Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene

Lizhong decoction inhibits porcine epidemic diarrhea virus in vitro and in vivo

ETHNOPHARMACOLOGICAL RELEVANCE

Lizhong decoction (LZD) is a frequently utilized traditional Chinese remedy for diarrhea. It is unknown how effective it is as an antiviral against PEDV infection.

AIM OF THE STUDY

In vitro and in vivo PEDV infection models were used to evaluate the anti-PEDV potential of LZD extract.

MATERIALS AND METHODS

LC-MS was used for qualitative analysis of LZD. The antiviral effect of LZD against PEDV using flow cytometry (FC), Quantitative real-time polymerase chain reaction (QPCR), immunofluorescence assay (IFA) analysis in Vero and IPEC-J2 cells. Additionally, we measured the survival rate, clinical symptoms, body weights, fecal scores, temperature, histological analysis, and viral load in a model of newborn piglets infected with PEDV in order to assess the antiviral impact of LZD in vivo.

RESULTS

In total, 648 compounds were identified, including 144 Alkaloids, 128 Terpenoids, etc. LZD effectively suppressed PEDV replication in vitro. According to time of addition experiments, LZD mostly inhibited PEDV during the viral life cycle's replication stages. During PEDV infection, LZD can Significantly decrease the apoptotic rate of IPEC-J2 cells and Vero cells. In comparison to the model group, LZD was able to decrease the viral titers in the infected piglets' intestinal and visceral tissues, ameliorate their intestinal pathology, cause a significant increase in body weight growth and increase the piglet survival rate.

CONCLUSION

Our findings indicate that the aqueous solution derived from LZD suppressed PEDV replication both in vitro and in vivo, indicating its potential as a candidate for pharmaceutical development.

Isolation and Characterization of Contemporary Bovine Coronavirus Strains

Bovine coronavirus (BCoV) poses a threat to cattle health worldwide, contributing to both respiratory and enteric diseases. However, few contemporary strains have been isolated. In this study, 71 samples (10 nasal and 61 fecal) were collected from one farm in Ohio in 2021 and three farms in Georgia in 2023. They were screened by BCoV-specific real-time reverse transcription-PCR, and 15 BCoV-positive samples were identified. Among them, five BCoV strains from fecal samples were isolated using human rectal tumor-18 (HRT-18) cells. The genomic sequences of five strains were obtained. The phylogenetic analysis illustrated that these new strains clustered with US BCoVs that have been detected since the 1990s. Sequence analyses of the spike proteins of four pairs of BCoVs, with each pair originally collected from the respiratory and enteric sites of one animal, revealed the potential amino acid residue patterns, such as D1180 for all four enteric BCoVs and G1180 for three of four respiratory BCoVs. This project provides new BCoV isolates and sequences and underscores the genetic diversity of BcoVs, the unknown mechanisms of disease types, and the necessity of sustained surveillance and research for BCoVs.

Progress of research on coronaviruses and toroviruses in large domestic animals using reverse genetics systems

The generation of genetically engineered recombinant viruses from modified DNA/RNA is commonly referred to as reverse genetics, which allows the introduction of desired mutations into the viral genome. Reverse genetics systems (RGSs) are powerful tools for studying fundamental viral processes, mechanisms of infection, pathogenesis and vaccine development. However, establishing RGS for coronaviruses (CoVs) and toroviruses (ToVs), which have the largest genomes among vertebrate RNA viruses, is laborious and hampered by technical constraints. Hence, little research has focused on animal CoVs and ToVs using RGSs, especially in large domestic animals such as pigs and cattle. In the last decade, however, studies of porcine CoVs and bovine ToVs using RGSs have been reported. In addition, the coronavirus disease-2019 pandemic has prompted the development of new and simple CoV RGSs, which will accelerate RGS-based research on animal CoVs and ToVs. In this review, we summarise the general characteristics of CoVs and ToVs, the RGSs available for CoVs and ToVs and the progress made in the last decade in RGS-based research on porcine CoVs and bovine ToVs.

Virological evaluation of natural and modified attapulgite against porcine epidemic diarrhoea virus

BACKGROUND

The Porcine Epidemic Diarrhea Virus (PEDV) has caused significant economic losses in the global swine industry. As a potential drug for treating diarrhea, the antiviral properties of attapulgite deserve further study.

METHODS

In this study, various methods such as RT-qPCR, Western blot, viral titer assay, Cytopathic Effect, immunofluorescence analysis and transmission electron microscopy were used to detect the antiviral activity of attapulgite and to assess its inhibitory effect on PEDV.

RESULTS

When exposed to the same amount of virus, there was a significant decrease in the expression of the S protein, resulting in a viral titer reduction from 10-5.613 TCID50/mL to 10-2.90 TCID50/mL, which represents a decrease of approximately 102.6 folds. Results of cytopathic effect and indirect immunofluorescence also indicate a notable decrease in viral infectivity after attapulgite treatment. Additionally, it was observed that modified materials after acidification had weaker antiviral efficacy compared to powdered samples that underwent ultrasonic disintegration, which showed the strongest antiviral effects.

CONCLUSION

As a result, Attapulgite powders can trap and adsorb viruses to inhibit PEDV in vitro, leading to loss of viral infectivity. This study provides new materials for the development of novel disinfectants and antiviral additives.

Research progress of porcine epidemic diarrhea virus S protein

Porcine epidemic diarrhea virus (PEDV) is a single-stranded RNA virus with a capsid membrane that causes acute infectious gastrointestinal disease characterized by vomiting, diarrhea, and dehydration in swine. Piglets are more susceptible to PEDV than adults, with an infection rate reaching 90% and a fatality rate as high as 100%. Moreover, PEDV has a rapid transmission rate and broad transmission range. Consequently, PEDV has caused considerable economic losses and negatively impacted the sustainability of the pig industry. The surface spike (S) glycoprotein is the largest structural protein in PEDV virions and is closely associated with host cell fusion and virus invasion. As such, the S protein is an important target for vaccine development. In this article, we review the genetic variation, immunity, apoptosis-induction function, virulence, vaccine potential, and other aspects of the PEDV S protein. This review provides a theoretical foundation for preventing and controlling PEDV infection and serves as a valuable resource for further research and development of PEDV vaccines.

Maternal immunization and vitamin A sufficiency impact sow primary adaptive immunity and passive protection to nursing piglets against porcine epidemic diarrhea virus infection

Porcine epidemic diarrhea virus (PEDV) causes a highly contagious enteric disease with major economic losses to swine production worldwide. Due to the immaturity of the neonatal piglet immune system and given the high virulence of PEDV, improving passive lactogenic immunity is the best approach to protect suckling piglets against the lethal infection. We tested whether oral vitamin A (VA) supplementation and PEDV exposure of gestating and lactating VA-deficient (VAD) sows would enhance their primary immune responses and boost passive lactogenic protection against the PEDV challenge of their piglets. We demonstrated that PEDV inoculation of pregnant VAD sows in the third trimester provided higher levels of lactogenic protection of piglets as demonstrated by >87% survival rates of their litters compared with <10% in mock litters and that VA supplementation to VAD sows further improved the piglets' survival rates to >98%. We observed significantly elevated PEDV IgA and IgG antibody (Ab) titers and Ab-secreting cells (ASCs) in VA-sufficient (VAS)+PEDV and VAD+VA+PEDV sows, with the latter maintaining higher Ab titers in blood prior to parturition and in blood and milk throughout lactation. The litters of VAD+VA+PEDV sows also had the highest serum PEDV-neutralizing Ab titers at piglet post-challenge days (PCD) 0 and 7, coinciding with higher PEDV IgA ASCs and Ab titers in the blood and milk of their sows, suggesting an immunomodulatory role of VA in sows. Thus, sows that delivered sufficient lactogenic immunity to their piglets provided the highest passive protection against the PEDV challenge. Maternal immunization during pregnancy (± VA) and VA sufficiency enhanced the sow primary immune responses, expression of gut-mammary gland trafficking molecules, and passive protection of their offspring. Our findings are relevant to understanding the role of VA in the Ab responses to oral attenuated vaccines that are critical for successful maternal vaccination programs against enteric infections in infants and young animals.

