Immunological studies on Swine Influenza Virus in pigs: from gene to epitopes

Abstract

Swine Influenza Virus (SwIV) is an important pathogen in veterinary field with a great zoonotic potential and thus it is considered also a potential threat for public health. Surveillance and control of this pathogen in pigs is therefore crucial. Current methods of control are based on prophylaxis; in particular they are based on vaccines eliciting humoral response. Escaping capacity and high variability of SwIV make that the efficacy of those can be compromised; thus vaccines need to be periodically updated. This problem is shared in human health and thus rationally designed vaccines are being developed. Those are being designed to enhance T cell response against Influenza A Virus (IAV). T cell responses showed to be related with protection against IAV infection, targeting the highly conserved internal protein of the virus. This would solve the problems above cited. T cell epitopes of SwIV in pigs are just few and related to class I Swine Leucocytes Antigens (SLA). Reverse vaccinology is used in human health to identify T cells epitope; however, in pigs this has just recently been introduced and thus just few tools were available. The main aim of this work was to identify T cells epitopes in SwIV to be used in rationally designed vaccines. For this purpose, the following studies were performed. Surveillance of SwIV is fundamental to design a proper control. The epidemiological situation of SwIV in Spain needed to be updated and more genetic data were required to allow the use of reverse vaccinology. The study showed that the epidemiological situation of Spain was similar to other European countries in which circulating strains were closed related and evolving in the same way. However, some exceptions were found; one strain evolved divergently in Spain. Genetic shift has been suggested as a recent event in the evolution of those strains. In vitro assays to determinate binding affinities of epitopes to class I SLA (SLA-I) available were few and based on recombinant molecules. Therefore, in a first instance an in vitro tool based on native forms of SLA-I was attempted. MHC reconstitution assay for SLA-I was designed and almost entirely developed. C1R cells expressing the Babraham pigs allele SLA-1*es11 were generated. Finally, the denaturalization step of the assay was set-up. Reverse vaccinology was then applied to identify T cells epitopes. Epitopes of the virus selected as target were predicted in silico by NetMHCpan on Babraham SLA-I alleles (SLA-1*es11 and SLA-2*es22) and tested by ex vivo functional assays (IFNγ and proliferation responses) using cells from immunised Babraham inbred pigs. Unfortunately, this approach did not give any positive epitope. Additionally, T cells epitopes were empirically identified. Proteins M1 and NP of a human IAV were selected as target and thus dissected by using overlapping peptides and functional methods (IFNγ and proliferation responses) until finding T cells epitopes. The tests were performed using cells from IAV immunised Babraham inbred pigs. Two overlapping SLA-II epitope were found, NP405-416 and NP407-420. In another attempt, a more complex strategy of reverse vaccinology was used. This was previously used by other authors and it is based on a combination of methods: in silico prediction of epitopes by NetMHCpan and validation of results by using in vitro binding preferences of the selected SLA-I allele , an in vitro test binding assay and in vivo test by tetramers. Peptides were identified in animals infected and challenged with two heterologous SwIV. This strategy showed to be highly accurate and thus one immunodominant epitope (NA171-180) was identified. Overall, these data pave the way for rational design of vaccine against SwIV as well as providing new insight into pig responses to infection or immunization with IAV.

Date of Award	12 Nov 2015
Original language	English
Supervisor	Maria Montoya (Director) & Maria Merce Marti Ripoll (Tutor)