Identification by immunoinformatics of the B and T epitopes in F and HN proteins of Newcastle disease viruses isolated in Madagascar

doi:10.21203/rs.3.rs-5241453/v1

Although conventional vaccines are widely used, outbreaks of Newcastle disease (ND) are still observed in Madagascar. This situation encourages the search for a more effective vaccine against this disease. Therefore, this study aims to develop a "multi-epitopic vaccine" based on circulating strains of Newcastle disease virus (NDV). To achieve this, it focuses on identifying B and T epitopes present in the F and HN proteins of 12 NDV strains isolated in Madagascar, using immunoinformatics methods. The sequences of F and HN proteins are extracted from the NCBI database and analyzed using specialized servers such as Bepipred v2.0, NetMHIIpan 4.0, and NetCTL v1.2 to predict the epitopes. These epitopes are then evaluated for antigenicity, non-allergenicity, and localization in exo-membrane regions, using tools such as VaxiJen 2.0, AllerTop v2.0, and TMHMM v2.0. The results reveal the presence of 52 epitopes in the F proteins and 68 epitopes in the HN proteins, all located in the exo-membrane regions of NDV. These epitopes prove to be antigenic and non-allergenic, offering promising potential for the development of a multi-epitopic vaccine.

Bioinformatics

Newcatle Disease Virus

fusion protein

hemagglutinin-neuraminidase

epitopes

immunoinformatics

Newcastle disease (ND) is a highly contagious virosis that infects domestic poultry and other animals. It is caused by the Newcastle disease virus (NDV), belonging to the Orthoavulavirus genus, the Paramyxoviridae family and the Mononegavirales order [1]. Vaccination is the only effective strategy for preventing ND. In Madagascar, commercially available ND vaccines are generally based on strains belonging to genotypes II and III, whereas the NDV responsible for epizootics are genotype XI [2]. This situation reduces the efficacy of existing vaccines in terms of viral excretion [3]. The development of a new genotype-appropriate vaccine, based on antigens homologous to circulating strains, is therefore necessary to combat this viral shedding.

Genotype-adapted vaccines are generally produced using three approaches: (1) attenuation of a virulent strain by reverse genetics; (2) inactivation of a virulent strain circulating in the field; and (3) co-expression of F or HN proteins in vectors [4]. Although vaccines derived from these three approaches are considered safe and effective, their manufacturing processes are costly and time-consuming to complete [5]. To overcome these limitations, many researchers have focused on the development of "multi-epitope vaccines" combining epitopes capable of inducing a positive immune response against numerous virulent strains. Unlike previous approaches, the development of multi-epitope vaccines is rapid and inexpensive [6].

In order to develop a multi-epitopic vaccine based on NDV strains circulating in Madagascar, the present study first aims to identify all the B and T epitopes present in the F and HN proteins of NDV isolated in Madagascar, using immuno-informatic methods.

The prediction flow adopted is shown in Fig. 1.

Download sequences

Twelve F protein sequences and twelve HN protein sequences from NDV genotype XI from Madagascar were downloaded in FASTA format from the NCBI database (http://www.ncbi.nlm.nih.gov/protein). Details of these sequences are given in Table 1.

Table 1

List of sequences used in this study
Strains	Identification Number		Collection Date	References
Strains	F proteins	HN proteins	Collection Date	References
MG-1992	ADQ64395	ADQ64396	1992	[19]
MG-725	ADQ64389	ADQ64390	2008
MG-MEOLA	ADQ64398	ADQ64399	2008
MG-39	ADQ64401	ADQ64402	2008
MGMNJ	AGC23353	AGW43230	2009	[20]
MGF003C	AGC23347	AGW43224	2010
MGF082T	AGC23349	AGW43226	2010
MGF015C	AGC23348	AGW43225	2011
MGF120T	AGC23350	AGW43227	2011
MGF166	AGC23351	AGW43228	2011
MGF192C	AGC23352	AGW43229	2011
MGS1130T	AGC23354	AGW43231	2011

Prediction of continuous B epitopes

Continuous B-cell epitopes were predicted using the Bepipred2.0 Linear Epitope Prediction server (http://tools.iedb.org/bcell/) with a default threshold of 0.35. This server combines two different methods, including propensity scales for amino acids and the hidden Markov model [7]. In the results, only continuous B epitopes containing at least 6 amino acids are retained.