Genetic evolution and phylogenetic analysis of porcine epidemic diarrhea virus strains circulating in and outside China with reference to a wild type virulent genotype CHYJ130330 reported from Guangdong Province, China

During the last decade, porcine epidemic diarrhea virus has detrimental consequences on swine industry, due to severe outbreaks especially in the suckling piglets. In March 2013, an outbreak was reported on a commercial swine farm in Guangdong Province, Southern China. A wild-type PEDV strain named as CHYJ130330 was identified, complete genome was sequenced and deposited in GenBank (accession no. KJ020932). The molecular epidemiological including evolutionary characteristics and pathogenicity assessment were explored during this study with particular interest and focus to develop this candidate strain for new vaccine. The isolates from China pre- and post-2013 shared 96.5-97.2% and 97-99% nt identity respectively with wild-type CHYJ130330 strain which during experimental studies has demonstrated high virulence and 100% mortality in 104 TCID50 group piglets within 5 days. The 22 reference strains selected from other parts of the world shared 98-99% identity with our sequence except Chinese (CV777) and S. Korean (vir.DR13, SM98 and atten.DR13) strains sharing 96.8, 97.6, 96.6 and 97.1% identity respectively. The phylogenetic tree revealed most strains reported after 2013 in GII genogroup while the prototype (CV777), S.korean and earlier Chinese (JS2008, 85-7mutant, Atten.vaccine, SD-M, LZC and CH/S) were GI Group. The amino acid sequence of CHYJ130330 E and M protein is highly conserved while ORF3 and N protein having 9 and 17 amino acid substitutions respectively in comparison to CV777 strain. The comparison of full length genome and the structural proteins revealed variations signifying that PEDV variant strains are still the main source of outbreaks in spite of continuous vaccination and also explain the variable trend of large scale outbreaks during this decade as compared to sporadic tendency of disease found before 2010. It is evident from this study that Chinese strains display significant level of mixing with the strains reported from other countries. The strain CHYJ130330 was also adapted successfully to Vero cell line and has shown high virulence in piglets. The information/findings will be helpful to develop a strategy for control of PEDV and have also shown that CHYJ130330 strain has strong virulence and is a more popular clinical strain in recent years, which has the potential to be developed into PEDV vaccine.

Porcine Epidemic Diarrhea: Insights and Progress on Vaccines

Porcine epidemic diarrhea (PED) is a swine-wasting disease caused by coronavirus infection. It causes great economic damage to the swine industry worldwide. Despite the continued use of vaccines, PED outbreaks continue, highlighting the need to review the effectiveness of current vaccines and develop additional vaccines based on new platforms. Here, we review existing vaccine technologies for preventing PED and highlight promising technologies that may help control PED virus in the future.

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.

Elucidating the biological characteristics and pathogenicity of the highly virulent G2a porcine epidemic diarrhea virus

Since the large-scale outbreak of porcine epidemic diarrhoea (PED) in 2010, caused by the genotype 2 (G2) variant of the porcine epidemic diarrhoea virus (PEDV), pig farms in China, even those vaccinated with the G2b vaccine, have experienced infections from the G2a variant, leading to significant economic losses. This study successfully isolated the G2a strain DY2020 from positive small intestine contents (SICs) by blind passage on Vero cells for four generations. The SICs were taken from Daye, Hubei Province, China. The biological characteristics were identified by indirect immunofluorescence assay (IFA) and transmission electron microscopy (TEM). The growth kinetics of the strain on Vero cells were detected by TCID50, and the virus titre could reach 107.35 TCID50 ml-1 (SD: 5.07×106). The pathogenicity towards colostrum-deprived piglets was conducted by assessing faecal viral shedding, morphometric analysis of intestinal lesions, and immunohistochemical staining. The results showed that DY2020 was highly virulent to colostrum-deprived piglets, with severe watery diarrhoea and other clinical symptoms appeared at 6 h post-infection (h p.i.), and all died within 30 h. Pathological tissue examination results showed that the lesions mainly occurred in the intestines of piglets, causing pathological changes such as shortening of intestinal villi. In summary, the discovery of the G2a strain DY2020 in this study is of great significance for understanding Hubei PEDV and provides an important theoretical basis for the development of new efficient PEDV vaccines.

A recombination-resistant genome for live attenuated and stable PEDV vaccines by engineering the transcriptional regulatory sequences

IMPORTANCE

Coronaviruses are important pathogens of humans and animals, and vaccine developments against them are imperative. Due to the ability to induce broad and prolonged protective immunity and the convenient administration routes, live attenuated vaccines (LAVs) are promising arms for controlling the deadly coronavirus infections. However, potential recombination events between vaccine and field strains raise a safety concern for LAVs. The porcine epidemic diarrhea virus (PEDV) remodeled TRS (RMT) mutant generated in this study replicated efficiently in both cell culture and in pigs and retained protective immunogenicity against PEDV challenge in pigs. Furthermore, the RMT PEDV was resistant to recombination and genetically stable. Therefore, RMT PEDV can be further optimized as a backbone for the development of safe LAVs.

An Advanced Multiplex Real-Time Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Rapid and Reliable Detection of Porcine Epidemic Diarrhea Virus and Porcine Internal Positive Control

For rapid and reliable detection of porcine epidemic diarrhea virus (PEDV) from pig clinical samples, a multiplex, real-time, reverse transcription loop-mediated isothermal amplification (mqRT-LAMP) was developed using two sets of primers and assimilating probes specific to the PEDV N gene and the Sus scrofa β-actin gene, which was used as an endogenous internal positive control (EIPC) to avoid false-negative results. The assay specifically amplified both target genes of PEDV and EIPC in a single reaction without any interference but did not amplify other porcine viral nucleic acids. The limit of detection was 10 copies/μL, 100-fold lower than that of a reverse transcription-polymerase chain reaction (RT-PCR) and equivalent to that of quantitative/real-time RT-PCR (qRT-PCR). This assay has high repeatability and reproducibility with coefficients of variation < 4.0%. The positive signal of the mqRT-LAMP assay was generated within 25 min, demonstrating advantages in rapid detection of PEDV over RT-PCR or qRT-PCR assay, which require at least 2 h turnaround times. In clinical evaluation, the detection rate of PEDV by mqRT-LAMP assay (77.3%) was higher than that of RT-PCR assay (69.7%), and comparable to qRT-PCR (76.8%) with almost 100% concordance (kappa value 0.98). The developed mqRT-LAMP assay can serve as an advanced alternative method for PEDV diagnosis because it has high sensitivity and specificity, rapidity, and reliability even in resource-limited laboratories.

Rescue of a Live-Attenuated Porcine Epidemic Diarrhea Virus HSGP Strain Using a Virulent Strain and a Partially Attenuated Strain

In South Korea in 2013, the G1-based vaccine failed to prevent an outbreak of G2b-type porcine epidemic diarrhea virus (PEDV), which is more pathogenic than the traditional G1-type strain, thereby allowing the virus to spread. In 2017 and 2018, field samples were cultured sequentially on Vero cells to isolate HS (virulent) and SGP-M1 (partially attenuated) strains, respectively, of the G2b type. The HS strain harbors a single amino acid (aa) change and two aa deletions in the N-terminal domain of S1 (⁵⁵I⁵⁶G⁵⁷E→⁵⁵K⁵⁶Δ⁵⁷Δ). The SGP-M1 strain harbors a seven aa deletion in the C-terminal domain of S2 (^1380~1386ΔFEKVHVQ). By co-infecting various animal cells with these two strains (HS and SGP-M1), we succeeded in cloning strain HSGP, which harbors the mutations present in the two original viruses. The CPE pattern of the HSGP strain was different from that of the HS and SGP-M1 strains, with higher viral titers. Studies in piglets showed attenuated pathogenicity of the HSGP strain, with no clinical symptoms or viral shedding, and histopathologic lesions similar to those in negative controls. These findings confirm that deletion of specific sequences from the S gene attenuates the pathogenicity of PEDV. In addition, HSGP strains created by combining two different strains have the potential for use as novel attenuated live vaccine candidates.

Porcine epidemic diarrhea virus: an update overview of virus epidemiology, vaccines, and control strategies in South Korea

Porcine epidemic diarrhea virus (PEDV) has posed significant financial threats to the domestic pig industry over the last three decades in South Korea. PEDV infection will mostly result in endemic persistence in the affected farrow-to-finish (FTF) herds, leading to endemic porcine epidemic diarrhea (PED) followed by year-round recurrent outbreaks. This review aims to encourage collaboration among swine producers, veterinarians, and researchers to offer answers that strengthen our understanding of PEDV in efforts to prevent and control endemic PED and to prepare for the next epidemics or pandemics. We found that collaboratively implementing a PED risk assessment and customized four-pillar-based control measures is vital to interrupt the chain of endemic PED in affected herds: the former can identify on-farm risk factors while the latter aims to compensate for or improve weaknesses via herd immunity stabilization and virus elimination. Under endemic PED, long-term virus survival in slurry and asymptomatically infected gilts ("Trojan Pigs") that can transmit the virus to farrowing houses are key challenges for PEDV eradication in FTF farms and highlight the necessity for active monitoring and surveillance of the virus in herds and their environments. This paper underlines the current knowledge of molecular epidemiology and commercially available vaccines, as well as the risk assessment and customized strategies to control PEDV. The intervention measures for stabilizing herd immunity and eliminating virus circulation may be the cornerstone of establishing regional or national PED eradication programs.

