Advances in Bioinformatics
Volume 2016 (2016), Article ID 5484972, 5 pages
http://dx.doi.org/10.1155/2016/5484972

Research Article

Prediction and In Silico Identification of Novel B-Cells and T-Cells Epitopes in the S1-Spike Glycoprotein of M41 and CR88 (793/B) Infectious Bronchitis Virus Serotypes for Application in Peptide Vaccines

Faruku Bande,1,2 Siti Suri Arshad,¹ Mohd Hair Bejo,1,3 Saeid Kadkhodaei,⁴ and Abdul Rahman Omar1,3

¹Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia
²Department of Veterinary Services, Ministry of Animal Health and Fisheries Development, PMB 2109, Usman Faruk Secretariat, Sokoto State, Nigeria
³Laboratory of Vaccine and Immunotherapeutic, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan, Malaysia
⁴Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 Serdang, Malaysia

Received 8 March 2016; Revised 30 May 2016; Accepted 1 August 2016

Academic Editor: Rita Casadio

Copyright © 2016 Faruku Bande et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract.

Bioinformatic analysis was used to predict antigenic B-cell and T-cell epitopes within the S1 glycoprotein of M41 and CR88 IBV strains. A conserved linear B-cell epitope peptide, , was identified in M41 IBV strains while three such epitopes types namely, , , and , were predicted in CR88 IBV strains. Analysis of MHCI binding peptides in M41 IBV strains revealed the presence of 15 antigenic peptides out of which 12 were highly conserved in 96–100% of the total M41 strains analysed. Interestingly three of these peptides, GGPITYKVM²⁰⁸, WFNSLSVSI³⁵⁶, and YLADAGLAI⁴⁷², relatively had high antigenicity index (>1.0). On the other hand, 11 MHCI binding epitope peptides were identified in CR88 IBV strains. Of these, five peptides were found to be highly conserved with a range between 90% and 97%. However, WFNSLSVSL³⁵⁸, SYNISAASV⁸⁸, and YNISAASVA⁸⁹ peptides comparably showed high antigenicity scores (>1.0). Combination of antigenic B-cells and T-cells peptides that are conserved across many strains as approach to evoke humoral and CTL immune response will potentially lead to a broad-based vaccine that could reduce the challenges in using live attenuated vaccine technology in the control of IBV infection in poultry.

1. Introduction

Infectious bronchitis virus (IBV) is a single stranded, enveloped RNA virus belonging to the family Coronaviridae, order Nidovirales [1]. The virus causes infectious bronchitis (IB), a contagious disease associated with huge economic loses in poultry industry worldwide [2]. Of major concern in the control of IB is the continued emergence of variant IBV strains that differ in terms of their tissue tropism, pathogenicity, and cross protection. Over the years, serological and molecular studies have been carried out extensively to determine the epidemiology of local IBV strains. Remarkably, both classical and variants IBV strains have been reported in different countries [3]. Among the widely identified IBV strains are IBV M41 (classical strain), originally recognized in USA [4, 5], and CR88 (variant strain otherwise known as 793/B or 4/91) which was first reported in Europe [3, 6, 7].

Over the years, control of IBV infection largely depends on vaccination using live attenuated and killed vaccines. However, one of the challenges with live attenuated IB vaccines is that such vaccines are reported to encourage mutation and recombination, thus leading to the emergence of new variant strains. Live attenuated vaccines have also been linked with reversion to virulence, severe disease, and increased mortality rate [8–10]. On the other hand, killed vaccines induce humoral but not cell mediated immune (CMI) response and in most cases require adjuvants as well as repeated boosting especially in laying chickens and breeder flocks. These challenges therefore necessitate the needs for novel broad vaccines for the control of IB in poultry [11]. To achieve this, stimulation of both humoral (B-cell) and cell mediated immune (CMI) responses is considered very essential for any candidate vaccine [12]. Neutralizing antibodies are important in removing freely circulating IB virus, whereas cytotoxic T- lymphocytes (CTL) response is crucial for the control and clearance of virally infected cells. The latter is achieved through MHCI immune surveillance as well as antigen presentations which is the function of MHCI molecule and both have been associated with the epitope within the S1 glycoprotein [13, 14]. While much has been documented on MHC restricted allele in human and mouse models, little information is available on the biological functions of these molecules in poultry [15]. A large binding groove of 2101 MHCI molecule identified in B21 chicken line is thought to confer conformational flexibility to the crucial Arg9 residue which allows remodeling of key peptide-binding sites and play a role in the resistance against poultry viral infections [16]. Chicken MHC B–F molecules have been structurally and functionally linked to mammalian MHC class I molecules and involved in antigen presentation to the CD8⁺ T lymphocytes, which is crucial in antiviral immune response [17]. Interestingly, the S1 glycoprotein of IBV (520 aa) contains different immune epitopes responsible for both antibodies and CTL-based immune responses, thus playing major protective role as viral antigenic determinant [18].

