Characterization of Chinese Porcine Epidemic Diarrhea Virus with Novel Insertions and Deletions in Genome

Isolation and characterization of a novel S1-gene insertion porcine epidemic diarrhea virus with low pathogenicity in newborn piglets

Porcine epidemic diarrhea virus (PEDV) causes diarrhea and vomiting in piglets, leading to a mortality rate of 100%. Due to the high frequency of mutation, it is important to monitor the evolution of PEDV and develop potential vaccine candidates. In this study, two PEDV strains (ZJ2022 and ZQ2022) were identified by PCR. These strains were subsequently isolated, and their genome sequences, growth characteristics, and pathogenicity were compared. Phylogenetic and recombination analyses revealed that both strains belonged to GIIa-subgroup, and ZQ2022 was identified as a recombinant strain derived from ZJ2022. Further sequence analysis showed that the ZJ2022 strain had a modified top region of the S1 protein due to a three amino acid insertion (T380_Y380insGGE) in the S1 gene. According to the virus growth curve, ZJ2022 exhibited better cellular adaptation than ZQ2022, with higher viral titers from 8 hpi to 24 hpi. Additionally, ZQ2022 exhibited a high level of pathogenicity, causing severe diarrhea in piglets at 36 hpi and a 100% mortality rate by 96 hpi. In contrast, ZJ2022 showed lower pathogenicity, inducing severe diarrhea in piglets at 60 hpi, with a mortality rate of 60% at 96 hpi and 100% at 120 hpi. In summary, our findings provided evidence of the undergoing mutations in Chinese PEDV strains. Furthermore, the S gene insertion strain ZJ2022 exhibited strong cellular adaptability and low pathogenicity, making it a potential candidate strain for vaccine development.

Genetic characterization and phylogenetic analysis of the S genes of porcine epidemic diarrhea virus isolates from China from 2020 to 2023

Porcine epidemic diarrhea virus (PEDV) is an enteric coronavirus that has been the main cause of diarrhea in piglets since 2010 in China. The aim of this study was to investigate sequence variation and recombination events in the spike (S) gene of PEDV isolates from China. Thirty complete S gene sequences were obtained from PEDV-positive samples collected in six provinces in China from 2020 to 2023. Phylogenetic analysis showed that 10% (3/30) belonged to subtype GII-a, 6.67% (2/30) were categorized as subtype GII-b, 66.67% (20/30) were categorized as subtype GII-c, and 16.66% (5/30) were clustered with the S-INDEL strains. Amino acid sequence alignments showed that, when compared to strains of other subtypes, the GII-c strains had two characteristic amino acid substitutions (N139D and I289M). Five S-INDEL subtype strains had a single amino acid deletion (139N) and four amino acid substitutions (N118G, T137S, A138S, and D141G). Recombination analysis allowed six putative recombination events to be identified, one involving recombination between GII-c strains, two involving GII-c and GII-b strains, two involving GII-c and GI-a strains, and one involving GII-a and GI-b strains. These results suggest that recombination between PEDV strains has been common and complex in recent years and is one of the main reasons for the continuous variation of PEDV strains.

Phylogenetic and Genetic Variation Analysis of Porcine Epidemic Diarrhea Virus in East Central China during 2020-2023

Porcine epidemic diarrhea virus (PEDV) is a major causative pathogen of a highly contagious, acute enteric viral disease. This study evaluated the emergence of nine variants in Jiangsu and Anhui provinces of China from 2020 to 2023. S gene-based phylogenetic analysis indicated that three variants belong to the G1c subgroup, while the other six strains are clustered within the G2c subgroup. Recombination analyses supported that three variants of the G1c subgroup were likely derived from recombination of parental variants FR0012014 and a donor variant AJ1102. In addition, there are novel mutations on amino acid 141-148 and these likely resulted in changes in antigenicity in the three variants. These results illustrated that the study provides novel insights into the epidemiology, evolution, and transmission of PEDV in China.

