Comparative Sequence Analysis on Different Strains of Swine Influenza Virus Sub-type H1N1 for Neuraminidase and Hemagglutinin

The swine flu is an infectious disease of swine and human, causing a huge amount of death to both. The aim of this study was to analyse the mutation possibility of swine influenza virus sub-type A/Swine/Nebraska/(H1N1) from swine of Nebraska. The H1N1 amino acid sequences of neuraminidase (GenBank Acc. No: ABR28650) and hemagglutinin (GenBank Acc. No: ABR28647) were analyzed for mutations using BLASTP and ClustalW programs. Our in silico analysis predicted that hemagglutinin and neuraminidase of swine influenza virus are sensitive to mutations at positions 225, 283 and 240, 451 respectively. These mutations were significant for its pathogenic nature because they are involved in change in polarity or hydrophobicity. Domain and motif search shows that mutations were detected in NA (T240A, G451S) and HA (I283V) at a predicted site of N-myristoylation. Secondary structure analysis predicted that no structural conformation changes were observed in HA and NA at positions 225, 283 and 240, 451 respectively. The program PROTMUTATION was developed in Perl CGI programming using Needleman-Wunsch algorithm for global sequence alignment. This program was used to monitor the mutations and predicts the trend of mutations.

[1]  M. Nei,et al.  MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. , 2007, Molecular biology and evolution.

[2]  J. Paulson,et al.  Receptor determinants of human and animal influenza virus isolates: differences in receptor specificity of the H3 hemagglutinin based on species of origin. , 1983, Virology.

[3]  Gregory C Gray,et al.  Cases of swine influenza in humans: a review of the literature. , 2007, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[4]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[5]  C. Scholtissek,et al.  Pigs as ‘Mixing Vessels’ for the Creation of New Pandemic Influenza A Viruses , 1990 .

[6]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[7]  R. Webster,et al.  Independence of Evolutionary and Mutational Rates after Transmission of Avian Influenza Viruses to Swine , 1999, Journal of Virology.

[8]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[9]  Yoshihiro Kawaoka,et al.  Molecular Basis for the Generation in Pigs of Influenza A Viruses with Pandemic Potential , 1998, Journal of Virology.

[10]  R D Appel,et al.  Protein identification and analysis tools in the ExPASy server. , 1999, Methods in molecular biology.

[11]  J. Gordon,et al.  The biology and enzymology of eukaryotic protein acylation. , 1988, Annual review of biochemistry.

[12]  Tamanna Anwar,et al.  In silico Analysis of Genes Nucleoprotein, Neuraminidase and Hemagglutinin: A Comparative Study on Different Strains of Influenza A (Bird Flu) Virus Sub-Type H5N1 , 2006, Silico Biol..

[13]  R. Grand,et al.  Acylation of viral and eukaryotic proteins. , 1989, The Biochemical journal.

[14]  R. Webster,et al.  Diversity of influenza viruses in swine and the emergence of a novel human pandemic influenza A (H1N1) , 2009, Influenza and other respiratory viruses.