Pioneering Structural Study of Porcine Coronavirus

Today, we are highlighting the research of a completely different team at the University of Minnesota. The Minnesota Supercomputing Institute provides advanced research computing infrastructure and expertise to advance and accelerate research and foster innovation and discoveries.

MSI PIs Wei Zhang (research associate professor, Diagnostic and Biological Sciences) and Fang Li (associate professor, Veterinary and Biomedical Sciences) have published a new paper that describes some of their continuing research into the structure of coronaviruses. These are a large group of viruses that includes such deadly diseases as SARS and MERS. Coronaviruses have four forms, known as α-, β-, γ-, and δ-coronavirus, which affect different hosts. For example, β-coronaviruses affect only mammals, while the δ form affects both birds and mammals.

The coronavirus structure includes a feature called a “spike protein,” which allows the virus to attach to the host’s cells. The spike proteins of α- and β-coronavirus have been well studied. The spike protein of the δ-coronavirus, however, is described for the first time in this paper. The researchers used cryo-electron microscopy, a fast-developing technology in which protein molecules are studied under ultra-cold temperatures with an electron microscope. This technology was used to determine the structure of the spike protein of porcine δ-coronavirus (PdCoV), a lethal virus infecting pigs, elucidating how PdCoV infects pigs cells and evades the host immune system. This is the first atomic-resolution cryo-electron microscopic study from the state of Minnesota, and is a milestone in the structural biology field at the University of Minnesota.

Zhang Li spike protein porcine deltacoronavirus

Image Description: Overall structure of PdCoV S-e in the prefusion conformation. (A) Schematic drawing of PdCoV S-e (spike ectodomain). S1, receptor-binding subunit. S2, membrane fusion subunit. GCN4-His6, GCN4 trimerization tag followed by His6 tag. S1-NTD, N-terminal domain of S1. S1-CTD, C-terminal domain of S1. CH-N and CH-C, central helices N and C. FP, fusion peptide. HR-N and HR-C, heptad repeats N and C. Residues in shaded regions (N terminus, GCN4 tag, and His6 tag) were not traced in the structure. (B) Cryo-EM maps of PdCoV S-e with atomic model fitted in. The maps have a contour of 6.6 σ. (C) Cryo-EM structure of prefusion PdCoV S-e. Each of the monomeric subunits is colored differently. (D) Structure of a monomeric subunit in the prefusion conformation. The structural elements are colored in the same way as those in panel A. Image and description, J Shang et al., J Virol. 92:e01556-17 (2018). © American Society for Microbiology.

The paper was published in late 2017 on the website of the Journal of Virology: J Shang, Y Zhang, Y Yang, Q Geng,W Tai, L Du, Y Zhou, W ZhangF Li. 2018. Cryo-Electronic Microscopy Structure of Porcine Deltacoronavirus Spike Protein in the Prefusion StateJournal of Virology 92 (4): e01556-17. doi: 10.1128/JVI.01556-17.

This report comes from the MSI research highlights.


Science Page: Herd-level prevalence and incidence of porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus(PDCoV) in swine herds in Ontario, Canada

This is our Friday rubric: every week a new Science Page from the Bob Morrison’s Swine Health Monitoring Project. The previous editions of the science page are available on our website.

This week, we are sharing a report regarding the prevalence of Porcine Deltacoronavirus and Porcine Epidemic Diarrhea virus in swine herds from Ontario.

Key Points

  • Cumulative incidence of PED and PDCoV in Canada is decreasing according to data coming from the industry for the year 2014, 2015 and 2016.
  • PED showed a cyclical pattern when looking at the number of farms infected. However, PDCoV showed a more erratic pattern with no clear trends.
  • Industry driven disease control programs provide useful information to understand temporal evolution and disease patterns.

The primary goal of this study was to estimate herd-level incidence and prevalence measures for PEDV and PDCoV in swine herds in Ontario (Canada) between January 2014 and December 2016, based on industry data (Ontario Swine Health Advisory Board (OSHAB) Disease Control Program (DCP)).

The full paper was published in the Transboundary and Emerging Diseases journal.

Ajayi PED Deltacoronavirus prevalence in swine herd Ontario

Herd-level incidence risk and rate of two novel porcine coronaviruses (PEDV and PDCoV) in Ontario swine herds between 2014 and 2016, and estimated prevalence of positive cases at the end of each year based on data provided in the Ontario Swine Health Advisory Board (OSHAB) Disease Control Program (DCP) database (average number of herds for 2014–2016 = 1093).

PED showed a cyclical pattern over the three years of the study while PDCoV showed a more erratic pattern. Incidence decreased over time between 2014 and 2016 in both, PED and PDCoV.

You can also read our report on the prevalence of PDCoV in the USA.

Science Page: Porcine Deltacoronavirus positive cases in the US: Where are we today?

This is our Friday rubric: every week a new Science Page from the Bob Morrison’s Swine Health Monitoring Project. The previous editions of the science page are available on our website.

This week, we are sharing a report from the MSHMP team regarding the prevalence of Porcine Deltacoronavirus in the US herds participation in MSHMP.

Key Points

  • Porcine Deltacoronavirus (PDCoV) was first reported in the US in 2014.
  • Monitoring of PDCoV cases showed that it is still present in pig herds from the United States.
  • PDCoV testing and reporting must continue in order to increase our understanding of the disease.

Porcine Deltacoronavirus (PDCoV) was first detected in the US in 2014. The complete genome of a United States’ PDCoV isolate was characterized by Marthaler et al. (2014), which was ~99% similar to a virus detected in Hong Kong.

Clinical signs may be similar to Porcine Epidemic Diarrhea (PED) and Transmissible gastroenteritis coronavirus (TGEV), including acute diarrhea, mild to moderate vomiting, and ultimately death especially in neonatal pigs.

PDCoV continues to be present in the United States swine herd. Since March, 2017 PDCoV cases have been passively reported to MSHMP. Over this period of time, 37 cases have been reported by six participant systems.

MSHMP Porcine deltacoronavirus prevalence US 2017-2018
Monthly number of PDCoV cases since March 2017

Since November 2017, 24 PDCoV cases were communicated to MSHMP, representing 67% of the reported cases.

PDCoV still occurs in the US at an apparent low number of reported cases. Swine producers and veterinarians must stay vigilant for clinical signs compatible with PDCoV and continue to test for this pathogen.