cord-000699-2mfbqs8i	2012	To the Editor: Beginning in October 2010, porcine epidemic diarrhea (PED), caused by a coronaviral infection affecting pigs, emerged in China in an outbreak characterized by high mortality rates among suckling piglets. The partial S gene deduced amino acid sequences were compared and also showed a high degree of homology (98.0%-100.0%); they had 85.3%-98.7% identity with all reference strains listed in online Technical Appendix Table 2 , 98.0%-98.7% with Thailand strains, and 93.3%-94.7% with vaccine strain CV777 (data not shown). These results showed that PEDV was present in sow milk (online Technical Appendix Table 3 ), but the detection rate was lower for these samples (40.8%) than for the fecal samples (82.0%). Our fi ndings show that PEDV was identifi ed not only in fecal samples from sick piglets, as expected, but also in the milk of the sow, which suggests vertical transmission of the virus.
cord-001658-algzczs8	2015	title: Complete Genome Sequence of a Porcine Epidemic Diarrhea Virus from a Novel Outbreak in Belgium, January 2015 Here, we report the complete genome sequence (28,028 nt) of a PEDV strain isolated during a novel outbreak in Belgium. Therefore, the complete genome of this novel isolate, BEL/15V010/2015, was unraveled by next-generation sequencing, in order to assess its genetic relation to other PEDV isolates circulating around the globe. Complete genome sequence of a highly prevalent isolate of porcine epidemic diarrhea virus in South China Complete genome sequence of a novel porcine epidemic diarrhea virus in south China Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States Emergence of Porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States
cord-001956-jpk854i3	2016	title: Complete Genome Sequence of a Porcine Epidemic Diarrhea Virus Strain from Vietnam, HUA-14PED96, with a Large Genomic Deletion A highly virulent strain of Porcine epidemic diarrhea virus (PEDV) causing severe diarrhea has recently emerged in Vietnam. Genomic sequences from a novel strain, HUA-14PED96, isolated from a Vietnamese piglet with serious diarrhea show relatively high identity with U.S.-like PEDV strains, and have a 72-nt deletion in the open reading frame 1a (ORF1a) gene. In this study, we sequenced the complete genome of a Vietnamese strain of PEDV, HUA-14PED96, and analyzed it to understand the molecular characteristics and diversity of PEDVs in Vietnam. Phylogenetic analysis using the nucleotide sequences of the full-length genomes of PEDVs revealed that HUA-14PED96 belonged to the G2 group. The complete genome sequence of PEDV strain HUA-14PED96 has been deposited in GenBank under accession no. Complete genome characterization of porcine epidemic diarrhea virus in Vietnam A novel strain of porcine epidemic diarrhea virus in Vietnamese pigs
cord-003328-vvle1q1e	2018	To examine whether CRISPR/Cas9-mediated gene editing could generate LTβR null alleles in IPEC-J2 cells, we randomly selected two biallelic mutation clones (1-10# and 1-22#) and compared their LTβR expression levels to those of wild-type IPEC-J2 cells (hereafter designated LTβR +/+ ) by real-time PCR. Since PEDV infection destroys epithelial barrier integrity [22] , and LTβR signaling was reported to limit mucosal damage through the IL-22-IL-23 pathway [10] , we examined the expression levels of LTβR downstream genes by semi-quantitative PCR, including VCAM1, IL-22 and IL-23, in PEDV-infected cells. We detected expression levels of IL-6 and IL-8 in infected cells, and the data showed that both genes were significantly decreased in infected LTβR −/− IPEC-J2 cells ( Figure 5C ). Since it has been demonstrated that PEDV infection destroys epithelial barrier integrity [22] and LTβR signaling limits mucosal damage through the IL-22-IL-23 pathway [10] , we detected expression levels of VCAM1, IL-22 and IL-23 in both cell types by semi-quantitative PCR.
cord-003503-t6cnjwpd	2019	Acknowledging the absence of a thorough investigation at the geographic level, we used 2014 outbreak sequence information from the Taiwan government''s open access databases plus GenBank records to analyze PEDV dissemination among Taiwanese pig farms. The data indicate that the 2014 Taiwan PEDV epidemic resulted from the spread of multiple strains, with strong correlations identified with pig farm numbers and sizes (measured as animal concentrations), feed mill numbers, and the number of slaughterhouses in a specifically defined geographic area. To determine specific temporal and geographic relationships associated with PEDV strain transmission, we used phylogenetic, phylodynamic and phylogeographic methods to systematically evaluate potential temporal and spatial transmission routes among Taiwanese swine farms during the 2014 outbreak. However, to date very few research efforts in Asia have utilized full genome sequencing for determining geographic structures due to the high costs and enormous amounts of computational time Phylogeographic investigation of 2014 porcine epidemic diarrhea virus transmission in Taiwan required for analyses [33, 34] .
cord-003587-zminzrov	2019	title: Visual detection of porcine epidemic diarrhea virus using a novel reverse transcription polymerase spiral reaction method The aim of this study was to establish a novel reverse transcription polymerase spiral reaction (RT-PSR) assay for the rapid detection of porcine epidemic diarrhea virus (PEDV). This new method for PEDV detection was 10 times more sensitive than the conventional reverse transcription-polymerase chain reaction (RT-PCR) assay. To decrease the time required for PEDV detection, PCR-related methods focused on the amplification of viral nucleic acids have been developed, which have been shown to be more efficient, highly sensitive and specific, even at different stages of the disease, when compared to immunological diagnostic methods. The polymerase spiral reaction (PSR) [14] is a novel nucleic acid isothermal amplification method that has the advantages of simplicity, rapidity, accuracy, and low cost when compared to conventional PCR.
cord-003899-a4w2nnos	2019	title: Dietary 25-Hydroxyvitamin D(3) Supplementation Alleviates Porcine Epidemic Diarrhea Virus Infection by Improving Intestinal Structure and Immune Response in Weaned Pigs We found that high dose 25-hydroxyvitamin D(3) supplementation could ease intestinal injury and inhibit intestinal immune response induced by porcine epidemic diarrhea virus (PEDV), suggesting that feeding a high dose of 25-hydroxyvitamin D(3) could be used as an approach against PEDV infection. ABSTRACT: We conducted this experiment to determine if feeding 25-hydroxyvitamin D(3) (25(OH)D(3)) to weaned pigs would alleviate porcine epidemic diarrhea virus (PEDV) infection and immune response. Porcine epidemic diarrhea virus (PEDV) infection causes severe damage to the intestinal function and barrier integrity of pigs [1] , leading to diarrhea, vomiting, dehydration, and high mortality in piglets [2] . In summary, the results of the current study indicate that dietary supplementation of 155.5 µg/kg 25(OH)D 3 alleviated the severity of diarrhea of piglets infected with PEDV by improving the intestinal structure and immune response, and maintaining regular intestinal function.
cord-003973-pnareltx	2019	
cord-004713-gzts5h0y	1985	A pathogenetic study of pleural effusion disease (PED) in rabbits was made, using the virulent PED agent or virus (PEDV) and an avirulent derivate of this isolate. Support for this contention is the enhancement of virulence of PED virus (PEDV) observed in the "natural" disease and --after its isolation --by continued serial propagation in rabbits at intervals of 3---10 days (Fig. 1) . However, there is also evidence which might suggest that increasing time of persistence of virulent virus in the individual rabbit host may operate in the reverse direction by selecting a population of predominantly avirulent PEDV particles, which appear to be unable to cause disease unless undergoing new rabbit passages at short intervals (t, 6). After infection with the avirulent derivate, the isolates from serum obtained during the entire period of viraemia were demonstrable in serum dilution 10 -1 to 10 -a, but the primary rabbit inoculation of these dilutions never resulted in clinical signs of PED.
cord-004727-9sniu39j	1981	Baby rabbits surviving infection with pleural effusion disease virus (PEDV) developed viraemia persisting for at least six months. The demonstration of pleural effusion disease (PED) virus as passenger of rabbit testicular suspensions of Treponema pallidum in several laboratories shows that this virus can be transmitted from rabbit to rabbit by testicular fluids at intervals of 7--14 days, i.e. the customary time between intratesticular inoculation and harvest of treponemes from the testes (3, 6, 7) . Infected and uninfected rabbits remained together in the same cage for a period of 90--180 days, and their blood was examined for PEDV at 30-day intervals from time of inoculation. To observe if the virus present in blood would retain inability to provoke clinical disease, serial rabbit passages of infectious serum from p.i. days 90, t20, 150 and 180 were carried out at 7-day intervals.
cord-009526-ghm1hvei	2016	Porcine epidemic diarrhea virus (PEDV) belongs to the Coronaviridae family; this family includes a wide variety of viruses that affect humans and other animals, causing respiratory and gastroenteric diseases (Weiss & Navas-Martin 2005) . The degree to which the small percentage of na€ ıve suckling piglets recover during PED outbreaks in the wider industry is unknown, as is the biological mechanisms involved, but two main hypothesis can be suggested: (i) survival can be related to variation in the intestinal receptor used by PEDV to gain entry to intestinal epithelial cells (the ANPEP gene) or (ii) as summarized by Schneider & Ayres (2008) and Ayres & Schneider (2012) , survival and recovery can be related to particular host immune responses that enhance viral clearance, increase cell epithelial regeneration rate or reduce viral replication rate. In this study, our aim was to investigate genome-wide differences between dead and recovered suckling piglets from commercial farms during PED outbreaks. Table S1 Number of dead and recovered piglets from the PEDV outbreak in each considered farm.
cord-010053-kniq2mbw	2019	title: Molecular characteristics and pathogenic assessment of porcine epidemic diarrhoea virus isolates from the 2018 endemic outbreaks on Jeju Island, South Korea Genetic and phylogenetic analyses revealed that the re-emergent Jeju Island PEDV isolates were most closely related to the pandemic genogroup 2b (G2b) strains that were responsible for the 2013-2014 global outbreaks, suggesting a direct introduction of the virus from the mainland of South Korea via unknown contaminating sources . In this study, we determined the complete genome sequences of field isolates on Jeju Island to investigate the diversity of the PEDVs responsible for the ongoing endemic outbreaks. Attenuation of an original US porcine epidemic diarrhea virus strain PC22A via serial cell culture passage Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene
cord-014932-web2tdef	2009	The structure genes spike (S), nucleocapsid (N), membrane (M), small membrane (sM) of a porcine epidemic diarrhea virus (PEDV) strain DX isolated in Gansu province, North-west of China, were cloned, sequenced and compared with published sequences of PEDV strains. The N gene was cloned using two primers which contained Nco I and BamH I restriction enzyme sites and subcloned into expression vector pET30a. Cloning and sequence analysis of the N gene of porcine epidemic diarrhea virus LJB/03 Cloning and sequence analysis of the N gene of porcine epidemic diarrhea virus LJB/03 Cloning and sequence analysis of the Korean strain of spike gene of Porcine epidemic diarrhea virus and expression of its neutralizing epitope in plants Cloning and Sequence Analysis of the Nucleocapsid Gene of Porcine Epidemic Diarrhea Virus Chinju99 Cloning and sequence analysis of the spike gene of Porcine epidemic diarrhea virus Chiju99
cord-016858-pbjj50bx	2015	PEDV antigens in frozen tissues are visualized as green staining in the cytoplasm of infected cells by fluorescent dyes conjugated with antibodies when activated by exciting light of a specific wavelength under a fluorescence microscope. In FFPE tissues, PEDV antigens are visualized as red staining in the cytoplasm of infected cells by the deposition of the substrate chromogen, Fast Red. 2013 to present, has led to a substantial loss of piglets (more than 10 % of US swine population). Viral antigens in frozen, fi xed cells, or tissues can be detected by immunohistochemistry (IHC) (or immunohistochemical staining) using specifi c antibodies labeled with fl uorescent dyes, such as Alexa Fluor ® 488 and fl uorescein isothiocyanate (FITC), or enzymes, such as alkaline phosphatase (AP) and peroxidase. Monoclonal antibody-based immunohistochemical detection of porcine epidemic diarrhea virus antigen in formalin-fi xed, paraffi n-embedded intestinal tissues
cord-033488-du8heorx	2020	(A) Sera from five mice from each group immunized with a negative control (wild-type crude extract, G1) or a positive control (commercial vaccine, G2) or the crude extract containing COE-GCN4pII (G3) were mixed, diluted 200 times and used as a primary antibody for detecting 1 µg of purified PEDV antigen. Different levels of PEDV-specific IgG (B), IgA (C), and IgM (D) antibodies in each mouse sera group were calculated as the reciprocal of the geometric mean titer of the five mice of each group vaccinated with the negative control (wild-type crude extract, G1) or the positive control (commercial vaccine, G2) or the crude extract containing COE-GCN4pII (G3). Therefore, plant crude extract containing the trimeric COE protein had the level of IgG antibodies similar to that of commercial vaccines against the PEDV DR13 strain after the third injection. Therefore, we concluded that plant crude extract containing the trimeric COE protein had a strong immunogenicity and induced a neutralizing antibody titer similar to that of the commercial vaccine against the attenuated PEDV DR13 strain.
cord-252121-s1zxu5vo	2014	
cord-252772-f3fctcru	2020	Moreover, we demonstrated that PEDV escaped IFN-λ responses by substantially upregulating the suppressor of cytokine signaling protein 1 (SOCS1) expression, which impaired the induction of IFN-stimulated genes (ISGs) and dampened the IFN-λ antiviral response and facilitated PEDV replication in Vero E6 cells. Compared with a mock uninfected control, PEDV did not increase the expression of IFNλ transcripts as observed until 12 hpi, and then gradually induced IFN-λ expression, indicating that PEDV infection elicits type III IFN expression at the late stage of infection instead of the early stage of infection in the Vero E6 cells (Figure 1A) , which was consistent with the results in porcine enteroids (Li et al., 2019) . In the current study, we observed that PEDV elicited substantially increased IFN-λ expression in Vero E6 cells only after 24 hpi (Figure 1A) , which is consistent with the results observed in porcine enteroids following PEDV infection (Li et al., 2019) , indicating that PEDV has evolved mechanisms to escape IFN-λ antiviral response instead of IFN-λ production at the late stage of infection.
cord-254192-86ksgl5t	2019	Here, to resolve the mechanism responsible for the disparity between IFN-λ3 and type I IFN in anti-mucosal virus infection, we compared the transcription profiles induced by the two IFNs in porcine intestinal epithelial (IPEC-J2) cells by RNA-Seq. Our results showed that the pretreatment of IPEC-J2 cells with IFN-λ3 resulted in the differential expression of 983 genes. Here, to resolve the mechanism responsible for the disparity between IFN-λ3 and type I IFN in anti-mucosal virus infection, we compared the transcription profiles induced by the two IFNs in porcine intestinal epithelial (IPEC-J2) cells by RNA-Seq. Our results showed that the pretreatment of IPEC-J2 cells with IFN-λ3 resulted in the differential expression of 983 genes. In this study, we comprehensively compared the transcriptional profiling of IFN-λ3-and IFN-α-induced genes in a porcine intestinal epithelial cell line (IPEC-J2) and verified the RNA-Seq results by reverse transcriptase quantitative PCR (RT-qPCR) in vitro, and further confirmed the transcriptional profile difference in crypt-derived porcine enteroids.