Comparative Review of the State of the Art in Research on the Porcine Epidemic Diarrhea Virus and SARS-CoV-2, Scope of Knowledge between Coronaviruses

This review presents comparative information corresponding to the progress in knowledge of some aspects of infection by the porcine epidemic diarrhea virus (PEDV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronaviruses. PEDV is an alphacoronavirus of great economic importance due to the million-dollar losses it generates in the pig industry. PEDV has many similarities to the SARS-CoV-2 betacoronavirus that causes COVID-19 disease. This review presents possible scenarios for SARS-CoV-2 based on the collected literature on PEDV and the tools or strategies currently developed for SARS-CoV-2 that would be useful in PEDV research. The speed of the study of SARS-CoV-2 and the generation of strategies to control the pandemic was possible due to the knowledge derived from infections caused by other human coronaviruses such as severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS). Therefore, from the information obtained from several coronaviruses, the current and future behavior of SARS-CoV-2 could be inferred and, with the large amount of information on the virus that causes COVID-19, the study of PEDV could be improved and probably that of new emerging and re-emerging coronaviruses.

Immunogenicity and protective efficacy of recombinant adenovirus expressing a novel genotype G2b PEDV spike protein in protecting newborn piglets against PEDV

IMPORTANCE

Porcine epidemic diarrhea (PED) is a highly infectious and economically significant gastrointestinal disorder that affects pigs of all ages. Preventing and controlling PED is achieved by immunizing sows with vaccines, enabling passive piglet immunization via colostrum. The prevalence of G2b porcine epidemic diarrhea virus (PEDV) continues in China despite the use of commercial vaccines, raising questions regarding current vaccine efficacy and the need for novel vaccine development. Adenovirus serotype 5 (Ad5) has several advantages, including high transduction efficiency, a wide range of host cells, and the ability to infect cells at various stages. In this study, we expressed the immunogenic proteins of spike (S) using an Ad5 vector and generated a PED vaccine candidate by inducing significant humoral immunity. The rAd5-PEDV-S prevented PED-induced weight loss, diarrhea, and intestinal damage in piglets. This novel vaccine candidate strain possesses the potential for use in the pig breeding industry.

The Characterization and Pathogenicity of a Recombinant Porcine Epidemic Diarrhea Virus Variant ECQ1

Porcine epidemic diarrhea virus (PEDV), a re-emerging enteropathogenic coronavirus, has become the predominant causative agent of lethal diarrhea in piglets, resulting in huge economic losses in many countries. Furthermore, the rapid variability of this virus has increased the emergence of novel variants with different pathogenicities. In this study, 633 fecal samples collected from diarrheic piglets in China during 2017-2019 were analyzed, and 50.08% (317/633) of these samples were PEDV-positive. The full-length spike (S) genes of 36 samples were sequenced, and a genetic evolution analysis was performed. The results showed that thirty S genes belonged to the GII-a genotype and six S genes belonged to the GII-b genotype. From the PEDV-positive samples, one strain, designated ECQ1, was successfully isolated, and its full-length genome sequence was determined. Interestingly, ECQ1 is a recombinant PEDV between the GII-a (major parent) and GII-b (minor parent) strains, with recombination occurring in the S2 domain of the S gene. The pathogenicity of ECQ1 was assessed in 5-day-old piglets and compared with that of the strain EHuB2, a representative of GII-a PEDV. Although both PEDV strains induced similar fecal viral shedding in the infected piglets, ECQ1 exhibited lower pathogenicity than did EHuB2, as evidenced by reduced mortality and less severe pathological changes in the intestines. These data suggest that PEDV strain ECQ1 is a potential live virus vaccine candidate against porcine epidemic diarrhea.

