Immunoinformatics approach for predicting epitopes in HN and F proteins of Porcine rubulavirus

Abstract

Porcine rubulavirus (PRV), which belongs to the family Paramyxoviridae, causes blue eye disease in pigs, characterized by encephalitis and reproductive failure in newborn and adult pigs, respectively. There is no effective treatment against PRV and no information on the effectiveness of the available vaccines. Continuous outbreaks have occurred in Mexico since the early 1980s, which have caused serious economic losses to pig producers. Vaccination can be used to control this disease. Searching for effective antigen candidates against PRV, we first sequenced the PAC1 F protein, then we used various immunoinformatics tools to predict antigenic determinants of B-cells and T-cells against the two glycoproteins of the virus (HN and F proteins). Finally, we used AutoDock Vina to determine the binding energies. We obtained the F gene sequence of a PRV strain collected in the early 1990s in Mexico and compared its amino acid profile with previous and more recent strains, obtaining an identity similarity of 97.78 to 99.26%. For the F proteins, seven linear B-cell epitopes, six conformational B-cell epitopes and twenty-nine T-cell MHC class I epitopes were predicted. For the HN proteins, sixteen linear B-cell epitopes, seven conformational B-cell epitopes and thirty-four T-cell MHC class I epitopes were predicted. The ATRSETDYY and AAYTTTTCF epitopes of the HN protein might be important for neutralizing the viral infection. We determined the in silico binding energy between the predicted epitopes on the F and HN proteins and swine MHC-I molecules. The binding energy of these epitopes ranged from-5.8 to-7.8 kcal/mol. The present study aimed to assess the use of HN and F proteins as antigens, either as recombinant proteins or as a series of peptides that could activate different responses of the immune system. This may help identify relevant immunogens, saving time and costs in the development of new vaccines or diagnostic tools.

Identification of Immunogenic Linear B-Cell Epitopes in C. burnetii Outer Membrane Proteins Using Immunoinformatics Approaches Reveals Potential Targets of Persistent Infections

“…As previously shown in Table 4, between 20% and 33% of responders to the epitopes OMP-H (51)(52)(53)(54)(55)(56)(57)(58)(59) , OMP-H (91-106) , Com-1 (57)(58)(59)(60)(61)(62)(63)(64)(65)(66)(67)(68)(69)(70)(71)(72)(73)(74)(75)(76) , Com-1 (191)(192)(193)(194)(195)(196)(197)(198)(199)(200)(201)(202)(203)(204)(205)(206) , and OMP-P1 (215-227) presented high levels of specific antibodies. Aiming to explore these data, we compared the clinical features of high responders (HR: RI > 2), low responders (LR: 1 > RI ≤ 2), and nonresponders (NR: RI ≤ 1) to each studied peptide.…”

“…Moreover, in the C. burnetii-reactive group, the frequencies of response against the epitopes OMP-H (51-59) (65%), OMP-H (91-106) (50%), Com-1 (57-76) (58%), Com-1 (191-206) (58%), and OMP-P1 (215-227) (15 responders; 58%) were higher than 50%. Moreover, the frequency of response to OMP-P1 (197-209) (23%) was statistically lower than the frequencies of response to OMP-H (51-59) (p = 0.0047), Com-1 (57)(58)(59)(60)(61)(62)(63)(64)(65)(66)(67)(68)(69)(70)(71)(72)(73)(74)(75)(76) , Com-1 (191)(192)(193)(194)(195)(196)(197)(198)(199)(200)(201)(202)(203)(204)(205)(206) , and OMP-P1 (215-227) (p = 0.0227) (Figure 2b). Despite these differences, we 2c).…”

“…The antigenicity of predicted linear epitopes was evaluated using the VaxiJen algorithm. Based on this evaluation, eight predicted epitopes were considered antigenic, among which were the four sequences predicted as linear B-cell epitopes by the three used algorithms (OMP-H (51)(52)(53)(54)(55)(56)(57)(58)(59) , OMP-H (98)(99)(100)(101)(102)(103)(104)(105)(106) , Com-1 (57)(58)(59)(60)(61)(62)(63)(64)(65)(66)(67)(68)(69)(70)(71)(72)(73)(74)(75)(76) , and Com-1 (191)(192)(193)(194)(195)(196)(197)(198)(199)(200)(201)(202)(203)(204)…”

“…Regarding the exposition of epitopes on protein quaternary structures, predicted epitopes OMP-H (51)(52)(53)(54)(55)(56)(57)(58)(59) and OMP-H (91-106) (Figure 1a,b), Com-1 (191-206) (Figure 1c,d), and OMP-P1 (197)(198)(199)(200)(201)(202)(203)(204)(205)(206)(207)(208)(209) and OMP-P1 (215-227) (Figure 1e,f) were exposed on the trimer surface, and did not interact with other chains in the oligomeric structure; meanwhile, the epitopes Com-1 (57)(58)(59)(60)(61)(62)(63)(64)(65)(66)(67)(68)(69)(70)(71)(72)(73)(74)(75)(76) , Com-1 (26-34) (Figure 1d), and OMP-P1 (98-106) (Figure 1e) presented, 25%, 78%, and 56%, respectively, of their sequences interacting with other chains when the predicted OMP trimeric structure was analyzed. Therefore, predicted epitopes Com-1 (26-34) (Figure 1d…”

Future perspectives on swine viral vaccines: where are we headed?

“…Pig vaccine applications to date have included viral infections such as IAV, PCV2, and ASFV [ 121 ]. Recently, this approach has also been utilized to predict epitopes and proteins for porcine rubulavirus [ 122 ].…”