Zeitschrift für Proteomik und Bioinformatik
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Comparative Sequence Analysis on Different Strains of Swine Influenza Virus Sub-type H1N1 for Neuraminidase and Hemagglutinin

Deepak Kumar Sharma, Anil Kumar Rawat, Shipra Srivastava, Rajeev Srivastava and Ajay Kumar

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.