Development of Effective PEDV Vaccine Candidates Based on Viral Culture and Protease Activity

Porcine epidemic diarrhea (PED) is a highly contagious disease that has been reported annually in several Asian countries, causing significant economic losses to the swine livestock industry. Although vaccines against the porcine epidemic diarrhea virus (PEDV) are available, their efficacy remains questionable due to limitations such as viral genome mutation and insufficient intestinal mucosal immunity. Therefore, the development of a safe and effective vaccine is necessary. In this study, a virulent Korean strain of PEDV, CKT-7, was isolated from a piglet with severe diarrhea, and six different conditions were employed for serial passage of the strain in a cell culture system to generate effective live attenuated vaccine (LAV) candidates. The characteristics of these strains were analyzed in vitro and in vivo, and the CKT-7 N strain was identified as the most effective vaccine candidate, with a viral titer peak of 8.67 ± 0.29 log₁₀TCID₅₀/mL, and no mortality or diarrhea symptoms were observed in five-day-old piglets. These results indicate that LAV candidates can be generated through serial passage with different culture conditions and provide valuable insights into the development of a highly effective LAV against PEDV.

Phylogenetic and Spatiotemporal Analyses of Porcine Epidemic Diarrhea Virus in Guangxi, China during 2017–2022

Since 2010, porcine epidemic diarrhea virus (PEDV) has swept across China and spread throughout the country, causing huge economic losses. In this study, 673 diarrhea samples from 143 pig farms in Guangxi during 2017–2022 were collected and detected for PEDV. Ninety-eight strains were selected for S1 gene analyses and these strains were classified into four subgroups (G1b, G2a, G2b and G2c), accounting for 1.02 (1/98), 75.51 (74/98), 16.33 (16/98) and 7.14% (7/98) of the total, respectively. Importantly, an increased number of strains in the G2c subgroup was found from 2019 onwards. Bayesian analysis revealed that Guigang may have been the epicenter of PEDVs in Guangxi. In addition, Guigang was identified as the primary hub from which PEDVs spread via two routes, namely Guigang–Wuzhou and Guigang–Laibin. Moreover, several coinfections of novel PEDV variants bearing large deletions in the partial S1 protein and PEDVs possessing an intact partial S1 protein were found in pigs. Further recombination analyses indicated that two of the strains, 18-GXNN-6 and 19-GXBH-2, originated from intra-genogroup recombination. Together, our data revealed a new profile of PEDV in Guangxi, China, which enhances our understanding of the distribution, genetic characteristics and evolutionary profile of the circulating PEDV strains in China.

Molecular and Structural Evolution of Porcine Epidemic Diarrhea Virus

To analyze the evolutionary characteristics of the highly contagious porcine epidemic diarrhea virus (PEDV) at the molecular and structural levels, we analyzed the complete genomes of 647 strains retrieved from the GenBank database. The results showed that the spike (S) gene exhibited larger dS (synonymous substitutions per synonymous site) values than other PEDV genes. In the selective pressure analysis, eight amino acid (aa) sites of the S protein showed strong signals of positive selection, and seven of them were located on the surface of the S protein (S1 domain), suggesting a high selection pressure of S protein. Topologically, the S gene is more representative of the evolutionary relationship at the genome-wide level than are other genes. Structurally, the evolutionary pattern is highly S1 domain-related. The haplotype networks of the S gene showed that the strains are obviously clustered geographically in the lineages corresponding to genotypes GI and GII. The alignment analysis on representative strains of the main haplotypes revealed three distinguishable nucleic acid sites among those strains, suggesting a putative evolutionary mechanism in PEDV. These findings provide several new fundamental insights into the evolution of PEDV and guidance for developing effective prevention countermeasures against PEDV.

Current State of Molecular and Serological Methods for Detection of Porcine Epidemic Diarrhea Virus