Currently, the use of peptide based DNA vaccines represents a novel strategy for addressing challenges associated with the control of viral infections [19, 20]. This technology may employ the use of in silico analysis to predict novel B-cells and T-cells immune epitopes for further use in their in vivo applications. One of the innovations in using this technology is the ability to incorporate several epitope peptides directed against different viruses and/or multiple virus strains into one single delivery system with the view to induce broad and specific immune response in single administration [11]. To date, only few epitope based peptide vaccines have been developed and evaluated against IB [20, 21]. The objective of this study therefore is to identify novel B-cells and T-cell epitopes within the S1 glycoprotein of M41 and CR88 IBV strains. The antigenicity of the predicted peptides was also evaluated.

2. Materials and Methods

2.1. Nucleotide Sequence Retrieval

Nucleotide sequences containing complete S1-gene of homologous to M41 and CR88 IBV strains were retrieved from NCBI database and translated into deduced amino acid sequences for further analysis. Consensus amino acid sequences from the two datasets (M41 and CR88) were used to predict B- and T-cells epitope peptides within S1 glycoprotein. The criteria used for the selection of M41 and CR88 were simply based on epidemiological relevance of the two strains in terms of their wide geographic distribution as classical and variant IBV strains, respectively. All sequences were assembled with Geneious® software R7 version [22]. The names and accession numbers of IBV sequences used in this study are presented in Supplementary File 1 in Supplementary Material available online at http://dx.doi.org/10.1155/2016/5484972.

2.2. Prediction of B-Cell Epitope

Epitopes associated with B-cells were predicted using the BepiPred epitope prediction server version 1.0 [23]. Similarly, antigenicity index of the predicted epitopes was analysed using VaxiJen v2.0 online antigen prediction tool http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html [22]. Prediction criteria were set at 75% classifier specificity and 20 epitope lengths with an overlap. The location of the predicted epitope within transmembrane regions was evaluated using TMHMM [24]. Only epitope present at the surface of the membrane was selected and further analysed for antigenicity. For this search, target organism was narrowed to viruses and only scores above 0.4 thresholds were considered as a good antigenic epitope. Further, conservancy analysis was carried out using IEDB tools available http://tools.immuneepitope.org/tools/conservancy/iedb_input [25].

2.3. Prediction of T-Cell Epitopes

The T-cell epitope prediction was carried out using ProPred-1 software which covers 47 MHC class-I alleles. Both proteasome and immune-proteasome were set at 5% threshold by MHC class I and only peptides with proteosomal cleavage site at the C terminus were considered [26].

2.4. Epitope Conservancy Analysis

Immune epitopes were analysed for conservancy and variability using IEDB conservation analysis tool: http://tools.immuneepitope.org/tools/conservancy/iedb_input [25].

3. Results

3.1. Nucleotide Sequence Retrieval

A total of 86 M41 and 72 CR88 IBV isolates were considered in this study. However, to build the consensus sequence, one isolate from each data set was removed due to some unidentified amino acid at one or two positions. The M41 IBV isolates were found to have an average nucleotides sequence length of 1614 (537 aa) while CR88 isolates had an average length of 1653 (553 aa).

3.2. B-Cell Epitope Prediction and Conservancy Analysis

Analysis of M41 associated linear B-cell epitopes revealed the presence of six unique B-cells peptides within the S1 glycoprotein. Of these, only YTSNETTDVTS175–185 peptide was found to be antigenic (Table 1).

