Working Paper Article Version 1 This version is not peer-reviewed

Quantifying the Persistence of Vaccine-related T cell Epitopes in Circulating Swine Influenza A Strains from 2013-2017

Version 1 : Received: 16 March 2021 / Approved: 17 March 2021 / Online: 17 March 2021 (10:55:56 CET)

A peer-reviewed article of this Preprint also exists.

Journal reference: Vaccines 2021
DOI: 10.3390/vaccines9050468


When swine flu vaccines and circulating influenza A virus (IAV) strains are poorly matched, vaccine-induced antibodies may not protect from infection. Highly conserved T cell epitopes may, however, have a disease-mitigating effect. The degree of T cell epitope conservation among circulating strains and vaccine strains can vary, which may also explain differences in vaccine efficacy. Here, we evaluate a previously developed conserved T cell epitope-based vaccine and determine the persistence of T cell epitope conservation over time. We used a pair-wise homology score to define conservation between the vaccine’s swine leukocyte antigen (SLA) class I and II-restricted epitopes and T cell epitopes found in 1,272 swine IAV strains sequenced between 2013 and 2017. Twenty-four of the 48 total T cell epitopes included in the epitope-based vaccine were highly conserved and found in >1,000 circulating swine IAV strains over the five-year period. In contrast, commercial swine IAV vaccines developed in 2013 exhibited declining conservation with the circulating IAV strains over the same five-year period. Conserved T cell epitope vaccines may be useful adjunct for commercial swine flu vaccines and to improve protection against influenza when antibodies are not cross-reactive.


Swine IAV; Immunoinformatics; T cell epitope conservation


LIFE SCIENCES, Biochemistry

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