Molecular characterization of porcine epidemic diarrhea virus associated with outbreaks in southwest China during 2014-2018

Molecular characterization of porcine epidemic diarrhea virus in Sichuan from 2023 to 2024

Porcine Epidemic Diarrhea (PED) is an acute, highly contagious disease caused by Porcine Epidemic Diarrhea Virus (PEDV). It is characterized by symptoms such as diarrhea, vomiting, and dehydration in pigs of all ages, with particularly severe outcomes in neonatal pigs. In this study, a total of 254 samples were collected from Sichuan Province between 2023 and 2024 to investigate the prevalence and genetic characteristics of PEDV. The overall prevalence of PEDV was found to be 19.3 %, with regional prevalence rates of 26.5 % in the Guangyuan region and 14.3 % in the Suining region. Phylogenetic analysis revealed that the G2c genotype was the predominant circulating strain. Furthermore, sequence analysis demonstrated that the six isolates exhibited greater sequence similarity to the AJ1102 vaccine strain than to the CV7777 strain. Notably, consistent mutations were observed in the G2b and G2c genotypes, including the insertion of four amino acids (QGVN) at positions 59-62, as well as amino acid substitutions at positions 140 and 161 in the G2b and G2c strains, respectively. Moreover, the G1c (S-INDEL) strain displayed amino acid losses and gains at positions 140 and 160, respectively. N-glycosylation site analysis of the S proteins from both the isolates and the vaccine strains revealed the absence of an N-glycosylation site at position 510 in all isolates. Notably, the SC/GY/2022 isolate contained only six N-glycosylation sites throughout the S protein, which is significantly fewer than those found in the vaccine strains. These findings provide a comprehensive understanding of the epidemiology of PEDV in Sichuan Province and offer valuable insights for the development of more effective immunological prevention and control strategies against PEDV.

Molecular characteristics of the immune escape of coronavirus PEDV under the pressure of vaccine immunity

Coronaviruses have undergone evolutionary changes and mutations in response to the immune pressures exerted by vaccines and environmental factors, resulting in more severe consequences during breakthrough infections. Nevertheless, the specific correlation between the evolutionary mutations of coronaviruses and immune pressures remains ambiguous. Swine coronavirus-porcine epidemic diarrhea virus (PEDV)-has existed for decades. This study utilized in vivo preparation of polyclonal antibodies against the PEDV and identified critical neutralizing epitopes through serial in vitro passaging. Then, the recombinant mutated strains were successfully constructed. In vitro experiments confirmed the ability of the rA1273P strain to escape neutralization by polyclonal antibodies. Both in vitro cell studies and in vivo animal experiments revealed that the strain maintains virulence and pathogenicity while evading antibody pressure post-vaccination. The pathogenicity of the strain while evading immune pressure is comparable to wild-type strains. A comparison of the S protein gene between vaccine strains and clinical strains identified mutations in 1273 amino acid positions in clinical strains. In conclusion, this study identified a novel PEDV S protein neutralizing site under immune pressure through serial passaging, indicating that the 1,273th amino acid position is prone to mutation under prolonged antibody pressure, enhancing the virus's ability to escape hosts. This study offers new insights into the interpretation of coronavirus escape immune pressure and provides technical support for monitoring and predicting the variation and evolution of coronavirus.IMPORTANCECoronaviruses represent an ongoing public health threat because of high variability. Since 2010, the emergence of highly pathogenic porcine epidemic diarrhea virus (PEDV) strains has resulted in significant economic losses to the global pig industry. PEDV undergoes evolution and mutation under external immune pressure, rendering it an increasingly challenging target for prevention and control measures. Here, we prepared the polyclonal antibodies against PEDV and identified a novel neutralization epitope on the S protein (1,273th amino acids) through serial in vitro passaging. Furthermore, our findings indicate that the mutation of A1273P in the S protein did not alter the virulence of the PEDV but significantly enhanced its ability to escape and infect the host in vitro and in vivo. Finally, we found that the 1,273 amino acid position of the S gene has been mutated to varying degrees in clinical PEDV strains. This work provides a specific correlation between the evolutionary mutations of coronaviruses and immune pressures.

Epidemiological investigation, isolation, and pathogenicity of porcine epidemic diarrhea virus subtype G2c in Sichuan province

Continued outbreaks of porcine epidemic diarrhea are causing serious economic losses to the swine industry in China. To monitor the prevalence, genetic mutations, and pathogenicity of porcine epidemic diarrhea virus (PEDV), 172 samples were collected from eight cities in Sichuan Province from 2020 to 2022. RT-PCR analysis revealed that 25.0% (43/172) of samples were positive for PEDV. Phylogenetic analysis of 17 S gene sequences (encoding the spike protein) showed that G2c was the main genotype circulating in Sichuan. One strain, Leshan-s-2020 (G2a), was identified as a recombinant resulting from inter-lineage recombination between the KM609212/LYG/2015 (G2a) and MianYang-s-2020 (G2a) strains in the S2 domain. In addition, the G2c strain YB2201, which was highly virulent in 4-day-old piglets, was successfully isolated. The results of this study enrich our understanding of the epidemiology of PEDV, the genetic characteristics and pathogenicity of the PEDV strains circulating in China, and the role of recombination in their evolution. These findings may contribute to the development of antigen detection reagents and vaccines.

Isolation, pathogenicity, and an infectious cDNA clone of the prevalent G2c variant of porcine epidemic diarrhea virus in China

Porcine epidemic diarrhea virus (PEDV) is a major enteric coronavirus causing diarrhea in piglets, and the recent prevalence of its G2c variant poses a significant threat to the pig industry in China. In this study, we successfully isolated a G2c variant strain (designated EHuB4) from a pig farm experiencing an outbreak of severe diarrhea in China, and constructed its full-length cDNA infectious clone using CRISPR/Cas9 technology. The parental EHuB4 strain and its rescued virus, rEHuB4, exhibited similar biological characteristics in Vero cells, including rapid cytopathic effects and the formation of large syncytia, suggesting strong cell fusion ability and replication efficiency. Pathogenicity experiments in piglets demonstrated that both EHuB4 and rEHuB4 caused severe diarrhea and mortality, further confirming that the prevalence of the G2c variant may be the primary reason for the current high incidence of PED outbreaks. We also analyzed the mutation frequency and variation tendency in the amino acids encoded by the EHuB4 Spike (S) gene and identified multiple high-frequency mutation sites located not only in the S1 subunit but also in the intermediate region between heptad repeat 1 (HR1) and HR2. Furthermore, these mutations have persisted since 2011 and may be closely related to virus prevalence, host adaptation, and pathogenicity. In summary, this study not only characterizes the genetic evolution and pathogenicity of the prevalent G2c strain but also provides a valuable molecular tool for developing novel vaccines through the established full-length cDNA infectious clone.

