Identification of a Newly Conserved SLA-II Epitope in a Structural Protein of Swine Influenza Virus

Baratelli, Massimiliano; Morgan, Sophie; Hemmink, Johanneke D.; Reid, Elizabeth; Carr, B. Veronica; Lefèvre, Eric A.; Montaner-Tarbes, Sergio; Charleston, Bryan; Fraile, Lorenzo; Tchilian, Elma; Montoya, María

doi:10.3389/fimmu.2020.02083

Cited by 3 publications

(2 citation statements)

References 29 publications

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“…Bioinformatic methods using a machine learning approach serve as an effective strategy to identify vaccine candidates for human (Guo et al 2022;Hajialibeigi et al 2021; Kibria et al 2022) and swine pathogens, including ASFV (Gao et al 2021), in uenza A virus (Baratelli et al 2020;Fan et al 2018), and porcine circovirus type 2 (Bandrick et al 2020). Machine learning methods used to identify epitopes in the design of multi-epitope vaccines consider the biological presentation and activation of ASFV epitopes.…”

Section: Introductionmentioning

confidence: 99%

Multi-epitope vaccine design of African swine fever virus considering T cell and B cell immunogenicity

Chen,

Ho,

et al. 2024

Preprint

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T and B cell activation are equally important in triggering and orchestrating adaptive host responses to design multi-epitope African swine fever virus (ASFV) vaccines. However, few design methods have considered the trade-off between T and B cell immunogenicity when identifying promising ASFV epitopes. This work proposed a novel Pareto front-based ASFV screening method PFAS to identify promising epitopes for designing multi-epitope vaccines utilizing five ASFV Georgia 2007/1 sequences. To accurately predict T cell immunogenicity, four scoring methods were used to estimate the T cell activation in the four stages, including proteasomal cleavage probability, transporter associated with antigen processing transport efficiency, class I binding affinity of the major histocompatibility complex, and CD8 + cytotoxic T cell immunogenicity. PFAS ranked promising epitopes using a Pareto front method considering T and B cell immunogenicity. The coefficient of determination between the Pareto ranks of multi-epitope vaccines and survival days of swine vaccinations was R2 = 0.95. Consequently, PFAS scored complete epitope profiles and identified 72 promising top-ranked epitopes, including 46 CD2v epitopes, two p30 epitopes, 10 p72 epitopes, and 14 pp220 epitopes. PFAS is the first method of using the Pareto front approach to identify promising epitopes that considers the objectives of maximizing both T and B cell immunogenicity. The top-ranked promising epitopes can be cost-effectively validated in vitro. The Pareto front approach can be adaptively applied to various epitope predictors for bacterial, viral and cancer vaccine developments. The MATLAB code of the Pareto front method was available at https://github.com/NYCU-ICLAB/PFAS.

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Section: Introductionmentioning

confidence: 99%

Multi-epitope vaccine design of African swine fever virus considering T cell and B cell immunogenicity

Chen,

Ho,

et al. 2024

Preprint

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“…As an animal model with a defined genetic background and limited heterozygosity, the inbred Babraham pig holds great potential for the research community, and several recent studies have used it to investigate immune responses in the pig while leveraging the breed’s minimal genomic variability (Lefevre et al 2012; Nicholls et al 2012; Nicholls et al 2016; Tungatt et al 2018; Baratelli et al 2020; Edmans et al 2021; Martini et al 2021). The breed was initially developed from commercial Large White pigs at The Babraham Institute (Cambridge, UK) in the 1970s as a model organism, and is currently the only extant large inbred pig breed available for research (Schwartz et al 2018).…”

Section: Introductionmentioning

confidence: 99%

A highly-contiguous genome assembly of the inbred Babraham pig (Sus scrofa) quantifies breed homozygosity and illuminates porcine immunogenetic variation

Schwartz,

Farrell,

Freimanis

et al. 2023

Preprint

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The inbred Babraham pig serves as a valuable biomedical model for research due to its high level of homozygosity, including in the major histocompatibility complex (MHC) loci and likely other important immune-related gene complexes, which are generally highly diverse in outbred populations. As the ability to control for this diversity using inbred organisms is of great utility, we sought to improve this resource by generating a long-read whole genome assembly of a Babraham pig. The Babraham genome wasde novoassembled using PacBio long-reads and error-corrected using Illumina short-reads. The assembled contigs were then mapped to the current porcine reference assembly, Sscrofa11.1, to generate chromosome-level scaffolds. The resulting Babraham pig assembly is nearly as contiguous as Sscrofa11.1 with a contig N50 of 34.95 Mb and contig L50 of 23. The remaining sequence gaps are generally the result of poor assembly across large and highly repetitive regions such as the centromeres and tandemly duplicated gene families, including immune-related gene complexes, that often vary in gene content between haplotypes. We also further confirm homozygosity across the Babraham pig MHC and characterize the allele content across several immune-related gene complexes, including the contiguous assemblies of the antibody heavy chain locus and leukocyte receptor complex. The Babraham pig genome assembly provides an alternate highly contiguous porcine genome assembly as a resource for the livestock genomics community. The assembly will also aid biomedical and veterinary research that utilizes this animal model such as when controlling for genetic variation is critical.

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A genome assembly and transcriptome atlas of the inbred Babraham pig to illuminate porcine immunogenetic variation

Schwartz,

Farrell,

Freimanis

et al. 2024

Immunogenetics

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The inbred Babraham pig serves as a valuable biomedical model for research due to its high level of homozygosity, including in the major histocompatibility complex (MHC) loci and likely other important immune-related gene complexes, which are generally highly diverse in outbred populations. As the ability to control for this diversity using inbred organisms is of great utility, we sought to improve this resource by generating a long-read whole genome assembly and transcriptome atlas of a Babraham pig. The genome was de novo assembled using PacBio long reads and error-corrected using Illumina short reads. Assembled contigs were then mapped to the porcine reference assembly, Sscrofa11.1, to generate chromosome-level scaffolds. The resulting TPI_Babraham_pig_v1 assembly is nearly as contiguous as Sscrofa11.1 with a contig N50 of 34.95 Mb and contig L50 of 23. The remaining sequence gaps are generally the result of poor assembly across large and highly repetitive regions such as the centromeres and tandemly duplicated gene families, including immune-related gene complexes, that often vary in gene content between haplotypes. We also further confirm homozygosity across the Babraham MHC and characterize the allele content and tissue expression of several other immune-related gene complexes, including the antibody and T cell receptor loci, the natural killer complex, and the leukocyte receptor complex. The Babraham pig genome assembly provides an alternate highly contiguous porcine genome assembly as a resource for the livestock genomics community. The assembly will also aid biomedical and veterinary research that utilizes this animal model such as when controlling for genetic variation is critical.

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Identification of a Newly Conserved SLA-II Epitope in a Structural Protein of Swine Influenza Virus

Cited by 3 publications

References 29 publications

Multi-epitope vaccine design of African swine fever virus considering T cell and B cell immunogenicity

Multi-epitope vaccine design of African swine fever virus considering T cell and B cell immunogenicity

A highly-contiguous genome assembly of the inbred Babraham pig (Sus scrofa) quantifies breed homozygosity and illuminates porcine immunogenetic variation

A genome assembly and transcriptome atlas of the inbred Babraham pig to illuminate porcine immunogenetic variation

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