Porcine epidemic diarrhea virus (PEDV), a member of the Coronaviridae family, is the etiological agent of an acute and devastating enteric disease that causes moderate-to-high mortality in suckling piglets. The accurate and early detection of PEDV infection is essential for the prevention and control of the spread of the disease. Many molecular assays have been developed for the detection of PEDV, including reverse-transcription polymerase chain reaction (RT-PCR), real-time RT-PCR (qRT-PCR) and loop-mediated isothermal amplification assays. Additionally, several serological methods have been developed and are widely used for the detection of antibodies against PEDV. Some of them, such as the immunochromatography assay, can generate results very quickly and in field conditions. Molecular assays detect viral RNA in clinical samples rapidly, and with high sensitivity and specificity. Serological assays can determine prior immune exposure to PEDV, can be used to monitor the efficacy of vaccination strategies and may help to predict the duration of immunity in piglets. However, they are less sensitive than nucleic acid-based detection methods. Sanger and next-generation sequencing (NGS) allow the analysis of PEDV cDNA or RNA sequences, and thus, provide highly specific results. Furthermore, NGS based on nonspecific DNA cleavage in clustered regularly interspaced short palindromic repeats (CRISPR)–Cas systems promise major advances in the diagnosis of PEDV infection. The objective of this paper was to summarize the current serological and molecular PEDV assays, highlight their diagnostic performance and emphasize the advantages and drawbacks of the application of individual tests.

Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype

Porcine epidemic diarrhea virus (PEDV), which classified in the genus Alphacoronavirus, family Coronaviridae, is one of the most important pathogens that cause heavy economic losses in pig industry. Although intensive mutation and recombination analysis of PEDV strains were provided, systematic genome analysis were needed to elucidate the evolution mechanism and codon usage adaptation profiles of the pathogen. Here, a comprehensive investigation was carried out to reveal the systematic evolutionary processes of synonymous codon usage and host-adapted evolution phenotype of PEDV genome. We found a low codon usage bias (CUB) in PEDV genome and that nucleotide compositions, natural selection, mutation pressure and geographical diversity shapes the codon usage patterns of PEDV, with natural selection dominated the overall codon usage bias in PEDV than the others. By using the relative codon deoptimization index (RCDI) and similarity index (SiD) analysis, we observed that genotype II PEDV strains showed the highest level of adaptation phenotype to Sus scrofa than another divergent clade. To the best of our knowledge, this is the first comprehensive report elaborating the codon usage and host adaptation of PEDV. The findings offer an insight into our understanding of factors involved in PEDV evolution, adaptation and fitness toward their hosts.

Changes in the spike and nucleocapsid protein of porcine epidemic diarrhea virus strain in Vietnam-a molecular potential for the vaccine development?

Background

Porcine epidemic diarrhea virus (PEDV) is a dangerous virus causing large piglet losses. PEDV spread rapidly between pig farms and caused the death of up to 90% of infected piglets. Current vaccines are only partially effective in providing immunity to suckling due to the rapid dissemination and ongoing evolution of PEDV.

Methods

In this study, the complete genome of a PEDV strain in Vietnam 2018 (IBT/VN/2018 strain) has been sequenced. The nucleotide sequence of each fragment was assembled to build a continuous complete sequence using the DNASTAR program. The complete nucleotide sequences and amino acid sequences of S, N, and ORF3 genes were aligned and analyzed to detect the mutations.

