In-silico vaccine matching and its validation through in-vivo immune protection analysis for imported and indigenous vaccines against recent field isolate of avian influenza H9N2

The ability of influenza viruses to incessantly mutate makes these viruses to circulate in the field continuously. Every year, economic losses are faced by poultry industry due to vaccine failure. The current study was designed to bridge the gap by using various bioinformatics tools. For B-cells, HA protein of study virus showed 85.45% epitopes conservancy with vaccine 4 (local vaccine) whereas 54.54%, 67.27% and 43.63% were found conserved in vaccines 3, 2 and 1 (imported vaccines) respectively. For NA protein of study virus, 87.03% epitopes were found conserved in vaccine 4 whereas in vaccines 3, 2 and 1, 18.14%, 50% and 37.03% were found conserved respectively. Slight different results were obtained for T-cells. For MHC-1, vaccine 2 showed highest conservancy of 70% with HA protein of our study virus whereas, vaccine 1 and 3 showed 50% and vaccine 4 showed 60% conservancy. In case of NA protein 90%, 54%, 45% and 36% epitopes were conserved in vaccines 4, 3, 2 and 1 respectively against MHC-1 molecules. For MHC-2, HA protein of our study virus, vaccine 2 and 4 showed 84% conservancy whereas vaccine 1 and 3 showed 53% conservancy. While for NA protein, 100%, 28%, 71%, and 57% epitopes were conserved in vaccines 4, 3, 2 and 1 against MHC-2 molecules. In-vivo trials also supported in-silico results. Groups vaccinated with vaccine 1 and 3 respectively, showed significant levels of morbidity and post-challenge virus shedding through buccal and cloacal swab as compared to vaccine 2 and 4 respectively. Our study shows that there is a need of continuous evaluation and upgradation of seed virus of H9N2 vaccines, for this purpose in-silico analysis is a reliable and efficient method.