Advances in porcine epidemic diarrhea virus research: genome, epidemiology, vaccines, and detection methods

Porcine epidemic diarrhea (PED) is a highly contagious intestinal disease caused by the porcine epidemic diarrhea virus (PEDV). The economic impact of PEDV on the global pig industry has been significant, resulting in considerable losses. This paper presents a review of the latest research progress on PEDV genome, molecular epidemiology, vaccine development, and molecular detection methods. It was determined that the genetic diversity of the PEDV spike (S) gene was closely associated with the epidemiological trend of PEDV. The prevalence of S gene variants of different genotypes exhibited variability across regions and pig populations. Epidemiological analyses have demonstrated that PEDV can be transmitted via multiple routes, including direct contact, airborne aerosol, and water source contamination. With regard to vaccine research, the available vaccines can be classified into several categories, including live-attenuated vaccines, inactivated vaccines, subunit vaccines, bacterial vector vaccines, viral vector vaccines, mRNA vaccines, etc. Each of these has distinctive characteristics in terms of immunogenicity, protection efficiency, and safety. Molecular detection methods, including PCR-based methods, isothermal amplification techniques, immunological assays, and biosensors, play an important role in the diagnosis and monitoring of PEDV. Furthermore, this paper examines the current developments in PEDV research and identifies the key areas of future investigation. The objective of this paper is to establish a theoretical foundation for the prevention and control strategies of PED, and to provide a point of reference for further research on the genomics, epidemiology, vaccine development and detection methods of PEDV.

Towards developing multistrain PEDV vaccines: Integrating basic concepts and SARS-CoV-2 pan-sarbecovirus strategies

Porcine epidemic diarrhea virus (PEDV) is a major pathogen impacting the global pig industry, with outbreaks causing significant financial losses. The genetic variability of PEDV has posed challenges for vaccine development since its identification in the 1970s, a problem that intensified with its global emergence in the 2010s. Since current vaccines provide limited cross-protection against PEDV strains, and the development of multistrain PEDV vaccines remains an underexplored area of research, there is an urgent need for improved vaccine solutions. The rapid development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines and ongoing pan-sarbecovirus vaccine research, have demonstrated the potential of next-generation vaccine platforms and novel antigen design strategies. These advancements offer valuable insights for the development of multistrain PEDV vaccines. This review summarizes key aspects of PEDV virology and explores multistrain vaccine development considering SARS-CoV-2 vaccine innovations, proposing a framework for developing next-generation PEDV vaccine solutions.

CRISPR/Cas system and its application in the diagnosis of animal infectious diseases

Infectious diseases are a serious threat to the existence of animals and humans' life. In the 21st century, the emergence and re-emergence of several zoonotic and non-zoonotic global pandemic diseases of socio-economic importance has affected billions of humans and animals. The need for expensive equipment and laboratories, non-availability of on-site testing abilities, with time-consuming and low sensitivity and specificity issues of currently available diagnostic techniques to identify these pathogenic micro-organisms on a large scale highlighted the need for developing cheap, portable environment friendly diagnostic methods. In recent years, these issues have been addressed by clustered regularly interspaced palindromic repeats (CRISPR)-based diagnostic platforms that have transformed the molecular diagnostic field due to their outstanding ultra-sensitive nucleic acid detecting capabilities. In this study, we highlight the types, potential of different Cas proteins, and amplification systems. We also illuminate the application of currently available CRISPR integrated setups on the diagnosis of infectious diseases, majorly in food-producing animals (pigs, ruminants, poultry, and aquaculture), domestic pets (dogs and cats), and diseases of zoonotic importance. We conclude the challenges and future perspectives of using these systems to rapidly diagnose and treat other infectious diseases and also develop control strategies to prevent the spread of pathogenic organisms.

Isolation and characterization of porcine epidemic diarrhea virus with mutations in the spike gene in China

Porcine epidemic diarrhea (PED) caused by porcine epidemic diarrhea virus (PEDV) has caused enormous economic losses to the global swine industry. Due to frequent mutations in the spike (S) gene of PEDV, commercial vaccines used today are gradually losing their protective efficacy against variants. It's significant to monitor the S gene of PEDV variants and understand its evolutionary trend. In this study, we report four novel PEDV strains isolated from Sichuan, Guangdong and Shanxi Provinces and determined their S gene sequences. Phylogenetic analysis showed that they all belong to GII genotype. Amino acid alignment revealed a unique mutation pattern. We also predicted their three-dimensional structures and continuous B-cell epitopes and compared them to those of the vaccine strain. Our study provides references for understanding the evolution of S gene and antigenic change of S protein, which are of great significance for formulating the prevention and control of PEDV.

Pyrococcus furiosus Argonaute-mediated porcine epidemic diarrhea virus detection

Porcine epidemic diarrhea virus (PEDV), an enteric coronavirus, induces severe vomiting and acute watery diarrhea in unweaned piglets. The pig industry has suffered tremendous financial losses due to the high mortality rate of piglets caused by PEDV. Consequently, a simple and rapid on-site diagnostic technology is crucial for preventing and controlling PEDV. This study established a detection method for PEDV using recombinase-aided amplification (RAA) and Pyrococcus furiosus Argonaute (PfAgo), which can detect 100 copies of PEDV without cross-reactivity with other pathogens. The entire reaction of RAA and PfAgo to detect PEDV does not require sophisticated instruments, and the reaction results can be observed with the naked eye. Overall, this integrated RAA-PfAgo cleavage assay is a practical tool for accurately and quickly detecting PEDV. KEY POINTS: • PfAgo has the potential to serve as a viable molecular diagnostic tool for the detection and diagnosis of viral genomes • The RAA-PfAgo detection technique has a remarkable level of sensitivity and specificity • The RAA-PfAgo detection system can identify PEDV without needing advanced equipment.

Prevalence and genetic diversity of porcine epidemic diarrhea virus in Southwest China during 2020-2022

Porcine epidemic diarrhea (PED), caused by porcine epidemic diarrhea virus (PEDV), has been frequently occurring in the southwestern region of China over the past few years, continuously affecting the development of the swine industry. However, the genetic diversity and prevalence of PEDV strains circulating in the swine population in southwestern China in recent years have not been well studied. To address this gap, a total of 478 clinical samples were collected from 125 pig farms experiencing piglet diarrhea in 18 cities in southwestern China. The detection results revealed that 227 out of 478 samples tested positive for PEDV nucleic acid, with a positivity rate of 47.49%. Complete S gene sequences of 28 PEDV strains were obtained and classified into four subgroups, G1-a subgroup (classical strain), G1-b subgroup (S-INDEL), and two G2 subgroups (G2-a and G2-b), accounting for 17.86% (5/28), 3.57% (1/28), 35.71% (10/28), 42.86% (12/28) of the total sequenced strains, respectively. The coexistence of multiple genotypes indicates the complex genetic background and prevalence of PEDV in southwest China. Amino acid comparisons of the S proteins showed that the 28 PEDV strains sequenced in the study showed different patterns of variation in the epitope domains compared to vaccine strains belonging to different genotypes and contained many unique amino acid mutations compared to the reference strains, which might lead to immune escape of PEDV. The complex epidemiology of PEDV with multiple subgroups co-circulating in Southwest China underscores the importance of selecting appropriate vaccine strains based on locally prevalent strains and the ongoing need for epidemiological surveillance of PEDV. The emergence of new variant strains also highlights the urgency of developing updated vaccines, and effective management practices remain crucial for controlling PED outbreaks in pig farms.