CTL epitope prediction

The NetCTLv1.2 server (https://www.cbs.dtu.dk/services/NetCTL/) was used to predict the cytotoxic T lymphocyte (CTL) epitopes present in the target proteins using the default threshold value of 0.75. The prediction is made using HLA alleles, as the immunocomputer servers do not possess chicken MHC alleles. In addition, three epitope characteristics including TAP transport efficiency, C-terminal cleavage and MHC-I binding peptides were combined in the prediction [8]. CTL epitopes with a combined score ≤ 1.0 percentile rank were selected.

HTL epitope prediction

The NetMHCIIpan4.0 server (http://www.cbs.dtu.dk/services/NetMHCIIpan/) was used to predict T helper lymphocyte (HTL) epitopes in F and HN proteins. This server predicted peptide binding to all HLA-II alleles (HLA-DR, HLA-DQ, HLA-DP), using artificial neural networks [9]. Peptide length was set at 15-mer and other parameters were used by default.

Analysis of antigenicity, allergenicity and membrane topology of epitopes

The antigenicity of predicted epitopes was analyzed with the VaxiJen v2.0 server (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html) using a threshold of 0.4 [10]. In addition, the allergenicity and membrane topology of epitopes found to be antigenic are respectively analyzed in the AllerTOP v2.0 server (https://www.ddg-pharmfac.net/AllerTOP/) [11] and TMHMM v.20 (https://services.healthtech.dtu.dk/services/TMHMM-2.0/) [12].

Results and interpretation

Identification of continuous B epitopes

BepiPred 2.0 proposed 150 continuous B epitopes, including 72 for F proteins and 78 for HN proteins. However, only 18 of these 150 predicted continuous B epitopes (5 for F proteins and 13 for HN proteins) were found to be antigenic, non-allergenic and localized in the exo-membrane region (Table 2). Of these, the epitopes E1 and E15 are respectively the most antigenic in F and HN proteins. The continuous B epitopes identified in HN proteins are more numerous than those identified in F proteins.

Table 2

Continuous B epitopes in NDV F and HN proteins
Proteins	Epitope	Position	Peptide	Score VaxiJen	Allergenicity	Membrane topology
F protein	E₁	29–36	TSSLDGRP	1,3312	NA	EM
	E₂	222–232	GPQITSPALTQ	0,4337	NA	EM
	E₃	222–233	GPQITSPALTQL	0,4637	NA	EM
	E₄	250–262	LTKLGVGNNQLSS	0,7468	NA	EM
	E₅	349–357	RVVTFPMSP	0,6366	NA	EM
HN protein	E₆	52–79	TPGDLAGIPTEISRAEERITSTLSSNRD	0,4949	NA	EM
	E₇	52–79	TPGDLAGIPTEITRAEERITSALSSNR*	0,5048	NA	EM
	E₈	52–80	TPGDLAGIPTEISRAEERITSTLSSNRDV	0,4563	NA	EM
	E₉	52–80	TPGDLAGIPTEISRAEERITSTLSSNRDI*	0,4749	NA	EM
	E₁₀	108–170	TSLSYQINGAANNSGCGAPVHDPDYIGGIGKELIVDDTSEVTSFYPSAFQEHLNFIPAPTTGS	0,4673	NA	EM
	E₁₁	108–170	TSLSYQINGAANTSGCGAPVHDPDYIGGIGKELIIDDTSEVTSFYPSAFQEHLNFIPAPTTGS*	0,4377	NA	EM
	E₁₂	108–171	TSLSYQINGAANNSGCGAPVHDPDYIGGIGKELIVDDTSEVTSFYPSAFQEHLNFIPAPTTGSG	0,4415	NA	EM
	E₁₃	109–171	SLSYQINGAANNSGCGAPVHDPDYIGGIGKELIVDDTSEVTSFYPSAFQEHLNFIPAPTTGSG	0,4226	NA	EM
	E₁₄	161–170	NFIPAPTTGS	0,7259	NA	EM
	E₁₅	280–292	QYHEKDLDVITLF	0,7614	NA	EM
	E₁₆	321–364	KPNSPSDIAQEGRYVIYKRYNDTCPDEQDYQIRMAKSSYKPGRF	0,6749	NA	EM
	E₁₇	321–364	KPNSLSDIAQEGRYVIYKRYNDTCPDEQDYQIRMAKSSYKPERF*	0,7293	NA	EM
	E₁₈	380–385	TSLGED	0,6376	NA	EM

(*) = Mutant epitopes, NA = Non-allergenic, EM = Exo-membrane

Identification of CTL epitopes

NetCTLv1.2 predicted 364 CTL epitopes, including 161 in F proteins and 203 in HN proteins. Of these, only 74 CTL epitopes (35 in F proteins and 39 in HN proteins) are antigenic, non-allergenic, non-toxic and located in the exo-membrane region (Table 3). Of these, the E epitopes 44 and E71 are the most antigenic in F and HN proteins respectively. Thus, CTL epitopes identified in HN proteins are more numerous than those identified in F proteins.