cord-254317-n2knqj4z	2018	Porcine epidemic diarrhea virus (PEDV) variants having a large deletion in the N-terminal domain of the S1 subunit of spike (S) protein were designated as S1 NTD-del PEDVs. They replicate well in experimentally infected pigs. Effect of mucin, bile and bile acids on the infection of PEDV icPC22A and icPC22A-S1Δ197 in Vero and IPEC-DQ cells Viruses (icPC22A or icPC22A-S1Δ197) were mixed with different concentrations of BM (0, 0.1, 0.3, 0.5 mg/mL) or PGM (0, 0.5, 1.0, 2.5, 5.0 mg/mL). Compared with the peak fecal PEDV N gene shedding titer (11.6 ± 0.2 log 10 copies/mL) of piglets in the icPC22A group (1 dpi), pigs in the coinfection group had a significantly higher peak titer (13.6 ± 0.7 log 10 copies/mL) ( Fig. 1B and Table 2 ) at a delayed time point (1.5 dpi). S1 NTD-del PEDV replicated to a lower peak titer in coinfection than that in single virus infection in both Vero cells and IPEC-DQ cells.
cord-254405-yc1q20fz	2018	Furthermore, we cultured the virus and screened for attenuated PEDV strains by analyzing the genovariations that occurred during passaging -confirming the results in animal experiments. [27] analyzed a cell culture-adapted PEDV (passage 100) strain with a smaller ORF3 gene and found it to have lower virulence relative to the wild-type virus. Molecular characterization of the ORF3 and S1 genes of porcine epidemic diarrhea virus non S-INDEL strains in seven regions of China Comparative genomic analysis of classical and variant virulent parental/attenuated strains of porcine epidemic diarrhea virus Isolation and identification of porcine epidemic diarrhea virus strain HBMC2012 and its pathogenicity in piglet Cloning and further sequence analysis of the spike gene of attenuated porcine epidemic diarrhea virus DR13 Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China
cord-255238-adpn5fb9	2017	Isolation and propagation of the pathogen in cell culture resulted in discovery of a novel swine enteric alphacoronavirus (tentatively named SeACoV) related to the bat coronavirus HKU2 identified in the same region a decade ago. Most recently, several chimeric SeCoV strains with a TGEV genomic backbone replaced by a PEDV spike (S) gene were identified from swine fecal samples in Europe (Akimkin et al., 2016; Belsham et al., 2016; Boniotti et al., 2016) , implying that novel SeCoV pathogens could emerge by inter-CoV recombination under co-infection. In this study, we report the isolation and genetic characterization of a novel swine enteric alphacoronavirus (tentatively named SeACoV), related to a bat enteric coronavirus, from a pig farm that reported newborn-piglet diarrhea in southern China in 2017.
cord-255607-dbexsugq	2020	Our preliminary results revealed that endogenous TANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3), the key components in the IFN signaling pathway were downregulated in PEDV infected IPEC-J2 cells by iTRAQ analysis. Moreover, PEDV nsp15 can directly degrade the RNA levels of TBK1 and IRF3 dependent on its EndoU activity to suppress IFN production and constrain the induction of IFN stimulated genes (ISGs), by which PEDV antagonizes the host innate response to facilitate its replication. Previous studies suggest that PEDV can restrain host innate immune response by different strategies, such as by degradation or cleavage of key factors essential the IFN signaling pathway [25, 26] , competitive interaction between viral encoded proteins and modulators for IFN production [27, 28] , or localization changes of antiviral components [29] .
cord-255773-b4re5bky	2016	
cord-255862-84u3c33m	2017	In this research, we investigated whether escin derivatives 1–7 (including new compounds 2, 3, 5 and 6), without the angeloyl or tigloyl groups and with modified glycosidic linkages by hydrolysis, have PEDV inhibitory effects with less cytotoxicity. Interestingly, compounds 1-7 isolated from the fraction with the two-step hydrolysis were evaluated to have much lower cytotoxic effects than compounds 8-10 from the n-BuOH part at concentration of 20 lM (Fig. S22) . As compounds 8-10 showed strong cytotoxic effects on Vero cells at 20 lM, their PEDV inhibitory activities were evaluated at a concentration of 2 lM. 33 To measure the expression level of viral RNA encoding nucleocapsid and spike proteins, compounds 4 and 6 were treated in Vero cells at a concentration of 40 lM and total RNA was extracted for reverse transcription followed by polymerase chain reaction using the primers for PEDV (STable 1 ).
cord-257136-zpeh8pmc	2019	To develop a simple, rapid, accurate, and high-throughput detection method for diagnosis and differential diagnosis on swine enteric coronaviruses, specific primers and probes were designed based on the highly conserved regions of transmissible gastroenteritis virus (TGEV) N, porcine epidemic diarrhea virus (PEDV) M, porcine deltacoronavirus (PDCoV) M, and porcine enteric alphacoronavirus (PEAV) N genes respectively. To develop a simple, rapid, accurate, and high-throughput detection method for diagnosis and differential diagnosis on swine enteric coronaviruses, a TaqMan-probe-based multiplex real-time RT-qPCR assay was established to simultaneously detect TGEV, PEDV, PEAV, and PDCoV from the same reaction vial. To establish a high-specific multiplex real-time RT-qPCR for the detection and differential diagnosis of swine enteric coronaviruses, primer sets, and TaqMan probes were designed targeting the highly conserved regions of PEDV or PDCoV M genes and TGEV or PEAV N genes, based on bioinformatics analysis of each virus.
cord-258546-1tf5ggfo	2016	Since outbreaks of porcine epidemic diarrhea virus (PEDV) in the United States in 2013, explosive outbreaks of PED in South Korea have infected all age groups of pigs in 2014–2015 year. PED outbreaks re-occurred in Korea in 2013, however, it was demonstrated that the emerging PEDVs were not variants of old Korean isolates or attenuated vaccine strains (Chung et al., 2015) . This study tested whether PEDV isolated recently was crossed neutralized by serum of pigs which were vaccinated with Korean PED oral vaccine (Attenuated DR13 strain, Green Cross Veterinary Product Co., Ltd., Yong-In, Korea). Comparative genome analysis and molecular epidemiology of the reemerging porcine epidemic diarrhea virus strains isolated in Korea ISolation of porcine epidemic diarrhea virus during outbreaks in South Korea Isolation of porcine epidemic diarrhea virus (PEDV) in Korea Heterogeneity in spike protein genes of porcine epidemic diarrhea viruses isolated in Korea
cord-259296-qsaewje2	2020	
cord-259324-g8kv4pvq	2011	In this study, we assessed the feasibility of producing a protective antigen for the PEDV spike protein 1 using duckweed, Lemna minor. Transgene integration and expression of the PEDV spike protein 1 gene were confirmed by genomic PCR and RT-PCR and western blot analysis of transgenic Lemna, respectively. In this study, we report the stable transformation and expression of a protective antigen for PEDV in Lemna minor with potential for use as an effective complement to the diets of animals. Fronds were then blotted onto sterile filter paper, and co-cultivated with Agrobacterium tumefaciens strain EHA105 harboring the PEDV spike protein 1 gene fused to a c-myc tag for 72 h on antibiotic-free ½MS1BA medium. PCR products of the expected size (330 bp) corresponding to primers designed on the internal PEDV spike protein 1 gene were detected from kanamycin-resistant Lemna, whereas no DNA band corresponding to the target gene was detected in untransformed wild-type Lemna.
cord-259794-6qoksn00	2017	Porcine epidemic diarrhea virus (PEDV) replicates in the cytoplasm of infected cells, but its nucleocapsid (N) protein localizes specifically to the nucleolus. The results suggest potential linkages among viral strategies for the regulation of cell survival activities, possibly through an interaction of N protein with NPM1 which prevents its proteolytic cleavage and enhances cell survival, thus ultimately promoting the replication of PEDV. In this study, to determine the intracellular distribution of N protein at the protein level, PEDV-infected Vero E6 cells were lysed, separated into nuclear and cytoplasmic fractions, and analyzed by western blotting. This study was based on different lines of evidence, reflecting both in vivo and in vitro situations, and demonstrated that PEDV N protein is able to associate with the major nucleolar protein NPM1 of Vero E6 cells (Fig. 2) ; we failed to detect an interaction with the fibrillarin or nucleolin (See Supplementary Fig. S2 ).
cord-260107-gqbtkf0x	2015	In the present study, one Korean PEDV strain, KOR/KNU-141112/2014, was successfully isolated and serially propagated in Vero cells for over 30 passages. Our genomic analyses indicated that the Korean isolate KNU-141112 is genetically stable during the first 30 passages in cell culture and is grouped within subgroup G2b together with the recent re-emergent Korean strains. Our data indicated that KNU-141112 isolate is relatively stable during the first 30 passages in cell culture and is classified into subgroup G2b that includes PEDV strains responsible for recent severe outbreaks in Korea and the US. Although virus isolation in cell culture from clinical samples of naturally or experimentally infected pigs is fastidious, recent studies reported the successful isolation and propagation of several US original PEDV strains using Vero cells (Chen et al., 2014; Oka et al., 2014) . Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene
cord-260835-ck9z5xsd	2017	Results showed PEDV infection was restricted to pAPN and pAPN domain VII expressing NIH3T3 cells. Also, PEDV harvested from pAPN or domain VII expressing NIH3T3 cells was induced indirect plaques in Vero cells confirming successful entry and replication. In the current study, by constitutive expression of pAPN in non-susceptible NIH3T3 cells, we have sought to annotate the previous findings stipulating pAPN receptor function for PEDV. Susceptibility assays showed infection in pAPN domain-VII expressing cells but virus entry was abrogated in absence of seventh domain (pAPN DI-VI ) as shown in (Fig. 5A) . PEDV was also reported to interact with pAPN in porcine enterocytes (Li et al., 2009) , and is capable of infecting MDCK and ST cells expressing the pAPN receptor (Oh et al., 2003; Nam and Lee, 2010) . In our study, to determine the specific interactive point of pAPN wt with PEDV, domain mutants were expressed stably in NIH3T3 cells.
cord-261036-zdhg4axx	2010	PEDV obtained after ten passages through the brains (MK-p10) had increased virulence for mice, and its fusion activity in cultured cells exceeded that of the original strain. One of these (an H-to-R substitution at residue 1,381) was first detected in PEDV isolated after eight passages, and both this virus (MK-p8) and MK-p10 showed enhanced syncytium formation relative to the original MK strain and viruses isolated after two, four, and six passages, suggesting the possibility that the H-to-R mutation was responsible for this activity. Expression of the receptor protein for mouse hepatitis virus (MHV) and severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) in cultured cells confers susceptibility to each of these viruses [2, 4, 25] . In the present study, we isolated a strain of PEDV that was more virulent than the original tissue-culture-adapted virus after passage through mouse brain cells. To investigate viral virulence and replication in mouse brains, 0-day-old mice were infected i.c. with 5,000 PFU of PEDV and monitored daily for clinical features; they were also weighed daily.
cord-261043-f9w310tp	2019	With recent advances in predictive analytics showing promise for health and disease forecasting, the primary objective of this study was to apply machine learning predictive methods (random forest, artificial neural networks, and classification and regression trees) to provincial PEDV incidence data, and in so doing determine their accuracy for predicting future PEDV trends. With 10-fold cross validation performed on the entire dataset, the overall accuracy was 0.68 (95% CI: 0.60 – 0.75), 0.57 (95% CI: 0.49 – 0.64), and 0.55 (0.47 – 0.63) for the random forest, artificial neural network, and classification and regression tree models, respectively. For the additional models constructed with random training and test sets (using 10-fold cross validation on the entire dataset), the summary confusion matrix in Table 3 indicates overall accuracy values of 68%, 57%, and 55% for random forest, neural nets, and classification trees respectively.
cord-261372-xjbs09gi	2010	A double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) based on the use of monoclonal antibodies was developed for the detection of porcine epidemic diarrhoea virus (PEDV). The objective of the present study was to develop a double antibody sandwich (DAS) ELISA, based on the use of monoclonal antibodies for PEDV detection in swine intestinal and faecal samples useful for routine examinations of field samples. It is already known that ELISA results depend on the clinical and pathological data: in intestinal contents and faecal specimens obtained from experimentally infected PEDV piglets, the virus shedding is detected with high consistency during the acute phase of disease, but much less frequently during the incubation period and the recovery phase (Callebaut et al., 1982) . Enzyme-linked immunosorbent assay for the detection of the coronavirus-like agent and its antibodies in pigs with porcine epidemic diarrhea
cord-261993-u2a26brw	2018	A more sensitive immunoplaque assay was able to detect virus from Styrofoam, metal, and plastic at 20 days post application, representing a 3-log loss of input virus on fomite materials. Virus recovery from surfaces of Styrofoam, nitrile gloves, aluminum foil, Tyvek ® coverall, metal, rubber, plastic, cardboard, and cloth showed no significant differences between the materials at RT, suggesting that storage temperature had a substantial influence on virus survival. Quantifiable viral RNA was detected in Styrofoam, Tyvek, and cardboard materials, although infectious PEDV titer decreased by 3 to 4 logs at 4 °C after 20 days. Quantifiable viral RNA was detected in Styrofoam, Tyvek, and cardboard materials, although infectious PEDV titer decreased by 3 to 4 logs at 4 °C after 20 days. Survivability of porcine epidemic diarrhea virus (pedv) in bovine plasma submitted to spray drying processing and held at different time by temperature storage conditions
cord-263439-oquk4t96	2014	Similar to other coronaviruses, PEDV spike protein mediates its cell entry by binding to cellular receptors and inducing membrane fusion between viral envelopes and cellular membranes. Taken together, our findings reveal that PEDV enters Vero cells via clathrin-mediated endocytosis and requires serine proteolysis during infection. Based on these observations, we concluded that an exogenous protease, like trypsin, was necessary to induce cell-cell fusion in PEDV-infected Vero cells but not essentially required for virus-cell entry. So, we hypothesized that PEDV entry into Vero cells under the trypsin-free condition most likely occurred inside endosomal compartments where cellular proteases might operate similar to trypsin, facilitating S-mediated fusion of PEDV with the endosomal membrane. The infection inhibition assay using various substrates that interfere with endocytosis or lysosomotropic agents revealed that PEDV enters Vero cells via clathrin-mediated endocytic uptake and delivery of virus to an acidic intracellular compartment.
