In silico prediction and analysis of influenza A ( H5N1) Indonesian virus neuraminidase protein epitopes as a clue for diagnostic tests and effective vaccines development

In silico prediction and analysis of influenza A ( H5N1) Indonesian virus neuraminidase protein epitopes as a clue for diagnostic tests and effective vaccines development
Zahra Latif ,^1,* Farida Behzadian ,² Zahra Barghi ,³ Maryam Saheh ,⁴ Behrokh Farahmand,⁵
1. Research Center of Bioscience and Biotechnology, Malek- Ashtar University of Technology, Tehran, Iran and Department of Influenza Virus Research and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Irann
2. Research Center of Bioscience and Biotechnology, Malek- Ashtar University of Technology, Tehran, Iran
3. Department of Influenza Virus Research and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
4. Department of Influenza Virus Research and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
5. Department of Influenza Virus Research and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
Introduction: In the year of 2007, the avian influenza outbreak which occurred in Indonesia caused mortality of almost 85% from detected avian influenza cases. Comparing the mortality rate in Indonesia to other countries with avian influenza outbreak, WHO announced the Highly Pathogenic Influenza (HPIV) Indonesia virus has the highest pathogenicity. Mutations with either antigenic shift or antigenic drift can influence the pathogenicity of the influenza virus. Studies on neuraminidase (NA) have been carried out because the protein has important roles in the infection process of the avian influenza virus and pathogenicity of birds to humans. So, the prediction of epitopes in protein provides a suitable primary immunodiagnostic antigen for the detection of the influenza A virus H5N1.
Methods: In silico analysis was done to find potential T-cell and B-cell epitopes. At first the nucleotides and protein sequences of neuraminidase of influenza A virus (A/Indonesia/5/2005(H5N1) were taken from NCBI Genbank ( Accession number: EU146623.1)and the open reading frame (ORF), a restriction site, expected molecular weight, and isoelectric point (pI) value were analyzed with Generunner and Prot Param softwares. The three-dimensional structure of the protein was predicted by the softwares available on the Expasysite. Amino acid sequence epitopes after NA gene expression for B lymphocytes and T lymphocytes by ABCpred and CTLpred respectively checked out and MHC class, I and II constructed for epitopes after NA gene expression was predicted in the IEDB database. The immunogenicity and stability indices of the amino the acid sequence was examined using Ellipro (an online tool that predicts the three-dimensional structures of protein using PDB format).
Results: As a result of the prediction of linear and discontinuous epitopes of the amino acid sequence of the protein neuraminidase and their antigenicity by the Ellipro database, the predicted epitope regions were fully visible on the three-dimensional molecular structure. Comparison of B-cell linear epitopes obtained from the first structure and discontinuous epitopes from the structures shows that there are some antigenic regions of the molecule in both structures that have the potential to stimulate the humoral immune system and produce antibodies. A result of MHC class I and II prediction observed showed that NA epitopes stimulate both cellular and humoral immune systems.
Conclusion: These results showed that this protein is a good candidate for the production of diagnostic tests and effective vaccines.
Keywords: H5N1 Indonesia, neuraminidase (NA), vaccine, diagnostic test, In silico.