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.

Isolation and characterization of porcine epidemic diarrhea virus with a novel continuous mutation in the S10 domain

Porcine epidemic diarrhea virus (PEDV), which re-emerged in China in 2010, has caused severe economic losses to the global pig industry. In this study, a PEDV strain, designated PEDV WMB, was isolated from piglets with severe diarrhea on a pig farm in Henan Province of China. Whole-genome sequencing and analysis revealed that the PEDV WMB strain belongs to subtype G2c and has a unique continuous mutation in the S1⁰ antigenic epitope of the S protein. Moreover, the virus-neutralization (VN) test indicated that polyclonal antibodies against the S1⁰ protein of other G1 and G2 strains showed reduced VN reactivity to PEDV WMB. The pathogenicity of PEDV WMB was further investigated in 3 day-old piglets. PEDV infection-related clinical symptoms and morphological lesions were observed and confirmed by histopathological and immunohistochemical examination (IHC). These results illustrated that continuous mutation of the S1⁰ epitope might affect the immunogenicity or pathogenicity of PEDV, providing evidence of the need to monitor the genetic diversity of the virus and develop effective measures to prevent and control PEDV.

Simultaneous detection and phylogenetic analysis of porcine epidemic diarrhea virus and porcine circovirus 4 in Henan province, China

Porcine circovirus 4 (PCV4) is a recently discovered circovirus that was first reported in 2019 in several pigs in Hunan province of China and has also been identified in pigs infected with porcine epidemic diarrhea virus (PEDV). To further investigate the coinfection and genetic diversity of these two viruses, 65 clinical samples (including feces and intestinal tissues) were collected from diseased piglets on 19 large-scale pig farms in Henan province of China, and a duplex SYBR Green I-based quantitative real-time polymerase chain reaction (qPCR) assay was developed for detecting PEDV and PCV4 simultaneously. The results showed that the limit of detection was 55.2 copies/μL and 44.1 copies/μL for PEDV and PCV4, respectively. The detection rate for PEDV and PCV4 was 40% (26/65) and 38% (25/65), respectively, and the coinfection rate for the two viruses was 34% (22/65). Subsequently, the full-length spike (S) gene of eight PEDV strains and a portion of the genome containing the capsid (Cap) gene of three PCV4 strains were sequenced and analyzed. Phylogenetic analysis showed that all of the PEDV strains from the present study clustered in the G2a subgroup and were closely related to most of the PEDV reference strains from China from 2011 to 2021, but they differed genetically from a vaccine strain (CV777), a Korean strain (virulent DR1), and two Chinese strains (SD-M and LZC). It is noteworthy that two PEDV strains (HEXX-24 and HNXX-24XIA) were identified in one sample, and the HNXX-24XIA strain had a large deletion at amino acids 31-229 of the S protein. Moreover, a recombination event was observed in strain HEXX-24. Phylogenetic analysis based on the amino acid sequence of the PCV4 Cap protein revealed that PCV4 strains were divided into three genotypes: PCV4a1, PCV4a2, and PCV4b. Three strains in the present study belonged to PCV4a1, and they had a high degree of sequence similarity (>98% identity) to other PCV4 reference strains. This study not only provides technical support for field investigation of PEDV and PCV4 coinfection but also provides data for their prevention and control.

Deletion of pentad residues in the N-terminal domain of spike protein attenuates porcine epidemic diarrhea virus in piglets

Our previous study revealed that tissue culture-adapted porcine epidemic diarrhea virus (PEDV) strains, namely KNU-141112-S DEL2/ORF3 and -S DEL5/ORF3, were attenuated to different extents in vivo, suggesting that their independent deletion (DEL) signatures, including 2-amino acid (aa; residues 56-57) or 5-aa (residues 56-60) DEL in the N-terminal domain (NTD) of the spike (S) protein, may contribute to the reduced virulence of each strain. To investigate whether each DEL in the NTD of the S1 subunit is a determinant for the virulence of PEDV, we generated two mutant viruses, named icS DEL2 and icS DEL5, by introducing the identical double or quintuple aa DEL into S1 using reverse genetics with an infectious cDNA clone of KNU-141112 (icKNU-141112). We then orally inoculated conventional suckling piglets with icKNU-141112, icS DEL2, or icS DEL5 to compare their pathogenicities. The virulence of both DEL mutant viruses was significantly diminished compared to that of icKNU-141112, which causes severe clinical signs and 100 % mortality. Interestingly, the degree of attenuation differed between the two mutant viruses: icS DEL5 caused neither diarrhea nor mortality, whereas icS DEL2 caused mild to moderate diarrhea, higher viral titers in feces and intestinal tissues, and 25 % mortality. Furthermore, the icS DEL5-infected piglets displayed no remarkable macroscopic and microscopic intestinal lesions, while the icS DEL2-infected piglets showed histopathological changes in small intestine tissues, including moderate-to-severe villous atrophy. Our data indicate that the loss of the pentad (⁵⁶GENQG⁶⁰) residues in S alone can be sufficient to give rise to an attenuated phenotype of PEDV.

Based on the Results of PEDV Phylogenetic Analysis of the Most Recent Isolates in China, the Occurrence of Further Mutations in the Antigenic Site S1° and COE of the S Protein Which Is the Target Protein of the Vaccine

The continuous challenge of existing vaccine systems by porcine epidemic diarrhea virus (PEDV) variant strains in recent years, it caused significant economic losses in the global swine industry. A PEDV virulent strain CH/HLJBQL/2022 was successfully isolated in China in this study. A genome-wide based phylogenetic analysis suggests that CH/HLJBQL/2022 belongs to the GII subtype, and 96.3%–99.6% homology existed in the whole genomes of other strains. For the first time, simultaneous mutations of four amino acids were found in the highly conserved membrane (M) and nucleocapsid (N) proteins, as well as five amino acid mutations that differed from the vast majority of strains in the spike (S) protein. Mutations in the M and S proteins were found to produce coils with different angles by building 2D and 3D structural models. Epitope analysis indicated that the isolates produced specific changes and that the transmembrane function of the M protein had not been affected. In addition, typing markers exist during strain evolution, but isolates are using the fusion of specific amino acids from multiple variant strains to add additional features, as also demonstrated by protein alignments and 3D models of numerous subtype strains. These results suggest that aa mutations in the M and S proteins may have changed the structure and antigenic epitope of the isolates and PEDV is evolving again on the basis of variants that have been found to counteract the immune network of the new vaccine.

Magnolol, a Neolignan-like Drug, Inhibits Porcine Epidemic Diarrhea Virus Replication in Cultured Cells

Porcine epidemic diarrhea virus (PEDV) is a destructive pathogen that continues to adversely affect the swine industry worldwide due to a current lack of vaccines and drugs capable of effective disease control. In the present study, the neolignan-like drug, magnolol (MAG), was tested for its ability to inhibit a Vero-cell adapted PEDV strain DR13^att. Our data revealed that MAG exhibited anti-PEDV activity in vitro, with IC₅₀ and CC₅₀ values of 28.21 μM and 57.28 μM, respectively. MAG was an efficient inhibitor of viral replication, and repression of viral proliferation was strongest when the host cells were exposed to MAG and the virus at the same time. Although our data indicate that MAG has the potential to be a useful PEDV control agent, in vivo testing of the drug, using animal hosts, is required.

A new PEDV strain CH/HLJJS/2022 can challenge current detection methods and vaccines

BACKGROUND

Porcine epidemic diarrhea virus (PEDV) variant strains cause great economic losses to the global swine industry. However, vaccines do not provide sufficient protection against currently circulating strains due to viral mutations. This study traced the molecular characteristics of the most recent isolates in China and aimed to provide a basis for the prevention and treatment of PEDV.

METHODS

We obtained samples from a Chinese diarrheal swine farm in 2022. Reverse transcription polymerase chain reaction and immunofluorescence were used to determine the etiology, and the full-length PEDV genome was sequenced. Nucleotide similarity was calculated using MEGA to construct a phylogenetic tree and DNASTAR. Mutant amino acids were aligned using DNAMAN and modeled by SWISS-MODEL, Phyre2 and FirstGlance in JMOL for protein tertiary structure simulation. Additionally, TMHMM was used for protein function prediction.