cord-265679-7gzont7l	2018	In this study, the antiviral activity of a cationic amphibian antimicrobial peptide Caerin1.1 against porcine epidemic diarrhea virus (PEDV) was evaluated by an in vitro system using Vero cells. Vero cells cultured in 24-well plates were washed with PBS for 3 times and inoculated respectively with single medium, or single PEDV, or PEDV pre-incubated with different concentrations of Caerin1.1. PEDV suspensions containing different concentrations of Caerin1.1 were pre-incubated for 1 h at 37 • C, and were serially diluted before they were inoculated on the 80% confluent Vero cell monolayers grown in the 96-well plates, followed by washing 3 times with PBS. As shown in Figure 4 , Vero cells were infected with PEDV (200 pfu) pre-incubated with different concentrations of Caerin1.1. As shown in Figure 4 , Vero cells were infected with PEDV (200 pfu) pre-incubated with different concentrations of Caerin1.1.
cord-266571-qbskh1uu	2002	Lymphocyte proliferative responses were evaluated in mucosal (mesenteric lymph nodes) and systemic (spleen and blood) lymphoid tissues of conventional piglets inoculated with the virulent or attenuated isolates of porcine epidemic diarrhoea virus (PEDV) strain CV-777 and challenged 21 days later with the virulent isolate of the same virus. Virus-specific lymphoproliferative responses of systemic tissues (spleen and blood) and mesenteric lymph nodes were studied in conventional piglets after primary inoculation with the virulent, wild type, strain CV-777 of PEDV or its cell culture attenuated form and after challenge, 3 weeks later, with a high dose of the virulent virus. Correlations between lymphocyte proliferative responses in mononuclear cells collected from mesenteric lymph nodes, blood and spleen from pigs inoculated with virulent or attenuated PEDV or mock-inoculated and protection against challenge 21 days later with virulent PEDV.
cord-266660-0wq77k6y	2014	title: Comparative genome analysis and molecular epidemiology of the reemerging porcine epidemic diarrhea virus strains isolated in Korea We detected three PEDV strains from ten small intestine samples from piglets with acute diarrhea and we determined the complete genome sequences of the reemerging Korean PEDV field isolates, except for the noncoding regions from both ends. This study aimed to determine the complete genome sequence of the reemerging Korean PEDV strain and to investigate their genetic relationship with other strains using comparative genome analysis and phylogenetic analysis. In addition, all available complete genome sequences of PEDV isolates from Korea were included in the alignment to compare the recent Korean strains with previous endemic Korean PEDV strains. Multiple alignment with other PEDV complete genomes indicated that the reemerging Korean strains possess genome sequences, which are distinct from those of previous Korean field strains (Fig. 1) .
cord-267446-rpv19oy6	2011	
cord-268010-1m5h3krw	2016	
cord-269013-ge7nmgsa	2014	title: Complete Genome Sequence of Porcine Epidemic Diarrhea Virus in Vietnam Porcine epidemic diarrhea virus (PEDV) has emerged in Vietnam since 2009. Herein, full-length genome sequences are reported for three PEDV isolates from pigs displaying severe diarrhea from farms located in northern and southern provinces of Vietnam. The full-length genome sequence suggests that PEDV variants circulating in Vietnam swine farms are novel variants with changes in the spike structure. Completion of the porcine epidemic diarrhoea coronavirus (PEDV) genome sequence Sequence analysis of the partial spike glycoprotein gene of porcine epidemic diarrhea viruses isolated in Korea Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in south China 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
cord-272031-o2hx667i	2015	Mortality in piglets less than two weeks old varied from 0 to 100 %, but it was usually lower than that described in outbreaks of diarrhoea caused by transmissible gastroenteritis virus (TGEV) which is another porcine coronavirus classically recognized as a cause of diarrhoea disease in swine. Although some reports have suggested that they could be associated with differences in the virulence of PEDV isolates, exhaustive challenge studies using pig adapted virus (not cell culture adapted isolates) in suckling piglets are needed to elucidate the role of the strain. The detection of PEDV specific antibodies is very useful, not for the investigation of diarrhoea outbreaks, but to determine whether an animal or a herd has previously been infected by this virus. Genetic characterization of porcine epidemic diarrhoea virus (PEDV) isolates from southern Vietnam during 2009-2010 outbreaks
cord-272480-276r1lh7	2019	title: Isolation and recombinant analysis of variants of porcine epidemic diarrhea virus strains from Beijing, China The strains in this study are indicated by underline Isolation and recombinant analysis of variants of porcine epidemic diarrhea virus strains from… 297 Frequent mutation and recombination of genes may occur in epidemics of PEDV. The phylogenetic trees showed that, these PEDV isolates from the Beijing area belonged to group II, while the traditional vaccine strain, CV777, belonged to group I based on the comparison of several important genes in PEDV, such as ORF1a/1b, S, M, N, E, and ORF3. Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in south China Sequence and phylogenetic analysis of nucleocapsid genes of porcine epidemic diarrhea virus (PEDV) strains in China Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea
cord-272728-inndwa61	2018	At PID 3 when vomiting had ceased, mean numbers of serotonin-positive EC cells per microscopic area (×250) were significantly (P < .05) increased in duodenum but reduced in ileum of the PEDV-inoculated pigs, compared with the corresponding negative controls, but they did not differ in mid-jejunum and colon (Table 1) . Histologic lesions and the distribution based on Table 1 Mean numbers ( ± SDM) of serotonin-positive enterochromaffin cells by immunohistochemistry in the crypt layers and entire or lower half of villi of duodenum, mid-jejunum, ileum, and colon per microscopic area, at ×250 magnification, of conventional 9-day-old nursing pigs inoculated with virulent US PEDV strain PC21A or mock at post-inoculation days (PIDs) 1, 3, and 5.
cord-272729-nbgdmavr	2012	
cord-272973-kzaowysv	2018	
cord-273610-cfoq3r3i	2014	To investigate the evolutionary process by which porcine epidemic diarrhea virus (PEDV) in the United States hypothetically descended from strains in China, we analyzed PEDV-positive samples collected in China during January 2012–July 2013. To investigate the evolutionary process by which porcine epidemic diarrhea virus (PEDV) in the United States hypothetically descended from strains in China, we analyzed PEDV-positive samples collected in China during January 2012-July 2013. The exception is the N gene-based tree, in which the AH2012 was grouped more closely to the sublineage associated with the United States than the strains in the designated ZMDZY sublineage (online Technical Appendix Figure 1 ). It is possible that replacement of a region within the partial S-ORF3-E-M-partial N region of the AH2012 strain with a corresponding fragment close to the ZMDZY sublineage (including several newly identified strains) resulted in a recombinant strain related to emergence of this virus in swine in the United States. Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States
cord-273705-0oyzg5tq	2018	title: Impact of dietary spray-dried bovine plasma addition on pigs infected with porcine epidemic diarrhea virus Experimental data suggest that the addition of spray-dried plasma (SDP) to pig feed may enhance antibody responses against certain pathogens and negatively impact virus survival. The aim of this study was to determine the effect of bovine SDP (BovSDP) in the pig diet on acute porcine epidemic diarrhea virus (PEDV) infection. The results indicate that addition of BovSDP induced an earlier anti-PEDV antibody response in pigs experimentally infected with PEDV thereby reducing clinical disease and the amount and duration of viral shedding during acute PEDV infection. Starting with arrival in the research facility and for the duration of the study, all pigs were fed the same standard commercial corn-soybean meal-dried whey-based diet ( Table 2 ) except for the diet of the PEDV-BovSDP group, which was supplemented with 5% spray-dried commercial bovine plasma replacing soy protein concentrate on an equal total lysine basis ( Figure 1 ).
cord-273712-r2akpce8	2016	In the same beta group, the receptors for mouse hepatitis virus (MHV) and bovine coronavirus (BCoV) are carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) and a sugar, respectively, despite their high sequence homology Peng et al., 2012) . In our study, we compared the efficiency of pseudotyped viruses with S proteins from different groups of CoVs. Furthermore, the cell tropisms of TGEV and PEDV were characterized by live and pseudotyped viruses. Therefore, we compared the S protein amino acid sequences of CoVs from different groups, including SARS-CoV, MHV, HCoV-229E, TGEV, PEDV, HCoV-OC43, BCoV, and IBV (Gen-Bank accession numbers ABD72982.1, AAR92025.1, NP_073551.1, ABG89335.1, NP_598310.1, AAT84362.1, ABM66810.1, and NP_040831.1, respectively) using ClustalW ( Figure 1B ). Lentiviruses pseudotyped with SARS-CoV S protein could efficiently infect 293T cells expressing ACE2, and the pseudovirus level after entry reached 10 6 relative light units (RLU) ( Figure 2B ). To further study the cellular entry of CoVs, we used live PEDV and TGEV to infect different cell lines.
cord-273745-mwjh5se7	2014	Three phage-displayed peptides designated H, S and F that recognize porcine aminopeptidase N (pAPN), the cellular receptor of porcine transmissible gastroenteritis virus (TGEV) were able to inhibit cell infection by TGEV. When Vero cells were pre-treated with peptide (cell pretreatment assay) prior to virus infection (Fig. 1B) , little changes in virus titers were observed between the control and peptide treatment groups; some small effects were observed with the rabbit anti-PEDV neutralizing antibodies. Finally, in the virus pretreatment assays where PEDV was incubated with peptides prior to cell infection (Fig. 1C) , the results indicated that both peptides H and S inhibited PEDV infectivity where EC 50 values were approximately 1 μg/ml and 62.5 μg/ml, respectively. Results clearly show that peptide H had no demonstrable effects on TGEV or PrV even at very high peptide concentrations (1 mM/ml) (Fig. 3) suggesting that a non-specific reactivity with virus envelopes is unlikely to be the cause for attenuating PEDV infectivity.
cord-274765-3wzht843	1999	The field isolate of porcine epidemic diarrhea virus (PEDV) was serially passaged in Vero cells. The cell passaged PEDV, designated KPEDV-9, was tested for its pathogenicity in the neonatal pigs, immunogenicity and safety in the pregnant sows. The results of this study supported that the attenuated virus derived from serial passage could be applied as vaccine for protecting suckling piglets against PEDV infection. In this study, we investigated the attenuation of PEDV through serial passages in Vero cell cultures and its prophylactic eect in pregnant sows. Nevertheless, when compared with the wild PEDV, the animals inoculated with the high passage level of virus did not show any severe signs of diarrhea or death in piglets, supporting attenuation. Development of an Elispot for the detection of antibody secreting cells against the porcine epidemic diarrhea virus (PEDV) in dierent tissues
cord-275499-25dp6u68	2019	In this study, we successfully demonstrated that the microbial community structure of colonic mucosa and content differed significantly between healthy and PEDV-infected piglets. Likewise, previous research has shown that the proportions of Escherichia-Shigella, Enterococcus, Fusobacterium, and Veillonella increased significantly in PEDV-infected piglets, while those of short-chain fatty acid (SCFA)-producing bacteria (e.g., Rikenellaceae_RC9_gut_group, Butyricimonas, and Alistipes) underwent a decrease [21] . Some bacteria from Firmicutes and Bacteroidetes were enriched in healthy piglets, while some from Proteobacteria and Fusobacteria were more abundant in PEDV-infected groups. To better characterize the intestinal microbiomes of healthy versus PEDV-infected piglets, we recommend that future studies fully examine virome diversity using a larger sample size and metagenomic de novo sequencing of the gut microbial genome. Dynamic change of gut microbiota during porcine epidemic diarrhea virus infection in suckling piglets Changes in cecal microbiota community of suckling piglets infected with porcine epidemic diarrhea virus
cord-276542-lxwls664	2020	
cord-276989-441aclcc	2020	title: Development of a rapid immunochromatographic strip test for the detection of porcine epidemic diarrhea virus specific SIgA in colostrum On the strip, a gold-labeled anti-SIgA SC mAb was applied to a conjugate pad; purified PEDV particles and goat anti-mouse antibodies were blotted onto a nitrocellulose membrane to form the test and control lines, respectively. Therefore, the aim of this study was to develop a simple and rapid immunochromatographic test strip incorporating a colloidal gold-labeled anti-SIgA SC mAb probe for the detection of anti-PEDV-specific SIgA in swine, and to compare its performance with an indirect SIgA ELISA based on the whole PEDV virus (Cong et al., 2019) . To test for colostrum, we diluted the samples 1: 20 in sample buffer and mixed thoroughly then, 100 μL of the solution was dispensed onto the sample pad well of the strip apparatus to determine the presence of PEDV specific SIgA, as described above.
cord-277194-mj85mpo2	2019	title: Factors Associated With Time to Elimination of Porcine Epidemic Diarrhea Virus in Individual Ontario Swine Herds Based on Surveillance Data Factors associated with time to elimination are likely reflective of the complexity of infection control practices applied in herds with different demographics and population structures, seasonal variability in the pathogen transmissibility, and the availability of resources to manage an emerging production-limiting disease. Therefore, the objective of this study was to determine time to PEDV elimination in Ontario swine herds infected between 2014 and 2017, on the basis of records from the DCP database; and to identify factors associated with the likelihood of elimination. A Cox''s proportional hazard model was constructed to investigate the effect of explanatory variables including herd type, season of diagnosis and year of diagnosis on the time to eliminate PEDV from the premises.
cord-278641-8lh5y7j0	2020	
cord-279598-xzionafe	2019	title: Identification of Neutralizing Monoclonal Antibodies Targeting Novel Conformational Epitopes of the Porcine Epidemic Diarrhoea Virus Spike Protein However, E10E-1-10, which targets a novel neutralizing epitope as shown with ICC staining, was also capable of binding to the full-length PEDV spike protein as well as truncated PEDV proteins, S 1-639 , S 1-575 , S 1-509 , S 1-501 , and S 1-485 with appropriate dilution effects. Similar to the results obtained by ICC staining, E10E-1-10 showed no binding ability www.nature.com/scientificreports www.nature.com/scientificreports/ toward PEDV S 1-435 by ELISA and therefore, an NmAb targeting a novel epitope of the new variant of PEDV specifically at a.a. 435-485 in the S1 region was confirmed. To further determine whether the binding of neutralizing epitopes require conformational integrity, immunodot blotting was performed by denaturing the various truncated PEDV spike proteins. Cell Attachment Domains of the Porcine Epidemic Diarrhea Virus Spike Protein Are Key Targets of Neutralizing Antibodies
cord-279784-o80x8nj7	2019	
cord-279794-hn5vmic0	2018	Molecular clock analysis showed that divergence of the GII‐c subgroup spike gene occurred in April 2010, suggesting that the subgroup originated from recombination events before the PEDV re‐emergence outbreaks. Consistent with our previous research (Wang, Fang, & Xiao, 2016a) , the phylogenetic tree indicated that the complete PEDV genomes evolved into two separate genogroups, GI (classical) and GII (variant), as presented in Figure 1a . Genetic variation of nucleocapsid genes of porcine epidemic diarrhea virus field strains in China Detection and molecular diversity of spike gene of porcine epidemic diarrhea virus in China Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China Complete genome sequence of a recombinant porcine epidemic diarrhea virus strain Evolutionary and epidemiological analyses based on spike genes of porcine epidemic diarrhea virus circulating in Thailand
cord-279813-mrei5kih	2017	
cord-279903-z0wf1wli	2014	title: Development and evaluation of a duplex real-time RT-PCR for detection and differentiation of virulent and variant strains of porcine epidemic diarrhea viruses from the United States In this study, the development and validation of a duplex real-time RT-PCR assay for detection and differentiation of the variant and the virulent strains of PEDV currently circulating in the US was reported. However, since the M gene is highly conserved between the virulent and the variant strains of PEDV in the US, this real-time RT-PCR assay cannot differentiate between the two strains of PEDV. Therefore, the aim of this study was to develop a duplex real-time RT-PCR which would detect and differentiate the virulent strain from the variant strain of PEDV. In conclusion, we have developed a duplex real-time RT-PCR assay that reliably detects and differentiates the virulent strain and variant strain of PEDV.