Results

The full-length genome was determined with 28,031 nucleotides in length which consisted of the 5'UTR, ORF1ab, S protein, ORF3, E protein, M protein, N protein, and 3'UTR region. The phylogenetic analysis showed that the IBT/VN/2018 strain was highly virulent belonged to the G2b subgroup along with the Northern American and Asian S-INDEL strains. Multiple sequence alignment of deduced amino acids revealed numerous mutations in the S, N, and ORF3 regions including one substitution ⁷⁶⁶P > L⁷⁶⁶ in the epitope SS6; two in the S⁰subdomain (¹³⁵DN¹³⁶ > ¹³⁵SI¹³⁶ and N¹⁴⁴> D¹⁴⁴); two in subdomain S^HR1 at aa ¹⁰⁰⁹L > M¹⁰⁰⁹ and ¹⁰⁸⁹S > L¹⁰⁸⁹; one at aa ¹²⁷⁹P > S¹²⁷⁹ in subdomain S^HR2 of the S protein; two at aa ³⁶⁴N > I³⁶⁴ and ³⁷⁸N > S³⁷⁸ in the N protein; four at aa ²⁵L > S²⁵, ⁷⁰I > V⁷⁰, ¹⁰⁷C > F¹⁰⁷, and ¹⁶⁸D > N¹⁶⁸ in the ORF3 protein. We identified two insertions (at aa ⁵⁹NQGV⁶² and aa ¹⁴⁵N) and one deletion (at aa ¹⁶⁸DI¹⁶⁹) in S protein. Remarkable, eight amino acid substitutions (²⁹⁴I > M²⁹⁴, ³¹⁸A > S³¹⁸, ³³⁵V > I³³⁵, ³⁶¹A > T³⁶¹, ⁴⁹⁷R > T⁴⁹⁷, ⁵⁰¹SH⁵⁰² > ⁵⁰¹IY⁵⁰², ⁵⁰⁶I > T⁵⁰⁶, ⁶⁸²V > I⁶⁸², and ⁷⁷⁷P > L⁷⁷⁷) were found in S^A subdomain. Besides, N- and O-glycosylation analysis of S, N, and ORF3 protein reveals three known sites (25^G+, 123^N+, and 62^V+) and three novel sites (144^D+, 1009^M+, and 1279^L+) in the IBT/VN/2018 strain compared with the vaccine strains. Taken together, the results showed that mutations in the S, N, and ORF3 genes can affect receptor specificity, viral pathogenicity, and the ability to evade the host immune system of the IBT/VN/2018 strain. Our results highlight the importance of molecular characterization of field strains of PEDV for the development of an effective vaccine to control PEDV infections in Vietnam.

Novel Method for Isolation of Porcine Epidemic Diarrhea Virus with the Use of Suspension Vero Cells and Immunogenicity Analysis

In February and December of 2019, two large-scale outbreaks of diarrhea were observed in the same swine farm with 3,000 sows in Shanghai, China. We successfully isolated two porcine epidemic diarrhea virus (PEDV) isolates (strains shxx1902 and shxx1912 in February and December, respectively) from clinical samples in this farm using suspension Vero cells. A third PEDV strain (SH1302) tested positive in another farm of Shanghai, China, in 2013 and was also isolated using suspension Vero cells. The three isolates were better adapted to growth in adherent Vero cells through serial passages in the suspension Vero cells. The three isolated strains were detected positive by an immunofluorescence assay (IFA) and observed through electron microscopy. Phylogenetic analysis of the complete genomic sequence demonstrated that shxx1902 (the 5th passage) and shxx1912 (the 5th passage) clustered with a new GII subgroup (GII-c), which consisted of SINDEL strains from America (e.g., OH851), and their S gene belonged to GII-a. Both strains(the 35th passage) have incurred dramatic changes in their genomes compared with the 5th passage. The 5th and 35th passages of SH1302 belonged to the GI-b genotype. The anti-N protein antibody titer of the strain shxx1902 was elevated to the same level as the vaccine strain (CV777) in mice. The use of the suspension Vero cells to isolate and propagate PEDV provides an effective approach for studies of the epidemiological characteristics and vaccine development of this virus.

Porcine epidemic diarrhea virus infection blocks cell cycle and induces apoptosis in pig intestinal epithelial cells

Porcine epidemic diarrhea virus (PEDV) is responsible for the acute infectious swine disease porcine epidemic diarrhea (PED). PED causes damage to the intestine, including villus atrophy and shedding, leading to serious economic losses to the pig industry worldwide. We carried out an in vitro study to investigate cell apoptosis and the cell cycle in a PEDV-infected host using transcriptomic shotgun sequencing (RNA-Seq) to study gene responses to PEDV infection. Results revealed that the PEDV infection reduced proliferation activity, blocked the cell cycle at S-phase and induced apoptosis in IPEC-J2 cells. The expression of gene levels related to ribosome proteins and oxidative phosphorylation were significantly up-regulated post-PEDV infection. Although the significantly down-regulated on PI3K/Akt signaling pathway post-PEDV infection, the regulator-related genes of mTOR signaling pathway exerted significantly up-regulated or down-regulated in IPEC-J2 cells. These results indicated that ribosome proteins and oxidative phosphorylation process were widely involved in the pathological changes and regulation of host cells caused by PEDV infection, and PI3K/AKT and mTOR signaling pathways played a vital role in antiviral regulation in IPEC-J2 cells. These data might provide new insights into the specific pathogenesis of PEDV infection and pave the way for the development of effective therapeutic strategies.