RESULTS

A PEDV virulent strain CH/HLJJS/2022 was successfully isolated in China. A genome-wide based phylogenetic analysis suggests that it belongs to the GII subtype, and 96.1-98.9% homology existed in the whole genomes of other strains. For the first time, simultaneous mutations of four amino acids were found in the highly conserved membrane (M) and nucleocapsid (N) proteins, as well as eight amino acid mutations that differed from the vast majority of strains in the spike (S) protein. Three of the mutations alter the S-protein spatial structure. In addition, typing markers exist during strain evolution, but isolates are using the fusion of specific amino acids from multiple variant strains to add additional features, as also demonstrated by protein alignments and 3D models of numerous subtype strains.

CONCLUSION

The newly isolated prevalent strain CH/HLJJS/2022 belonged to the GII subtype, and thirteen mutations different from other strains were found, including mutations in the highly conserved m and N proteins, and in the S1° and COE neutralizing epitopes of the S protein. PEDV is breaking through original cognitions and moving on a more complex path. Surveillance for PEDV now and in the future and improvements derived from mutant strain vaccines are highly warranted.

Characterization and pathogenicity of the porcine epidemic diarrhea virus isolated in China

Piglet diarrhea caused by the porcine epidemic diarrhea virus (PEDV) is a common problem on pig farms in China associated with high morbidity and mortality rates. In this study, three PEDV isolates were successfully detected after the fourth blind passage in Vero cells. The samples were obtained from infected piglet farms in Jilin (Changchun), and Shandong (Qingdao) Provinces of China and were designated as CH/CC-1/2018, CH/CC-2/2018, and CH/QD/2018. According to the analysis of the complete S protein gene sequence, the CH/CC-1/2018 and CH/CC-2/2018 were allocated to the G2b branch, while CH/QD/2018 was located in the G1a interval and was closer to the vaccine strain CV777. Successful detection and identification of the isolated strains were carried out using electron microscopy and indirect immunofluorescence. Meanwhile, animal challenge experiments and viral RNA copies determination were used to compare the pathogenicity. The results showed that CH/CC-1/2018 in Changchun was more pathogenic than CH/QD/2018 in Qingdao. In conclusion, the discovery of these new strains is conducive to the development of vaccines to prevent the pandemic of PEDV, especially that the CH/CC-1/2018, and CH/CC-2/2018 were not related to the classical vaccine strain CV777.

Experimental Infection of Pigs with Recent European Porcine Epidemic Diarrhea Viruses

Porcine epidemic diarrhea virus (PEDV), belonging to the genus Alphacoronavirus, can cause serious disease in pigs of all ages, especially in suckling pigs. Differences in virulence have been observed between various strains of this virus. In this study, four pigs were inoculated with PEDV from Germany (intestine/intestinal content collected from pigs in 2016) and four pigs with PEDV from Italy (intestine/intestinal material collected from pigs in 2016). The pigs were re-inoculated with the same virus on multiple occasions to create a more robust infection and enhance the antibody responses. The clinical signs and pathological changes observed were generally mild. Two distinct peaks of virus excretion were seen in the group of pigs inoculated with the PEDV from Germany, while only one strong peak was seen for the group of pigs that received the virus from Italy. Seroconversion was seen by days 18 and 10 post-inoculation with PEDV in all surviving pigs from the groups that received the inoculums from Germany and Italy, respectively. Attempts to infect pigs with a swine enteric coronavirus (SeCoV) from Slovakia were unsuccessful, and no signs of infection were observed in the inoculated animals.

Development of a Next-Generation Vaccine Platform for Porcine Epidemic Diarrhea Virus Using a Reverse Genetics System

For the past three decades, the porcine epidemic diarrhea virus (PEDV) has remained an enormous threat to the South Korean swine industry. The scarcity of an effective method for manipulating viral genomes has impeded research progress in PEDV biology and vaccinology. Here, we report the development of reverse genetics systems using two novel infectious full-length cDNA clones of a Korean highly pathogenic-G2b strain, KNU-141112, and its live attenuated vaccine strain, S DEL5/ORF3, in a bacterial artificial chromosome (BAC) under the control of a eukaryotic promoter. Direct transfection of cells with each recombinant BAC clone induced cytopathic effects and produced infectious progeny. The reconstituted viruses, icKNU-141112 and icS DEL5/ORF3, harboring genetic markers, displayed phenotypic and genotypic properties identical to their respective parental viruses. Using the DNA-launched KNU-141112 infectious cDNA clone as a backbone, two types of recombinant viruses were generated. First, we edited the open reading frame 3 (ORF3) gene, as cell-adapted strains lose full-length ORF3, and replaced this region with an enhanced green fluorescent protein (EGFP) gene to generate icPEDV-EGFP. This mutant virus presented parental virus-like growth kinetics and stably retained robust EGFP expression, indicating that ORF3 is dispensable for PEDV replication in cell culture and is a tolerant location for exogeneous gene acceptance. However, the plaque size and syncytia phenotypes of ORF3-null icPEDV-EGFP were larger than those of icKNU-141112 but similar to ORF3-null icS DEL5/ORF3, suggesting a potential role of ORF3 in PEDV cytopathology. Second, we substituted the spike (S) gene with a heterologous S protein, designated S51, from a variant of interest (VOI), which was the most genetically and phylogenetically distant from KNU-141112. The infectious recombinant VOI, named icPEDV-S51, could be recovered, and the rescued virus showed indistinguishable growth characteristics compared to icKNU-141112. Virus cross-neutralization and structural analyses revealed antigenic differences in S between icKNU-141112 and icPEDV-S51, suggesting that genetic and conformational changes mapped within the neutralizing epitopes of S51 could impair the neutralization capacity and cause considerable immune evasion. Collectively, while the established molecular clones afford convenient, versatile platforms for PEDV genome manipulation, allowing for corroborating the molecular basis of viral replication and pathogenesis, they also provide key infrastructural frameworks for developing new vaccines and coronaviral vectors.

Development of an indirect ELISA to detect PEDV specific IgA antibody based on a PEDV epidemic strain

Background

Porcine epidemic diarrhea (PED), a swine epidemic disease caused by porcine epidemic diarrhea virus (PEDV), is characterized by severe watery diarrhea, vomiting, dehydration and high mortality in piglets, and has caused serious economic losses to the global porcine industry. The level of PEDV IgA antibody is a key marker to assess the extent of passive immunity of the resistance against PEDV infection. However, current commercial structure proteins-based kits for detection of PEDV antibody are not affordable, and those kits require complicated antigen preparation procedures, which cannot meet the scope of economic benefits of many large-scale pig companies in China. Therefore, there is an urgent need to develop an accurate, simple, and economical method for IgA detection in clinical samples. In this study, an indirect ELISA (i-ELISA) method was developed based on a purified PEDV epidemic strain (NH-TA2020).

Results

The results show that optimal working dilution ratios of PEDV antigen and HRP anti-swine IgA are at 1: 1000 and 1:15000 respectively. The sensitivity of this method is high with the maximum dilution of samples up to 1:160, and coefficients of variation (CV) of both the intra assays and inter assays were no more than 15%. In addition, the relative sensitivities of the i-ELISA were above 90% compared with values from commercial kits in both serum and oral fluid samples.

Conclusions

Our results suggested that the i-ELISA developed in this study was an accurate, simple, and economical method for PEDV-IgA detection in clinical samples.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03419-w.

Prevention and Control of Porcine Epidemic Diarrhea: The Development of Recombination-Resistant Live Attenuated Vaccines

Porcine epidemic diarrhea (PED), causing up to 100% mortality in neonatal pigs, is a highly contagious enteric disease caused by PED virus (PEDV). The highly virulent genogroup 2 (G2) PEDV emerged in 2010 and has caused huge economic losses to the pork industry globally. It was first reported in the US in 2013, caused country-wide outbreaks, and posed tremendous hardship for many pork producers in 2013–2014. Vaccination of pregnant sows/gilts with live attenuated vaccines (LAVs) is the most effective strategy to induce lactogenic immunity in the sows/gilts and provide a passive protection via the colostrum and milk to suckling piglets against PED. However, there are still no safe and effective vaccines available after about one decade of endeavor. One of the biggest concerns is the potential reversion to virulence of an LAV in the field. In this review, we summarize the status and the major obstacles in PEDV LAV development. We also discuss the function of the transcriptional regulatory sequences in PEDV transcription, contributing to recombination, and possible strategies to prevent the reversion of LAVs. This article provides insights into the rational design of a promising LAV without safety issues.