cord-280183-fxhkfjl6	1992	
cord-280564-kgoczioe	2017	title: Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs In the sample, we observed the presence of a small Torovirus contig of 256 bp, which was included in the phylogenetic tree (Fig. 1A , Torovirus/BEL/2015), showing very low similarity with the gene insertion found in the recombinant virus. The enterovirus genome region before the torovirus insertion (VP1-VP4, 2 A, 2B, and 2 C) showed its highest similarity on the amino-acid level (94.5%) with EVG/Porcine/USA/Texas1/ 2014 (Fig. 1C) . In addition to confirming the presence of the enterovirus-torovirus recombinant using Sanger sequencing, we used proteomics to infer whether the protein of the insertion could be found in the sample. Taking the metagenomics data, the Sanger sequence confirmation and the proteomics results all together we can conclude that this recombinant virus is present in the sample and that the inserted protein is being expressed.
cord-282466-r2sjv9ih	2019	Porcine epidemic diarrhoea (PED) is a highly contagious and devastating enteric disease of pigs caused by porcine epidemic diarrhoea virus (PEDV), an enveloped, single-stranded RNA virus belonging to the Alphacoronavirus genus of the Coronaviridae family. Heavy economic losses in the pig-farming industry were sustained in the USA between 2013 and 2015 when PEDV spread very quickly and resulted in epidemics. The purpose of this review is a description of the current status of porcine epidemic diarrhoea in European pigs and the risk presented by the introduction of PEDV to Poland in comparison to the epidemics in the USA. Pathogenesis comparison between the United States porcine epidemic diarrhoea virus prototype and S-INDEL-variant strains in conventional neonatal piglets Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States Characterizing the rapid spread of porcine epidemic diarrhea virus (PEDV) through an animal food manufacturing facility
cord-284322-synuzaxm	2010	To confirm these initial observations, we established a cell culture model of mixed infections with Chlamydia and a cell culture-adapted porcine epidemic diarrhea virus (ca-PEDV) and hypothesized that this would result in the generation of persistent chlamydial forms. In contrast, dual infections with ca-PEDV and Chlamydia pecorum resulted in the exclusive production of aberrant inclusions containing between 2-50 ABs. Chlamydial inclusions in viral syncytia grew even larger than in non-viral infected Vero cells. The changes of chlamydial inclusion size by subsequent virus addition to Chlamydia abortus are different to those we observed in the Chlamydia pecorum dual infection experiments. TEM examinations of mixed infections (ca-PEDV and Chlamydia abortus or Chlamydia pecorum) revealed aberrant chlamydial inclusions containing fewer bacteria than typical inclusions and were located in viral syncytia or single cells without viral infection. Enlarged chlamydial inclusions were described in that study in the ca-PEDV co-infection model with Chlamydia abortus and Chlamydia pecorum but no further ultrastructural analysis has been subsequently performed.
cord-286831-ni7qfjk9	2008	Following this, 0.09 mL of diluted virus suspension of PEDV containing CCID 50 (50% cell culture infective dose) of the virus stock to produce a appropriate cytopathic effects within 2 days after infection and 0.01 mL of medium supplemented with typsin-EDTA containing an appropriate concentration of the compounds were added. Current antiviral drugs, natural compounds and flavonoids were further studied for their inhibitory effects on replication of the PEDV and cytotoxicity in Vero cells, among which ribavirin, tannic acid, coumarin and interferon-␣ exhibited the activities with IC 50 of 4.1, 47.4, 9 g/mL and 0.52 unit, respectively. A similar result was obtained in control infections with treated ribavirin (Fig. 1 ), but antiviral activity was shown to be lower than that of Q7R. Trials of ribavirin in this study showed that the drug had favorable effects on antiviral activity in Vero cells infected with PEDV.
cord-287913-pe6ot11q	2007	title: Effects of epidermal growth factor on atrophic enteritis in piglets induced by experimental porcine epidemic diarrhoea virus Epidermal growth factor (EGF) promotes gastrointestinal mucosal recovery by stimulating the mitogenic activity of intestinal crypt epithelial cells. The aim of this study was to determine the effects of EGF on atrophic enteritis induced in piglets by experimental infection with porcine epidemic diarrhoea virus (PEDV) strain Dr13. EGF stimulates proliferation of intestinal crypt epithelial cells and promotes recovery from atrophic enteritis in PEDV-infected piglets. Most PEDV + EGF piglets had moderate diarrhoea from 24 to 36 hpi and severe diarrhoea Table 1 Mean ratio of villous height to crypt depth (VH:CD) in piglets infected with porcine epidemic diarrhoea virus with (PEDV + EGF) or without (PEDV only) epidermal growth factor relative to uninfected piglets (control) This study has shown that EGF enhances proliferation of intestinal crypt epithelial cells and promotes the recovery of damaged villi in piglets infected with PEDV.
cord-287947-7kjxbd6t	2020	Collectively, our data indicated that GLY inhibited PEDV infection and decreased proinflammatory cytokine secretion via the HMGB1/TLR4-mitogen-activated protein kinase (MAPK) p38 pathway. Western blotting showed that TAK induced moderately decreased porcine epidemic diarrhea virus nucleocapsid (PEDV-N) protein expression in a dose-dependent manner, and about 73% PEDV-N protein decreased when treating with 10 μM concentration of TAK (Figure 2A) , demonstrating the fact that TLR4 might regulate PEDV infection. Western blotting showed that TAK induced moderately decreased porcine epidemic diarrhea virus nucleocapsid (PEDV-N) protein expression in a dose-dependent manner, and about 73% PEDV-N protein decreased when treating with 10 μM concentration of TAK (Figure 2A) , demonstrating the fact that TLR4 might regulate PEDV infection. In this study, we explored GLY-inhibited PEDV infection and decreased proinflammatory cytokine production through effects on the HMGB1/TLR4-p38 pathway. In this study, we explored GLY-inhibited PEDV infection and decreased proinflammatory cytokine production through effects on the HMGB1/TLR4-p38 pathway.
cord-288058-oilurica	2020	To determine the effect of APN on coronavirus replication, the enterocytes were precultured with 1µg/mL hydrocortisone, 50 µM spermidine, 1 µg/mL insulin, 0.1 µM Wnt agonist, or 1% intestinal contents for 24 h prior to inoculation with PEDV CV777 Vero adapted strain, CV777 fecal suspension, and TGEV Miller. To determine the effect of APN on coronavirus replication, the enterocytes were precultured with 1µg/mL hydrocortisone, 50 µM spermidine, 1 µg/mL insulin, 0.1 µM Wnt agonist, or 1% intestinal contents for 24 h prior to inoculation with PEDV CV777 Vero adapted strain, CV777 fecal suspension, and TGEV Miller. The results show that pretreatment of primary enterocytes with hydrocortisone, spermidine, porcine insulin, Wnt agonist, and intestinal contents could stimulate the expression of APN and enhance the infection of PEDV CV777 Vero adapted and non-adapted strains and the TGEV Miller in the enterocytes.
cord-288253-wqrhiq08	2015	
cord-289026-v09m2fzw	2018	
cord-290819-zhywlf6r	2020	title: The antiviral protein viperin interacts with the viral N protein to inhibit proliferation of porcine epidemic diarrhea virus In the early stage of virus infection, the pattern recognition receptor (PRR) signaling pathway of the host cell is activated to induce interferon production, activating interferon-stimulated genes (ISGs) that encode antiviral proteins that exert antiviral effects. Increased expression of interferon and viperin and decreased replication of PEDV with a clear reduction in the viral load were observed in PEDV-infected IPEC-J2 cells. After virus infection, pattern recognition receptors recognize released viral nucleic acids and activate downstream signaling pathways to promote the production of specific transcription factors and type I interferons [25] . These results indicate that PEDV infection upregulates the expression of interferon and viperin in IPEC-J2 cells. This study showed that the expression of type I interferon increases and that of viperin is also upregulated in IPEC-J2 cells infected with PEDV.
cord-290833-m0wodqr3	2019	In this study, 10 surfactin analogues were obtained by chemical synthesis and evaluated to determine their anti-PEDV activities, hemolytic activities, and critical micelle concentrations. The production of designer surfactins, made by changing the number and composition of amino acids and fatty acids has proven to be an effective strategy for screening large numbers of lipopeptides for biological activity, but most current research focuses on their anticancer [4] , antimicrobial [5] and insulin delivery [6] properties but not on their antiviral potential. Time of addition assays were performed to determine whether the SLP5 exerts its anti-PEDV effect at the same stage during infection as surfactin. As expected for a normal component of the cell membrane, DEPE did not affect PEDV replication at any stage, while SLP5 and surfactin exhibited antiviral activity at specific stages. SLP5 also has two fewer hydrophobic amino acids than surfactin, this reduces the cost of synthesis while having little effect on antiviral activity.
cord-292101-lnap47kp	2015	
cord-292690-1p1gnpgf	2020	title: Recombinant Lactobacillus acidophilus expressing S(1) and S(2) domains of porcine epidemic diarrhea virus could improve the humoral and mucosal immune levels in mice and sows inoculated orally In order to develop a new effective vaccine for the current PEDV, oral vaccines were generated by transferring eukaryotic expression recombinant plasmids carrying the S(1) and S(2) (antigenic sites of the S protein) epitopes of PEDV into a swine-origin Lactobacillus acidophilus (L. The results showed that oral administration of the VP1 gene of foot-and-mouth disease virus using Lactobacillus as a carrier could produce a higher antibody titer than injection, and induce humoral and cellular immunity (Li et al., 2007) . High-level mucosal and systemic immune responses induced by oral administration with Lactobacillus-expressed porcine J o u r n a l P r e -p r o o f epidemic diarrhea virus (PEDV)
cord-292734-2g2ym81n	2008	The piglets were euthanized at 1, 2, or 3 days post-inoculation (DPI) to measure the villous height:crypt depth (VH:CD) ratio and to collect fecal samples for RT-PCR and virus isolation. No significant differences in mean VH:CD ratio and clinical symptoms (diarrhea, vomiting, dehydration, and anorexia) were observed between the PEDV/PGAR-infected and PEDV-infected groups of piglets at 1, 2 and 3 DPI; however, at 2 and 3 DPI, PGAR was detected in all fecal samples by RT-PCR and virus isolation. The aim of this study was to determine the impact of PGAR co-infection on PEDV pathogenicity by subjecting piglets experimentally co-infected by PEDV and PGAR to evaluation of clinical signs (severity in diarrhea, dehydration, and dehydration) and histological morphometric analysis (villous height: crypt depth) in mid-jejunum where PEDV lesions were evident.
cord-292958-k5d5fo3i	2017	
cord-293458-jb7u9xn6	2016	
cord-293512-rcwwx7qw	2016	
cord-294559-u0r7oh9z	2019	title: A new immunochromatographic assay for on-site detection of porcine epidemic diarrhea virus based on monoclonal antibodies prepared by using cell surface fluorescence immunosorbent assay For rapid detection of PEDV, a new immunochromatographic assay (ICA) based on monoclonal antibodies (mAbs) was developed in this study. To compare its accuracy to other traditional detection methods, 27 swine stool samples from south of China were investigated with the new developed ICA, commercial strip and RT-PCR. Relying on signals emitted from gold nanoparticles labeled mAb (AuNPs-mAb), a new ICA was developed for sensitive, specific and on-site detection of PEDV in swine stool in China. They were capture and detection mAb, the size of gold nanoparticles, the type of sample pad, the type of conjugate pad, the type of Nitrocellulose membrane, the type of absorbent pad, the amount of tween-20 addition and the spray volume of AuNPs-mAb. The optimization methods are shown in the supplemental materials.
cord-295534-bwa4wz94	2015	
cord-296791-h8ftslps	2006	
cord-298401-4szmu1dh	2017	
cord-298685-qxkxjxsz	2016	Pathogenesis studies with the prototype strain CV777 showed severe villous atrophy in neonatal pigs and the virus-animal interactions showed many similarities with transmissible gastro-enteritis virus (TGEV), another porcine coronavirus. Also, after a first epidemic phase of the new PEDV, the virus often persisted on breeding-finishing farms in weaned and feeder pigs (endemic PED). Results of pathogenesis studies obtained in caesarean derived, colostrum deprived neonatal pigs upon inoculation with the European prototype strain CV777 of the seventies, were practically identical to those observed more recently in Asia and in the USA epidemics with the so-called "original US PEDV strains" Stevenson et al., 2013; Kim and Chae, 2003) . In a serological study in Belgium in 1986, PEDV was associated with diarrhea in 13 out of 16 groups of feeder pigs after arrival in fattening farms (Callebaut et al., 1986) But, the virus remained prevalent in the swine populations of Western Europe during the eighties.
cord-298922-k568hlf4	2015	Among the disease-related functions, certain anti-viral pathways and proteins, such as the RIG-I-like receptor, Rap1, autophagy, mitogen-activated protein kinase, PI3K-Akt and Jak-STAT signaling pathways, and integrin β2/β3 and cystatin-C proteins, represented potential factors in PEDV infection. In our current study, we used a quantitative proteomics approach based on an iTRAQ tandem mass spectrometry (MS/MS) technique to identify proteins differentially expressed between PEDV-infected and mock-infected Vero E6 cells. To verify the differential expression of the selected DEPs, equivalent volumes of the cell lysate replicates from the PEDV-infected (V1-V3) and mock-infected (C1-C3) Vero E6 cells were pooled into the V and C samples, respectively, and western blotting was performed as described above, with the following exceptions: a 1:1000 dilution of the polyclonal antibodies anti-␤ tubulin, anti-integrin-␤3, anti-cystatin-C, anti-protein S100-A2, anti-apolipoprotein E4, and anti-centrin from rabbit (Beijing Biosynthesis Biotechnology, Beijing, China) was used as the primary antibody, and a 1:5000 dilution of the HRP-conjugated goat anti-rabbit IgG (Sigma-Aldrich, St. Louis, USA) was used as the secondary antibody.
