Identification of a Novel Linear B-Cell Epitope on the Nucleocapsid Protein of Porcine Deltacoronavirus

Abstract

Porcine deltacoronavirus (PDCoV), first identified in 2012, is a swine enteropathogen now found in many countries. The nucleocapsid (N) protein, a core component of PDCoV, is essential for virus replication and is a significant candidate in the development of diagnostics for PDCoV. In this study, monoclonal antibodies (mAbs) were generated and tested for reactivity with three truncations of the full protein (N1, N2, N3) that contained partial overlaps; of the five monoclonals chosen tested, each reacted with only the N3 truncation. The antibody designated 4E88 had highest binding affinity with the N protein and was chosen for in-depth examination. The 4E88 epitope was located to amino acids 308-AKPKQQKKPKK-318 by testing the 4E88 monoclonal for reactivity with a series of N3 truncations, then the minimal epitope, 309-KPKQQKKPK-317 (designated EP-4E88), was pinpointed by testing the 4E88 monoclonal for reactivity with a series of synthetic peptides of this region. Homology analysis showed that the EP-4E88 sequence is highly conserved among PDCoV strains, and also shares high similarity with sparrow coronavirus (HKU17), Asian leopard cat coronavirus (ALCCoV), quail coronavirus (UAE-HKU30), and sparrow deltacoronavirus (SpDCoV). Of note, the PDCoV EP-4E88 sequence shared very low similarity (<22.2%) with other porcine coronaviruses (PEDV, TGEV, PRCV, SADS-CoV, PHEV), demonstrating that it is an epitope that can be used for distinguishing PDCoV and other porcine coronavirus. 3D structural analysis revealed that amino acids of EP-4E88 were in close proximity and may be exposed on the surface of the N protein.

Phylogenetic Classification of Global Porcine Deltacoronavirus (PDCoV) Reference Strains and Molecular Characterization of PDCoV in Taiwan

“…B-cell epitopes are an important factor in viral immunogenicity [ 33 ]. A previous study identified the B-cell antigenic epitope EP-4E88 (309KPKQQKKPK317) within the N protein [ 20 ], and this finding is inconsistent with the finding from our PDCoV/104-553/TW-2015 strain that highlighted a point mutation at the aa position (Pro-to-Ser [P310S]) (data not shown). As a highly conserved component of PDCoV, N protein mutations might dynamically alter the protein structure or antigenic recognition.…”

Porcine Coronaviruses: Overview of the State of the Art

“…The results support the understanding of the prevalence and evolution characteristics of PDCoV in China (Zhang M et al 2019). Recent results revealed that the PDCoV EP-4E88 sequence shared very low similarity (\ 22.2%) with other porcine CoV (PEDV, TGEV, PRCV, SADS-CoV, PHEV), demonstrating that it is an epitope that can be used for distinguishing PDCoV and other porcine CoV (Fu et al 2020).…”

The Novel Insight of SARS-CoV-2 Molecular Biology and Pathogenesis and Therapeutic Options

“…SARS-CoV-2 utilized a particular pattern to bind RNA with data on atomic resolution (Kang et al, 2020). Since N protein is a surface protein and has less variation than S protein, it can be suggested as a vaccine candidate for SARS-CoV-2 Fu et al, 2020). In silico analysis suggests that the effect of the two drugs, Glycyrrhizic acid and the phytochemical Theaflavi, on N proteins can be examined as one of the treatment options (Ray et al, 2020).…”