Determination of restriction sites of hemagglutinin, neuraminidase and nucleoprotein encoding genes of H1N1 and H7N9 strains of influenza virus
- Journal of Microbiology & Experimentation
Buriachenko SV, Stegniy BT
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Introduction: Influenza virus (family Orthomyxoviridae) is the causative agent of influenza-an acute, highly contagious disease of the respiratory and gastrointestinal tract. The most important influenza virus virulence factors are surface proteins - hemagglutinin and neuraminidase, as well as nucleoprotein. These substances also have antigenic properties. High variability of the genes which are encoding these proteins leads to the emergence of strains with new antigenic properties every 1-2 years, which allows the virus to overcome strain-specific immunity in the population and to receive epidemic spread. Diagnosis and mapping of the genome of the virus due to its high level of variability requires high-quality and highly sensitive molecular methods, such as the technique of restriction fragment length polymorphism (RFLP). The aim of this work was to determine the restriction sites of hemagglutinin, neuromidinase and nucleoprotein genes and to model the RFLP analysis of Influenza virus using the pathogenic H1N1 and H7N9 strains with the help of bioinformatic methods in silico.
Materials and methods: The restriction fragment length polymorphism assay was performed on the nucleotide sequences of HA, NA, and NP genes encoding hemagglutinin, neuraminidase, and nucleoprotein, H1N1, and H7N9 influenza strains which were taken from the GenBank database of the National Center for Biotechnology (NCBI). The restriction sites were found, their location on the genes was examined, and the nucleotide distances between them were calculated. Restriction enzyme was detected for further performing of RFLP analysis. The RFLP analysis with restrictase to the well-established sites was modeled and the sizes of its products in silico were determined. The studies were performed using VectorNTI-11.
Result: Common and unique RFLP analysis products for HA, NA and NP genes of H1N1 and H7N9 influenza strains have been identified. The distribution of RFLP analysis products by electrophoresis in silico is shown. The possibility of using restriction fragment length polymorphism to identify strains of H1N1 and H7N9 influenza virus was shown.
influenza virus, strain H1N1, strain H7N9, hemagglutinin, neuraminidase, nucleoprotein, restriction sites