cord-299345-2i48ld8d	2019	Pairwise identity analysis of the whole genome sequences revealed that PEDV/Belgorod/dom/2008 is an intermediate between PEDV and transmissible gastroenteritis virus (TGEV) strains. Based on the phylogenetic analysis of the M gene, the PEDV/Belgorod/ dom/2008 isolate belongs to the same clade as other virulent Russian PEDV strains, indicating a high degree of sequence homogeneity in the M gene (Fig. 3a) isolate is genetically distinct and does not belong to any group (Fig. 3b ). The identification of recombinant regions in PEDV/Belgorod/dom/2008 can be useful for further analysis of evolutionary variability, epidemiology, and development of a new diagnostic gene-based assay for porcine epidemic diarrhea virus. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China
cord-299988-jaekryq5	2020	title: Re-emergence of porcine epidemic diarrhea virus in a piglet-producing farm in northwestern Germany in 2019 After initial confirmation of PEDV by real-time RT-PCR, fecal material and small intestine samples from affected pigs were subjected to metagenomic analyses employing next-generation sequencing. Phylogenetic analyses showed high identities among the PEDV sequences obtained from samples of different animals and a close relation to recent strains from Hungary and France. After reports from Asia, that a new PEDV variant caused considerable losses [12, 13] , that highly virulent PEDV variant emerged also in the United States (US) in 2013, with swine farms experiencing explosive epidemics affecting all age classes of animals, with up to 95% mortality in suckling pigs [2, 14] . Emergence of porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences
cord-301175-6alsigxk	2015	
cord-301347-22lt6h40	2016	Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. Despite excising a large portion of the genome prior to analysis, the Bayesian trees illustrate two distinct entries of PEDV into the US and characterize the evolution of PEDV compared to other CoVs. Modeling of the pAPN RBD region has revealed that Asian strains have increasing diversity compared to previously developed vaccines, and the variability in both the American and Asian strains needs to be considered for future vaccine development. Phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in central China based on the ORF3 gene and the main neutralization epitopes Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene
cord-301355-9lswjro2	2015	title: Development of an enzyme-linked immunosorbent assay for the monitoring and surveillance of antibodies to porcine epidemic diarrhea virus based on a recombinant membrane protein Therefore, the accurate diagnosis, serological monitoring, and surveillance of specific antibodies in pigs resulting from porcine epidemic diarrhea virus (PEDV) infection or vaccination would be essential in helping to control the spread of PED. To detect PEDV antibodies in eight herds, 382 serum samples were collected from sows that had been immunized with a PED vaccine, and screened using the developed ELISA in parallel with a serum neutralization (SN) assay. To determine the specificity of the developed ELISA, crossreactivity was assessed by determining the reactivity of the purified antigen with serum samples containing antibodies against TGEV, PRV, PRRSV, PCV2, CSFV and PEDV. Development and evaluation of enzyme-linked immunosorbent assay based on recombinant nucleocapsid protein for detection of porcine epidemic diarrhea (PEDV) antibodies
cord-301655-6nxhvvm4	2019	In order to determine and compare which of the viral proteins may be useful as diagnostic antigens, whole virus (WV) particles and a panel of structural and nonstructural PEDV proteins [spike subunit 1 (S1), the C-terminal part of ORF3 (ORF3C), envelope (E), nonstructural protein 1 (Nsp1), Nsp2, Ac (acidic domain of Nsp3), and ADRP (ADP-ribose-1-monophosphatase domain of Nsp3), expressed individually in bacterial and/or mammalian cells] were tested for reactivity with sera from PEDV-infected pigs by ELISA and/or western blot analysis. In this study, a panel of recombinant PEDV ORFs encoding structural and nonstructural proteins were expressed in mammalian and/or bacterial cells and screened for reactivity with porcine sera from seven provinces of China by ELISA and/or western blot analysis, in order to determine which antigen is most suitable as a diagnostic marker for PEDV infection.
cord-302083-9q1i20o6	2020	
cord-302286-wu6csxve	2007	
cord-302323-vvo8a4hp	2015	To determine whether these mutations lead to changes in antigenicity, as suggested by the failure of PEDV vaccines in China, we first optimized the codons of typical S genes of the CV777 vaccine strain (G1 subtype) and LNCT2 strain (G2 subtype) and expressed the recombinant full-length sequence of the S protein in a eukaryotic expression system. The findings of this study confirmed that the recombinant S protein was highly immunogenic in Cross serum neutralization (SN) between the S proteins of the two PEDV subtypes and anti-S PAbs. Reciprocals of PEDV neutralizing antibody titers were expressed as the dilution inhibiting PEDV infection by 50 %, which was calculated as follows: Log50 % neutralizing titer = L-d (s-0.5), where L is the log of the lowest dilution factor, d is the difference between the dilution factors, and s is the sum of the ratios of positive wells Variation between porcine epidemic diarrhea virus subtypes 545 mice and could effectively induce production of antibodies, especially neutralizing antibodies.
cord-302503-7s9f8wje	2020	In October 2010, a severe PED outbreak caused by a highly virulent PEDV variant emerged in southern China with high mortality ranging from 70 to 100%; the result was devastating damage to the pig farm industry and tremendous economic losses, and later, the PEDV variant spreads to other countries, e.g., USA, Canada, and Mexico ( For the early and rapid detection of PEDV, different types of PCR methods have been developed. A TaqMan probe-based real-time PCR to differentiate porcine epidemic diarrhea virus virulent strains from attenuated vaccine strains Development and evaluation of a duplex real-time RT-PCR for detection and differentiation of virulent and variant strains of porcine epidemic diarrhea viruses from the United States Development of a TaqMan-based real-time RT-PCR assay for the detection of SADS-CoV associated with severe diarrhea disease in pigs
cord-302819-oj33i2ma	2014	On the SDPP sample that was tested, the following N gene rRT-PCR results were observed: C t of 35.84 for PBS supernatant after 10 000 g, C t of 36.74 for the PBS pellet after 10 000 g, C t of 38.83 for the PBS + Nonidet P-40 Comparison of S protein gene sequences obtained from bioassay piglets versus those of field cases. No significant difference was observed in the kinetics of N gene rRT-PCR positivity in animals that were inoculated with the three SDPP samples that were tested, suggesting that each contained infectious virus. Negative contrast staining electron microscopy of fecal samples collected at 4 dpi from the SDPP-inoculated piglets and the positive control group piglets showed the presence of virus-like particles consistent with coronavirus virions. Similar virus-like particles were also found in the content of the small intestine of a SDPP-inoculated piglet at 7 dpi and a positive control group contact piglet at 5 days post-contact.
cord-302890-eenijt7f	2019	To examine the inhibitory effects of shRNAs against N on target gene expression during PEDV replication, IEC cells were transfected with or without 1 µg, 2 µg, or 4 of µg shR-N307, shR-N463, and shR-N1071 or 4 µg of shR-NC for 24 h and infected with 100 TCID 50 /mL PEDV strain CV777 or LNCT2. To examine the inhibitory effects of shRNAs against N on target gene expression during CV777 and LNCT2 replication, IEC cells were transfected with indicated plasmids for 24 h and then infected with PEDV CV777 orLNCT2 strain (100 TCID 50 /mL). To examine the inhibitory effects of shRNAs against N on target gene expression during CV777 and LNCT2 replication, IEC cells were transfected with indicated plasmids for 24 h and then infected with PEDV CV777 orLNCT2 strain (100 TCID 50 /mL).
cord-303186-2hxlx1j2	2019	
cord-305156-w6iqeayr	2018	
cord-305315-0qt7eth0	2015	
cord-305859-vt8vwo3y	2017	Fecal virus shedding, seroconversion and histopathology were evaluated in 3-7-year-old gnotobiotic calves orally inoculated with porcine deltacoronavirus (PDCoV) (9.0-9.6 log(10) genomic equivalents [GE] of OH-FD22-P5; n=4) or porcine epidemic diarrhea virus (PEDV) (10.2-12.5 log(10) GE of PC21A; n=3). In PDCoV-inoculated calves, an acute but persisting fecal viral RNA shedding and PDCoV-specific serum IgG antibody responses were observed, but without lesions or clinical disease. Our study demonstrated that Gn calves orally inoculated with the PDCoV strain OH-FD22 (ICs of cell-culture grown PDCoV from infected Gn pigs) develop an acute infection with persistent fecal PDCoV RNA shedding and PDCoVspecific serum IgG antibody responses, but show no signs of significant intestinal lesions or clinical disease [8] . In our study, there were no detectable fecal viral RNA shedding, virus-specific serum IgG antibody responses, histological lesions, and clinical disease in Gn calves orally inoculated with the PEDV strain PC21A (ICs of wild-type PEDV-infected Gn pigs) [6] .
cord-306502-jkqg1qal	2014	title: An evaluation of contaminated complete feed as a vehicle for porcine epidemic diarrhea virus infection of naïve pigs following consumption via natural feeding behavior: proof of concept Here we provide proof of concept of this risk by describing a novel means for recovering PEDV-contaminated complete feed material from commercial swine sites and conducting an in vivo experiment to prove its infectivity. Clinical signs of PEDV infection (vomiting and diarrhea) and viral shedding were observed in both the Positive control and Treatment group'' post-consumption with virus and microscopic lesions detected in intestinal samples No evidence of infection was observed in the Negative controls. As more data regarding the risk of PEDV transmission via complete feed are needed, we conducted a study to test the risk of PEDV-contaminated complete feed using a novel on-farm sampling method for virus detection in feed along with an in vivo experiment (swine bioassay) using at-risk feed material.
cord-306517-tls0849i	2017	To characterize the Central European PEDV strains regarding their virulence in suckling piglets, and to assess the protective effect of maternally derived antibodies (MDA), four trial groups were randomly assigned, each consisting of two pregnant sows and their litter. To induce MDA in a subset of piglets, two sows received a cell culture-adapted PEDV strain, and another two sows were inoculated with field material from German PED outbreaks. Subsequently, all piglets were inoculated with the corresponding PEDV strains at an age of 3 to 6 days, and virus shedding, clinical signs and occurrence of specific antibodies were assessed. Piglets without MDA and inoculated with the cell culture-adapted virus (PEDV EU, group A2) started vomiting 24 hours post inoculation (hpi), and showed diarrhea from 36 hpi. All sows, which were inoculated with PEDV prior to farrowing (groups A1 and B1), showed IgG isotype antibodies in blood and colostrum samples at the day of farrowing using the ELISA assays mentioned above.
cord-307110-eiobmxp2	2019	In total 137 cat serum samples and 25 FCoV type 1 or type 2-specific antisera were screened for the presence of antibodies against the S1 receptor binding subunit of the CoV spike protein, which is immunogenic and possesses low amino acid sequence identity among coronavirus species. Synthetic sequences of 12 coronavirus spike S1 subunits (HCoV-HKU1 (GB: YP_173238.1), MERS-CoV (GB:YP_009047204.1), SARS-CoV (GB: AAX16192.1), HCoV-OC43 (GB: AAR01015.1), HCoV-229E (GB: NP_073551.1), HCoV-NL63 (GB: YP_003767.1), TGEV (GB: ABG89325.1), PEDV (GB: AOG30832.1), BCoV (GB: P15777.1), PDCoV (GB: AML40825.1), FCoV type 1 (GB: FJ938060.1), FCoV type 2 (GB: AY994055.1)) and different domains of PEDV S1 subunit (S1 0 and S1 A-D , as identified and described in [40] ) were cloned into pCAGGS expression plasmids as described previously [41] .
cord-307408-6wfx0wey	2013	title: Phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in central China based on the ORF3 gene and the main neutralization epitopes In this study, we aimed to investigate the molecular epidemiology and antigenic variability of PEDV field strains based on analysis of ORF3 and a portion of the S gene encoding three neutralizing epitopes (aa 499-638, 748-755, and 764-771) of the S protein. To further investigate the molecular epidemiology of this virus, we chose the ORF3 gene and a partial S gene encoding a region including three neutralization epitopes for studying the evolutionary characteristic and antigenic variation of PEDV. Based on the sequence analysis of ORF3 and partial S genes of PEDV, molecular epidemiology was conducted using 14 field strains from central China. Sequence and phylogenetic analysis of nucleocapsid genes of porcine epidemic diarrhea virus (PEDV) strains in China
cord-308170-uqezwbzn	2014	title: An evaluation of a liquid antimicrobial (Sal CURB®) for reducing the risk of porcine epidemic diarrhea virus infection of naïve pigs during consumption of contaminated feed For the purpose of a positive control, a separate group of piglets was allowed to ingest non-treated (Sal CURB®-free) feed also spiked with stock PEDV (Ct = 25.22). Clinical signs of PEDV infection (vomiting and diarrhea) and viral shedding in feces were observed in the positive control group 2–3 days post-consumption of non-treated feed. Furthermore, the results from the positive control group provide additional proof of concept regarding the ability of contaminated feed to serve as a risk factor for PEDV infection of naïve piglets. The results of this study provide initial proof of concept that the application of a liquid antimicrobial product (Sal CURB®) reduced the risk of PEDV infection through contaminated feed.
cord-308344-ao9z00t7	2017	title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation Among 17 PEDV samples isolated from individual pigs, all of them contained at least two distinct genotypes with large genomic deletions, and 94.1% of them were found to consist of strains with an intact S gene. In this study, variants with large deletions in the S gene were found in eight primary and nine recurrent outbreaks from 16 pig farms, and they mostly (94.1%) coexisted with PEDV strains with an intact S gene. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene New porcine epidemic diarrhoea virus variant with a large deletion in the spike gene identified in domestic pigs
cord-309359-85xiqz2w	2015	Continuous emergence of multiple mutant strains from several regions has aggravated porcine epidemic diarrhea endemic conditions and highlighted the need for new vaccines based on the current circulating PEDV. Genetic variabil ity and phylogeny of current Chinese porcine epidemic diarrhea virus strains based on spike, ORF3, and mem brane genes Molecular characteriza tion and phylogenetic analysis of membrane protein genes of porcine epidemic diarrhea virus isolates in China Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States Molecular epidemiology and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea Cell culture isolation and sequence analysis of genetically diverse US porcine epi demic diarrhea virus strains including a novel strain with a large deletion in the spike gene Genetic characterization of porcine epidemic diarrhea vi rus (PEDV) isolates from southern Vietnam during 2009 2010 outbreaks
cord-309693-f2htekhz	2017	To develop an effective bivalent oral vaccine against TGEV and PEDV infection, the D antigenic site of the TGEV spike (S) protein and the major antigen site (core neutralizing epitope—COE) of the PEDV S protein were used as immunogens, and the enhanced green fluorescent protein (eGFP) gene was used as a reporter to construct genetically engineered Lactobacillus casei rLpPG(F)-T7g10-eGFP-6D-COE. The results showed that levels of anti-PEDV and anti-TGEV serum immunoglobulin G (IgG) and mucosal secreted immunoglobulin A (sIgA) antibodies obtained from the mice immunized with rLpPG(F)-T7g10-eGFP-6D-COE, as well as the proliferation levels of lymphocytes, were significantly higher than those in mice orally administered phosphate-buffered saline (PBS) or rLpPG-T7g10. This was evidenced by significantly higher levels of virus-neutralizing antibodies, anti-PEDV/TGEV serum IgG, and mucosal sIgA in mice orally immunized with rLpPG F -T7g10-eGFP-6D-COE, compared to the levels for the rLpPG-T7g10 or PBS groups.
