Two novel neutralizing antigenic epitopes of the s1 subunit protein of a QX-like avian infectious bronchitis virus strain Sczy3 as revealed using a phage display peptide library

Revealing Novel-Strain-Specific and Shared Epitopes of Infectious Bronchitis Virus Spike Glycoprotein Using Chemical Linkage of Peptides onto Scaffolds Precision Epitope Mapping

The avian coronavirus, infectious bronchitis virus (IBV), is an economically important infectious disease affecting chickens, with a diverse range of serotypes found globally. The major surface protein, spike (S), has high diversity between serotypes, and amino acid differences in the S1 sub-unit are thought to be responsible for poor cross-protection afforded by vaccination. Here, we attempt to address this, by using epitope mapping technology to identify shared and serotype-specific immunogenic epitopes of the S glycoprotein of three major circulating strains of IBV, M41, QX, and 4/91, via CLIPS peptide arrays based on peptides from the S1 sub-units. The arrays were screened with sera from chickens immunised with recombinant IBV, based on Beau-R backbone expressing heterologous S, generated in two independent vaccination/challenge trials. The screening of sera from rIBV vaccination experiments led to the identification of 52 immunogenic epitopes on the S1 of M41, QX, and 4/91. The epitopes were assigned into six overlapping epitope binding regions. Based on accessibility and location in the hypervariable regions of S, three sequences, 25YVYYYQSAFRPPNGWHLQGGAYAVVNSTN54, 67TVGVIKDVYNQSVASI82, and 83AMTVPPAGMSWSVS96, were selected for further investigation, and synthetic peptide mimics were recognised by polyclonal sera. These epitopes may have the potential to contribute towards a broader cross-protective IBV vaccine.

Antigenic and molecular characterization of isolates of the Brazilian genotype BR-I (GI-11) of infectious bronchitis virus supports its recognition as BR-I serotype

The antigenic and molecular characteristics of BR-I infectious bronchitis viruses (IBVs) isolated from Brazil are reported. IBVs isolated from commercial flocks with different clinical manifestations between 2003 and 2019 were submitted to antigenic and molecular characterization. The complete S1 glycoprotein gene of 11 field isolates was amplified and sequenced. The virus neutralization (VN) test showed 94.75% neutralization with a BR-I isolate and 30% or less against other worldwide reference strains. The nucleotide and amino acid sequence analyses revealed 84.3-100% and 83.5-100% identity among them, respectively. The identity values ranged from 57.1 to 82.6% for nucleotides and from 46.6-84.4% for amino acids compared with those of other genotypes. By phylogenetic tree analysis, the Brazilian isolates were branched into the BR-I genotype (lineage GI-11), which was differentiated from foreign reference strains. Selective pressure analyses of BR-I IBVs revealed evolution under purifying selection (negative pressure) for the complete S1 gene but four specific sites (87, 121, 279, and 542) under diversifying selection (positive pressure). Profiles of cleavage sites and potential N-glycosylation sites differed from those of other genotypes. The low molecular relationship among the Brazilian viruses and foreign serotypes was concordant with the VN test results. The low antigenic relatedness (ranging from 5.3-30% between Brazilian genotype BR-I and reference IBV serotypes of North America, Europe, and Asia) indicates that the BR-I genotype is a different serotype, referred to for the first time and hereafter as serotype BR-I. RESEARCH HIGHLIGHTSStrains of the BR-I genotype presented robust antigenic and molecular similarity.BR-I strains evolved under purifying selection mode (negative pressure).The BR-I genotype originated in Brazil and dispersed to other countries.BR-I genotype viruses can be referred to as the BR-I serotype.

Filamentous bacteriophages, natural nanoparticles, for viral vaccine strategies

Filamentous bacteriophages are natural nanoparticles formed by the self-assembly of structural proteins that have the capability of replication and infection. They are used as a highly efficient vaccine platform to enhance immunogenicity and effectively stimulate the innate and adaptive immune response. Compared with traditional vaccines, phage-based vaccines offer thermodynamic stability, biocompatibility, homogeneity, high carrying capacity, self-assembly, scalability, and low toxicity. This review summarizes recent research on phage-based vaccines in virus prevention. In addition, the expression systems of filamentous phage-based virus vaccines and their application principles are discussed. Moreover, the prospect of the prevention of emerging infectious diseases, such as coronavirus 2019 (COVID-19), is also discussed.

