Determination of the epitopic peptides of fig mosaic virus and the single-chain variable fragment antibody by mass spectrometry

The study of antibody-antigen interactions, through epitope mapping, enhances our understanding of antibody neutralization and antigenic determinant recognition. Epitope mapping, employing monoclonal antibodies and mass spectrometry, has emerged as a rapid and precise method to investigate viral antigenic determinants. In this report, we propose an approach to improve the accuracy of epitopic peptide interaction rate recognition. To achieve this, we investigated the interaction between the nucleocapsid protein of fig mosaic virus (FMV-NP) and single-chain variable fragment antibodies (scFv-Ab). These scFv-Ab maintain high specificity similar to whole monoclonal antibodies, but they are smaller in size. We coupled this with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The experimental design involved using two different enzymes to digest FMV-NP separately. The resulting peptides were then incubated separately with the desired scFv-Ab at different incubation times and antibody concentrations. This allowed us to monitor the relative rate of epitopic peptide interaction with the antibody. The results demonstrated that, at a 1:1 ratio and after 2 h of interaction, the residues 122-136, 148-157, and 265-276 exhibited high-rate epitopic peptide binding, with reductions in peak intensity of 78%, 21%, and 22%, respectively. Conversely, the residues 250-264 showed low-rate binding, with a 15% reduction in peak intensity. This epitope mapping approach, utilizing scFv-Ab, two different enzymes, and various incubation times, offers a precise and dependable analysis for monitoring and recognizing the binding kinetics of antigenic determinants. Furthermore, this method can be applied to study any kind of antigens.

Effectiveness of repeated influenza vaccination among the elderly population with high annual vaccine uptake rates during the three consecutive A/H3N2 epidemics

BACKGROUND

Annually, about 80% of the Korean elderly aged ≥65 years receive influenza vaccination. Repeated annual vaccination has been suggested as an important factor of poor influenza vaccine effectiveness (VE), though reported conflicting results.

METHODS

During the consecutive A/H3N2-dominant influenza seasons between 2012 and 2015, we comparatively evaluated the VE (repeated vs. current season only) against laboratory-confirmed influenza, pneumonia and hospitalization in the elderly aged ≥65 years with influenza-like illness (ILI). Clinical and demographic data were collected prospectively, and vaccination status of prior and current seasons was verified using the immunization registry data of Korean Centers for Disease Control and Prevention.

RESULTS

During the first A/H3N2-dominant season in 2012-2013, influenza vaccine showed statistically significant effectiveness against influenza A infection only and when vaccinated in the current season only (VE 53%, 95% CI 15-77). In the latter two seasons (2013-2015 years), the adjusted VE for influenza A was indistinguishable between repeated vaccination and vaccination in the current season only.

CONCLUSION

During consecutive influenza A/H3N2 epidemics, poor influenza vaccine effectiveness may be more pronounced among the elderly population with a high annual vaccine uptake rate.

Computational analysis of envelope glycoproteins from diverse geographical isolates of bovine leukemia virus identifies highly conserved peptide motifs

BACKGROUND

Bovine leukemia virus (BLV) is a deltaretrovirus infecting bovine B cells and causing enzootic bovine leucosis. The SU or surface subunit, gp51, of its envelope glycoprotein is involved in receptor recognition and virion attachment. It contains the major neutralizing and CD4+ and CD8+ T cell epitopes found in naturally infected animals. In this study, we aimed to determine global variation and conservation within gp51 in the context of developing an effective global BLV vaccine.

RESULTS

A total of 256 sequences extracted from the NCBI database and collected in different parts of the world, were studied to identify conserved segments along the env gene sequences that encode the gp51 protein. Using the MEME server and the conserved DNA Region module for analysis within DnaSP, we identified six conserved segments, referred to as A-F, and five semi-conserved segments, referred to as G-K. The amino acid conservation ranged from 98.8 to 99.8% in conserved segments A to F, while segments G to K had 89.6-95.2% conserved amino acid sequence. Selection analysis of individual segments revealed that residues of conserved segments had undergone purifying selection, whereas, particular residues in the semi-conserved segments are currently undergoing positive selection, specifically at amino acid positions 48 in segment K, 74 in segment G, 82 in segment I, 133 and 142 in segment J, and residue 291 in segment H. Each of the codons for these six residues contain the most highly variable nucleotides within their respective semi-conserved segments.