Evolution Characterization and Pathogenicity of a Porcine Reproductive and Respiratory Syndrome Virus Isolate from a Pig Farm in Shandong Province, China

In recent years, porcine reproductive and respiratory syndrome virus (PRRSV) strains have been experiencing extensive recombination in Chinese swine farms. This recombination usually happens in NADC30/34 strains and highly pathogenic (HP) PRRSV strains. This study identified a new PRRSV isolate that shared 99% and 99.1% nucleotide identity with CH-1a and CH-1R at the genomic level, respectively. After purification by viral plaque assay, this isolate was named PRRSV CSR1801. The isolate did not experience any recombination with other PRRSV strains common in swine herd epidemics in China, which means it still maintains the stable features of the classical PRRSV strain and did not easily recombine with other PRRSV strains. Further analysis of the pathogenicity of the PRRSV isolate CSR1801 was performed in piglets. The results indicated that none of the inoculated piglets showed the typical clinical manifestations of PRRS, which presented with runny noses, rough back hair, rectal temperatures always below 40.5 °C, and no deaths. Additionally, no obvious histopathological lesions such as severe interstitial pneumonia could be observed in the lungs of the piglets. Hence, the PRRSV isolate CSR1801 should be classified as a classical-like PRRSV strain. This classical PRRSV strain showed genetic stability and maintained low pathogenicity. This study may provide new clues for further understanding the genetic evolution and pathogenicity of PRRSV and may also be an important reference for the prevention and control of PRRS in swine farms.

Genetic Characteristics and Pathogenicity of a Novel Porcine Epidemic Diarrhea Virus with a Naturally Occurring Truncated ORF3 Gene

Porcine epidemic diarrhea virus (PEDV) is the major pathogen that causes diarrhea and high mortality in newborn piglets, with devastating impact on the pig industry. To further understand the molecular epidemiology and genetic diversity of PEDV field strains, in this study the complete genomes of four PEDV variants (HN2021, CH-HNYY-2018, CH-SXWS-2018, and CH-HNKF-2016) obtained from immunized pig farms in central China between 2016 to 2021 were characterized and analyzed. Phylogenetic analysis of the genome and S gene showed that the four strains identified in the present study had evolved into the subgroup G2a, but were distant from the vaccine strain CV777. Additionally, it was noteworthy that a new PEDV strain (named HN2021) belonging to the G2a PEDV subgroup was successfully isolated in vitro and it was further confirmed by RT-PCR that this isolate had a large natural deletion at 207–373 nt of the ORF3 gene, which has never been reported before. Particularly, in terms of pathogenicity evaluation, colostrum deprivation piglets challenged with PEDV HN2021 showed severe diarrhea and high mortality, confirming that PEDV HN2021 was a virulent strain. Hence, PEDV strain HN2021 of subgroup G2a presents a promising vaccine candidate for the control of recurring porcine epidemic diarrhea (PED) in China. This study lays the foundation for better understanding of the genetic evolution and molecular pathogenesis of PEDV.

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.

The spike glycoprotein genes of porcine epidemic diarrhea viruses isolated in China

The porcine epidemic diarrhea virus (PEDV) causes a highly contagious disease in pigs, which is one of the most devastating viral diseases of swine in the world. In China, PEDV was first confirmed in 1984 and PEDV infections occurred sporadically from 1984 to early 2010. From late 2010 until present, PEDV infections have swept every province or region in China. In this study, we analyzed a total of 186 full-length spike genes and deduced proteins of all available complete genomes of PEDVs isolated in China during 2007–2019. A total of 28 potential recombination events were identified in the spike genes of PEDVs in China. Spike gene recombination not only expanded the genetic diversity of PEDVs in the GII genogroup, but also resulted in the emergence of a new evolutional branch GI-c during 2016–2018. In addition, comparative analysis of spike proteins between GI-a prototype virulent CV777 and GII strain AJ1102 reveals that the amino acid variations could affect 20 potential linear B cell epitopes, demonstrating a dramatic antigen drift in the spike protein. These results provide a thorough view of the information about the genetic and antigenic diversity of PEDVs circulating in China and therefore could benefit the development of suitable strategies for disease control.

Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication

Background

Coronavirus (CoV) nonstructural protein 14 (nsp14) has exoribonuclease (ExoN) activity, responsible for proofreading and contributing to replication fidelity. It has been reported that CoVs exhibit variable sensitivity to nsp14-ExoN deficiency. Betacoronavirus murine hepatitis virus (MHV) and severe acute respiratory syndrome (SARS)-CoV were viable upon nsp14-ExoN deficiency. While betacoronavirus Middle East respiratory syndrome (MERS)-CoV and SARS-CoV-2 were non-viable with disabled nsp14-ExoN. In this study, we investigated the nsp14-ExoN deficiency of alphacoronavirus porcine epidemic diarrhea virus (PEDV) in viral pathogenesis using reverse genetics.

Results

Eight nsp14-ExoN deficient mutants, targeting the predicted active sites and the Zinc finger or mental-coordinating sites, of PEDV were designed. Only one mutant E191A with a mutation in the Mg²⁺-binding site was rescued using the infectious clone of PEDV PC22A strain (icPC22A). The passage no.1–3 (P1-3) of E191A grew to very low titers in Vero cells. To evaluate the pathogenesis of the E191A, 4 or 5-day-old gnotobiotic pigs were inoculated orally with 100 TCID₅₀/pig of the E191A-P1, icPC22A, or mock. All mock pigs did not shed virus in feces or show clinical signs. All pigs inoculated with icPC22A shed high viral RNA levels, had severe diarrhea, and died by 6 days post-inoculation (dpi). In contrast, only 3 pigs (3/4, 75%) in the E191A-P1 group shed low levels of viral RNA and 2 pigs had moderate diarrhea at acute infection phase. At 22 dpi, each pig was challenged orally with 10⁶ plaque forming unit of virulent icPC22A. All pigs in the mock group developed severe diarrhea and 2 of the 5 pigs died. Pigs in the E191A-P1 group had less severe diarrhea and no pigs died. Sanger sequencing analysis revealed that the viral genome in the fecal sample of one E191A-P1-inoculated pig and the P4 virus passaged in vitro lost the E191A mutation, suggesting the genetic instability of the E191A mutant.

Conclusion

The recombinant PEDV variants carrying mutations at the essential functional sites within nsp14-ExoN were either lethal or genetically unstable. Our finding further confirmed the critical role of nsp14-ExoN in CoV life cycle, suggesting that it may be a target for the design of universal anti-CoV drugs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13578-021-00598-1.

Identification of cellular proteins interacting with PEDV M protein through APEX2 labeling

Membrane (M) proteins of coronaviruses are the most abundant component of the virus envelope and play crucial roles in virus assembly, virus budding and the regulation of host immunity. To understand more about these functions in the context of PEDV M protein, forty host cell proteins interacting with the M protein were identified in the present study by exploiting the proximity-labeling enzyme APEX2 (a mutant soybean ascorbate peroxidase). Bioinformatic analysis showed that the identified host cell proteins were related to fifty-four signal pathways and a wide diversity of biological processes. Interaction between M and five of the identified proteins (RIG-I, PPID, NHE-RF1, S100A11, CLDN4) was confirmed by co-immunoprecipitation (Co-IP). In addition, knockdown of PPID and S100A11 genes by siRNA significantly improved virus production, indicating that the proteins encoded by the two genes were interfering with or down-regulating virus replication in infected cells. Identification of the host cell proteins accomplished in this study provides new information about the mechanisms underlying PEDV replication and immune evasion. SIGNIFICANCE: PEDV M protein is an essential structural protein implicated in viral infection, replication and assembly although the precise mechanisms underlying these functions remain enigmatic. In this study, we have identified 40 host cell proteins that interact with PEDV M protein using the proximity-labeling enzyme APEX2. Co-immunoprecipitation subsequently confirmed interactions between PEDV M protein and five host cell proteins, two of which (S100A11 and PPID) were involved in down-regulating virus replication in infected cells. This study is significant in that it formulates a strategy to provide new information about the mechanisms relating to the novel functions of PEDV M protein.

Isolation and Identification of a Recombinant Porcine Epidemic Diarrhea Virus With a Novel Insertion in S1 Domain

Porcine epidemic diarrhea virus (PEDV) is the major pathogen that causes diarrhea and high mortality in newborn piglets with devastating impact to the pig industry. Recombination and mutation are the main driving forces of viral evolution and genetic diversity of PEDV. In 2016, an outbreak of diarrhea in piglets occurred in an intensive pig farm in Central China. A novel PEDV isolate (called HNAY) was successfully isolated from clinical samples. Sequence analysis and alignment showed that HNAY possessed 21-nucleotide (nt) insertion in its S1 gene, which has never been reported in other PEDV isolates. Moreover, the sequence of the insertion was identical with the sequence fragment in PEDV N gene. Notably, the HNAY strain exhibited two unique mutations (T500A and L521Y) in the neutralizing epitopes of the S1 protein that were different from those of other PEDV variant strains and CV777-based vaccine strains. Additionally, PEDV HNAY might be derived from a natural recombination between two Chinese variant PEDV strains. Animal experiments demonstrated that HNAY displayed higher pathogenicity compared with two other clinical isolates. This study lays the foundation for better understanding of the genetic evolution and molecular pathogenesis of PEDV.