Development of a safe and broad-spectrum attenuated PEDV vaccine candidate by S2 subunit replacement

Porcine epidemic diarrhea (PED) has caused serious economic losses to the swine livestock industry. Due to the rapid variation in the PEDV) genome, especially the spike (S) protein, the cross-protection ability of antibodies between different vaccine strains is weakened. Hence, the rapid development of safe, broad-spectrum and highly effective attenuated PEDV vaccine still needs further research. Here, we found that the replacement of the S2 subunit had little effect on S protein immunogenicity. Moreover, the chimeric virus (YN-S2DR13), the S protein of the YN strain was replaced by the DR13 S2 subunit, which lost its trypsin tropism and increased its propagation ability (approximately 1 titer) in Vero cells. Then, the pathogenesis of YN-S2DR13 was evaluated in neonatal piglets. Importantly, quantitative real-time PCR, histopathology, and immunohistochemistry confirmed that the virulence of YN-S2DR13 was significantly reduced compared with that of YN. Immunization with YN-S2DR13 induced neutralizing antibodies against both YN and DR13 in weaned piglets. In vitro passaging data also showed that YN-S2DR13 had good genetic stability. Collectively, these results suggest that YN-S2DR13 has significant advantages as a novel vaccine candidate, including a capacity for viral propagation to high titers with no trypsin requirement and the potential to provide protection against both PEDV G1 and G2 strains infections. Our results also suggests that S2 subunit replacement using reverse genetics can be a rapid strategy for the rational design of live attenuated vaccines for PEDV.

IMPORTANCE

Emerging highly virulent porcine epidemic diarrhea virus (PEDV) G2 strains has caused substantial economic losses worldwide. Vaccination with a live attenuated vaccine is a promising method to prevent and control PED because it can induce a strong immune response (including T- and B-cell immunity). Previous studies have demonstrated that the S2 subunit of the PEDV spike (S) protein is the determinant of PEDV trypsin independence. Here, we evaluated the pathogenicity, tissue tropism, and immunogenicity of the chimeric virus (YN-S2DR13) via animal experiments. We demonstrated that YN-S2DR13 strain, as a trypsin independent strain, increased intracellular proliferation capacity, significantly reduced virulence, and induced broad-spectrum neutralization protection against PEDV G1 and G2 strains. In vitro passaging data also validated the stability of YN-S2DR13. Our results showed that generating a chimeric PEDV strain that is trypsin-independent by replacing the S2 subunit is a promising approach for designing a live attenuated vaccine for PEDV in the future.

Whole-Genome Analysis of Porcine Epidemic Diarrhea Virus from Yunnan, China

Porcine epidemic diarrhea virus (PEDV) is a member of the genus α-coronavirus and causes severe diarrhea in piglets, leading to enormous economic losses in the pig industry. To understand the epidemic variation of PEDV strains in Yunnan province, three PEDV strains (YN2021, YNLP 2022, and YNBS 2022) and one commercially available attenuated vaccine strain (Attenuated AJ1102-R) that were previously isolated were sequenced and compared with the representative PEDV strains. NJ phylogenetic analysis showed that YN2021 strain and Attenuated CV777 strain were clustered into GI-b subtype, while YNLP 2022 and YNBS 2022 belong to GII-b subtype, accompanying ZJCZ4 and Attenuated AJ1102-R. RDP analysis revealed that YNLP 2022 was a genome recombination from both GII-b strain PEDV-7C and GII-a strain YN1, of which the recombination region is in the range nt4994-7605. YNBS 2022 strain was another recombination originated from GII-b subtype strain 17GXZC-1ORF3c and GII-a subtype strain PEDV-CHZ, of which the counterpart is in the range nt16399-22326. The Yunnan strain of PEDV was analyzed for the first time from the whole-genome perspective, and comprehensive analysis showed that the Yunnan strains have high genetic variation. This study may shed new light on the current PEDV infections in Yunnan and pave the way toward further control of PEDV infections.

Neutralizing VHH Antibodies Targeting the Spike Protein of PEDV

Porcine epidemic diarrhea virus (PEDV) is a highly contagious coronavirus that infect pigs' intestinal epithelial cells, causing high morbidity and mortality. Due to the rapid mutation of PEDV, vaccine efficacy is uncertain, prompting exploration of alternative treatments. Nanobodies, also known as variable heavy chain domains of heavy chain-only antibodies (VHHs), offer significant potential in biomedical applications due to their small size and high specificity. In this study, yeast two-hybrid technology was employed to screen for eight specific VHH sequences targeting the PEDV S protein from a synthetically constructed nanobody yeast library. The VHH genes were then cloned into expression plasmids for recombinant protein production, and the resulting VHHs (termed PEDV S-VHHs) were purified. Indirect immunofluorescence assay (IFA) and Western blotting analysis confirmed that these VHHs specifically bind to both PEDV and its S protein. Neutralization assays demonstrated that seven PEDV S-VHHs exhibited potent neutralizing activity against PEDV. Additionally, a combination of these seven antibodies showed enhanced antiviral effects. Preliminary predictions were also made regarding the binding sites between these VHHs and PEDV. The PEDV S-VHHs described in this study hold potential as candidates for the prevention and treatment of PEDV infection.

The prevalence and shedding of porcine epidemic diarrhea virus in intensive swine farms of China from 2022 to 2023

Porcine epidemic diarrhea has emerged as a significant threat to the global swine industry. The shedding and exposure status of porcine epidemic diarrhea virus (PEDV) in intensive farms is not completely understood. In this study, a total of 56,598 clinical samples collected from 256 intensive pig farms in 20 provinces in China from 2022 to 2023, were evaluated for PEDV using quantitative real-time PCR. The overall PEDV prevalence was 11.78 % and 28.45 % at the sample and farm levels, respectively, which are relatively high in Northern China and the fourth and first quarter of the year. The PEDV-positive rates and viral loads in suckling piglet herds were higher than those in growing-finishing pigs and multiparous sows. Meanwhile, 15.61 % of pig pens, 9.51 % of corridors, 9.4 % of office areas, 9.23 % of production personnel, and 8.33 % of pig cart driver samples were positive for PEDV, indicating potential biosafety gaps in intensive pig farms. In addition, 93.41 % of inguinal lymph node tissue samples contained viral nucleic acids, revealing a possible persistent infection of PEDV in pig herds. Our study presents the first report of the large-scale detection of PEDV in intensive pig farms, which constitutes indirect evidence of virus circulation in pig herds. This study provides valuable data for preventing and controlling PEDV infection in the future.

