Comparative Genomic Analysis of Classical and Variant Virulent Parental/Attenuated Strains of Porcine Epidemic Diarrhea Virus

Fangzhou Chen,Xiaozhen Guo,Qigai He,Zhonghua Li,Yinxing Zhu,Shiyi Ye,Meizhou Wu,Xugang Ku

doi:10.3390/v7102891

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.

Highlights

Porcine epidemic diarrhea virus (PEDV) belongs to genus Alphacoronavirus, family Coronaviridae, and it is an enveloped, single-stranded, positive-sense RNA virus with a genome of about 28 kb [1]
We concluded that YN15, YN60 and YN144 were cell culture adapted compared to the original YN1 strain because their total and peak virus titers were higher and growth curves shorter than the YN1 strain (Figure 1E,F)
The passages YN15 and later were cell-culture-adapted compared to the original YN1 strain, and the viral titers of YN1, YN15, YN60, and YN144 were continuously increasing. These results suggested that the nucleotide and aa changes of passages YN15 and later might contribute to the cell culture adaptation of these strains

Summary

Introduction

Porcine epidemic diarrhea virus (PEDV) belongs to genus Alphacoronavirus, family Coronaviridae, and it is an enveloped, single-stranded, positive-sense RNA virus with a genome of about 28 kb [1]. The PEDV, a dangerous pathogen for the global swine industry, is the causative agent of porcine epidemic diarrhea (PED), which is characterized by watery diarrhea, dehydration and weight loss in adult pigs, and is lethal in piglets [2]. In October 2010, the outbreak of PED was reported in China, causing huge economic losses [6], and the etiologic agent was identified as the variant PEDV [7]. After first being reported in the United States (US) in May 2013 [10], the Chinese AH2012 strain and other variant strains were reported in South Korea, Taiwan, Mexico, Germany, and some other regions, causing significant economic losses to the global pig industry [7,8,9,10,11,12,13,14]

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Results

Discussion

Conclusion