cord-310579-tnxokfwu	2020	title: Molecular Characterization of Porcine Epidemic Diarrhea Virus and Its New Genetic Classification Based on the Nucleocapsid Gene In the phylogenetic trees inferred from the D1-D2 datasets of the S gene ( Figure 2 , Supplementary Figures S1 and S2) , the PEDV strains were classified into five sub-genogroups (G1a, G1b, G2a, G2b, and G2c), which were previously designated [8] . In the phylogenetic trees inferred from the D1-D2 datasets of the S gene ( Figure 2 , Supplementary Figures S1 and S2) , the PEDV strains were classified into five sub-genogroups (G1a, G1b, G2a, G2b, and G2c), which were previously designated [8] . Supported by high posterior probability values (0.90-1), the phylogenetic trees inferred from the D3-D4 datasets of the N gene (Figure 3, Supplementary Figures S3 and S4) suggested that the classification of PEDV strains into four S gene-based sub-genogroups G1a, G1b, G2b, G2a/G2c was more reliable. Sequence and phylogenetic analysis of nucleocapsid genes of porcine epidemic diarrhea virus (PEDV) strains in China
cord-311255-zaa8i9vh	2014	Abstract The present study sought to investigate whether porcine epidemic diarrhea virus (PEDV) induces apoptosis and to elucidate the mechanisms associated with apoptotic cell death after PEDV infection. Interestingly, mitochondrial apoptosis-inducing factor (AIF) was found to translocate to the nucleus during PEDV infection, and AIF relocalization was completely abrogated by the presence of cyclosporin A (CsA), an inhibitor of cyclophilin D (CypD) that is an essential component of the mitochondrial permeabilization transition pore (mPTP) complex. Altogether, our results indicate that a caspase-independent mitochondrial AIF-mediated pathway plays a central role in PEDV-induced apoptosis to facilitate viral replication and pathogenesis. Therefore, in this study, we aimed to determine if PEDV induces apoptosis following infection in vitro and in vivo and to define the specific pathways involved in apoptotic death of virus-infected cells.
cord-311561-eiys4mbf	2014	title: Full-Length Genome Sequence of a Variant Porcine Epidemic Diarrhea Virus Strain, CH/GDZQ/2014, Responsible for a Severe Outbreak of Diarrhea in Piglets in Guangdong, China, 2014 The full-length genome sequence of a variant porcine epidemic diarrhea virus (PEDV) strain, CH/GDZQ/2014, was determined. Here, we report the full-length genome sequence of a variant PEDV isolate, CH/GDZQ/2014, which is responsible for a severe outbreak of diarrhea in Guangdong, southern China, in March 2014. CH/GDZQ/2014 was a very virulent field PEDV strain isolated from Guangdong Province in southern China. Complete genome sequence of porcine epidemic diarrhea virus strain AJ1102 isolated from a suckling piglet with acute diarrhea in China Complete genome sequence of a Chinese virulent porcine epidemic diarrhea virus strain Complete genome sequence of a very virulent porcine epidemic diarrhea virus strain, CH/ GDGZ/2012, isolated in Southern China Complete genome sequence of novel porcine epidemic diarrhea virus strain GD-1 in China
cord-313126-7hrjzapj	2019	Nineteen complete TGEV genomes and a single strain of porcine respiratory coronavirus (PRCV) from the US were generated and compared to historical strains to investigate the evolution of these endemic coronaviruses. The "variant" genotype shared similar unique deletions and amino acid changes with the recent PRCV strain identified in this study, suggesting a recombination event occurred between the ''''variant'''' TGEV and PRCV. Complete genomic sequences, a key residue in the spike protein and deletions in nonstructural protein 3b of US strains of the virulent and attenuated coronaviruses, transmissible gastroenteritis virus and porcine respiratory coronavirus
cord-313691-6wq64h2b	2020	This study aimed to observe the comparative pathogenicity and cross-protection between G1a and G2a PEDVs, and thus find a new insight into the antigenicity and immunogenicity of PEDVs. The results of the present study demonstrated that the G2a-based inactivated vaccine could provide sterilizing immunity against both highly virulent homologous and heterologous PEDV challenges. The findings of this study might explain the underlying mechanism that severe PED and deaths still occurred among the neonatal piglets of which CV777-based PEDV vaccine were administered in China, and imply G2a-based PEDV vaccine used in this study might be a good vaccine candidate for PEDV which may provide solid protection against circulating highly virulent PEDVs. ABSTRACT: To date, two genotypes, i.e., genotype 1 (G1) and genotype 2 (G2), of porcine epidemic diarrhea virus (PEDV) have been identified in swine, while the cross protection between the G2a and G1a subgenotypes is undetermined.
cord-314751-i9rxesrg	2014	In this study, a codon-optimized PEDV S1 gene containing amino acid residues 25–738 was synthesized based on a multiple alignment of the S amino acid sequences of PEDV field isolates and used to establish a stable porcine cell line constitutively expressing the PEDV S1 protein. In the present study, therefore, we first synthesized a full-length, codon-optimized PEDV S1 gene and then generated a stable porcine-origin cell line constitutively expressing the recombinant S1 protein. These results were coincident with the rabbit study described above, since the rabbit antisera generated by immunization with the recombinant S1 protein also contained low levels of neutralizing antibodies to the heterologous PEDV vaccine strain. In the present study, the first aim was to stably express the full-length, codon-optimized S1 gene of PEDV in porcine-origin cells and to evaluate the immunogenicity and efficacy of the recombinant S1 protein.
cord-315885-iu5wg5ik	2013	title: Full-Length Genome Sequence of a Plaque-Cloned Virulent Porcine Epidemic Diarrhea Virus Isolate (USA/Iowa/18984/2013) from a Midwestern U.S. Swine Herd The complete genome sequence of PEDV strain USA/Iowa/18984/2013 was submitted to GenBank under the accession no. Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States Complete genome sequence of porcine epidemic diarrhea virus strain AJ1102 isolated from a suckling piglet with acute diarrhea in China Complete genome sequence of a Chinese virulent porcine epidemic diarrhea virus strain Complete genome sequence of a recombinant porcine epidemic diarrhea virus strain from eastern China Complete genome sequence of a highly prevalent isolate of porcine epidemic diarrhea virus in south China Complete genome sequence of a variant porcine epidemic diarrhea virus strain isolated in central China Complete genome sequence of novel porcine epidemic diarrhea virus strain GD-1 in China
cord-316134-lkd2mj27	2020	Investigation of possible molecular interactions between components of PEDV, PDCoV and TGEV and their influence on replication of each virus would provide a crucial insight into comprehensive understanding of these CoVs. Of all viral proteins, we have chosen to start with the N protein, as it is among the most abundant and ubiquitous structural proteins in infected cells. For viral infection in the transient CoV N expression experiment, VeroE6 cells were transfected with 1 or 2 μg of pCAGGS-PEDV N-Myc, pCAGGS-PDCoV N-HA, pCAGGS-TGEV N-FLAG, or the empty pCAGGS vector and were incubated for 24 h to allow for protein expression. To investigate how this protein-protein interaction might affect PEDV replication, we transiently transfected VeroE6 cells with varying amounts of the pCAGGS plasmid expressing N proteins from either PDCoV or TGEV for 24 h before infection with PEDV-mCherry (MOI = 0.0001) and followed the course of viral replication for each condition.
cord-316908-8ti75mru	2020	Given that the differences in gene sequences and pathogenicity between classical and mutant strains of PEDV may lead to diverse invasion mechanisms, this study focused on the cellular entry pathways and cellular transport of the PEDV GI and GII subtype strains in Vero cells and IPEC-J2 cells. To clarify the specific endocytic pathways, systematic research methods were used and showed that PEDV enters cells via the clathrinand caveolae-mediated endocytosis pathways, in which dynamin II, clathrin heavy chain, Eps15, cholesterol, and caveolin-1 were indispensably involved. Our results showed that two the subtypes of PEDV utilized clathrin-, caveolae-, and lipid raft-mediated endocytosis to enter the Vero and IPEC-J2 cells, but the utilization efficiency of each endocytic pathway varied depending on the different genotypes and types of cells. We demonstrated that PEDV GI subtype GDS09 and GII subtype GDS01 strains could enter Vero and IPEC-J2 cells via the clathrin-, caveolae-, and lipid raft-mediated endocytosis pathways.
cord-317496-6o2upns3	2019	In this line, we engineered an attenuated virus based on the transmissible gastroenteritis virus (TGEV) genome, expressing a chimeric spike protein from a virulent United States (US) PEDV strain. The rTGEV-RS-SPEDV vaccine candidate was also attenuated in three-week-old animals that were used to evaluate the protection conferred by this virus, compared with the protection induced by infection with a virulent PEDV US strain (PEDV-NVSL). Interestingly, Viruses 2019, 11, 682 9 of 18 when viral RNA was isolated from feces of 21-day-old piglets at seven days post-vaccination (see below) and rTGEV-RS-SPEDV virus was sequenced, the same modifications were observed. An attenuated chimeric rTGEV virus expressing the ectodomain of a virulent US PEDV S protein (rTGEV-RS-SPEDV) was engineered as vaccine candidate for PEDV and evaluated in a young piglet model system. An attenuated chimeric rTGEV virus expressing the ectodomain of a virulent US PEDV S protein (rTGEV-RS-SPEDV) was engineered as vaccine candidate for PEDV and evaluated in a young piglet model system.
cord-319460-n4ezxnjc	2016	During summer 2014, animals on two farms displaying mild clinical signs were detected as positive for PEDV by PCR (Boniotti et al., 2016) , and at the beginning of 2015 a new severe epidemic wave occurred (Efsa Ahaw Panel, 2014) . We conducted a longitudinal study by sampling the feces and blood of piglet groups from each farm at fixed intervals during a 2-5 months period, and then we determined PEDV shedding and the antibody presence. The highest fecal PEDV RNA shedding titer was observed in 3-6 day-old piglets with mean values (among shedding animals) of 5.9, 5.6, 5.6, and 6.2 log 10 copies/mL on F1, F2, F3, and F4, respectively ( Figure 1B; Supplementary Table 3 ). Determining the viral loads and shedding rates of PEDV in real field situations during outbreaks is important in evaluating the virulence of a strain and in predicting the susceptibility of infected animals, at different ages and in the various farm units, within a herd.
cord-319712-3dikelw6	2014	title: Survivability of porcine epidemic diarrhea virus (PEDV) in bovine plasma submitted to spray drying processing and held at different time by temperature storage conditions Bovine plasma was inoculated with porcine epidemic diarrhea virus (PEDV) at an average final titer of 4.2 log10 TCID(50)/mL to determine the effect of spray drying on viral inactivation. Furthermore, and since April 2013, very similar PEDV strains to the Chinese variants have been Veterinary Microbiology 174 (2014) [427] [428] [429] [430] [431] [432] Bovine plasma was inoculated with porcine epidemic diarrhea virus (PEDV) at an average final titer of 4.2 log10 TCID 50 /mL to determine the effect of spray drying on viral inactivation. A second objective was to determine survival time of PEDV inoculated on spray-dried bovine plasma when stored under different temperatures (4, 12 and 22 8C) for different periods of time (0, 7, 14 and 21 days).
cord-320559-up1q3k6q	2018	Porcine epidemic diarrhea virus (PEDV) is the highly contagious, causative agent of an economically important acute enteric disease in pigs of all ages. In total, 838 blood samples from sows from 267 farms and 101 samples from wild boars were collected from May till November 2014 and tested for antibodies against PEDV by ELISA. The number of required blood samples from animals and farms to estimate the seroprevalence of PEDV in Dutch sow herds was calculated based on the following assumptions: PEDV is highly contagious and no vaccination against this virus was carried out in the Netherlands. For the detection of PEDV antibodies in serum samples an in-house indirect ELISA based on the viral spike (S) protein S1-part of the G2b strain GDU (Non-S-INDEL, GenBank KU985230.1) was used, similar as the ELISA previously described (Gerber et al., 2014) .
cord-321739-dnuu6jok	2015	The Ohio swine operation (Figure 1 ), consisting of 3 multi-site, farrow-to-finish production flows (referred to as flows A-C, each having two breed-wean sites) and a multiplier herd (referred to as D, with a single breedwean site) had no prior cases of PEDV and was determined to have effective biosecurity measures in place evidenced by the absence of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) during more than the prior seven years. Beyond the sow unit, a wean-to-finish barn in flow A that received pigs on January 10 th from both flow A breed-wean units (A1 and A2) reported loose stools on January 12 th and had confirmation of PEDV with RT-PCR positive fecal samples collected the same day. On that same day, an oral fluid sample from one of the nurseries in flow B that received pigs from both flow B breed-wean units (B1 and B2) on January 15 th , 17 th , and 20 th , 2014 tested PEDV PCR positive ( Figure 1B ).
cord-321814-vt6yio6x	2012	In this study, we isolated a PEDV strain designated CHGD-01 from piglet intestines using Vero cell cultures, and its specific cytopathic effects were confirmed in susceptible cells by direct immunofluorescence testing and electron microscopy. Amino acid sequence analysis based on individual virus genes indicated a close relationship between the spike protein gene of CHGD-01 and the field strain KNU0802 in Korea. Phylogenetic analyses of the S protein amino acid sequences revealed that all PEDV strains in this study could be separated into two groups: CHGD-01 belonged to Group 2, which also contained the two Japanese isolates Kawahira and NK, eight Korean field strains (Chinju99, KNU-0801, KNU-0802, and KNU-0901-KNU-0905) and two Chinese strains (BJ-2011-1 and CH/FJND-3/2011), which were deposited in GenBank in 2011 ( Figure 3b ). Molecular characterization and phylogenetic analysis of membrane protein genes of porcine epidemic diarrhea virus isolates in China
cord-321953-yql6gpd3	2017	Therefore, this report was conducted using the complete sequence of the S gene and powerful Bayesian phylogeographic reconstructions to clarify the putative origin of PEDV in Ecuador, revealing the wide expansion of the emergent PEDV strains, which caused the first PEDV outbreak in this country. To perform sequence comparison analyses and to establish the phylogenetic relationships of PEDV sequence from Ecuador, alignments using the consensus sequence of complete S gene available at GenBank database (Supplementary Information Table S1 ) were conducted by the algorithm ClustalW included in the program BioEdit Sequence Alignment Editor [33] . The phylogeographic study revealed the emergence of the Chinese PEDV strains followed by spreading to US in 2013 (Figures 3(a) and 3(b), Supplementary Material Video S1). Complete genome sequence of a porcine epidemic diarrhea S gene indel strain isolated in France in
cord-321992-lk2ao6m8	2015	In the present study, we investigated the innate immune responses such as cytokine and NK cell activity as well as changes in frequencies of T cells to examine if differences coincide with the higher disease severity of suckling versus weaned pigs. The infected weaned pigs also had significantly higher NK cell frequencies in blood and ileum at PID 5 (P < 0.05) compared to infected suckling pigs ( Fig. 2A and B) . In infected suckling and weaned groups, peak IFN␣, IL-12 and TNF␣ levels coincided with onset of diarrhea and fecal PEDV RNA shedding and peak serum PEDV RNA titers (PIDs 1 and 3, respectively); and (4) Frequencies of CD3+CD4+ T cells were significantly higher in ileum of suckling pigs than in weaned pigs, whereas there was no difference in frequency of CD3+CD8+ T cells.