Prevalence and genetic evolution analysis of porcine epidemic diarrhea virus and porcine circovirus type 2 in Sichuan Province, China, from 2023 to 2024

Introduction

Porcine circovirus type 2 (PCV2) and Porcine epidemic diarrhea virus (PEDV) are highly prevalent in Sichuan, significantly affecting the swine industry's development. PCV2, known for its immunosuppressive effects, can compromise pigs' immune systems, while PEDV typically causes diarrhea in piglets, leading to high mortality rates. Despite their impact, recent studies on the epidemiology and genetic diversity of PCV2 and PEDV within Sichuan Province remain limited.

Methods

This study examines clinical samples from 352 diarrheal piglets across 63 pig farms in 17 regions of Sichuan Province, revealing positivity rates of 42.33% (149/352) for PCV2 and 50.28% (177/352) for PEDV, with a co-infection rate of 27.56% (97/352). Notably, the highest positivity rates were observed in Ziyang for PCV2 at 61.90% (13/21), and in Meishan for PEDV at 73.81% (31/42), both regions also reported the highest co-infection rates of 47.62%.

Results and discussion

Seasonal analysis indicated that PEDV infections peaked during winter, whereas PCV2 showed no significant seasonal trends. Phylogenetic analysis identified 14 PCV2 strains, categorizing 2 as PCV2b (14.29%), 10 as PCV2d (71.43%), and 2 as PCV2e (14.29%). Among the 16 PEDV strains, 2 were classified as G1a (12.5%) and 14 as G2a (87.5%), with PCV2d and PEDV G2a identified as the predominant strains in the region. The study also highlights a high mutation rate at the antigenic sites of both viruses, potentially affecting vaccine efficacy. These findings underscore the need for ongoing surveillance and vaccine development tailored to the prevalent strains to improve control measures within the province.

Phylogenetic Analysis of Porcine Epidemic Diarrhea Virus (PEDV) during 2020-2022 and Isolation of a Variant Recombinant PEDV Strain

Porcine epidemic diarrhea (PED) is an acute, highly contagious, and infectious disease caused by porcine epidemic diarrhea virus (PEDV). PEDV can affect pigs of all ages, with 50~100% mortality in neonatal piglets and substantial economic losses in the swine industry. In the present study, 347 fecal and intestinal samples were collected from seven regions in China during 2020-2022. A comprehensive molecular investigation of the spike (S) gene of PEDV strains was carried out, which included phylogenetic analysis of the obtained PEDV sequences. Epidemiological surveillance data indicate that the GIIc subgroup strains are widely distributed among pigs. A PEDV strain was successfully isolated from positive small intestine samples and identified through RT-PCR detection using specific N gene primers of PEDV, indirect immunofluorescence assay (IFA), TEM analysis, genome sequencing, and full-length S gene analysis, named PEDV/SC/2022. RDP and SimPlot analysis showed that the isolate originated from the recombination of PEDV/AH2012 and PEDV/AJ1102. In conclusion, our findings contribute to the current understanding of PEDV epidemiology and provide valuable information for the control of PED outbreaks in China.

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.

Phylogenetic and Evolutionary Analysis of Porcine Epidemic Diarrhea Virus in Guangxi Province, China, during 2020 and 2024

The variant porcine epidemic diarrhea virus (PEDV) has caused considerable economic losses to the global pig industry since 2010. In this study, a total of 5859 diarrhea samples were collected from different pig farms in China's Guangxi province during January 2020 and March 2024 and tested for PEDV using RT-qPCR. The positivity rate of PEDV was 11.90% (697/5859). Ninety-two PEDV-positive samples were selected based on sampling time, and the sampling region for amplification, sequencing, and analysis of the S1, M, and N genes. Phylogenetic analysis of the S1 gene revealed that all strains from Guangxi province were distributed in three subgroups, i.e., 81.5% (75/92) in the G2a subgroup, 4.3% (4/92) in the G2b subgroup, and 14.1% (13/92) in the G2c subgroup. The sequence analysis revealed that the S1 gene sequences from Guangxi province had higher homology with the variant strains than with the classical strains, showing as high as 99.2% with the variant strain AJ1102 and only 94.3% with the classical strain CV777. Recombination analysis revealed that the GX-BS08-2023 strain (G2c) from Guangxi province originated from inter-lineage recombination between the GX-BS09-2023 (G2a) and CH-JN547228-2011 (G1a) strains. In addition, the S1 gene of the G2a and G2b subgroup strains shared many mutations and insertions. There were common mutations of N143D and P235L in the G2a subgroup. Evolutionary analysis revealed that all Guangxi strains belonged to the G2 genotype. These strains have spread rapidly since the PEDV variant strains that emerged in 2010, weakened until 2021, and then remained stable. In conclusion, the results revealed the latest genetic evolution of circulating PEDV strains in Guangxi province in recent years, providing important information for preventing and controlling PEDV infection. Currently, the G2a subgroup strains are the predominant strains circulating in pig herds in Guangxi province, southern China.

Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus in Xinjiang, China, from 2020 to 2022

In recent years, the pig industry in Xinjiang, China, has been severely impacted by outbreaks of porcine epidemic diarrhea (PED), despite vaccination efforts. In this study, we investigated the genetic characteristics of currently prevalent porcine epidemic diarrhea virus (PEDV) strains in the region. We collected 548 samples from animals with suspected PED on large-scale pig farms in Xinjiang. Of these, 258 tested positive for PEDV by RT-PCR, yielding an overall positivity rate of 47.08%. S1 gene sequencing and phylogenetic analysis were conducted on 23 randomly selected RT-PCR-positive samples. Three endemic strains of PEDV (PEDV/CH/XU/2020, PEDV/CH/XK/2020, and PEDV/CH/XA/2020) were isolated, and their complete genome sequences were analyzed for evidence of genetic recombination. Sequence comparison of the S gene indicated significant variations in the S1 gene of the Xinjiang strains compared to the vaccine strains CV777, AJ1102, and LWL, with 90.2%-98.5% nucleotide sequence identity. Notably, both the N-terminal and C-terminal domains of the S protein showed significant variation. Genetic evolutionary analysis identified the GIIa subtype as the dominant genotype among the epidemic strains in Xinjiang. Recombination analysis revealed inter-subtype recombination events in the PEDV/CH/XK/2020 and XJ1904-34 strains. These findings highlight the extensive genetic variation in the predominant GIIa genotype of PEDV in Xinjiang, which does not match the genotype of the currently used vaccine strains. These data may guide further efforts toward the development of effective vaccines for the control of PED.

