Journal of Proteomics & Bioinformatics - Open Access Research Article JPB/Vol.1/July 2008 J Proteomics Bioinform Volume 1(4) :219-226(2008) - 219 ISSN:0974-276X JPB, an open access journal Modeling of RNA Secondary Structure of Non Structural Gene and Evolutionary Stability of the Influenza Virus Through In Silico Methods Pallavi Somvanshi 1* , Vijai Singh 2 and M. Arshad 3 2 Aquatic Microbes Section, National Bureau of Fish Genetic Resources, Canal ring road, PO- Dilkusha, Lucknow-226002. India, Email: vijai15@rediffmail.com 3 Department of Zoology, University of Lucknow, Lucknow, E-mail: arshadm123@rediffmail.com Abstract An influenza virus is an important pathogen causing disease in the birds and further transmits to humans globally. The genome of Influenza virus encodes highly conserved non structural gene (NS1), which is thermody- namically stable in the evolution. Total 32 NS1 nucleotide sequences of Influenza A virus H5N1 strain varied from 831 to 875 bp were used to construct the phylogeny and nine major clades were obtained. The computa- tional tool was used to model the RNA secondary structure of nine different strains of Influenza A virus. The thermodynamic free energy ranges between -222.90 to -251.10 Kcal/mol of the NS which may provide new in- sight to understand the evolutionary stability and pathogenesis of Influenza virus. Keywords : Influenza Avirus, NS1; RNA secondary structure; Free energy; Evolution Introduction An outbreak of avian influenza A virus of the H5N1 subtype was spread to poultry in Asian countries. The trans- mission of influenza virus from birds to humans in Hong Kong with outbreaks H5N1 strains of avian influenza A virus Hiorrimoton and Kawaoka (2005) and highly pathogenic influ- enza A virus H5N1 was identified among the poultry in re- public of Korea Fouchier et al. (2005). An outbreak of highly pathogenic avian influenza (HPAI) H5N1 virus was reported from India in 2006. Phylogenetic analyses revealed that Indian isolates were grouped in the mixed-migratory bird sub-lineage of the Eurasian lineage. In the phylogeny analysis viruses were probably introduced to India from China via Europe because they share a direct ancestral relationship with the Indian isolates Kamal et al. (2007). Influenza viruses are pleomorphic RNA viruses belong- ing to the Orthomyxoviridae family. The genome of influ- enza virus is segmented and consists of single stranded nega- tive sense RNA; it encodes the 8 structural proteins and non structural gene (NS1). The Influenza virus proteins such as two surface proteins hemagglutinin (HA) and neuramini- dase (NA) Fouchier et al. (2005) and other proteins like three RNA polymerase (PA, PB1 and PB2). Nucleoprotein (NP) and matrix protein (M1 and M2) also play role in the cell cycle. The non structural gene (NS1) provides evolu- tionary stability and replication of Influenza virus Wan et al. (2007). Several reports are available on the role of NS of the Influenza virus. The avian influenza virus NS encoding pro- tein induces the apoptosis in the human Lam et al. (2008). The NS protein contributes in the pathogenesis and small fragment have deleted from the NS gene that have been reported as the attenuated vaccine for the chickens Zhu et Received July 01, 2008; Accepted July 16, 2008; Published July 17, 2008 Citation: Pallavi S, Vijai S, Arshad M (2008) Modeling of RNA Secondary Structure of Non Structural Gene and Evolution- ary Stability of the Influenza Virus Through In Silico Methods. J Proteomics Bioinform 1: 219-226. doi:10.4172/jpb.1000026 Copyright: © 2008 Pallavi S, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. *Corresponding author: Pallavi Somvanshi, Bioinformatics Centre, Biotech Park, Sector-G Jankipuram, Lucknow-226021, Uttar Pradesh, India, E-mail: psomvanshi@gmail.com; Tel: +91 522 4012076; Fax: +91 522 4012081 Bioinformatics Centre,Biotech Park, Sector-G Jankipuram, Lucknow-226021, Uttar Pradesh, India, E-mail: psomvanshi@gmail.com 1