Bacterial artificial chromosome-based reverse genetics system for cloning and manipulation of the full-length genome of infectious bronchitis virus

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Reverse genetics system to clone attenuated IBV C-78 full-length genome in a BAC.

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Rescued virus from BAC-cloned C-78 show parental virus properties.

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Genetic manipulation of BAC-cloned C-78 using Red-mediated recombination in E. coli.

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Construction of S gene recombinant C-78 by swapping with the S gene of virulent IBV.

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S gene determines neutralization specificity but not virulence and tissue-tropism.

Avian infectious bronchitis virus (IBV) causes highly contagious respiratory reproductive and renal system diseases in chickens, and emergence of serotypic variants resulting from mutations in the viral S gene hampers vaccine management for IBV infection. In this study, to facilitate the molecular analysis of IBV pathogenesis and the development of a new-generation IBV vaccine, we established a reverse genetics system (RGS) for cloning the full-length cDNA of the IBV C-78E128 attenuated strain in a bacterial artificial chromosome (BAC). The BAC-cloned C-78E128 cDNA generated infectious viruses with biological properties of the parental C-78E128 strain with regard to an avirulent phenotype, tissue tropism and induction of virus neutralizing (VN) antibody in vivo. To assess the feasibility of genetic manipulation of the IBV genome using the BAC-based RGS, the S gene of the BAC-cloned C-78E128 cDNA was replaced with that of the IBV S95E4 virulent strain, which differs from the C-78E128 strain in serotype and tissue tropism, by bacteriophage lambda Red-mediated homologous recombination in Escherichia coli (E. coli). The resultant S gene recombinant virus was found to be avirulent and fully competent to induce a serotype-specific VN antibody against the S95 strain; however, the S gene recombinant virus did not fully recapitulate the tissue tropism of the S95E4 strain. These data imply that serotype-specific VN immunogenicity, but not tissue-tropism and pathogenicity, of IBV is determined by the viral S gene. The IBV BAC-based RGS that enables cloning and manipulation of the IBV virus genome entirely in E. coli provides a useful platform for the molecular analyses of IBV pathogenesis and the development of rationally designed IBV recombinant vaccines.

Phage Display Technique as a Tool for Diagnosis and Antibody Selection for Coronaviruses

Phage display is one of the important and effective molecular biology techniques and has remained indispensable for research community since its discovery in the year 1985. As a large number of nucleotide fragments may be cloned into the phage genome, a phage library may harbour millions or sometimes billions of unique and distinctive displayed peptide ligands. The ligand–receptor interactions forming the basis of phage display have been well utilized in epitope mapping and antigen presentation on the surface of bacteriophages for screening novel vaccine candidates by using affinity selection-based strategy called biopanning. This versatile technique has been modified tremendously over last three decades, leading to generation of different platforms for combinatorial peptide display. The translation of new diagnostic tools thus developed has been used in situations arising due to pathogenic microbes, including bacteria and deadly viruses, such as Zika, Ebola, Hendra, Nipah, Hanta, MERS and SARS. In the current situation of pandemic of Coronavirus disease (COVID-19), a search for neutralizing antibodies is motivating the researchers to find therapeutic candidates against novel SARS-CoV-2. As phage display is an important technique for antibody selection, this review presents a concise summary of the very recent applications of phage display technique with a special reference to progress in diagnostics and therapeutics for coronavirus diseases. Hopefully, this technique can complement studies on host–pathogen interactions and assist novel strategies of drug discovery for coronaviruses.

Peptide enzyme-linked immunosorbent assay (pELISA) as a possible alternative to the neutralization test for evaluating the immune response to IBV vaccine

BACKGROUND

Infectious bronchitis virus (IBV), a coronavirus, is one of the most important poultry pathogens worldwide due to its multiple serotypes and poor cross-protection. Vaccination plays a vital role in controlling the disease. The efficacy of vaccination in chicken flocks can be evaluated by detecting neutralizing antibodies with the neutralization test. However there are no simple and rapid methods for detecting the neutralizing antibodies.

RESULTS

In this study, a peptide enzyme-linked immunosorbent assay (pELISA) as a possible alternative to the neutralization test for evaluating the immune response to IBV vaccine was developed. The pELISA could indirect evaluate neutralizing antibody titers against different types of IBV in all tested sera. The titers measured with the pELISA had a coefficient of 0.83 for neutralizing antibody titers.