Table 3

CTL epitopes in NDV F and HN proteins
Proteins	Epitope	Position	Peptide	Score VaxiJen	Allergenicity	Membrane topology
F protein	E₁₉	12–20	FPMPTVLIV	0,4136	NA	EM
	E₂₀	19–27	IVLALGCVR	1,2102	NA	EM
	E₂₁	20–28	VLALGCVRL	1,3961	NA	EM
	E₂₂	35–43	RPLAAAGIV	0,4797	NA	EM
	E₂₃	117–125	FVGAVIGSV	0,4429	NA	EM
	E₂₄	119–127	GAVIGSVAL	0,7104	NA	EM
	E₂₅	119–127	GAIIGSVAL*	0,5387	NA	EM
	E₂₆	121–129	VIGSVALGV	1,1096	NA	EM
	E₂₇	121–129	IIGSVALGV*	0,9459	NA	EM
	E₂₈	205–213	QVGVELSLY	0,8613	NA	EM
	E₂₉	212–220	LYLTELTTV	0,8958	NA	EM
	E₃₀	227–235	SPALTQLTI	0,9003	NA	EM
	E₃₁	240–248	NLAGSNMDY	0,8480	NA	EM
	E₃₂	245–253	NMDYLLTKL	0,7282	NA	EM
	E₃₃	300–308	ATYLETLSV	0,4129	NA	EM
	E₃₄	329–337	VIEELDTSY	0,5085	NA	EM
	E₃₅	379–387	LTTPYLTLK	0,7754	NA	EM
	E₃₆	383–391	YLTLKGSVI	0,6714	NA	EM
	E₃₇	427–435	LSLDGITLR	0,8224	NA	EM
	E₃₈	428–436	SLDGITLRL	0,5295	NA	EM
	E₃₉	432–440	ITLRLSGEF	0,7007	NA	EM
	E₄₀	504–512	YIVLTVVSL	1,2955	NA	EM
	E₄₁	505–513	IVLTVVSLV	1,1583	NA	EM
	E₄₂	506–514	VLTVVSLVF	0,9971	NA	EM
	E₄₃	509–517	VVSLVFGML	1,0571	NA	EM
	E₄₄	511–519	SLVFGMLSL	1,6161	NA	EM
	E₄₅	512–520	LVFGMLSLV	1,4689	NA	EM
	E₄₆	513–521	VFGMLSLVL*	0,9617	NA	EM
	E₄₇	513–521	VFGVLSLVL	0,8891	NA	EM
	E₄₈	516–524	MLSLVLICY*	1,2434	NA	EM
	E₄₉	516–524	VLSLVLICY	1,0715	NA	EM
	E₅₀	517–525	LSLVLICYL	1,2555	NA	EM
	E₅₁	518–518	SLVLICYLM	0,8804	NA	EM
	E₅₂	519–527	LVLICYLMY	0,7853	NA	EM
	E₅₃	536–544	LLWLGNNTL	0,4064	NA	EM
HN protein	E₅₄	22–30	RLAFRIAIL	1,2391	NA	EM
	E₅₅	22–30	RLAFRISIL*	1,3115	NA	EM
	E₅₆	23–31	LAFRIAILL	1,1265	NA	EM
	E₅₇	23–31	LAFRISILL*	1,1814	NA	EM
	E₅₈	25–33	FRIAILLLI	0,6820	NA	EM
	E₅₉	25–33	FRISILLLI*	0,7761	NA	EM
	E₆₀	29–37	ILLLITIIL	0,4397	NA	EM
	E₆₁	29–37	ILLLITITL*	1,0588	NA	EM
	E₆₂	30–38	LLLITIILA	0,4607	NA	EM
	E₆₃	30–38	LLLITITLA*	1,1094	NA	EM
	E₆₄	31–39	LLITIILAL	0,4530	NA	EM
	E₆₅	31–39	LLITITLAL*	0,9878	NA	EM
	E₆₆	36–44	ILALSTATL	0,5396	NA	EM
	E₆₇	36–44	TLALSTAAL*	0,4753	NA	EM
	E₆₈	95–103	ALLSTESVI	0,5043	NA	EM
	E₆₉	132–140	YIGGIGKEL	0,7564	NA	EM
	E₇₀	148–156	VTSFYPSAF	0,4192	NA	EM
	E₇₁	177–185	SFDISATHY	1,7398	NA	EM
	E₇₂	203–211	HQYLAIGVL	1,4544	NA	EM
	E₇₃	203–211	HQYLALGVL*	1,4158	NA	EM
	E₇₄	205–213	YLALGVLRT	1,1717	NA	EM
	E₇₅	273–281	GRLGFDGQY	1,9611	NA	EM
	E₇₆	274–282	RLGFDGQYH	1,3727	NA	EM
	E₇₇	281–289	YHEKDLDVI	1,3509	NA	EM
	E₇₈	299–307	YPGVGGGSF	1,0615	NA	EM
	E₇₉	312–320	VWFPVYGGL	0,4965	NA	EM
	E₈₀	321–329	KPNSPSDIA	0,5389	NA	EM
	E₈₁	321–329	KPSSPSDIA*	0,7347	NA	EM
	E₈₂	390–398	VSPNTVTLM	0,6229	NA	EM
	E₈₃	397–405	LMGAEGRVL	0,4415	NA	EM
	E₈₄	405–412	LTVGTSHFL	0,6614	NA	EM
	E₈₅	406–413	TVGTSHFLY	0,5265	NA	EM
	E₈₆	418–426	SSYFSPALL	0,7036	NA	EM
	E₈₇	419–427	SYFSPALLY	0,6322	NA	EM
	E₈₈	468–476	GVYTDPYPL	0,6599	NA	EM
	E₈₉	469–477	VYTDPYPLV	0,6099	NA	EM
	E₉₀	470–478	YTDPYPLVF	1,0589	NA	EM
	E₉₁	551–559	TLFGEFRIV	0,4567	NA	EM
	E₉₂	557–565	RIVPLLVEI	1,1852	NA	EM