cord-322475-i29t7ce8	2012	title: Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) samples from field cases in Fujian, China In this study, we investigated molecular diversity, phylogenetic relationships, and protein characterization of Fujian field samples with other PEDV reference strains. Phylogenetic analysis based on S1 or sM gene, which have high levels of variations, indicated that each sample was related to the specific reference strain, and this finding was consistent with the protein characterization prediction analysis. In order to analyze the phylogenetic relationships between the 3 Fujian samples and other PEDV strains isolated in various regions worldwide, we constructed 2 phylogenetic trees using the deduced amino acid sequences of S1 and sM, respectively (Fig. 3) . Molecular characterization and phylogenetic analysis of membrane protein genes of porcine epidemic diarrhea virus isolates in China Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea
cord-322683-wkrj6n1d	2020	title: Cellular Poly(C) Binding Protein 2 Interacts with porcine epidemic diarrhea virus Papain-Like Protease 1 and Supports Viral Replication Taken together, these data demonstrated that PLP1 negatively regulated the production of type 1 interferon by interacting with PCBP2 and promoted PEDV replication. The PEDV N protein interacts with the TANK-binding kinase, blocking its association with interferon regulatory factor 3 (IRF3) and thus inhibiting IRF3 activation and type I IFN production (Ding et al., 2014; Hu et al., 2018) . PCBP2 expression is induced following viral infection and acts as a negative regulator of mitochondrial antiviral signaling protein (MAVS), triggering its degradation (You et al., 2009) . Although significant progress has been made in understanding PEDV evasion of innate immune responses, the mechanism of interaction between viral and host cell proteins remains unclear. In the present study, we demonstrated that PLP1 interacted with PCBP2 to inhibit IFN-β production and promote PEDV replication.
cord-327000-oyg3oyx1	2020	
cord-329227-sqetz7h6	2018	The amounts of PEDV S proteins in the ERGIC, in other organelles, or on the cell surface are likely regulated by two nearby motifs in its cytoplasmic tail (CT): a tyrosine-based motif, Yxx⌽ (x is any residue and ⌽ is a bulky hydrophobic residue: F, M, I, L, or V), and an ER retrieval signal (ERRS), KVHVQ (10) (11) (12) (13) , as well as other viral and cellular proteins. One study demonstrated that a single amino acid substitution in this motif (KVHVQ to KVRVQ) weakens the intracellular retention function of the S proteins of the 10th passage of a murine-adapted PEDV variant, MK-P10 (18) , resulting in enhanced syncytium formation in Vero cells. In this study, we evaluated the phenotypes of transiently expressed S mutants containing mutations or deletions in these two motifs in mammalian cells and the virulence of three representative recombinant PEDVs in gnotobiotic piglets.
cord-330035-0d6w8xyd	2017	The addition of exogenous cholesterol to MβCD-treated cells moderately restored the infectivity of porcine nidoviruses, indicating that the presence of cholesterol in the target cell membrane is critical for viral replication. The addition of exogenous cholesterol to MβCD-treated cells moderately restored the infectivity of porcine nidoviruses, indicating that the presence of cholesterol in the target cell membrane is critical for viral replication. Furthermore, pharmacological sequestration of cellular cholesterol efficiently blocked both virus attachment and internalization and, accordingly, markedly affected subsequent post-entry steps of the replication cycle, including viral RNA and protein biosynthesis and progeny virus production. Further experiments revealed that pharmacological depletion of cellular cholesterol primarily interferes with virus binding and penetration and subsequently influences post-entry stages of the PRRSV and PEDV replication cycle, including viral genomic and sg RNA synthesis, viral protein expression, and virus production.
cord-330475-mameyzih	2014	Furthermore, by utilizing fusion proteins with green fluorescent protein (GFP), deletion mutations or site-directed mutagenesis of PEDV N protein, coupled with live cell imaging and confocal microscopy, it was revealed that, a region spanning amino acids (aa), 71–90 in region 1 of the N protein was sufficient for nucleolar localization and R87 and R89 were critical for its function. The B23.1-DsRed fusion protein was used to tag the nucleolus, so we could analyze nucleolar localization properties and colocalization in cotransfected cells by live cell imaging (direct fluorescence) or confocal microscopy. These expression plasmids were transfected into Vero E6 cells, the nuclear was stained with DAPI at 24 h post-transfection indicated that amino acids 148-220 directed AcGFP to the cytoplasm and nucleus and had a subcellular localization similar to AcGFP.
cord-330772-i7cfmw9x	2019	The in vitro toxicity and antiviral ability of the surfactin-like peptide in the BLFP crude extract against PEDV were evaluated using the Vero cells. To study the antiviral activity of BLFP crude extract against PEDV, the biosurfactants were added at different time points during the viral infection. No statically significant difference in the average daily gain was noted among all groups each week BLFP crude extract with PEDV-infected cells during the whole study. Similarly, extracellular viral RNA levels in PEDV-infected cells cultured with biosurfactants were significantly lower than those without BLFP crude extract 24 and 48 HPI (Fig. 8b) . b Extracellular viral RNA levels in the supernatants of PEDV-infected Vero cells treated with or without BLFP crude extract were determined by real-time reverse transcription (RT)-PCR. d Intracellular viral RNA levels in the supernatants of PEDV-infected Vero cells treated with or without BLFP crude extract were determined by real-time RT-PCR.
cord-330825-apfcql4m	2016	title: Phylogenetic tracking of current porcine epidemic diarrhea virus (PEDV) strains in the Philippines Since the receptor-binding sites and majority of the neutralization epitopes are located in the S1 portion, this region has been subjected to sequencing and molecular analysis to determine the genetic relatedness of different PEDV viruses [1] [2] [3] . Using data from swine farms in these provinces and diagnosis data from the College of Veterinary Science and Medicine in Central Luzon State University, the incidence is 67 % in Pampanga, 79 % in Tarlac, 61 % in Batangas, and 90 to 100 % in Agusan. This is the first report of PEDV S1 gene sequences from the provincial PEDV hotspots of the Philippines, which include Batangas, Pampanga, Tarlac and Agusan. Phylogenetic analysis of the spike (S) gene of the new variants of porcine epidemic diarrhoea virus in Taiwan Molecular characterization of the spike and ORF3 genes of porcine epidemic diarrhea virus in the Philippines
cord-331509-p19dg1jw	2020	title: Porcine epidemic diarrhea virus: Viral RNA detection and quantification using a validated one-step real time RT-PCR In this study we described the development and validation of a SYBR™ Green one-step RT-qPCR according to the French norm NF U47-600, for the detection and quantification of PEDV viral RNA. Specificity and sensitivity, limit of detection (LoD), limit of quantification (LQ), linearity, intra and inter assay variability were evaluated using transcribed RNA and fecal and jejunum matrices spiked with virus. For a rapid, accurate and reliable diagnosis of PED in the veterinary laboratory, a method for the detection of PEDV viral RNA has been developed and more importantly validated according to the "Association Francaise de NORmalisation" (AFNOR) French NF U47-600 norm entitled "requirement and recommendation for the implementation, development and validation of PCR in animal health" (AFNOR, 2015a; AFNOR, 2015b) . This method should help harmonize detection and quantification of viral RNA from PEDV belonging to both S-non-INDEL and S-INDEL strains in both field and experimental settings.
cord-331542-wy068c6o	2020	The antisera titers were determined by indirect ELISA, western blot and IFA after four immunizations to find the important immunodominant region of S1, and then purified the immunodominant region of S1 protein and immunized mice to generate the special antibodies, and then used recombinant peptides to determine the B-cell epitopes of monoclonal antibodies. To accurately identify the immunodominant region of S1, the purified truncated S1 proteins (SA, SB, SC, SD and SE) were used to immunize BALB/c mice to prepare Fig. 1 Detection of recombinant proteins'' antigenicity for polyclonal antisera (PcAbs) by indirect ELISA, western blot and IFA. The indirect ELISA and western blot analysis showed that the SE polyclonal antisera had the highest antibody titers against PEDV S1 protein ( Fig. 1a and b) , suggesting that SE protein was the important immunodominant region of S1.
cord-331652-oc5s1if2	2016	
cord-331919-6kistim2	2012	Another report revealed that PEDV has caused enteric disease with devastating impact since the first identification of PEDV in 1992 in Korea, and recent, prevalent Korean PEDV field isolates are closely related to Chinese field strains but differ genetically from European strains and vaccine strains [45] . For instance, it is possible to estimate the potential transmission of PEDV by comparing viral shedding load with a standard internal control DNA curve [72] , as well as to perform multiplex RT-PCR to detect PEDV in the presence of various viruses [73] -a technique that is particularly useful for rapid, sensitive, and cost-effective diagnosis of acute swine viral gastroenteritis). Shorter periods of virus shedding, as well as reduced severity and duration of diarrhoea in piglets, result from higher titres of serum antibodies; complete protection from PEDV infection prevents shedding after exposure to viral challenge [90] . Development of an ELISA for the detection fo antibody isotypes against porcine epidemic diarrhoea virus (PEDV) in sow''s milk
cord-332811-kjgah8ts	2015	title: Immunoprophylactic effect of chicken egg yolk antibody (IgY) against a recombinant S1 domain of the porcine epidemic diarrhea virus spike protein in piglets A codon-optimized PEDV S1 gene consisting of amino acid residues 25–749 was synthesized and used to establish a stable porcine cell line constitutively expressing a recombinant PEDV S1 protein containing the chicken immunoglobulin Fc fragment at its C-terminus. Moreover, oral passive immunization using chicken IgY raised against the PEDV S1 protein was found to control and prevent PED post-challenge in suckling piglets. All neonatal piglets except for animals in the control group were inoculated orally with 1 ml of the small-intestine homogenate containing 10 4 TCID 50 /ml PEDV field virus determined using real-time RT-PCR as described previously [10] . Immunoprophylactic effect of chicken egg yolk immunoglobulin (IgY) against porcine epidemic diarrhea virus (PEDV) in piglets
cord-334218-bkjfy66e	2016	title: Impact of Mated Female Nonproductive Days in Breeding Herd after Porcine Epidemic Diarrhea Virus Outbreak The objectives of the present study were to investigate the effects between a 1-year period before and after PEDV outbreak on a sow''s reproductive traits on a commercial pig farm in Taiwan. The average number of mated females, average parity of farrowed sows, number of matings, number of farrowings, FR, RR, number of abortions, LMFY, percentage of sows mated by 7 days after weaning, WFSI, FI, NPDs, replacement rates of sows and sow culling rates of preand post-PEDV outbreak periods were compared using a Mann-Whitney test. In the present study, we compared the productivity index of gilts and sows between 1 year pre-and post-PEDV outbreak in a Taiwanese breeding herd. Impact of porcine epidemic diarrhea virus infection at different periods of pregnancy on subsequent reproductive performance in gilts and sows
cord-336517-v7z62tld	2018	Further studies suggest that PEDV PL2 pro exhibits much higher DUB activity than that of SARS-and MERS-CoV PL pro s and can be inhibited by the anti-leukemia drug 6-thioguanine (6TG). Previous studies suggested that the Ubl domain was not involved in the catalytic activity of SARS-and MERS-CoV PL pro s (Chou et al., 2012; Clasman et al., 2017) . Overall, the secondary, tertiary and quaternary structures of the PEDV PL2 pro catalytic core are similar to those of SARS-and MERS-CoV PL pro s, even though their sequence identity is only 22-25% (Fig. S1 ). In contrast, previous studies suggested that the binding site of 6TG for SARS-and MERS-CoV PL pro s may be near the catalytic triad''s cysteine residue due to its competitive pattern of inhibition Chou et al., 2008) . Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin
cord-339012-4juhmjaj	2020	Instead, PEDV down-regulated the expression of a set of zinc finger proteins with putative antiviral activity and enhanced the expression of the transmembrane serine protease gene TMPRSS13 (alias MSPL) to support its own infection by virus-cell membrane fusion (Shi et al, 2017, Viruses, 9(5):114). Furthermore, by comprehensive datamining in biological and chemical databases and consulting related literature we identified sets of PEDV-response genes with potential to influence i) the metabolism of biogenic amines (e.g. histamine), ii) the formation of cilia and "synaptic clefts" between cells, iii) epithelial mucus production, iv) platelets activation, and v) physiological processes in the body regulated by androgenic hormones (like blood pressure, salt/water balance and energy homeostasis). The detected sets of differential expressed genes (DEGs) for PEDV and MRV were analyzed by gene set enrichment analysis (GSEA) using functional bioinformatic programs to retrieve biological processes (pathways and Gene Ontology terms [GO-term]) and associations with chemical compounds, including drugs.
