Genomic Motifs as a Novel Indicator of the Relationship between Strains Isolated from the Epidemic of Porcine Epidemic Diarrhea in 2013-2014

Time-calibrated phylogenomics of the porcine epidemic diarrhea virus: genome-wide insights into the spatio-temporal dynamics

Porcine epidemic diarrhea virus (PEDV), the causative agent of porcine epidemic diarrhea (PED), has led to tremendous economic losses in the global swine industry. Although the phylogeny of PEDV has been investigated extensively at the molecular level, there was no time-calibrated phylogenomic study on the virus. To improve insight into this topic, we analyzed 138 published genome sequences using the Bayesian coalescent analyses as well as Bayesian inferences and maximum likelihood methods. All of the global PEDV isolates were divided into six groups, except for one unclassified isolate. Of the six groups, Groups 1–5 comprised pandemic viruses while the remaining Group 6 contained classical isolates. Interestingly, the two clades, both pandemic and classical, consisted of clade-specific amino acid sequences in five genes: ORF1a, ORF1b, S, ORF3, and N. Within the pandemic clade, Group 1 and Group 2 originated from North America, whereas Group 3–Group 5 were derived from Asia. In Group 2, there was a common origin of S INDEL isolates. Within each group, there was no apparent association between temporal or geographic origin and heterogeneity of PEDVs. Our findings also showed that the PEDV virus evolved at a rate of 3.38 × 10⁻⁴ substitutions/site/year, and the most recent common ancestor of the virus emerged 75.9 years ago. Our Bayesian skyline plot analysis indicated that the PEDV had maintained constant effective population size excluding only a short period, around 2012, when a valley shaped decline in the effective number of infections occurred.

Factors associated with farm-level infection of porcine epidemic diarrhea during the early phase of the epidemic in Japan in 2013 and 2014

The objective of this study was to investigate factors that caused rapid spread during the early phase of the porcine epidemic diarrhea (PED) epidemic in Japan in 2013 and 2014. Anonymized datasets from all pig farms were provided by Kagoshima (709 farms) and Miyazaki Prefectures (506 farms). Semi-parametric survival analysis was conducted using the first 180 days from the first case on December 3, 2013 in Kagoshima Prefecture. To compare the hazard between different farm management types, univariable survival analysis was conducted. As farm sizes varied among different farm types, bivariable survival analysis was conducted for farm size categories and farm density per km² for each management type. A case-control study using a postal questionnaire survey was conducted in September 2014, and risk factor analysis was performed using generalized linear models with binomial errors. The hazard was significantly higher in farrow-to-finish farms than fattening farms [hazard ratio (HR) = 1.6, p < 0.01], but was not significantly different between reproduction and fattening farms (HR = 1.3, p = 0.16). In separate bivariable survival analyses for each farm type, large- and middle-scale farms had higher hazard than small-scale farms in fattening (HR = 5.8 and 2.6, respectively, both p < 0.01) and reproduction farms (HR = 4.0 and 3.6, respectively, both p < 0.01). In farrow-to-finish farms, large-scale farms had higher hazard than small-scale farms (HR = 2.8, p < 0.01), and higher farm density per km² was also a risk factor (HR = 7.6, p < 0.01). In the case-control study, questionnaires were returned from 78 PED virus-infected and 91 non-infected farms. The overall response rate was 34%. Risk factors of the final model were occurrence of porcine reproductive and respiratory syndrome in the past 5 years [odds ratio (OR) = 1.97, 95% confidence interval (CI): 0.97-4.00, p = 0.054], use of a common compost station (OR = 2.51, 95%CI: 1.08-5.83, p = 0.03), and use of a pig excrement disposal service (OR = 2.64, 95%CI: 1.05-6.63, p = 0.04). High hazard in farrow-to-finish farms suggested transmission from slaughterhouses to susceptible suckling piglets. Hazard associated with large-scale farms and high density might be due to frequent vehicle entrance and transmission by roads. Improvement of farm hygiene management and avoidance of risky practices associated with contact with pig excrement were keys in preventing invasion of PED virus to a farm.

The Identification and Characterization of Two Novel Epitopes on the Nucleocapsid Protein of the Porcine Epidemic Diarrhea Virus

Porcine epidemic diarrhea virus (PEDV) is a highly contagious coronavirus that causes severe diarrhea and death, particularly in neonatal piglets. The nucleocapsid protein (N protein) of PEDV presents strong immunogenicity and contributes to the cross-reactivity between PEDV and TGEV. However, the characterization of epitopes on the PEDV N protein remains largely unknown. Here, two monoclonal antibodies (MAbs) specific to the N protein of a PEDV strain, FJzz1/2011, were generated and screened against a partially overlapping library of 24 GST-fusion N protein-truncated constructs. We confirmed that residues 18–133 (designated NEP-D4) and residues 252–262 (designated NEP-D6) were the epitopes targeted by MAbs PN-D4 and PN-D6, respectively. Sequence analysis revealed that these two epitopes were highly conserved among PEDV strains but were significantly different from other members of the Coronavirinae subfamily. Western blot analysis showed that they could be specifically recognized by PEDV antisera but could not be recognized by TGEV hyperimmune antisera. Indirect immunofluorescence (IFA) assays confirmed no cross-reaction between these two MAbs and TGEV. In addition, the freeze-thaw cycle and protease treatment results indicated that NEP-D4 was intrinsically disordered. All these results suggest that these two novel epitopes and their cognate MAbs could serve as the basis for the development of precise diagnostic assays for PEDV.

Evolution, antigenicity and pathogenicity of global porcine epidemic diarrhea virus strains

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Evolution of global PEDV strains.

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Cross-reactivity between PEDV and other coronaviruses and antigenic variations among different PEDV strains.

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Pathologic features of different PEDV strains.

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Considerations for vaccine strain selection: PEDV virulence attenuation and in vivo cross-protection among PEDV variants.

Emerging and re-emerging coronaviruses cause morbidity and mortality in human and animal populations, resulting in serious public and animal health threats and economic losses. The ongoing outbreak of a highly contagious and deadly porcine epidemic diarrhea virus (PEDV) in Asia, the Americas and Europe is one example. Genomic sequence analyses of PEDV variants have revealed important insights into the evolution of PEDV. However, the antigenic variations among different PEDV strains are less explored, although they may contribute to the failure of PEDV vaccines in Asian countries. In addition, the evolution of PEDV results in variants with distinct genetic features and virulence differences; thus PEDV can serve as a model to explore the molecular mechanisms of coronavirus evolution and pathogenesis. In this article, we review the evolution, antigenic relationships and pathologic features of PEDV strains. This information and review of researches will aid in the development of strategies for control and prevention of PED.