(*) = Mutant epitopes, NA = Non-allergenic, EM = Exo-membrane

Identification of HTL epitopes

NetMHCIIpan 4.0 predicted 157 HTL epitopes, including 72 in F proteins and 85 in HN proteins. However, only 28 HTL epitopes (12 in F proteins and 16 in HN proteins) are antigenic, non-allergenic, non-toxic and localized in exo-membrane regions (Table 4). Of these, the E epitopes 93 and E111 are the most antigenic in F and HN proteins respectively. Thus, the HTL epitopes identified in HN proteins are more numerous than those identified in F proteins.

Tableau 4 : Les épitopes HTL dans les protéines F et HN de VMN

Proteins	Epitope	Position	Peptide	Score VaxiJen	Allergenicity	Membrane topology
F protein	E₉₃	8–22	WIPISPMPTILIALA	0,8658	NA	EM
	E₉₄	8–22	WIPIFPMPTVLIVLA*	0,4612	NA	EM
	E₉₅	34–48	GRPLAAAGIVVTGDK	0,4569	NA	EM
	E₉₆	35–49	RPLAAAGIVVTGDKA	0,5427	NA	EM
	E₉₇	118–132	VGAIIGSVALGVATA	0,8164	NA	EM
	E₉₈	126–139	ALGVATAAQITAAAA	0,8498	NA	EM
	E₉₉	235–249	IQALYNLAGSNMDYL	0,4999	NA	EM
	E₁₀₀	318–332	LVPKVVTQVGSVIEE	0,4500	NA	EM
	E₁₀₁	323–337	VTQVGSVIEELDTSH	0,6443	NA	EM
	E₁₀₂	452–466	DSQVIVTGNLDISTE	0,5541	NA	EM
	E₁₀₃	452–466	DSQVIVTGNLDISAE*	0,7456	NA	EM
	E₁₀₄	532–546	QQKTLLWLGNNTLDQ	0,4601	NA	EM
HN protein	E₁₀₅	43–57	ALIYSMEASTPGDLA	0,4307	NA	EM
	E₁₀₆	53–67	PGDLAGIPTEITRAE	0,4359	NA	EM
	E₁₀₇	129–143	DPDYIGGIGKELIVD	0,5995	NA	EM
	E₁₀₈	129–143	DPDYIGGIGKELIID*	0,6788	NA	EM
	E₁₀₉	130–144	PDYIGGIGKELIIDD	0,4315	NA	EM
	E₁₁₀	157–171	QEHLNFIPAPTTGSG	0,9029	NA	EM
	E₁₁₁	202–216	SHQYLAIGVLRTSAT	0,9224	NA	EM
	E₁₁₂	202–216	SHQYLALGVLRTSA*	0,8896	NA	EM
	E₁₁₃	218–232	RVLFSTLRSINLDDN	0,6104	NA	EM
	E₁₁₄	218–232	RVFFSTLRSINLDDN*	0,4580	NA	EM
	E₁₁₅	221–235	FSTLRSINLDDNQNR	0,6869	NA	EM
	E₁₁₆	317–331	YGGLKPNSPSDIAQE	0,5425	NA	EM
	E₁₁₇	379–393	STSLSEDPVLTVSPN	0,6043	NA	EM
	E₁₁₈	475–489	PLVFHRNHTLRGVFG	0,5237	NA	EM
	E₁₁₉	499–513	LNPVSAVFDNIARSR	0,5124	NA	EM
	E₁₂₀	555–569	EFRIVPLLVEILKDG	0,7710	NA	EM