Genome-wide analysis of long noncoding RNA profiles in Vero cells infected with porcine epidemic diarrhea virus

Porcine epidemic diarrhea (PED) is an acute enteric disease caused by porcine epidemic diarrhea virus (PEDV). In China, variant PEDV causes severe watery diarrhea, vomiting, and dehydration in piglets, leading to very high morbidity and mortality. However, the pathogenesis of PEDV is still not fully understood. In our study, we analyzed the long noncoding RNA (lncRNA) and mRNA expression profiles of PEDV GDgh16 in infected Vero cells at 60 h postinfection. A total of 61,790 annotated mRNAs, 14,247 annotated lncRNAs and 1290 novel lncRNAs were identified. A total of 227 annotated lncRNAs and 13 novel lncRNAs were significantly and differentially expressed after viral infection. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases were used to identify genes adjacent to the lncRNAs, and it was found that these lncRNAs were enriched in pathways related to immune and antiviral responses. Next, we selected candidate lncRNAs and their predicted target genes for study. RT-qPCR demonstrated that these lncRNAs and genes were differentially expressed after PEDV infection. Our study investigated the function of lncRNAs involved in PEDV infection, providing new insight into the pathogenic mechanisms of PEDV.

Characterization and evaluation of the pathogenicity of a natural recombinant transmissible gastroenteritis virus in China

Porcine transmissible gastroenteritis virus (TGEV) is one of the major etiological agents of viral enteritis and fetal diarrhea in suckling piglets. In this study, a TGEV JS2012 strain was isolated from the feces of piglets in Jiangsu Province, China. The phylogenetic analysis showed that TGEV JS2012 was placed between the Purdue and the Miller clusters. Analysis of recombination confirmed that TGEV JS2012 is a natural recombinant strain between Miller M6 and Purdue 115. Similar to Miller M6, virulent Purdue and China strain TS, in S gene the JS2012 maintained genetic integrity and the characteristics of the TGEV virulent strains. In vivo, TGEV JS2012 caused 100% mortality in newborn piglets, indicating the strong pathogenicity of this isolate. These results reveal that the JS2012 is a novel natural recombinant TGEV with high virulence. Our findings provide valuable information about genetic diversity and infection mechanism of the coronavirus family.

Epidemic and genetic characterization of porcine epidemic diarrhea virus strains circulating in the regions around Hunan, China, during 2017-2018

Outbreaks of porcine epidemic diarrhea (PED) caused by porcine epidemic diarrhea virus (PEDV) infection have caused high mortality of piglets and significant economic losses to the Chinese swine industry. In the current study, 184 specimens from pigs with or without signs of diarrhea were collected from 39 farms across eight provinces, mainly around Hunan, People's Republic of China, in 2017 to 2018 in order to obtain epidemiological information on PEDV infections in these regions. The results indicated an average PEDV-positive rate of 38.04% (70/184) and more-pronounced disease severity in diarrheic pigs (48.76%; 59/121) than in non-diarrheic pigs (17.46%; 11/63). Phylogenetic and sequence analysis demonstrated that 14 representative PEDV strains from 14 swine farms belonged to the G2 group (G2-a and G2-b subgroups) and displayed a high degree of genetic variation. In particular, two out of the 14 PEDV strains were found to have unique indels in the S1 gene. The strain HN-SY-2017-Oct had a 9-nucleotide (T¹¹⁵²GAAGCCAAT¹¹⁶⁰T) insertion, and the strain ZJ-2018-May had a 3-nucleotide (AAA) deletion at position 1126 in the S1 gene. A three-dimensional structural prediction revealed that these unique insertions might lengthen the loop on the surface or increase the likelihood of the surface protein being phosphorylated at ³⁸⁸Y, thereby affecting the virulence or pathogenicity of PEDV. Collectively, the data show that PED remains a severe threat to the pig industry and that variant PEDV stains are circulating in China. The updated PEDV epidemiological data will facilitate the design of PEDV vaccines and the application of effective measures for PED prevention.