cord-339546-m7rqr886	2002	An enzyme-linked immunospot (ELISPOT) has been developed to detect porcine epidemic diarrhea virus (PEDV)-specific antibody secreting cells (ASC) in gut associated lymphoid tissues (duodenum and ileum lamina propria and mesenteric lymph nodes) and systemic locations (spleen and blood) of conventional pigs so as to characterise the mucosal and systemic antibody response generated by the infection with PEDV. Memory antibody response to the PEDV was also studied by secondary in vitro stimulation of the mononuclear cells (MNC) isolated from mesenteric lymph nodes, spleen and blood. In order to evaluate the distribution of PEDV-speci®c ASC, MNC from mesenteric lymph nodes, lamina propria of duodenum and ileum, spleen and blood were recovered at various PID from PEDV exposed pigs and tested for antibody production by ELISPOT. Table 1 Numbers of isotype-specific ASC to PEDV (per 5 Â 10 5 MNC) in duodenum and ileum lamina propria, mesenteric lymph nodes (MLN), spleen and blood from pigs experimentally exposed to the virulent isolate of the PEDV strain CV-777 and sacrificed on PID 4, 7, 14, 21, 25 
cord-339871-jso21mbx	2018	To investigate the diversity of PEDVs responsible for the ongoing outbreaks in South Korea, in this study, we determined the full-length sequences of the S proteins of field isolates and complete genome sequences of representative strains identified throughout 2017. Based on the S gene sequences, therefore, PEDV can be genetically separated into two genogroup clusters, genogroup 1 (G1, classical and recombinant: low-pathogenic) and genogroup 2 (G2, field epizootic or panzootic: high-pathogenic), which are further divided into subgroups 1a and F I G U R E 1 Phylogenetic analysis based on nucleotide sequences of the spike genes (a) and full-length genomes (b) of porcine epidemic diarrhoea virus strains. Molecular characterization and phylogenetic analysis of membrane protein genes of porcine epidemic diarrhea virus isolates in China Full-genome sequence analysis of a variant strain of porcine epidemic diarrhea virus in South Korea Genomic and antigenic characterization of Porcine epidemic diarrhoea virus strains isolated from South Korea
cord-339924-tsmnkuhw	2014	title: Pathology of US Porcine Epidemic Diarrhea Virus Strain PC21A in Gnotobiotic Pigs To understand the progression of porcine epidemic diarrhea virus infection, we inoculated gnotobiotic pigs with a newly emerged US strain, PC21A, of the virus. For the pig-passaged PC21A strain, RT-PCR/PCR results were negative for transmissible gastroenteritis virus/porcine respiratory coronavirus (7), rotavirus groups A-C (8), caliciviruses (13, 14) , astroviruses (15) , circoviruses, enterovirus, kobuvirus, and bocavirus. Electron micrograph of a US porcine epidemic diarrhea virus (PEDV) particle detected in a field fecal sample collected during a 2013 outbreak of PED on a farm in Ohio, USA; the fecal sample from which PEDV strain PC21A in this study was obtained was from a pig on the same farm during the same outbreak. Emergence of Porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences
cord-340202-ikptxviu	2015	Sequencing and phylogenic analyses of the partial spike gene and ORF3 of PEDV demonstrated that all prevailing Japanese PEDV isolates belonged to novel genotypes that differed from previously reported strains and the two PEDV vaccine strains currently being used in Japan. Unlike vaccine strains, all prevailing field PEDV isolates in Japan were found to have a number of amino acid differences in the neutralizing epitope domain, COE, which may affect antigenicity and vaccine efficacy. This study aimed to evaluate the genetic characteristics and molecular epidemiology of the emergent Japanese PEDV isolates using genome analysis and phylogenetic analysis of the partial S gene and ORF3. To investigate the heterogeneity of the recent Japanese isolates and their genetic relationship with modified live vaccines, in addition to 2 PEDV vaccine strains (P5-V and 96-P4C6) used in Japan, representative isolates were selected for sequencing of the partial S gene and full ORF3 gene.
cord-340438-9q3ic0ye	2018	
cord-341469-7guojyay	2011	Especially, ORF3 gene analysis can be used for discrimination between vaccine and wild-type PEDVs. Sequence and phylogenetic analysis showed that recent, prevalent Korean PEDV field isolates have close relationships to Chinese field strains and differ genetically from European strains and vaccine strains used in Korea. Sequence analysis of the complete ORF3 genes showed that all PEDVs, including the Korean field isolates, fell into three groups, and group 3 had two subgroups (3-1 and 3-2), as can be seen in the phylogenetic tree (Fig. 2) . Genetic analysis based on complete M and ORF3 genes showed that each PEDV group had several unique characteristics, and these results indicated that specific groups of PEDVs may be differentiated from other PEDVs, including Korean field isolates, by specific nucleotide differences, but more PEDVs need to be analyzed for more accurate analysis.
cord-341521-dntkdwkj	2020	MATERIAL AND METHODS: We observed the effect of the PEDV SHpd/2012 strain on an infected Vero cell cycle through flow cytometry and Western blot, investigating the interrelationships of cell-cycle arrest, the DNA damage–signalling pathway caused by PEDV and the phosphorylation levels of the key molecules Chk.2 and H2A.X involved upstream and downstream in this pathway. We used inhibitors of ATM and Chk.2 to block the DNA damage-signalling pathway and to confirm whether PEDV infection can lead to cell-cycle arrest. We also treated cells with chemical inhibitors of ATM and Chk.2 to determine if cell-cycle arrest after PEDV infection was linked with activation of the DNA damage-signalling pathway. These results revealed that cell-cycle arrest after infection of Vero cells with PEDV was caused by activation of the DNA damage-signalling pathway.
cord-342923-prgorr3d	2018	title: Cellular hnRNP A1 Interacts with Nucleocapsid Protein of Porcine Epidemic Diarrhea Virus and Impairs Viral Replication Replication of PEDV was inhibited by silencing the expression of hnRNP A1 in CCL-81 cells, suggesting the positive effect of hnRNP A1 on PEDV infection. Previous studies have demonstrated hnRNP A1 could interact with N proteins of SARS Coronavirus and mouse hepatitis virus (MHV) [14, 19] . Our previous work has proved that hnRNP A1 underwent different regulations in jejunum tissues of piglets infected with PEDV virulent strain and its attenuated strain [20] . The beads were then washed with IP lysis buffer five times and boiled in sample buffer, and the proteins were subjected to SDS-PAGE, followed by immunoblotting analysis with anti-Flag PAb or anti-hnRNP A1 PAb. CCL-81 cells grown on coverslips were infected with PEDV YN144 strain, YN13 strain and CV777 strain, respectively, at a multiplicity of infection (MOI) 0.001.
cord-343132-qqhivgkq	2020	The results showed that the intracellular extracts of Ln. mesenteroides YPK30 possessed in vitro prophylactic, therapeutic, and direct-inhibitory effects against PEDV in the Vero cell model. As shown in Figure 3 , the metabolic activity of Vero cells pretreated with the intracellular extracts of Ln. mesenteroides, regardless of which strain, were similar to those pretreated with IFN-α2b (p > 0.05) but were significantly higher than the un-pretreated cells (p < 0.05), indicating that all the Ln. mesenteroides strains isolated from kefir grains possessed in vitro prophylactic effects against PEDV. durans, Lb. kefiri, Lc. lactis, and Ln. mesenteroides , were isolated from kefir grains, and the in vitro prophylactic effects of the intracellular extracts of these four species against PEDV infection in Vero cells were compared. Therefore, the in vitro prophylactic and therapeutic effects of the intracellular extracts of Ln. mesenteroides YPK30 against PEDV in Vero cells seem not be attributed to the direct interaction of bacterial components or metabolites with virus.
cord-343780-084lq92r	2018	title: Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan To investigate if PDCoV is also present in Taiwan, three swine coronaviruses—PDCoV, porcine epidemic diarrhea virus (PEDV), and transmissible gastroenteritis coronavirus (TGEV)—were tested using real-time reverse transcription polymerase chain reaction (rRT-PCR) in 172 rectal swab samples from piglets exhibiting diarrhea between January 2016 and May 2017 on 68 pig farms in Taiwan. Currently, there are at least three members of the family Coronaviridae that can cause diarrhea in pigs: transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), and porcine deltacoronavirus (PDCoV) [8] . Based on the real-time RT-PCR (rRT-PCR) detection results, the percentage of pig farms that were positive for at least of one of the coronaviruses was 25% for PDCoV (17/68), 22.1% for PEDV (15/68), and 2.9% for TGEV (2/68). Phylogeny analysis of PDCoV-N genes showed that PDCoVs found in Taiwan were highly similar in their nucleotide sequences to isolates from the United States, mainland China, and other countries (Fig. 1) .
cord-344309-6c2wttxg	2018	
cord-344421-rmnck42f	2018	Suckling piglets shed kobuvirus from one week of age, but an association between peak of viral shedding (10(6.42)–10(7.01) copies/swab) and diarrheic signs was not observed during a follow-up study. Third-generation sequencing using MinION (Oxford Nanopore Technologies, ONT) might be a useful and affordable diagnostic tool for swine veterinary medicine as it allows rapid sample preparation and real-time sequence analysis. The shedding of porcine kobuvirus, RVA and rotavirus C (RVC) was quantitatively investigated in 5 suckling pigs of the same farm from which the diarrheic feces originated. The third-generation sequencing device MinION (ONT), holds promise as a diagnostic platform, as it allows real-time sequencing and analyses of all DNA/RNA in a sample, theoretically without needing pre-amplification of viral nucleic acids. In the present study, a novel RT-qPCR assay, targeting the conserved 3D gene encoding the RNA-dependent-RNA-polymerase, was developed and used to assess, for the first time, longitudinal quantitative shedding kinetics of porcine kobuvirus in pigs under field conditions.
cord-344558-1jgqofbr	2001	A cloning strategy, which involves primers based on conserved regions in the predicted ORF1 products from other coronaviruses whose genome sequence has been determined, was used to amplify the equivalent, but as yet unknown, sequence of PEDV. Comparative amino acid sequence alignments revealed that PEDV is most closely related to human coronavirus (HCoV)-229E and transmissible gastroenteritis virus (TGEV) and less related to murine hepatitis virus (MHV) and infectious bronchitis virus (IBV). The alignment of the deduced amino acid sequences indicated that PEDV occupies an interesting intermediate position between the two well-characterized members of the group I coronaviruses, transmissible gastroenteritis virus (TGEV) and human coronavirus (HCoV)-229E. In order to obtain the first partial PEDV specific sequences, the predicted amino acid sequences of the HCoV-229E and TGEV polymerase ORFs were aligned and homologous regions identified. The deduced amino acid sequences of ORF1a and ORF1b from PEDV were aligned with the corresponding sequences of HCoV-229E, TGEV, MHV-A59, and IBV using PILEUP.
cord-344845-52rehsd5	2017	title: Evaluation of the efficacy of a commercial inactivated genogroup 2b-based porcine epidemic diarrhea virus (PEDV) vaccine and experimental live genogroup 1b exposure against 2b challenge The aim of this study was to compare the ability of G1b-based live virus exposure against use of a commercial G2b–based inactivated vaccine to protect growing pigs against G2b challenge. Under the study conditions a commercial inactivated G2b-based vaccine protected pigs against G2b challenge, as evidenced by reduction of PEDV RNA in feces for 3–4 logs during peak shedding and a shorter viral shedding duration. The oral, but not the intramuscular, experimental G1b-based live virus exposure induced a high anti-PEDV IgA response prior to challenge, which apparently did not impact PEDV shedding compared to POS-CONTROL pigs. Anti-PEDV IgA antibodies in serum samples were first detected in 8/8 EXP-ORAL-1b pigs at dpv 14 ( Figure 3 ).
cord-345940-adg264vb	2018	
cord-346457-2mq2aije	2020	RESULTS: In the study, a differential one-step quantitative real-time fluorescent reverse transcription recombinase polymerase amplification (real-time RT-RPA) method based on the PEDV universal real-time RT-RPA assay was established according to the ORF1 deletion sequences of three classical attenuated vaccine strains (PEDV attenuated vaccine KC189944, attenuated CV777 and DR13) and five Vero cell-adapted isolates (JS2008, SDM, SQ2014, SC1402, HLJBY), which could effectively differentiate PEDV classical attenuated vaccine strains from wild-type strains (PEDV classical wild strains and variant strains). The detection limits of PEDV RNA in the both PEDV real-time RT-RPA assays were 300 copies within 20 min at 39 °C, and the detection limits of classical attenuated vaccine strain CV777, Vero-cell-adapted isolate JS2008, and PEDV wild-type strain DX were 10(0.5) TCID(50)/100 μL, 10(1.1) TCID(50)/100 μL, and 10(1.2) TCID(50)/100 μL, respectively. CONCLUSION: This RPA method we developed is simple, time-effective, and safe and provides a reliable technical tool for the differential diagnosis and clinical epidemic surveillance of PEDV classical attenuated vaccine strains and wild-type strains.
cord-346872-k5d5793a	2018	
cord-347475-ttmactz0	2015	
cord-348669-mizygp4j	2016	
cord-349249-jwvz1ux2	2019	To combine the safety and efficacy advantages of inactivated and attenuated PEDV vaccines, respectively, in this study, we tested the hypothesis that subjecting PEDV virions to heat treatment at 44°C for 10 min to reversibly unfold structural proteins, followed by exposure to RNAse to fragment the genome, would result in a vaccine preparation with intact viral structure/antigenicity but highly diminished replicative abilities. to that of the spike protein-specific Abs. Strong virus neutralizing Ab responses, were detected in animals vaccinated with the heat and RNAse treated virions but not in the pigs which received the irradiated viral vaccine. Although the heat and RNAse treated virus culture was amplified after 3 passages in cell culture (Figure 2) , the absence its detection by RT-qPCR (Figure 4) , or immunohistochemistry (Table 1 and Figure 5 ) and the lack of strong Ab responses to the non-structural NP (Figure 3) , in vaccinated pigs prior to challenge indicates that active vaccine viral replication was absent in the host or was undetectable by the techniques used.
cord-353245-es7b1rs0	2015	Compared to the PEDV CV777 strain, CH/JX-1/2013 and CH/JX-2/2013 had some unique genetic characteristics in the proximal region of the 5''-UTRs. Phylogenetic analysis of the complete genomes and the structural proteins revealed that CH/JX-1/2013 and CH/JX-2/2013 had a close relationship with post-2010 Chinese PEDV strains and US strains identified in 2013. Genetic characteristics were observed between the two groups: 1) compared to genome sequences of the members in G1, four insertions, 20803G, 20810CAGGGTGTCAA20820, 20830G, 21042AAT21044 and two deletions, 20842A, 21097CGTGAT21102, existed in the N-terminal domain (NTD) of the S protein in G 2 members; 2) the three field PEDV strains of JS2008, JS2008new and SD-M together with two attenuated PEDV strains, DR13 and vaccine_KC189944, were clustered into subgroup 1b. Notably, an amino acid substitution was found in the middle of one neutralizing epitope Phylogenetic trees based on the complete genome, aa sequences of structural proteins and ORF3 of PEDV strains. Sequence and phylogenetic analysis of nucleocapsid genes of porcine epidemic diarrhea virus (PEDV) strains in China
cord-354052-x4ckzw64	2013	
cord-354729-dpaz01np	2019	title: Characterization and evolution of the coronavirus porcine epidemic diarrhoea virus HLJBY isolated in China A strain of porcine epidemic diarrhoea virus (PEDV), namely HLJBY, was isolated in Heilongjiang province, China. To investigate the molecular characteristics of PEDV HLJBY strain, UTR (5'' and 3'') and the nucleotide and predicted amino acid sequences of the nonstructural and structural proteins (replicase ORF1a/1b, S, ORF3, E, M, N) of PEDV HLJBY strain were compared with CV777. 399 nt deletions exhibited in ORF3 of PEDV HLJBY (Figure 2d ), and nucleotide sequence identity was 91.7%, and the amino acid sequence identity was 90.1% (Table 3 ). To investigate the evolution of PEDV, phylogenetic analysis based on the entire genomic nucleotide sequences of PEDV HLJBY strain The group Ⅲ was further divided into subgroup Ⅲa and Ⅲb. Characterization and evolution of the coronavirus porcine epidemic diarrhoea virus HLJBY isolated in China
cord-355119-sdg9zdc1	2016	
cord-355465-qjtifwhd	2018	
cord-355991-4zu69e0y	2018