title: Comparative Genomic Analysis of Classical and Variant Virulent Parental/Attenuated Strains of Porcine Epidemic Diarrhea Virus.
abstract: Since 2010, the variant porcine epidemic diarrhea virus (PEDV) has been the etiological agent responsible for the outbreak of porcine epidemic diarrhea (PED) worldwide. In this study, a variant PEDV strain YN1 was isolated, serially propagated on the Vero cells and was characterized for 200 passages. To better elucidate the molecular basis of Vero cell adaptation of variant PEDV strains, we sequenced, compared, and analyzed the full-genome sequences of parental YN1 and passages 15, 30, 60, 90, 144, and 200. The results showed that the variations increased with the viral passage. The nucleotides sequences of non-structural protein (NSP)2, NSP4-7, NSP10, NSP12 and NSP13 genes did not change during the Vero cell adaptation process. After comparison of the variation characteristic of classical, variant virulent/attenuated strains, it was found that attenuation of PEDV virus was associated with 9-26 amino acid (aa) changes in open reading frames (ORF) 1a/b and S protein, early termination in ORF3, 1-3 aa changes in E, M and N protein and some nucleotide sequences' synonymous mutations. The aa deletion at about 144 aa of S protein could be the attenuation marker for the PEDV. The pig study showed that the early termination in ORF3 was more important for virus cell adaptation than virus attenuation.
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China. chenfangzhou@webmail.hzau.edu.cn.
authors.forename: Fangzhou
authors.initials: F
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China. yingzizhu10@163.com.
authors.forename: Yinxing
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China. wumeizhou@mail.hzau.edu.cn.
authors.forename: Meizhou
authors.initials: M
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China. kuxugang84@163.com.
authors.forename: Xugang
authors.initials: X
authors.lastname: Ku
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China. yeshiyi@webmail.hzau.edu.cn.
authors.forename: Shiyi
authors.initials: S
authors.lastname: Ye
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China. yuxincangqiong@163.com.
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Li
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China. gxz0821@163.com.
authors.forename: Xiaozhen
authors.initials: X
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China. he628@mail.hzau.edu.cn.
authors.forename: Qigai
authors.initials: Q
authors.lastname: He
mesh_terms: D000220:Adaptation, Biological; D019943:Amino Acid Substitution; D000818:Animals; D002522:Chlorocebus aethiops; D018352:Coronavirus Infections / Q000662:veterinary / Q000821:virology; D014644:Genetic Variation; D016679:Genome, Viral; D050505:Mutant Proteins / Q000235:genetics; D053485:Porcine epidemic diarrhea virus / Q000235:genetics* / Q000254:growth & development / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D012692:Serial Passage; D013552:Swine; D013553:Swine Diseases / Q000821:virology; D014709:Vero Cells; D015678:Viral Structural Proteins / Q000235:genetics; D014774:Virulence
chemical_list: D050505:Mutant Proteins; D015678:Viral Structural Proteins
keywords: genomic analysis; variant PEDV; virus attenuation; virus cell adaptation