Origin and epidemic status of porcine epidemic diarrhea virus variants in China

From 2010, porcine epidemic diarrhea virus (PEDV) variants caused sequential outbreaks of disease in Asia and the United States. In this retrospective study, 49 complete spike (S) gene sequences were obtained from PEDV strains collected in China from 2014 to 2016. We observed that variant PEDV strains with novel insertions, deletions, and multiple S gene recombination types were present in China. In addition, mixed infections involving different variant strains were observed in some areas. Based on phylogenetic and recombination analyses, we determined that the newly emerged PEDV variants potentially originated via recombination between the earliest Chinese G1 genogroup strain, JS-2004-2 and earlier Korean pandemic strains. These findings provide important information for understanding ongoing PEDV outbreaks and suggest that novel variants make it more difficult to prevent PEDV infection.

Pathogenicity and immunogenicity of a new strain of porcine epidemic diarrhea virus containing a novel deletion in the N gene

Since late 2010, highly virulent PEDV G2-genotype strains have emerged globally extracting heavy losses on the pork industries of numerous countries. We investigated the characteristics of a field strain of PEDV (PEDV strain SH) isolated from a piglet with severe diarrhea on a farm in Shanghai China. Whole genome sequencing and analysis revealed that the SH strain belonged to subtype G2b and has a unique 12-aa deletion (aa 399-410) including the antigenic epitope NEP-1C9 (aa 398-406) of the N protein. PEDV SH strain is highly pathogenic to challenged newborn piglets, resulting in 100 % morbidity and mortality. Pathological examination revealed significant villus atrophy in the jejuna of infected piglets. Mice inoculated with inactivated PEDV SH produced antibodies against the N protein, but no antibodies against the deletions. These results illustrated that deletion of the NEP-1C9 epitope had no effect on the immunogenicity or pathogenicity of PEDV, providing evidence of the necessity to monitor the genetic diversity of the virus. Our study also contributes to development of candidate for vaccines and diagnostics that could differentiate pigs seropositive due to vaccination by conventional strains from wild virus infection.

Complete genome sequences of novel S-deletion variants of porcine epidemic diarrhea virus identified from a recurrent outbreak on Jeju Island, South Korea

Porcine epidemic diarrhea virus (PEDV) is a deadly epizootic swine coronavirus that is of importance to the world pork industry. Since the re-emergence of the virulent genotype 2b (G2b) in 2014, Jeju Island in South Korea has faced periodic outbreaks, leading to the occurrence of endemics in provincial herds. In this study, we examined the complete genome sequences and molecular characteristics of novel G2b PEDV variants with a two-amino-acid deletion in the neutralizing epitope of the spike (S) gene, which were concurrently identified on a re-infected farm and its neighboring farm on Jeju Island. Whole-genome sequencing of the Jeju S-DEL isolates KNU-1829 and KNU-1830 revealed the presence of a continuous 9-nucleotide deletion within the nonstructural protein coding region. Their genomes were 28,023 nucleotides in length, 15 nucleotides shorter than those of the classical G2b PEDV strains. The two S-DEL isolates had 96.4–99.2% and 98.3–99.7% identity at the S-gene and full-genome level, respectively, to other global G2b PEDV strains. Genetic and antigenic analyses indicated that the S-DEL isolates are most closely related to the primary strain identified from the initial exposure at the same farm, but the virus appears to undergo continuous evolution, possibly leading to antigenic drift under recurrent or endemic pressure. This study provides important information about the antigenic diversity of PEDV circulating in the endemic areas, which arises from continuous non-lethal mutations to ensure viral fitness in the host environment.