Epidemiological monitoring and genetic variation analysis of pathogens associated with porcine viral diarrhea in southern China from 2021 to 2023

Large-scale outbreaks of virus-associated severe diarrhea have occurred in pig populations since 2010. To investigate the prevalence and genetic evolution of the diarrhea-associated viruses responsible for the outbreaks, we tested 1,791 diarrhea samples collected from 213 pig farms in five provinces in southern China between 2021 and 2023. The test results showed that porcine epidemic diarrhea virus (PEDV) was the most frequently detected virus. The prevalence rates ranged from 47.40 to 52.22% in samples and 76.06% (162/213) in pig farms. Porcine rotavirus (PoRV) was the second common virus, with prevalence rates ranging from 25.81 to 50.81% in samples and 72.77%(155/213) in pig farms. Porcine delta coronavirus (PDCoV) was the third common virus, with prevalence rates ranging from 16.33 to 17.48% in samples and 38.50% (82/213) in pig farms. The detection rates of both transmissible gastroenteritis virus (TGEV) and porcine acute diarrheal syndrome coronavirus (SADS-CoV) were very low, less than 1.01% in samples and less than 3.76% in pig farms. In this study, we found SADS-CoV only in piglet diarrhea samples from Jiangxi, Guangdong, and Guangxi provinces in China, with a prevalence rate of 5.16% (11/213) in pig farms. Co-infection with these diarrhea-associated viruses is a common occurrence. The most common co-infections were PEDV and PoRV, with a prevalence rate of 6.64% (119/1,791), followed by PDCoV and PoRV, with a prevalence rate of 4.19% (75/1,791). Phylogenetic analyses showed that PEDV and PEDV variants prevalent in southern China during the past three years clustered into genotype GIIb and recombinant PEDV subtypes. Among the currently endemic PEDV, the most common mutations occurred in the collagenase equivalent (COE) and epitope regions of the spike gene. PoRV strains were mainly dominated by the G9 subtype, followed by the G5, G3 and G4 subtypes. Our results suggest that variant PEDV, PDCoV and PoRV are the main pathogens of swine diarrhea, and singular- or co-infection with pathogenic enteric CoV is common in pig herds in southern China. Therefore, prevention and control of porcine viral diarrhea should be given high attention.

Development of a multiplex reverse transcription-quantitative PCR (qPCR) method for detecting common causative agents of swine viral diarrhea in China

BACKGROUND

Diarrheal diseases caused by viral agents have led to a great morbidity, mortality, and economic loss in global pig industry. Porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), and group A porcine rotavirus (RVA) are main causative agents of swine viral diarrhea with similar clinical signs on Chinese farms and their co-infection is also common. However, it is still lack of a convenient method to detect these four agents.

METHODS

A TaqMan multiplex qPCR method was developed to detect PEDV, TGEV, PDCoV, and RVA, simultaneously. This method was then applied to investigate 7,342 swine fecal samples or rectal swabs, as well as 1,246 swine intestinal samples collected from 2075 farms in China in 2022.

RESULTS

Minimum detection limits of this method were 3 copies/µL for PEDV, 4 copies/µL for TGEV, 8 copies/µL for RVA, and 8 copies/µL for PDCoV, suggesting a good sensitivity. No signals were observed by using this method detecting other viral agents commonly prevalent in pigs, which is suggestive of a good specificity. Application of this method on investigating clinical samples demonstrated a relatively high positive rate for PEDV (22.21%, 1907/8588) and RVA (44.00%, 3779/8588). In addition, co-infection between PEDV and RVA was observed on 360 investigated farms, accounting for 17.35% (360/2075) of the farms where co-infection events were screened.

CONCLUSIONS

A TaqMan multiplex qPCR method targeting PEDV, TGEV, PDCoV, and RVA was developed in this study. This method demonstrated a good specificity and sensitivity on investigating these four common viruses responsible for viral diarrhea on Chinese pig farms, which represents a convenient method for the monitoring and differential diagnosis of swine viral diarrhea.

Isolation and Identification of a Tibetan Pig Porcine Epidemic Diarrhoea Virus Strain and Its Biological Effects on IPEC-J2 Cells

Porcine epidemic diarrhoea virus (PEDV) is a coronavirus that can cause severe watery diarrhoea in piglets, with high morbidity and mortality rates, seriously hindering the healthy development of the global swine industry. In this study, we isolated a strain of PEDV from Tibetan pigs and named it CH/GS/2022. Subsequently, we screened the apoptosis signals of PEDV-infected IPEC-J2 cells and studied the correlation between apoptosis signals and cell apoptosis. The results showed that different infections of PEDV induced different degrees of apoptosis in cells, and PEDV-induced cell apoptosis was dose-dependent. We then detected the expression of the p53, p38, JNK, Bax, and Bcl-2 genes in the apoptosis signal pathway. The results showed that 24 h after PEDV infection, the expression of the p53, p38, JNK, and Bax genes in IPEC-J2 cells increased significantly, while the expression of the Bcl-2 gene decreased significantly (p < 0.05). Subsequently, we used Western blot to detect the protein levels of these five genes, and the results showed that PEDV infection upregulated the expression of p53, p38, JNK, and Bax proteins (p < 0.05) while downregulating the expression of Bcl-2 protein (p < 0.05). Thus, it was initially inferred that PEDV infection could regulate cell apoptosis by activating the p53, p38, and JNK signalling pathways. Finally, we further investigated the apoptosis of the cells through the use of inhibitors. The results indicated that the p53 inhibitor Pifithrin-α has a significant inhibitory effect on the expression of the p53 protein after PEDV infection and can reverse the expression levels of Bax and Bcl-2 proteins. This suggested that p53 is involved in PEDV-induced cell apoptosis. Similarly, the p38 MAPK inhibitor SB203580 has an inhibitory effect on the expression of the p38 protein and can reverse the expression levels of Bax and Bcl-2 proteins. This suggested that p38 is also involved in PEDV-induced cell apoptosis. On the other hand, the JNK inhibitor SP600125 has no inhibitory effect on the expression of the JNK protein after PEDV infection, but the expression levels of Bax and Bcl-2 proteins have changed. Furthermore, it is noteworthy that SP600125 can inhibit the activity of apoptotic proteins but not their levels, resulting in reduced cell apoptosis. These preliminary results indicated that JNK may be involved in PEDV-induced IPEC-J2 cell apoptosis.

Porcine Epidemic Diarrhea Virus: Etiology, Epidemiology, Antigenicity, and Control Strategies in China

Porcine epidemic diarrhea virus (PEDV) is a porcine enteric coronavirus, which is one of the main causative agents of porcine epidemic diarrhea (PED), with 100% morbidity and 80-100% mortality in neonatal piglets. Since 2010, large-scale PED caused by highly pathogenic variants of PEDV has occurred successively in China and other countries in the world, posing a great threat to the global pig industry. It has been demonstrated in many investigations that the classic attenuated vaccine strain, PEDV CV777, is insufficient to fully protect against the PEDV variants. Moreover, the maternally derived antibodies elicited by inactivated vaccines also cannot completely protect piglets from infection. In addition, feedback feeding poses a risk of periodic PEDV recurrence in pig farms, making it challenging to successfully limit the spread of PEDV in China. This review focuses on the etiology, epidemiology, antigenicity, and control strategies of PEDV in China and provides information for the formulation of effective control measures.

