strain of CH/ZMDZY/11. P orcine epidemic diarrhea (PED) is a devastating enteric disease (1) caused by PED virus (PEDV), an RNA virus in the genus Alphacoronavirus, family Coronaviridae (2) . Presently, PEDV is posing a threat to the swine industry worldwide (3) (4) (5) (6) (7) . PED was first reported in England in 1971 (8) and has since been identified in many pig-raising countries, including European, American, and Asian countries (9) . In 2010, the largescale outbreaks of PED with high morbidity and mortality occurred in swine farms in China, resulting in huge economic losses (10, 11) . In April 2017, a PEDV outbreak occurred in a farrow-to-finish herd in southern China. The mortality rate of the disease ranged from 10% in weaning pigs to 95% in neonatal piglets. PEDV was identified by an established reverse transcription-PCR with primers specific to the N gene of PEDV. Subsequently, the whole-genome sequence of one representative strain of PEDV, designated CH/JXJA/2017, was determined according to the previously reported methodology (12) , and the data were assembled and annotated by Lasergene version 7.10 (DNAStar, Inc., USA). The (11) , and it had a nucleotide identity of 96.7% with the attenuated CV777 strain. Phylogenetic analysis based on the full-length genome sequences of PEDVs revealed that CH/JXJA/2017 belonged to genogroup 2 (G2). Interestingly, the CH/JXJA/2017 strain possessed two unique deletion and two insertion sites compared to the PEDV attenuated vaccine CV777 strain (nt 20811 to 20822, nt 21123 to 21128, nt 21054 to 21056, and nt 21105 to 21107) in the S gene, and one 4-amino-acid deletion ( 59 QGVN 62 ), one 2-amino-acid deletion ( 163 NI 164 ), and two single-amino-acid insertions ( 140 N and 157 H) were observed. Of note, the 4-amino-acid insertion site ( 59 QGVN 62 ) of CH/JXJA/2017 was in the S1 domain of the S protein, which was similar to CH/ZMDZY/ 11. These findings suggest that CH/JXJA/2017 was a novel PEDV variant. Further study is required to determine the biological properties of this novel variant of PEDV. Accession number(s). The complete genome sequence of PEDV strain CH/JXJA/ 2017 has been deposited in GenBank under the accession number MF375374. A new coronavirus-like particle associated with diarrhea in swine Completion of the porcine epidemic diarrhoea coronavirus (PEDV) genome sequence Mutations in the spike gene of porcine epidemic diarrhea virus associated with growth adaptation in vitro and attenuation of virulence in vivo Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea Phylogenetic analysis of porcine epidemic diarrhea virus field strains prevailing recently in China Genetic diversity of ORF3 and spike genes of porcine epidemic diarrhea virus in Thailand Epidemiology and vaccine of porcine epidemic diarrhea virus in China: a mini-review An apparently new syndrome of porcine epidemic diarrhoea Evolution, antigenicity and pathogenicity of global porcine epidemic diarrhea virus strains Porcine epidemic diarrhea virus infection: etiology, epidemiology, pathogenesis and immunoprophylaxis Porcine epidemic diarrhea in China Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea viruses associated with outbreaks of severe diarrhea in piglets in Jiangxi MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets This study was supported by the National Key Research and Development Program