An Exploratory Bioinformatic Investigation of Cats' Susceptibility to Coronavirus-Deriving Epitopes

Abstract

Coronaviruses are highly transmissible and pathogenic viruses for humans and animals. The vast quantity of information collected about SARS-CoV-2 during the pandemic helped to unveil details of the mechanisms behind the infection, which are still largely elusive. Recent research demonstrated that different class I/II human leukocyte antigen (HLA) alleles might define an individual susceptibility to SARS-CoV-2 spreading, contributing to the differences in the distribution of the infection through different populations; additional studies suggested that the homolog of the HLA in cats, the feline leukocyte antigen (FLA), plays a pivotal role in the transmission of viruses. With these premises, this study aimed to exploit a bioinformatic approach for the prediction of the transmissibility potential of two distinct feline coronaviruses (FCoVs) in domestic cats (feline enteric coronavirus (FeCV) and feline infectious peritonitis virus (FIPV)) using SARS-CoV-2 as the reference model. We performed an epitope mapping of nonapeptides deriving from SARS-CoV-2, FeCV, and FIPV glycoproteins and predicted their affinities for different alleles included in the three main loci in class I FLAs (E, H, and K). The predicted complexes with the most promising affinities were then subjected to molecular docking and molecular dynamics simulations to provide insights into the stability and binding energies in the cleft. Results showed the FLA proteins encoded by alleles in the FLA-I H (H*00501 and H*00401) and E (E*01001 and E*00701) loci are largely responsive to several epitopes deriving from replicase and spike proteins of the analyzed coronaviruses. The analysis of the most affine epitope sequences resulting from the prediction can stimulate the development of anti-FCoV immunomodulatory strategies based on peptide drugs.

Keywords: MHC; coronavirus; immunity system; peptides.

Figure 1

(A) Schematic representation of the MHC localization in the feline chromosome B2 (at the top) and the human chromosome 6 (at the bottom). (B) Superposition on the backbone atoms of two representative proteins encoded by class I HLA (orange ribbons) and FLA (blue ribbons).

Figure 2

Workflow of the investigation.

Figure 3

Sequence alignment of the peptides resulted in an EL score > 0.8 from NetMHCPan analysis. The frequency of finding the amino acid reported in the table in the corresponding position is indicated in a color scale (light orange for frequency > 10%, blue for frequency > 80%).

Figure 4

Cryo-EM structure of the moiety of SARS-CoV R1ab including the residues 4438–5337 (PDB ID: 6NUS [38]) in ribbon representation. The possible localization of _fipv-rEp4 is shown as blue CPK. The SARS-CoV R1ab sequence (UniProt ID: P0C6X7) aligned on FIPV R1ab (UniProt ID: Q98VG9, residues 4089–4988) reports 59.51% conserved residues in this domain and > 95% residues with similar chemical characteristics. The residues aligned reported at the bottom correspond to the moiety including _fipv-rEp4 (asterisk indicates conserved residues, colon indicates amino acids with high similarity, and dot indicates amino acids with low similarity).

Figure 5

Analysis of the possible epitope exposition in SARS-CoV-2 R1ab and FIPV R1ab in moieties predicted with AlphaFold2. The possible localization of the epitopes is shown as colored CPK.

Figure 6

(A) Cryo-EM structure of the monomer of SARS-CoV-2 S (PDB ID: 7WEB [39]) in ribbon representation. The possible localization of the FIPV S-deriving epitopes is shown in CPK visualization, while the actual localization of SARS-CoV-2 S-deriving epitopes is shown as transparent surfaces. The SARS-CoV-2 S sequence (UniProt ID: P0DTC2, residues 612–1206) aligned on FIPV S (UniProt ID: P10033, residues 760–1386) reports 35.47% conserved residues in this domain and >70% residues with similar chemical characteristics. The residues aligned reported in (B) correspond to the moieties including _fipv-sEp7, _fipv-sEp8, and _fipv-sEp9 (asterisk indicates conserved residues, colon indicates amino acids with high similarity, and dot indicates amino acids with low similarity). (C) Focus on the overlapping residues in the possible location of _fipv-sEp8 with the real location of _sars-sEp5.