Establishment of stable Vero cell lines expressing TMPRSS2 and MSPL: A useful tool for propagating porcine epidemic diarrhea virus in the absence of exogenous trypsin

Porcine epidemic diarrhea virus (PEDV) is the causative agent of porcine epidemic diarrhea, causing substantial economic losses to the swine industry worldwide. However, the development of PEDV vaccine is hampered by its low propagation titer in vitro, due to difficulty in adapting to the cells and complex culture conditions, even in the presence of trypsin. Furthermore, the frequent variation, recombination, and evolution of PEDV resulted in reemergence and vaccination failure. In this study, we established the Vero/TMPRSS2 and Vero/MSPL cell lines, constitutively expressing type II transmembrane serine protease TMPRSS2 and MSPL, in order to increase the stability and titer of PEDV culture and isolation in vitro. Our study revealed that the Vero/TMPRSS2, especially Vero/MSPL cell lines, can effectively facilitate the titer and multicycle replication of cell-adapted PEDV in the absence of exogenous trypsin, by cleaving and activating PEDV S protein. Furthermore, our results also highlighted that Vero/TMPRSS2 and Vero/MSPL cells can significantly enhance the isolation of PEDV from the clinical tissue samples as well as promote viral infection and replication by cell-cell fusion. The successful construction of the Vero/TMPRSS2 and Vero/MSPL cell lines provides a useful approach for the isolation and propagation of PEDV, simplification of virus culture, and large-scale production of industrial vaccine, and the cell lines are also an important system to research PEDV S protein cleaved by host protease.

Dynamic Dissection of the Endocytosis of Porcine Epidemic Diarrhea Coronavirus Cooperatively Mediated by Clathrin and Caveolae as Visualized by Single-Virus Tracking

Coronaviruses (CoVs) have caused severe diseases in humans and animals. Endocytic pathways, such as clathrin-mediated endocytosis (CME) and caveolae-mediated endocytosis (CavME), play an important role for CoVs to penetrate the cell membrane barrier. In this study, a novel CoV entry manner is unraveled in which clathrin and caveolae can cooperatively mediate endocytosis of porcine epidemic diarrhea coronavirus (PEDV). Using multicolor live-cell imaging, the dynamics of the fluorescently labeled clathrin structures, caveolae structures, and PEDV were dissected. During CavME of PEDV, we found that clathrin structures can fuse with caveolae near the cell plasma membrane, and the average time of PEDV penetrating the cell membrane was within ∼3 min, exhibiting a rapid course of PEDV entry. Moreover, based on the dynamic recruitment of clathrin and caveolae structures and viral motility, the direct evidence also shows that about 20% of PEDVs can undergo an abortive entry via CME and CavME. Additionally, the dynamic trafficking of PEDV from clathrin and caveolae structures to early endosomes, and from early endosomes to late endosomes, and viral fusion were directly dissected, and PEDV fusion mainly occurred in late endosomes within ∼6.8 min after the transport of PEDV to late endosomes. Collectively, this work systematically unravels the early steps of PEDV infection, which expands our understanding of the mechanism of CoV infection.IMPORTANCE Emerging and re-emerging coronaviruses cause serious human and animal epidemics worldwide. For many enveloped viruses, including coronavirus, it is evident that breaking the plasma membrane barrier is a pivotal and complex process, which contains multiple dynamic steps. Although great efforts have been made to understand the mechanisms of coronavirus endocytic pathways, the direct real-time imaging of individual porcine epidemic diarrhea coronavirus (PEDV) internalization has not been achieved yet. In this study, we not only dissected the kinetics of PEDV entry via clathrin-mediated endocytosis and caveolae-mediated endocytosis and the kinetics of endosome trafficking and viral fusion but also found a novel productive coronavirus entry manner in which clathrin and caveolae can cooperatively mediate endocytosis of PEDV. Moreover, we uncovered the existence of PEDV abortive endocytosis. In summary, the productive PEDV entry via the cooperation between clathrin and caveolae structures and the abortive endocytosis of PEDV provide new insights into coronavirus penetrating the plasma membrane barrier.

A portable, 3D printed, microfluidic device for multiplexed, real time, molecular detection of the porcine epidemic diarrhea virus, transmissible gastroenteritis virus, and porcine deltacoronavirus at the point of need

The porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine deltacoronavirus (PDCoV) are emerging/reemerging coronaviruses (CoVs) of neonatal pigs that cause great economic losses to pig farms and pork processors. Specific, rapid, and simple multiplex detection of these viruses is critical to enable prompt implementation of appropriate control measures. Conventional methods for molecular diagnosis require skilled personnel and relatively sophisticated equipment, restricting their use in centralized laboratories. We developed a low-cost, rapid, semi-quantitative, field deployable, 3D-printed microfluidic device for auto-distribution of samples and self-sealing and real-time and reverse transcription-loop-mediated isothermal amplification (RT-LAMP), enabling the co-detection of PEDV, TGEV and PDCoV within 30 minutes. Our assay's analytical performance is comparable with a benchtop, real-time RT-LAMP assay and the gold standard quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay with limits of detection of 10 genomic copies per reaction for PEDV and PDCoV, and 100 genomic copies per reaction for TGEV. Evaluation of clinical specimens from diseased pigs with our microfluidic device revealed excellent concordance with both benchtop RT-LAMP and qRT-PCR. Our portable RT-LAMP microfluidic chip will potentially facilitate simple, specific, rapid multiplexed detection of harmful infections in minimally equipped veterinary diagnostic laboratories and on-site in pigs' farms.

A Half-Day Genome Sequencing Protocol for Middle East Respiratory Syndrome Coronavirus

Recent coronavirus (CoV) outbreaks, including that of Middle East respiratory syndrome (MERS), have presented a threat to public health worldwide. A primary concern in these outbreaks is the extent of mutations in the CoV, and the content of viral variation that can be determined only by whole genome sequencing (WGS). We aimed to develop a time efficient WGS protocol, using universal primers spanning the entire MERS-CoV genome. MERS and synthetic Neoromicia capensis bat CoV genomes were successfully amplified using our developed PCR primer set and sequenced with MinION. All experimental and analytical processes took 6 h to complete and were also applied to synthetic animal serum samples, wherein the MERS-CoV genome sequence was completely recovered. Results showed that the complete genome of MERS-CoV and related variants could be directly obtained from clinical samples within half a day. Consequently, this method will contribute to rapid MERS diagnosis, particularly in future CoV epidemics.

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.

Chimeric Porcine Deltacoronaviruses with Sparrow Coronavirus Spike Protein or the Receptor-Binding Domain Infect Pigs but Lose Virulence and Intestinal Tropism

Porcine deltacoronavirus (PDCoV) strain OH-FD22 infects poultry and shares high nucleotide identity with sparrow-origin deltacoronaviruses (SpDCoV) ISU73347 and HKU17 strains. We hypothesized that the spike (S) protein or receptor-binding domain (RBD) from these SpDCoVs would alter the host and tissue tropism of PDCoV. First, an infectious cDNA clone of PDCoV OH-FD22 strain (icPDCoV) was generated and used to construct chimeric icPDCoVs harboring the S protein of HKU17 (icPDCoV-SHKU17) or the RBD of ISU73347 (icPDCoV-RBDISU). To evaluate their pathogenesis, neonatal gnotobiotic pigs were inoculated orally/oronasally with the recombinant viruses or PDCoV OH-FD22. All pigs inoculated with icPDCoV or OH-FD22 developed severe diarrhea and shed viral RNA at moderate-high levels (7.62-10.56 log10 copies/mL) in feces, and low-moderate levels in nasal swabs (4.92-8.48 log10 copies/mL). No pigs in the icPDCoV-SHKU17 and icPDCoV-RBDISU groups showed clinical signs. Interestingly, low-moderate levels (5.07-7.06 log10 copies/mL) of nasal but not fecal viral RNA shedding were detected transiently at 1-4 days post-inoculation in 40% (2/5) of icPDCoV-SHKU17- and 50% (1/2) of icPDCoV-RBDISU-inoculated pigs. These results confirm that PDCoV infected both the upper respiratory and intestinal tracts of pigs. The chimeric viruses displayed an attenuated phenotype with the loss of tropism for the pig intestine. The SpDCoV S protein and RBD reduced viral replication in pigs, suggesting limited potential for cross-species spillover upon initial passage.