CONCLUSIONS

The data described here show that the consensus amino acid sequence constitutes a strong candidate from which a global vaccine can be derived for use in countries where eradication by culling is not economically feasible. The most conserved segments overlap with amino acids in known immunodeterminants, specifically in epitopes D-D', E-E', CD8+ T-cell epitopes, neutralizing domain 1 and CD4+ T-cell epitopes. Two of the segments reported here represent unique segments that do not overlap with previously identified antigenic determinants. We propose that evidence of positive selection in some residues of the semi-conserved segments suggests that their variation is involved in viral strategy to escape immune surveillance of the host.

Emergence of antigenic variants within serotype A FMDV in the Middle East with antigenically critical amino acid substitutions

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The recent A-Iran-05 viruses circulating in the Middle East do not match with the existing vaccines.

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Full capsid sequence of 13 SIS-10 and SIS-12 viruses was generated.

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The r₁-values generated using antisera raised against two existing vaccines and a new vaccine.

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Amino acid changes in neutralizing antigenic sites 1, 2 and 4 were observed.

A new immunologically distinct strain (A-Iran-05) of foot-and-mouth disease virus serotype A emerged in the Middle East in 2003 that replaced the previously circulating strains (A-Iran-96 and A-Iran-99) in the region. This resulted in introduction of a new vaccine of this strain (A/TUR/2006) in 2006. Though this vaccine strain has been predominantly used to control FMD in the region, recent viruses isolated in 2012 and 2013 have shown antigenic drift and a poor match with it. In this study, we report the antigenic matching results and capsid sequence data of currently circulating viruses belonging to the SIS-10 and SIS-12 sub-lineages of A-Iran-05 (isolated in 2012 and 2013), highlighting the inadequacy of the currently used serotype A vaccines. Implications of these results in the context of FMD control in the Middle East are discussed.

An overview of bioinformatics tools for epitope prediction: implications on vaccine development

Exploitation of recombinant DNA and sequencing technologies has led to a new concept in vaccination in which isolated epitopes, capable of stimulating a specific immune response, have been identified and used to achieve advanced vaccine formulations; replacing those constituted by whole pathogen-formulations. In this context, bioinformatics approaches play a critical role on analyzing multiple genomes to select the protective epitopes in silico. It is conceived that cocktails of defined epitopes or chimeric protein arrangements, including the target epitopes, may provide a rationale design capable to elicit convenient humoral or cellular immune responses. This review presents a comprehensive compilation of the most advantageous online immunological software and searchable, in order to facilitate the design and development of vaccines. An outlook on how these tools are supporting vaccine development is presented. HIV and influenza have been taken as examples of promising developments on vaccination against hypervariable viruses. Perspectives in this field are also envisioned.

Genetic basis of antigenic variation in foot-and-mouth disease serotype A viruses from the Middle East

Foot-and-mouth disease viruses (FMDV) from serotype A exhibit high antigenic diversity. Within the Middle East, a strain called A-Iran-05 emerged in 2003, and subsequently replaced the A-Iran-96 and A-Iran-99 strains that were previously circulating in the region. Viruses from this strain did not serologically match with the established A/Iran/96 vaccine, although most early samples matched with the older A22/Iraq vaccine. However, many viruses from this strain collected after 2006 had poor serological match with the A22/Iraq vaccine necessitating the development of a new vaccine strain (A/TUR/2006). More recently, viruses from the region now exhibit lower cross-reactivity with the A/TUR/2006 antisera highlighting the inadequacy of the serotype A vaccines used in the region. In order to understand the genetic basis of these antigenic phenotypes, we have determined the full capsid sequence for 57 Middle Eastern viruses isolated between 1996 and 2011 and analysed these data in context of antigenic relationship (r1) values that were generated using antisera to A22/Iraq and A/TUR/2006. Comparisons of capsid sequences identified substitutions in neutralising antigenic sites (1, 2 and 4), which either individually or together underpin these observed antigenic phenotypes.

Molecular events leading to the creation of a pandemic influenza virus

Influenza A virus is a potent pathogen of annual respiratory illness with huge potential of causing occasional pandemics of catastrophic consequences. In April 2009, a novel, swine-origin influenza A H1N1/09 virus was identified in Mexico which continued to spread globally. This unique virus emerged from an avian, human, Eurasian swine viral strain and a North American swine strain belonging to the lineage of the 1930 swine virus. Till date H1N1/09 pandemic has been relatively mild and lacks the previously described molecular markers of influenza A pathogenicity and transmissibility. In this review, we will discuss the molecular and antigenic determinants of this virus and its designation as a low pathogenic strain, which carries the potential to develop into a devastating strain with subsequent mutations and reassortments.