Virus-like particle vaccines with epitopes from porcine epidemic virus and transmissible gastroenteritis virus incorporated into self-assembling ADDomer platform provide clinical immune responses in piglets

Introduction

Porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus (TGEV) are major intestinal coronaviruses that cause vomiting, diarrhea, dehydration, and mortality in piglets. These viruses coexist and lead to significant economic losses in the swine industry. Virus-like particles (VLPs) have emerged as promising alternatives to conventional inactivated vaccines due to their exceptional safety, efficacy, and ability to provide multi-disease protection with a single dose.

Methods

Our study focused on specific antigenic epitopes from the PEDV S protein (SS2 and 2C10 regions) and the TGEV S protein (A and D sites) as target candidates. These epitopes were integrated into the ADDomer framework, and we successfully generated recombinant proteins AD, AD-P, AD-T, and AD-PT using the baculovirus expression vector system (BEVS). By meticulously optimizing conditions in High Five cells, we successfully expressed and purified the recombinant proteins. Subsequently, we developed the recombinant ADDomer-VLP vaccine and conducted a comprehensive evaluation of its efficacy in piglets.

Results

Following ultrafiltration concentration and sucrose gradient centrifugation purification, the recombinant proteins self-assembled into VLPs as observed by transmission electron microscopy (TEM). Administration of the vaccine did not result in any adverse reactions in the immunized piglets. Additionally, no significant instances of fever were detected in any of the experimental groups, and there were no notable changes in average daily weight gain compared to the control group that received PBS. The recombinant ADDomer-VLP vaccines demonstrated strong immunogenicity, effectively stimulating the production of neutralizing antibodies against both PEDV and TGEV. Moreover, the recombinant ADDomer-VLP vaccine induced elevated levels of IFN-γ, IL-2, and IL-4, and enhanced cytotoxic T lymphocyte (CTL) activity in the peripheral blood of piglets.

Discussion

These recombinant VLPs have demonstrated the ability to induce strong cellular and humoral immune responses in piglets, making them an incredibly promising platform for the rapid and simplified development of epitope vaccines.

Biological Characteristics and Pathogenicity Analysis of a Low Virulence G2a Porcine Epidemic Diarrhea Virus

Since the outbreak caused by a porcine epidemic diarrhea virus (PEDV) variant in 2010, the current epidemic of PEDV genotype 2 (G2) has caused huge economic losses to the pig industry in China. In order to better understand the biological characteristics and pathogenicity of the current PEDV field strains, 12 PEDV isolates were collected and plaque purified during 2017 to 2018 in Guangxi, China. The neutralizing epitopes of the spike proteins and the ORF3 proteins were analyzed to evaluate genetic variations, and they were compared with the reported G2a and G2b strains. Phylogenetic analysis of the S protein showed that the 12 isolates were clustered into the G2 subgroup (with 5 and 7 strains in G2a and G2b, respectively) and that they shared 97.4 to 99.9% amino acid identities. Among them, one of the G2a strains, CH/GXNN-1/2018, which had a titer of 106.15 PFU/mL, was selected for pathogenicity analysis. Although piglets infected with the CH/GXNN-1/2018 strain exhibited severe clinical signs and the highest level of virus shedding within 24 h postinfection (hpi), recovery and decreased virus shedding were seen after 48 hpi, and no piglets died during the whole process. Thus, the CH/GXNN-1/2018 strain had low virulence in suckling piglets. Virus neutralizing antibody analysis showed that the CH/GXNN-1/2018 strain induced cross-protection against both homologous G2a and heterologous G2b PEDV strains as early as 72 hpi. These results are of great significance for understanding PEDV in Guangxi, China, and they provide a promising naturally occurring low-virulent vaccine candidate for further study. IMPORTANCE The current epidemic of porcine epidemic diarrhea virus (PEDV) G2 has caused huge economic losses to the pig industry. Evaluation for low virulence of the PEDV strains of subgroup G2a would be useful for the future development of effective vaccines. In this study, 12 field strains of PEDV were obtained successfully, and they were characterized from Guangxi, China. The neutralizing epitopes of the spike proteins and the ORF3 proteins were analyzed to evaluate antigenic variations. One of the G2a strains, CH/GXNN-1/2018, was selected for pathogenicity analysis, and it showed that the CH/GXNN-1/2018 strain had low virulence in suckling piglets. These results provide a promising naturally occurring low-virulent vaccine candidate for further study.

Insights and progress on epidemic characteristics, genotyping, and preventive measures of PEDV in China: A review

Porcine Epidemic Diarrhoea (PED) is an acute, extremely infectious intestinal disease of pigs caused by the Porcine Epidemic Diarrhoea Virus (PEDV). The virus can affect pigs of all breeds and age groups and shows varying degrees of symptoms, with piglets, in particular, being infected with mortality rates of up to 100%. PEDV was first identified in China in the 1980s and in October 2010 a large-scale PED outbreak caused by a variant of PEDV occurred in China, resulting in huge economic losses. Initially, vaccination can effectively prevent the classical strain, but since December 2010, the PEDV variant has caused "persistent diarrhoea" with severe vomiting, watery diarrhoea, and high morbidity and mortality in newborn piglets as the dominant clinical features, with a significant increase in morbidity and mortality. This indicates that PEDV strains have mutated during evolution and that traditional vaccines no longer provide effective cross-immune protection, so it is necessary to optimize immunization programs and find effective treatments through epidemiological surveys of PEDV to reduce the economic losses caused by infections with mutated strains. This article reviews the progress of research on the aetiology, epidemiological characteristics, genotyping, pathogenesis, transmission routes, and comprehensive control of PEDV infection in China.

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.

A Porcine Epidemic Diarrhea Virus Isolated from a Sow Farm Vaccinated with CV777 Strain in Yinchuan, China: Characterization, Antigenicity, and Pathogenicity

Porcine epidemic diarrhea virus (PEDV) is a porcine enteric coronavirus globally, causing serious economic losses to the global pig industry since 2010. Here, a PEDV CH/Yinchuan/2021 strain was isolated in a CV777-vaccinated sow farm which experienced a large-scale PEDV invasion in Yinchuan, China, in 2021. Our results demonstrated that the CH/Yinchuan/2021 isolate could efficiently propagate in Vero cells, and its proliferation ability was weaker than that of CV777 at 10 passages (P10). Phylogenetic analysis of the S gene revealed that CH/Yinchuan/2021 was clustered into subgroup GIIa, forming an independent branch with 2020-2021 isolates in China. Moreover, GII was obviously allocated into four clades, showing regional and temporal differences in PEDV global isolates. Notably, CH/Yinchuan/2021 was analyzed as a recombinant originated from an American isolate and a Chinese isolate, with a big recombinant region spanning ORF1a and S1. Importantly, we found that CH/Yinchuan/2021 harbored multiple mutations relative to CV777 in neutralizing epitopes (S10, S1A, COE, and SS6). Homology modelling showed that these amino acid differences in S protein occur on the surface of its structure, especially the insertion and deletion of multiple consecutive residues at the S10 epitope. In addition, cross-neutralization analysis confirmed that the differences in the S protein of CH/Yinchuan/2021 changed its antigenicity compared with the CV777 strain, resulting in a different neutralization profile. Animal pathogenicity test showed that CH/Yinchuan/2021 caused PEDV-typified symptoms and 100% mortality in 3-day-old piglets. These data will provide valuable information to understand the epidemiology, molecular characteristics, evolution, and antigenicity of PEDV circulating in China.