A strain of porcine deltacoronavirus: Genomic characterization, pathogenicity and its full-length cDNA infectious clone

As a novel enteropathogenic coronavirus, porcine deltacoronavirus (PDCoV) warrants further investigation. In this study, a Chinese PDCoV strain, designated CHN-HN-1601, was isolated from the faeces of a diarrhoeic piglet. After plaque purification, the genome was determined which shared 97.5%-99.5% nucleotide identities with 71 representative PDCoV strains available in the GenBank. The pathogenic properties of CHN-HN-1601 were evaluated using 5-day-old piglets. All inoculated piglets developed severe diarrhoea from 2 days post-infection (dpi) onwards. To our surprise, two periods of diarrhoea starting from 2 to 7 dpi and from 13 to 19 dpi were observed in affected piglets during the experiment. Faecal viral shedding of the inoculated piglets was detected by real-time RT-PCR, with viral shedding peaked at 4 and 16 dpi, respectively. At necropsy at 5 dpi, the main gross lesions included transparent, thin-walled and gas-distended intestines containing yellow watery contents. Further histopathological examinations, including haematoxylin and eosin staining, immunohistochemistry and RNAscope in situ hybridization, revealed that the virus infection caused severe villous atrophy of the small intestines, with PDCoV antigen and RNA mainly distributed in the cytoplasm of the villous epithelial cells of jejunum and ileum in piglets. The dynamic production of PDCoV-specific IgG and neutralizing antibodies in serum of the affected piglets was also assessed using a whole virus-based ELISA and an immunofluorescence assay-based neutralization test, respectively. Furthermore, a full-length cDNA infectious clone of CHN-HN-1601 was constructed using a bacterial artificial chromosome system. The rescued virus exhibited in vitro growth and pathogenic properties similar to the parental virus. Taken together, our study not only enriches the information of PDCoV, but also provides a useful reverse genetics platform for further pathogenesis exploration of the virus.

Evaluation of Cross-Protection between G1a- and G2a-Genotype Porcine Epidemic Diarrhea Viruses in Suckling Piglets

Simple Summary

Porcine epidemic diarrhea (PED), caused by PED virus (PEDV), is a devastating enteric disease in pigs worldwide. At least two genotypes (G1 and G2) and five subgenotypes (G1a, G1b, G2a, G2b, andG2c) of PEDV strains have been identified. To date, the reports on the antigenicity and immunogenicity of those viruses are limited and the results documented on cross-neutralization among different genotypes and/or subgenotypes of PEDV were inconsistent. This study aimed to observe the comparative pathogenicity and cross-protection between G1a and G2a PEDVs, and thus find a new insight into the antigenicity and immunogenicity of PEDVs. The results of the present study demonstrated that the G2a-based inactivated vaccine could provide sterilizing immunity against both highly virulent homologous and heterologous PEDV challenges. In contrast, the G1a-based inactivated vaccine could induce a sterilizing immune response against challenge of homologous strain CV777 and only provide partial protection for the challenge of a heterologous G2a PEDV CH/JX/01. The findings of this study might explain the underlying mechanism that severe PED and deaths still occurred among the neonatal piglets of which CV777-based PEDV vaccine were administered in China, and imply G2a-based PEDV vaccine used in this study might be a good vaccine candidate for PEDV which may provide solid protection against circulating highly virulent PEDVs.

Abstract

To date, two genotypes, i.e., genotype 1 (G1) and genotype 2 (G2), of porcine epidemic diarrhea virus (PEDV) have been identified in swine, while the cross protection between the G2a and G1a subgenotypes is undetermined. Hence, in the present study, we attempted to observe a comparative pathogenicity and cross protection of G1a (CV777) and G2a (CH/JX/01) PEDVs. Initially pregnant sows were vaccinated twice with the two kinds of inactivated G1a- and G2a-based PEDV vaccines, respectively and the delivered neonatal piglets were challenged with prototype isolates of G1a and G2a PEDVs, and then the pathogenicity and cross-protection in neonatal piglets were observed. The results showed that CH/JX/01, a highly virulent and dominant G2a PEDV strain currently circulating in China had more severe pathogenicity in vitro and in vivo, and induced more strong immune responses, including higher titers of sIgA in maternal milk than that induced by CV777 PEDV, a prototype of G1a PEDV strain. All piglets from the sows immunized with CH/JX/01 could not only survive when challenged with the homologous PEDV, but also be fully protected when challenged with heterogenous G1a PEDV. In contrast, the piglets from the sows immunized with CV777 could be protected when challenged with homologous PEDV and only partially protected when challenged with heterologous G2a strain of PEDV (CH/JX/01). The findings of this study provide new insights into the pathogenicity, antigenicity, and immunogenicity of currently circulating wild type G2a PEDV, which might be valuable for the development of novel PEDV vaccine candidates with improved efficacy.

Rapid Selective Detection of Potentially Infectious Porcine Epidemic Diarrhea Coronavirus Exposed to Heat Treatments Using Viability RT-qPCR

Coronaviruses (CoVs) cause severe respiratory, enteric, and systemic infections in a wide range of hosts, including humans and animals. Porcine epidemic diarrhea virus (PEDV), a member of the Coronaviridae family, is the etiological agent of porcine epidemic diarrhea (PED), a highly contagious intestinal disease affecting pigs of all ages. In this study, we optimized a viability real-time reverse transcriptase polymerase chain reaction (RT-qPCR) for the selective detection of infectious and heat-inactivated PEDV. PEMAX™, EMA™, and PMAxx™ photoactivable dyes along with PtCl₄ and CDDP platinum compounds were screened as viability markers using two RT-qPCR assays: firstly, on PEDV purified RNA, and secondly on infectious and thermally inactivated virus suspensions. Furthermore, PMAxx™ pretreatment matched the thermal inactivation pattern obtained by cell culture better than other viability markers. Finally, we further optimized the pretreatment by coupling viability markers with Triton X-100 in inoculated serum resulting in a better estimation of PEDV infectivity than RT-qPCR alone. Our study has provided a rapid analytical tool based on viability RT-qPCR to infer PEDV infectivity with potential application for feed and feed ingredients monitoring in swine industry. This development would allow for greater accuracy in epidemiological surveys and outbreak investigations.

Genetic Diversity of Porcine Epidemic Diarrhea Virus With a Naturally Occurring Truncated ORF3 Gene Found in Guangxi, China

Porcine epidemic diarrhea virus (PEDV) is one of the major enteric pathogens, causing severe enteric disease, resulting in enormous economic losses. The ORF3 gene encodes an accessory protein which is related to the infectivity and virulence of PEDV. In this study, 33 PEDV positive field samples were collected from Guangxi, from 2017 to 2019, and the genetic diversity of ORF3 was investigated. Thirty-eight strains of ORF3 were obtained, and these were composed of five strains of ORF3 named Guangxi naturally truncated strains that were 293 bp in length, with continuous deletions from 172 to 554 bp. The Guangxi naturally truncated strains encoded a truncated protein of 89 amino acids, which had clustered into a new group referred to as Group 3, and these might be involved in the variations of virulence. Three genotypes (G1-1 subgroup, G1-3 subgroup, and Group 3) existed simultaneously in Guangxi based on the genetic and evolutionary analysis of the ORF3 gene. The sequence information in the current study will hopefully facilitate the establishment of a diagnostic method that can differentiate the PEDV field stains. Continued surveillance will be useful for monitoring PEDV transmission. Differentiation of the ORF3 genes in PEDV field strains can help us to choose an appropriate PEDV vaccine candidate in the future and prevent outbreaks of PED more effectively.

Emergence and evolution of highly pathogenic porcine epidemic diarrhea virus by natural recombination of a low pathogenic vaccine isolate and a highly pathogenic strain in the spike gene

Outbreaks of a new variant of porcine epidemic diarrhea virus (PEDV) at the end of 2010 have raised interest in the mutation and recombination of PEDV. A PEDV strain (CN/Liaoning25/2018) isolated from a clinical outbreak of piglet diarrhea contained a 49-bp deletion in the ORF3 gene. This deletion is considered a genetic characteristic of low pathogenic attenuated vaccine strains. However, CN/Liaoning25/2018 was highly pathogenic. Complete genome sequencing, identity analysis, phylogenetic tree construction, and recombination analysis showed that this virus was a recombinant strain containing the Spike (S) gene from the highly pathogenic CN/GDZQ/2014 strain and the remaining genomic regions from the low pathogenic vaccine isolate SQ2014. Histopathology and immunohistochemistry results confirmed that this strain was highly pathogenic and indicated that intestinal epithelial cell vacuolation was positively correlated with the intensity and density of PEDV antigens. A new natural recombination model for PEDV was identified. Our results suggest that new highly pathogenic recombinant strains in the field may be generated by recombination between low pathogenic attenuated live PEDV vaccines and pathogenic circulating PEDV strains. Our findings also highlight that the 49-bp deletion of the ORF3 gene in low pathogenic attenuated vaccine strains will no longer be a reliable standard to differentiate the classical vaccine attenuated from the field strains.