CONCLUSIONS

The pELISA could detect antibodies against different types of IBV in all tested sera. The pELISA has the potential to evaluate samples for IBV-specific neutralizing antibodies and surveillance the infection of IBV.

Antigenic and Pathogenic Characteristics of QX-Type Avian Infectious Bronchitis Virus Strains Isolated in Southwestern China

The QX-type avian infectious bronchitis virus (IBV) is still a prevalent genotype in Southwestern China. To analyze the antigenicity and pathogenicity characteristics of the dominant genotype strains (QX-type), S1 gene sequence analysis, virus cross-neutralization tests, and pathogenicity test of eight QX-type IBV isolates were conducted. Sequence analysis showed that the nucleotide homology between the eight strains was high, but distantly related to H120 and 4/91 vaccine strains. Cross-neutralization tests showed that all eight strains isolated from 2015 and 2017 belonged to the same serotype, but exhibited antigenic variations over time. The pathogenicity test of the five QX-type IBV isolates showed that only three strains, CK/CH/SC/DYW/16, CK/CH/SC/MS/17, and CK/CH/SC/GH/15, had a high mortality rate with strong respiratory and renal pathogenicity, whereas CK/CH/SC/PZ/17 and CK/CH/SC/DYYJ/17 caused only mild clinical symptoms and tissue lesions. Our results indicate that the prevalent QX-type IBVs displayed antigenic variations and pathogenicity difference. These findings may provide reference for research on the evolution of IBV and vaccine preparation of infectious bronchitis (IB).

Evolution of infectious bronchitis virus in the field after homologous vaccination introduction

Despite the fact that vaccine resistance has been typically considered a rare phenomenon, some episodes of vaccine failure have been reported with increasing frequency in intensively-raised livestock. Infectious bronchitis virus (IBV) is a widespread avian coronavirus, whose control relies mainly on extensive vaccine administration. Unfortunately, the continuous emergence of new vaccine-immunity escaping variants prompts the development of new vaccines. In the present work, a molecular epidemiology study was performed to evaluate the potential role of homologous vaccination in driving IBV evolution. This was undertaken by assessing IBV viral RNA sequences from the ORF encoding the S1 portion of viral surface glycoprotein (S) before and after the introduction of a new live vaccine on broiler farms in northern-Italy. The results of several biostatistics analyses consistently demonstrate the presence of a higher pressure in the post-vaccination period. Natural selection was detected essentially on sites located on the protein surface, within or nearby domains involved in viral attachment or related functions. This evidence strongly supports the action of vaccine-induced immunity in conditioning viral evolution, potentially leading to the emergence of new vaccine-escape variants. The great plasticity of rapidly-evolving RNA-viruses in response to human intervention, which extends beyond the poultry industry, is demonstrated, claiming further attention due to their relevance for animal and especially human health.

Peptides with 16R in S2 protein showed broad reactions with sera against different types of infectious bronchitis viruses

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We examined the specific amino acids contributing to S2 epitopes in IBVs.

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16R in S2 protein was a key amino acid mediating the antigenicity of S2 protein.

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S2-derived peptides with 16R, but not those with 16 K, reacted with IBV-infected serum.

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Commercial ELISAs did not react with sera harboring all types of IBVs.

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S2-derived peptides with 16R could be novel antigens for anti-IBV vaccines.

Vaccination plays a vital role in controlling diseases caused by chicken infectious bronchitis virus (IBV). The continuously variant antigenicity of IBV limits the application of current vaccine strategies and serological diagnostic systems. S2 protein is an invariant that harbors broad neutralizing epitopes. However, little is known about the key amino acids that contribute to the broad-spectrum S2 epitopes. In this study, we aimed to elucidate the specific amino acids contributing to S2 epitopes. Site mutagenesis and peptide-based enzyme-linked immunosorbent assays (ELISAs) showed that 16R in S2 protein was a key amino acid mediating the antigenicity of S2 protein. S2-derived peptides with 16R, but not those with 16 K, could react with sera against different types of IBVs. Notably, a commercial ELISA kit for detection of antibodies against IBV did not react with sera against all types of IBVs. Taken together, these data demonstrated that S2-derived peptides with 16R could be used as novel marker-based antigens for developing both broad-spectrum vaccines and serological diagnostic kits to control IBV.