Table 1: Predicted antigenic B-cells linear epitopes within the S1 glycoprotein sequence of M41 IBV strains.

Position
Peptides
Length
Antigenicity

S33–44
AFRPGPGWHL
10
0.1545

S52–66
SSESNNAGSSSGCT
14
0.0842

S83–92
MTAPSSGMAW
10
0.0728

S175–185
YTSNETTDVTS
11
0.6727

S403–421
KSGGSRIQTATEPPVITQH
19
0.2319

Peptides in italic represent antigenic epitope considered.

Analysis of transmembrane potentials within the M41 IBV S1 gene showed that the predicted linear B-cell epitopes interact with the outside surface membrane especially with maximum threshold occurring at amino acid positions 280 to 290 (Figure 1).

Figure 1: Predicted linear B-cells epitopes and their locations to the surface membrane (yellow) in M41 IBV strains. Note: maximum transmembrane interaction was observed at a threshold of 2.4 within amino acid positions 280 to 290.

Interestingly, conservancy analysis showed that YTSNETTDVTS175–185 peptide is common in 82.35% of the M41 strains. On the other hand, a total of six antigenic epitope peptides were predicted in CR88 IBV strains; however, three of these peptides, NETNNAGSVSDCTAGT54–69, VSNASPNSGGVD279–290, and HPKCNFRPENI328–338 were demonstrated to be antigenic (Table 2). Further, conservancy analysis showed that the three CR88 associated antigenic B-cell peptides had 39.44%, 84.5%, and 43.66% conservancy rates, respectively.

Table 2: Predicted antigenic B-cells linear epitopes found in the S1 glycoprotein sequence of CR88 IBV strains.

Epitope position
Peptides
Length
Antigenicity

S33–44
AFRPGPGWHL
10
0.1545

S54–69
NETNNAGSVSDCTAGT
16
0.4237

S83–92
MTVPPNGMSW
10
0.0306

S279–290
VSNASPNSGGVD
12
0.7396

S328–338
HPKCNFRPENI
11
1.9437

S405–414
KSDGSRIQTR
10
0.3178

Peptides in italic represent antigenic epitope.

As with the M41 IBV strains, most of these epitopes are shown to interact with the surface at varying threshold (yellow) as depicted in Figure 2.

Figure 2: Linear B-cells epitope and their interaction with the surface membrane (yellow) in CR88 IBV strains. Note: the high east transmembrane interaction was predicted at the threshold of about 1.9 within the amino acid positions 280–290.

3.3. Prediction of T-Cell Epitope and Conservancy Analysis

3.3.1. Prediction of MHC-I Binding Epitopes

In M41 IBV strains, a total of 21 MHCI peptides were predicted at different amino acid positions; however, 15 of these peptides were found to be antigenic at various conservancy rates (98.82–100%). Three epitope peptides, GGPITYKVM²⁰⁸, WFNSLSVSI³⁵⁶, and YLADAGLAI⁴⁷² relatively have high antigenicity index (>1.0) as compared to other peptides (Table 3).

Table 3: Prediction of MHCI binding epitopes in the S1 glycoprotein of M41 IBV strains and their characteristic antigenicity scores.

Epitope position
Peptide sequence
Conservancy %
Antigenicity scores

18
VTPLLLVTL
98.82
0.8935

19
TPLLLVTLL
9882
0.7935

176
VNNLTSVYL
98.82
0.6733

192
SNETTDVTS
82.35
0.6575

208
GGPITYKVM
100
1.3364

214
KVMREVKAL
80.00
0.4479

356
WFNSLSVSI
98.82
1.1016

387
AYSYGGPSL
49.41
0.9013

462
NVTDSAVSY
100
0.6936

465
DSAVSYNYL
100
0.9786

467
AVSYNYLAD
100
0.5294

470
YNYLADAGL
96.47
0.5650

471
NYLADAGLA
96.47
0.9234

472
YLADAGLAI
96.47
1.0681

513
FVVSGGKLV
98.82
0.6146

Note: only epitopes with 0.4 and above scores are presented.