Isolation and recombinant analysis of variants of porcine epidemic diarrhea virus strains from Beijing, China

Porcine epidemic diarrhea virus (PEDV) is a highly infectious virus infecting pigs with high morbidity, especially for newborn piglets. Several PEDV strains were isolated from the intestinal tracts of diarrheic piglets from the Beijing area, China. Sequencing of the whole-genome of the PEDV isolates (GenBank numbers MG546687-MG546690) yielded sequences of 28033-28038 nt. The phylogenetic tree revealed that these strains from the Beijing area belonged to group II, while the vaccine strain, CV777, belonged to group I. We also determined the genetic correlation between these strains and CV777 strain. However, it showed that these strains in the Beijing area had unique mutations. The sequence identity of PEDV strains showed that these strains are most similar to these strains LZW, CH/JX-1/2013, USAIllinois972013, USAKansas1252014, CH/GDZQ/2014, SHQPYM2013, AJ1102, CHZMDZY11, KoreaK14JB01, and CHYJ130330, respectively. The possible recombination events indicate that PEDV in this studies were possibly recombinant strain formed by parent strains USAIllinois972013, KoreaK14JB01, CHYJ130330, and CHZMDZY11. These PEDV strains has been genetic recombination and mutations. The variant strains characterized in this study help to the evolutionary analysis of PEDV.

A novel duplex TaqMan probe-based real-time RT-qPCR for detecting and differentiating classical and variant porcine epidemic diarrhea viruses

Two different genotypes of porcine epidemic diarrhea virus (PEDV), the classical and variant strains, are classified by multiple insertions and deletions in their S genes. It is critical to detect and differentiate two genotypes in the pork industry to prevent PEDV outbreaks. In the present study, a novel duplex TaqMan RT-PCR was developed for detecting and differentiating PEDV strains in China. There was no cross-amplification between the two probes when using standard recombinant plasmids, and the specificity was further confirmed by using other seven non-PEDV swine pathogens. The minimum copies required for the detection of both classical and variant PEDV were 4.8 × 10² DNA copies/reaction. The repeatability of TaqMan RT-PCR was evaluated using standard recombinant plasmids and gave coefficients of variation 0.19-4.93. In recent 5 years, 79 clinical samples were collected from piglets with severe diarrhea in the Central China. Among these clinical samples, 51 were confirmed as PEDV positive by conventional RT-PCR, whereas 63 variant PEDV, 3 co-infections and 1 classical PEDV were confirmed by this duplex TaqMan RT-PCR, with viral loads of 10²-10⁸, 10²-10³, and 10⁴ copies/reaction, respectively. Therefore, the duplex TaqMan RT-PCR could be a useful method for detecting and differentiating variant and classical PEDV strains. The results showed that variant PEDV was prevalent in clinical samples in central China. Moreover, in this study, co-infection by PEDV strains was detected for the first time and might help explain the emergence of the novel recombinant PEDV in recent years.

Complete genome sequence of a novel S-insertion variant of porcine epidemic diarrhea virus from South Korea

Porcine epidemic diarrhea virus (PEDV) is an emerging and re-emerging viral pathogen of pigs that is causing significant economic concerns in the global pork industry. The virulent G2b PEDV subgroup, which was responsible for the 2013–2014 pandemics on the American and Asian continents, hit Jeju Island in 2014, which had been PEDV-free since 2004. This study presents molecular characterization of a novel PEDV variant with a 5-amino acid (aa) insertion (DTHPE) in the spike (S) gene (an S-insertion) that was identified in diarrheic piglets from Jeju Island. The genome of the PEDV strain KOR/KNU-1601/2016 was sequenced and analyzed to characterize the S-insertion variant circulating on Jeju Island. The full-length genome sequence of KNU-1601 is 28,053 nucleotides (nt) in length, which is 24 nt and 15 nt longer than the genome sequences of G1 classical and G2 epidemic field strains, respectively. KNU-1601 shares 99.5–99.6% nucleotide sequence identity at the genome level and 98.0–98.6% amino acid sequence identity at the S gene level with other global G2b PEDV strains. Genetic and phylogenetic analyses indicated that the KNU-1601 variant is most closely related to the G2b field isolates but appears to undergo continuous evolution in the field. These data advance our understanding of the genetic diversity and evolutionary characteristics of the PEDV field strains circulating in South Korea.