(*) = Mutant epitopes, NA = Non-allergenic, EM = Exo-membrane

In this study, the B and T epitopes present in the F and HN proteins of 12 NDV strains are identified by immunoinformatic methods. F and HN proteins were targeted because of their importance in the host immune response, and antibodies directed against these proteins can neutralize the virus [13]. In addition, the immunoinformatics method was chosen for its cost-effectiveness and speed compared with in vitro methods [14]. Researchers have also used it in their studies of NDV [15–17].

The criteria used to select the final epitopes are: (a) high antigenicity; (b) absence of allergenicity; and (c) localization in exo-membrane domains. Based on these criteria, the epitopes selected must be antigenic to induce effective humoral and cellular immune responses [6]. In addition, they must be non-allergenic to ensure that they do not provoke allergic reactions after administration [6]. Finally, they must be located in extra-membrane regions to be accessible to immune cells such as B and T lymphocytes.

As a result, 58 and 62 epitopes were respectively identified in the F and HN proteins of 12 NDV strains from Madagascar (Tableaux 2, 3 et 4). Remarkably, the number of epitopes discovered in HN proteins exceeds that found in F proteins, although previous studies have suggested that F protein is the main protective antigen of NDV and may provide more protective immunity than HN proteins [18]. This difference could be attributed to the relatively larger size of NDV HN proteins [18].

Most of these predicted epitopes have already been identified by other researchers in various virulent strains of NDV [15–17], and some have even been identified in vaccine strains [17]. Moreover, their prediction in this study as antigenic, non-allergenic and localized to the extra-membrane surface of the virus suggests that they could be exploited in the development of a broad-spectrum multi-epitopic vaccine against ND.

This study employs immunoinformatic methods to identify potential epitopes for epitopes relevant to a multi-epitopic vaccine, targeting the F and HN proteins of 12 strains of Newcastle disease virus from Madagascar. The results reveal the presence of 52 epitopes in the F protein and 68 epitopes in the HN protein. All these epitopes were found to be antigenic, non-allergenic and localized in exo-membrane regions. They could therefore be exploited in the future in silico and in vitro development of a multi-epitope vaccine against Newcastle disease.

Conflict of Interest

There is no conflict of interest to declare

Acknowledgements

The authors would like to thank IMVAVET for its support during the development of this work.

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The authors declare no competing interests.

Identification by immunoinformatics of the B and T epitopes in F and HN proteins of Newcastle disease viruses isolated in Madagascar

Status:

Version 1

Abstract

Figures

Introduction

Materials and methods

Download sequences

Prediction of continuous B epitopes

CTL epitope prediction

HTL epitope prediction

Analysis of antigenicity, allergenicity and membrane topology of epitopes

Results and interpretation

Identification of continuous B epitopes

(*) = Mutant epitopes, NA = Non-allergenic, EM = Exo-membrane

Identification of CTL epitopes

(*) = Mutant epitopes, NA = Non-allergenic, EM = Exo-membrane

Identification of HTL epitopes

Tableau 4 : Les épitopes HTL dans les protéines F et HN de VMN

(*) = Mutant epitopes, NA = Non-allergenic, EM = Exo-membrane

Discussion

Conclusion

Declarations

Conflict of Interest

Acknowledgements

References

Additional Declarations

Status:

Version 1