In the case of CR88 IBV strains, 18 MHCI epitope binding peptides were predicted. Of these, 11 peptides were found to be antigenic with most of the epitopes having conservancy rate ranging from 52.11% to 94.37% except peptide occurring at position S69 which is conserved in only 8.45%. Interestingly, WFNSLSVSL³⁵⁸, SYNISAASV⁸⁸, and YNISAASVA⁸⁹ demonstrated high antigenicity index compared to other predicted peptides (Table 4).

Table 4: MHCI associated antigenic peptide predicted on the S1 glycoprotein of CR88 IBV strains.

Epitope position
Peptide sequence
Conservancy %
Antigenicity

S18
GKPLLLVTL
69.01
0.9669

S69
NETNNAGSV
8.45
0.5716

S88
SYNISAASV
52.11
1.1186

S89
YNISAASVA
52.11
1.1067

S216
KVMKEVKAL
90.14
0.432

S358
WFNSLSVSL
80.28
1.1441

S467
EATANYSYL
94.37
0.8157

S472
YSYLADGGL
94.37
0.512

S473
SYLADGGLA
94.37
0.8439

S474
YLADGGLAI
97.18
0.9277

S479
GLAILDTSG
94.37
0.4147

4. Discussion

The use of bioinformatic and/or in silico analyses to understand infectious diseases as well as to predict novel vaccine candidate has been recently extended to poultry [27, 28]. Most of the epitopes responsible for virus neutralization have been mapped to be located within the first and third quarters of the linear S1 glycoprotein [13, 16]. The present study identified novel B-cells and T-cells epitopes presence in the S1 glycoprotein of M41 and CR88 IBV strains. Predicted antigenic B-cell epitopes were found to be highly conserved and demonstrated strong transmembrane potentials which probably predicts regions of virus-cell interaction. Linear B-cells epitopes located within the S1 region have been reported to play a role in virus neutralization. Using a phage display library, Zou et al. [29] identified two neutralizing linear B-cells epitopes within the S1 glycoprotein.

Recent studies have shown that chicken MHCI genes are categorized into MHCI associated genes (B-F) and MHCII (B-L) associated B-G genes, probably found only in poultry. Remarkably, this study has identified 21 and 18 MHCI binding peptides located within the S1 glycoproteins of M41 and CR88 IBV strains, respectively. Chickens with MHC homozygous B12 and B19 are reported to be more susceptible to infection with IBV-Grey strains as compared with B2/B2 and B5/B5 haplotype which often resist infection [30]. Recently, Tan et al. [21] used 4, 12, 15, and 19 chicken MHCI haplotypes to predict 21 CTL-peptide candidates in Massachusetts and Australian T strains. The study revealed that the constructed poly-CTL-epitope DNA vaccine was capable of inducing protection in 90% of the vaccinated chicken following challenge with SH1208 IBV strain. In a different study, Tian et al., 2008 [31] have identified seven T- and B-cells epitopes within the IBV S1 and S2 and NP proteins chimeric DNA vaccine derived from these epitope was found to be associated with 80% protection rate. Interestingly, the regions through which B-cells and T-cells epitope were predicted in this study correspond to the IBV receptor binding domain (RBD) which play a role in sufficient binding as well as entry of IBV viruses [32]. Similarly, epitopes peptides found within RBD have been reported in different study to induce neutralizing antibody response, for example, against human coronavirus and mouse hepatitis virus [33, 34].

5. Conclusion

This study predicted novel antigenic B-cells and T-cell epitopes within the S1 glycoprotein of M41 and CR88 IBV strains. The characteristic antigenicity index as well as epitope conservancy rates demonstrates potentials of the identified epitope peptides as polyvalent synthetic or DNA-based peptide vaccine for application in the control of IBV infection. The use of such vaccines will likely reduce the challenges associated with live attenuated vaccines and allow broad coverage of the target IBV strains.

Competing Interests

The authors declared no conflict of interests regarding the present publication.

Acknowledgments

The authors would like to thank the Universiti Putra Malaysia and Ministry of Science, Technology and Innovation (MOSTI), Project no. 02-01-04-SF1070 for funding the research.

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