Construction and immunogenicity of a trypsin-independent porcine epidemic diarrhea virus variant

Porcine epidemic diarrhea virus (PEDV) is a re-emerging enteropathogenic coronavirus that causes high mortality in neonatal piglets. The addition of trypsin plays a crucial role in the propagation of PEDV, but also increases the complexity of vaccine production and increases its cost. Previous studies have suggested that the S2' site and Y976/977 of the PEDV spike (S) protein might be the determinants of PEDV trypsin independence. In this study, to achieve a recombinant trypsin-independent PEDV strain, we used trypsin-dependent genotype 2 (G2) PEDV variant AJ1102 to generate three recombinant PEDVs with mutations in S (S2' site R894G and/or Y976H). The three recombinant PEDVs were still trypsin dependent, suggesting that the S2' site R894 and Y976 of AJ1102 S are not key sites for PEDV trypsin dependence. Therefore, we used AJ1102 and the classical trypsin-independent genotype 1 (G1) PEDV strain JS2008 to generate a recombinant PEDV carrying a chimeric S protein, and successfully obtained trypsin-independent PEDV strain rAJ1102-S2'_JS2008, in which the S2 (amino acids 894-1386) domain was replaced with the corresponding JS2008 sequence. Importantly, immunization with rAJ1102-S2'_JS2008 induced neutralizing antibodies against both AJ1102 and JS2008. Collectively, these results suggest that rAJ1102-S2'_JS2008 is a novel vaccine candidate with significant advantages, including no trypsin requirement for viral propagation to high titers and the potential provision of protection for pigs against G1 and G2 PEDV infections.

Triacetyl Resveratrol Inhibits PEDV by Inducing the Early Apoptosis In Vitro

PEDV represents an ancient Coronavirus still causing huge economic losses to the porcine breeding industry. Resveratrol has excellent antiviral effects. Triacetyl resveratrol (TCRV), a novel natural derivative of resveratrol, has been recently discovered, and its pharmacological effects need to be explored further. This paper aims to explore the relationship between PEDV and TCRV, which offers a novel strategy in the research of antivirals. In our study, Vero cells and IPEC-J2 cells were used as an in vitro model. First, we proved that TCRV had an obvious anti-PEDV effect and a strong inhibitory effect at different time points. Then, we explored the mechanism of inhibition of PEDV infection by TCRV. Our results showed that TCRV could induce the early apoptosis of PEDV-infected cells, in contrast to PEDV-induced apoptosis. Moreover, we observed that TCRV could promote the expression and activation of apoptosis-related proteins and release mitochondrial cytochrome C into cytoplasm. Based on these results, we hypothesized that TCRV induced the early apoptosis of PEDV-infected cells and inhibited PEDV infection by activating the mitochondria-related caspase pathway. Furthermore, we used the inhibitors Z-DEVD-FMK and Pifithrin-α (PFT-α) to support our hypothesis. In conclusion, the TCRV-activated caspase pathway triggered early apoptosis of PEDV-infected cells, thereby inhibiting PEDV infections.

Porcine Epidemic Diarrhea Virus: An Updated Overview of Virus Epidemiology, Virulence Variation Patterns and Virus-Host Interactions

The porcine epidemic diarrhea virus (PEDV) is a member of the coronavirus family, causing deadly watery diarrhea in newborn piglets. The global pandemic of PEDV, with significant morbidity and mortality, poses a huge threat to the swine industry. The currently developed vaccines and drugs are only effective against the classic GI strains that were prevalent before 2010, while there is no effective control against the GII variant strains that are currently a global pandemic. In this review, we summarize the latest progress in the biology of PEDV, including its transmission and origin, structure and function, evolution, and virus-host interaction, in an attempt to find the potential virulence factors influencing PEDV pathogenesis. We conclude with the mechanism by which PEDV components antagonize the immune responses of the virus, and the role of host factors in virus infection. Essentially, this review serves as a valuable reference for the development of attenuated virus vaccines and the potential of host factors as antiviral targets for the prevention and control of PEDV infection.

Isolation and oral immunogenicity assessment of porcine epidemic diarrhea virus NH-TA2020 strain: One of the predominant strains circulating in China from 2017 to 2021

Porcine epidemic diarrhea (PED) caused by porcine epidemic diarrhea virus (PEDV) is one of the most devastating diseases in the global pig industry due to its high mortality rate in piglets. Maternal vaccines can effectively enhance the gut-mammary gland-secretory IgA axis to boost lactogenic immunity and passive protection of nursing piglets against PEDV challenge. From 2017 to 2021, we collected 882 diarrhea samples from 303 farms in China to investigate the epidemiology of PEDV. The result showed that about 52.15% (158/303) of the farms were positive for PEDV with an overall detection rate of 63.95% (564/882) of the samples. The S1 fragments of S gene from 104 strains were sequenced for the phylogenetic analysis. A total of 71 PEDV strains (68.27%) sequenced in this study were clustered into the predominant G2c subgroup, while the newly-defined G2d strains (9.62%) were identified in three provinces of China. The NH-TA2020 strain of G2c subgroup was isolated and cultured, and its infection to piglets caused watery diarrhea within 24 ​h, indicating its strong pathogenicity. Oral administration of NH-TA2020 strain to pregnant gilts stimulated high levels of IgA antibody in colostrum. The piglets fed by the gilts above were challenged with NH-TA2020 strain or CH–HeB-RY-2020 strain from G2d subgroup, and the clinical symptoms and virus shedding were significantly reduced compared to the mock group. Our findings suggest that G2c subgroup is the predominant branch circulating in China from 2017 to 2021. Oral administration of NH-TA2020 enhances maternal IgA and lactogenic immune responses, which confer protection against the homologous and emerging G2d PEDV strains challenges in neonates.

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From 2017 to 2021, PEDV positive rate of Chinese farms and samples tested in this study was 52.15% and 63.95%, respectively.

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A total of 71 sequenced PEDV strains (68.27%) were clustered into the predominant G2c subgroup.

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The newly-defined G2d strains (9.62%) were identified in three provinces of China.

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NH-TA2020 strain belonging to the G2c subgroup was isolated and its strong pathogenicity was confirmed.

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The milk containing high levels of IgA antibody induced by NH-TA2020 strain could protect piglets against PEDV challenge.