Rapid differentiation of PEDV wild-type strains and classical attenuated vaccine strains by fluorescent probe-based reverse transcription recombinase polymerase amplification assay

Background

Porcine epidemic diarrhea virus (PEDV), an intestinal coronavirus that causes acute diarrhea and high mortality in suckling piglets, can result in high economic losses in the swine industry. In recent years, despite the use of China’s current vaccine immunization strategy, multiple types of PEDV strains were still found in immunized swine herds. Our research aims to explore a new rapid differentiation method to distinguish the different types of PEDV strains and assess the safety evaluation of classical attenuated vaccine strains in swine herds.

Results

In the study, a differential one-step quantitative real-time fluorescent reverse transcription recombinase polymerase amplification (real-time RT-RPA) method based on the PEDV universal real-time RT-RPA assay was established according to the ORF1 deletion sequences of three classical attenuated vaccine strains (PEDV attenuated vaccine KC189944, attenuated CV777 and DR13) and five Vero cell-adapted isolates (JS2008, SDM, SQ2014, SC1402, HLJBY), which could effectively differentiate PEDV classical attenuated vaccine strains from wild-type strains (PEDV classical wild strains and variant strains). The detection limits of PEDV RNA in the both PEDV real-time RT-RPA assays were 300 copies within 20 min at 39 °C, and the detection limits of classical attenuated vaccine strain CV777, Vero-cell-adapted isolate JS2008, and PEDV wild-type strain DX were 10^0.5 TCID₅₀/100 μL, 10^1.1 TCID₅₀/100 μL, and 10^1.2 TCID₅₀/100 μL, respectively. Both assays were highly specific for PEDV, showing no cross-reactivity with other enteral viruses.

Conclusion

This RPA method we developed is simple, time-effective, and safe and provides a reliable technical tool for the differential diagnosis and clinical epidemic surveillance of PEDV classical attenuated vaccine strains and wild-type strains.

New tropisms of porcine epidemic diarrhoea virus (PEDV) in pigs naturally coinfected by variants bearing large deletions in the spike (S) protein and PEDVs possessing an intact S protein

We previously reported the coinfection of novel porcine epidemic diarrhoea virus (PEDV) variants bearing large deletions in the S protein and PEDVs possessing an intact S protein (S-intact PEDV) in domestic pigs in Japan. The variants were frequently observed in pig farms with persistent or recurrent infection. To elucidate the role of the variants in persistent infections and their tropism properties, we genetically characterized and immunohistochemically detected PEDVs collected in primary and recurrent outbreaks in two persistently infected farms. Our results revealed coinfection of the PEDV variants bearing a 214-amino acid deletion in the S protein and S-intact PEDVs in the lungs of the naturally infected pigs. New tropisms of PEDV, including epithelial cells and submucosal glands of the airway tract, epithelial cells of the bile duct, and monocytes/macrophages were identified. The findings elucidate the mechanism of PEDV infection, epidemiology and pattern changes in the disease.

Replicative capacity of porcine deltacoronavirus and porcine epidemic diarrhea virus in primary bovine mesenchymal cells

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Gnotobiotic (Gn) calves were susceptible to infection with PDCoV, but not with PEDV.

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Cytopathic effects (CPE) were identified in two primary bovine mesenchymal cell types inoculated with PDCoV or PEDV.

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High PDCoV or PEDV RNA titers and PDCoV or PEDV antigens were also detected in inoculated cells.

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The in vitro observations only partially coincided with the corresponding in vivo data from Gn calves.

Unlike porcine epidemic diarrhea virus (PEDV) that infects only pigs, porcine deltacoronavirus (PDCoV) has the capacity to infect different animal species. In vivo gnotobiotic calves were previously confirmed to be susceptible to infection with PDCoV, but not with PEDV. We next investigated in vitro whether primary bovine cells are susceptible to PDCoV or PEDV infection. We conducted quantification of viral RNA in cell culture supernatants and immunofluorescent staining for the detection of PDCoV or PEDV antigen in two primary bovine cell types inoculated with the PDCoV strain OH-FD22 or PEDV strain PC22-P40 grown in LLC-PK or Vero cells, respectively, and supplemented with 1.25∼5 μg/mL of trypsin in the cell culture medium. The primary cells were isolated from the kidney or heart of a gnotobiotic calf, and both cell types were vimentin-positive, but E-Cadherin-negative, resembling mesenchymal cells. Similar to the previous in vivo observation, cytopathic effects (CPE) that consisted of enlarged and rounded cells, followed by cell shrinkage and detachment, were identified in the two primary cell types inoculated with PDCoV. Unexpectedly, similar CPE was also identified in the two cell types inoculated with PEDV. High PDCoV or PEDV RNA titers and PDCoV or PEDV antigens were detected in the cell culture supernatants and CPE-positive cells, respectively. Our study revealed that primary bovine mesenchymal cells are susceptible to infection with PDCoV and PEDV. The in vitro observation partially coincided with the corresponding in vivo data from gnotobiotic calves.

Development of a rapid and sensitive europium (III) chelate microparticle-based lateral flow test strip for the detection and epidemiological surveillance of porcine epidemic diarrhea virus

Porcine epidemic diarrhea virus (PEDV), a member of the genus Alphacoronavirus, is the predominant cause of severe enteropathogenic diarrhea in swine. A simple, rapid, specific, and sensitive method is critical for monitoring PEDV on pig farms. In this study, a simple and rapid lateral flow immunoassay detection system that integrates europium (Eu) (III) chelate microparticles was developed to identify PEDV in fecal swabs. This newly developed diagnostic sandwich immunoassay utilizes lateral flow test strips (LFTSs). The fluorescence peak heights of the test line (HT) and the control line (HC) were measured using a fluorescence strip reader, and the HT/HC ratio was used for quantitation. The limit of detection of PEDV with this LFTS was ??ten times the median tissue culture infectious dose (TCID₅₀) per mL??. Fecal swab samples were used to determine the cutoff value. Field samples, various PEDV strains and other viruses were used to determine the sensitivity and specificity of the Eu (III) chelate microparticle-based LFTSs, which were 97.8% and 100%, respectively, with a cutoff value of 0.05, as compared with reverse transcription polymerase chain reaction (RT-PCR). In samples from piglets experimentally infected with PEDV, the results were in high agreement with those obtained by RT-PCR. Epidemiological surveillance of PEDV using the LFTSs ??in areas threatened by African swine fever virus?? suggested that the PEDV positive rate on pig farms had significantly decreased, mainly due to the implementation of strict biosecurity measures. The results indicate that the Eu (III) chelate microparticle-based LFTS system is a rapid, sensitive, and reliable method for the identification of PEDV, indicating its suitability for epidemiological surveillance of PEDV infection.

Trypsin promotes porcine deltacoronavirus mediating cell-to-cell fusion in a cell type-dependent manner

Porcine deltacoronavirus (PDCoV) is a newly emerging threat to the global porcine industry. PDCoV has been successfully isolated using various medium additives including trypsin, and although we know it is important for viral replication, the mechanism has not been fully elucidated. Here, we systematically investigated the role of trypsin in PDCoV replication including cell entry, cell-to-cell membrane fusion and virus release. Using pseudovirus entry assays, we demonstrated that PDCoV entry is not trypsin dependent. Furthermore, unlike porcine epidemic diarrhea virus (PEDV), in which trypsin is important for the release of virus from infected cells, PDCoV release was not affected by trypsin. We also demonstrated that trypsin promotes PDCoV replication by enhancing cell-to-cell membrane fusion. Most importantly, our study illustrates two distinct spreading patterns from infected cells to uninfected cells during PDCoV transmission, and the role of trypsin in PDCoV replication in cells with different virus spreading types. Overall, these results clarify that trypsin promotes PDCoV replication by mediating cell-to-cell fusion transmission but is not crucial for viral entry. This knowledge can potentially contribute to improvement of virus production efficiency in culture, not only for vaccine preparation but also to develop antiviral treatments.