Evaluation of the genetic variability found in Brazilian commercial vaccines for infectious bronchitis virus

Infectious bronchitis virus (IBV) is currently one of the most important pathogens in the poultry industry. The H120 and Ma5 are the only viral strains approved by the Brazilian government as the constituent of vaccines. Despite the systematic vaccination in Brazil, IBV has not yet been controlled and diseases associated with this virus have been reported in vaccinated chickens. Here, we investigated the genetic variability of H120 and Ma5 strains present in the IBV vaccines from different Brazilian manufacturers. We performed DNA sequencing analyses of the S1 spike glycoprotein gene to investigate its genetic variability and the presence of viral subpopulations among vaccines, between batches, and also in each vaccine after a single passage was performed in chicken embryonated eggs. Our results revealed up to 13 amino acid substitutions among vaccines and some of them were localized in regions of the S1 glycoprotein that play a role in virus-host interaction. Secondary nucleotide peaks identified in the chromatogram for the S1 gene sequence revealed that all original vaccines (H120 and Ma5) were composed by different subpopulations of IBV. Moreover, new viral subpopulations were also found in vaccines after a single passage in chicken embryonated eggs. These findings indicate that H120 and Ma5 viral strains used in vaccines market in Brazil can still mutate very rapidly during replication, leading to amino acid substitutions in proteins involved in the stimulation of the immune response, such as the S1 glycoprotein. Therefore, our data suggest that the genetic variability of these viral strains should be taken into consideration to ensure an effective immune response against IBV.

Infectious bronchitis virus poly-epitope-based vaccine protects chickens from acute infection

Infectious bronchitis virus (IBV) causes major losses in the poultry industry. The safe and effective vaccine to control IBV spread is imperative. In the present study, we developed IBV S1 glycoprotein poly-epitope-based DNA vaccine pV-S1B+S1T consisting of SH1208 and Holte strain BF2-restricted T cell epitopes and Australian T strain dominant B cell neutralization epitopes. Specific pathogen-free chickens were vaccinated with pV-S1B+S1T and control plasmids twice to elicit strong humoral and cellular immune response, as indicated by viral neutralization titers and results of CD8⁺ T cell proliferation assays. A lethal dose of IBV SH1208 strain used for protection and challenge experiments at two weeks post-booster immunization following challenge protection and virus shedding reverse transcription quantitative PCR assay, indicated that pV-S1B+S1T protected against IBV and significantly reduced viral excretion. These results demonstrated that the IBV poly-epitope-based vaccine effectively prevents infection and represents a potential IBV vaccine.

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

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, YTSNETTDVTS^175–185, was identified in M41 IBV strains while three such epitopes types namely, VSNASPNSGGVD^279–290, HPKCNFRPENI^328–338, and NETNNAGSVSDCTAGT^54–69, 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.

Phylogenetic and antigenic analysis of avian infectious bronchitis virus in southwestern China, 2012-2016

The aim of this study was to decipher the molecular epidemiological and antigenic characteristics of infectious bronchitis virus strains (IBVs) isolated in recent years in southwestern China. A total of 24 field strains were isolated from diseased chickens between 2012 and 2016. Phylogenetic analysis based on S1 nucleotide sequences showed that 16 of the 24 isolates were clustered into four distinct genotypes: QX (37.5%), TW (16.7%, TWI and TWII), Mass (8.3%), and J2 (4.2%). The QX genotype was still the prevalent genotype in southwestern China. Recombination analysis of the S1 subunit gene showed that eight of the 24 field strains were recombinant variants that originated from field strains and vaccine strains. A new potential recombination hotspot [ATTTT(T/A)] was identified, implying that recombination events may become more and more common. The antigenicity of ten IBVs, including seven field strains and commonly used vaccine strains, were assayed with a viral cross-neutralization assay in chicken embryonated kidney cells (CEK). The results showed that the ten IBVs could be divided into four serotypes (Massachusetts, 793B, Sczy3, and SCYB). Sczy3 and 793B were the predominant serotypes. Six of the seven field isolates (all except for cK/CH/SCYB/140913) cross-reacted well with anti-sera against other field strains. In conclusion, the genetic and antigenic features of IBVs from southwestern China in recent years have changed when compared to the previous reports. The results could provide a reference for vaccine development and the prevention of infectious bronchitis in southwestern China.

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The QX genotype was still the prevalent genotype in southwestern China, 2012–2016.

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The Sczy3 and 793B were the predominant serotypes in analyzed IBVs.

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A new potential recombination hotspot [ATTTT(T/A)] in S1 gene was identified.