PEDV: Insights and Advances into Types, Function, Structure, and Receptor Recognition

Porcine epidemic diarrhea virus (PEDV) has been endemic in most parts of the world since its emergence in the 1970s. It infects the small intestine and intestinal villous cells, spreads rapidly, and causes infectious intestinal disease characterized by vomiting, diarrhea, and dehydration, leading to high mortality in newborn piglets and causing massive economic losses to the pig industry. The entry of PEDV into cells is mediated by the binding of its spike protein (S protein) to a host cell receptor. Here, we review the structure of PEDV, its strains, and the structure and function of the S protein shared by coronaviruses, and summarize the progress of research on possible host cell receptors since the discovery of PEDV.

Reverse transcription-enzymatic recombinase amplification coupled with CRISPR-Cas12a for rapid detection and differentiation of PEDV wild-type strains and attenuated vaccine strains

Porcine epidemic diarrhea virus (PEDV) is an enteric coronavirus that causes acute watery diarrhea and vomiting in unweaned piglets, and is associated with high mortality, thus causing severe economic losses in the pig industry. Currently, although attenuated vaccines are commonly used in commercial pig farms in China, they do not completely protect against all mutated wild-type strains. Existing nucleic acid assays have high sensitivity and specificity, but the complexity of the assay process and expensive instrumentation hinder disease detection. Here, reverse transcription–enzymatic recombinase amplification (RT-ERA) was combined with the CRISPR-Cas12a system to develop a rapid diagnostic method to distinguish PEDV wild-type strains from attenuated vaccine strains. The protocol used crRNA and RT-ERA amplification primers against open reading frame 3 (ORF3), followed by Cas12a/crRNA complex detection of predefined target sequences at 37 °C for 30 min, thus producing results visible to the naked eye under LED blue light. The assay is highly sensitive and specific, detecting as few as two copies of the target gene per test and showing no cross-reactivity with other porcine pathogens. Overall, this integrated RT-ERA pre-amplification and Cas12a/crRNA cleavage assay is a practical tool for reliable and rapid detection of PEDV for diagnostic differentiation.

The Novel PRRSV Strain HBap4-2018 with a Unique Recombinant Pattern Is Highly Pathogenic to Piglets

Currently, various porcine reproductive and respiratory syndrome virus (PRRSV) variants emerged worldwide with different genetic characteristics and pathogenicity, increasing the difficulty of PRRS control. In this study, a PRRSV strain named HBap4-2018 was isolated from swine herds suffering severe respiratory disease with high morbidity in Hebei Province of China in 2018. The genome of HBap4-2018 is 15,003 nucleotides in length, and compared with NADC30-like PRRSV, nsp2 of HBap4-2018 has an additional continuous deletion of five amino acids. Phylogenetic analysis based on complete genome and ORF5 showed that HBap4-2018 belonged to lineage 8 of PRRSV-2, which was characterized by highly variable genome. However, HBap4-2018 was classified into lineage 1 based on phylogenetic analysis of nsp2, sharing higher amino acid homology (85.3%-85.5%) with NADC30-like PRRSV. Further analysis suggested that HBap4-2018 was a novel natural recombinant PRRSV with three recombinant fragments in the genome, of which highly pathogenic PRRSV (HP-PRRSV) served as the major parental strains, while NADC30-like PRRSV served as the minor parental strains. Five recombination break points were identified in nsp2, nsp3, nsp5, nsp9 and ORF6, respectively, presenting a novel recombinant pattern in the genome. Piglets inoculated with HBap4-2018 presented typical clinical signs with a mortality rate of 60%. High levels of viremia and obvious macroscopic and histopathological lesions in the lungs were observed, revealing the high pathogenicity of HBap4-2018 in piglets.

Comparative Characterization and Pathogenicity of a Novel Porcine Epidemic Diarrhea Virus (PEDV) with a Naturally Occurring Truncated ORF3 Gene Coinfected with PEDVs Possessing an Intact ORF3 Gene in Piglets

Coinfection caused by various genotypes of porcine epidemic diarrhea virus (PEDV) is a new disease situation. We previously reported the coexistence of PEDV strains containing different ORF3 genotypes in China. In this study, the PEDV strains 17GXCZ-1ORF3d and 17GXCZ-1ORF3c were isolated and plaque-purified from the same piglet, which had a natural large deletion at the 172–554 bp position of the ORF3 gene or possessed a complete ORF3 gene, respectively. Meanwhile, 17GXCZ-1ORF3d had >99% nt identity with 17GXCZ-1ORF3c in the 5′UTR, ORF1a/1b, S, E, M, N and 3′UTR regions but only demonstrated low nucleotide identities (80.5%) in the ORF3 gene. To elucidate the pathogenicity, 7-day-old piglets were infected. Piglets infected with these two PEDV strains exhibited severe clinical signs and shed the virus at the highest level within 96 hpi. Compared with the piglets inoculated with the 17GXCZ-1ORF3c strain, the piglets inoculated with the 17GXCZ-1ORF3d strain had higher mortality rates (75% vs. 50%), an earlier onset of clinical signs with a significantly higher diarrhea score, lower VH:CD ratios and a higher percentage of PEDV-positive enterocytes. This study is the first to report PEDV coinfections with different ORF3 genotypes, and a PEDV strain with a large deletion in the ORF3 gene might have the advantage of a potential genetic marker, which would be useful during vaccine development.

Genetic characterization and phylogenetic analysis of porcine epidemic diarrhea virus in Guangdong, China, between 2018 and 2019

Porcine epidemic diarrhea virus (PEDV), a leading cause of piglet diarrhea outbreaks, poses a significant danger to the swine industry. The aim of this study was to investigate the epidemic characteristics of PEDV that was circulating in Guangdong province, one of China's major pig producing provinces. Clinical samples were collected from eight pig farms in Guangdong province between 2018 and 2019 and tested for the major porcine enteric pathogens, including PEDV, transmissible gastroenteritis virus (TGEV), Swine enteric coronavirus (SeCoV), Swine acute diarrhea syndrome coronavirus (SADS-CoV), porcine deltacoronavirus (PDCoV), and porcine rotavirus (RV). As a result, only PEDV and RV were detected at a rate of 47.0% (16/34) and 18.6% (8/34), respectively. Coinfectoin with PEDV and RV occurred at a rate of PEDV 12.5% (2/16). Subsequently, the full-length S gene sequences of 13 PEDV strains were obtained, and phylogenetic analysis suggested the presence of GII-c group PEDV strains in this region (non-S-INDEL). Two novel common amino acid insertions (55T/IG56 and 551L) and one novel glycosylation site (1199G+) were detected when the CV777 and ZJ08 vaccine strains were compared. Furthermore, intragroup recombination events in the S gene regions 51-548 and 2478-4208 were observed in the PEDV strains studied. In summary, the observations provide current information on the incidence of viral agents causing swine diarrhea in southern China and detailed the genetic characteristics and evolutionary history of the dominant PEDV field strains. Our findings will aid in the development of an updated vaccine for the prevention and control of PEDV variant strains.