Molecular and genetic analysis of NS gene from high pathogenic strains of the avian influenza (H5N1) virus isolated in Kazakhstan Olga V. Chervyakova ⁎, Vitaliy M. Strochkov, Kulyaisan T. Sultankulova, Nurlan T. Sandybayev, Valentin L. Zaitsev, Seidigapbar M. Mamadaliyev Research Institute for Biological Safety Problems, RK ME&S–Science Committee, Gvardeiskiy, Kordaiskiy rayon, Zhambylskaya oblast, 080409, Republic of Kazakhstan abstract article info Article history: Accepted 13 February 2011 Available online 19 February 2011 Received by A.J. van Wijnen Keywords: Phylogenetic relationship Genotype Pathogenicity factors Ways of infection introduction The high pathogenic strains of the avian influenza H5N1 virus isolated in Kazakhstan have NS of different genotypes. The influenza virus strains isolated in 2005 is of NS1E Qinghai genotype. A/swan/Mangystau/3/ 2006 strain is of NS2A genotype that is typical for Gs/Gd-like strains. The results of the analysis allow assuming that A/swan/Mangystau/3/2006 strain has been brought onto the territory of Kazakhstan from the European part of the continent along the Black Sea–Mediterranean flyway. © 2011 Elsevier B.V. All rights reserved. 1. Introduction A distinctive feature of the influenza virus is its unique aptitude for higher mutability as compared to other agents and for frequent mutations in genome (Suzuki, 2010). First of all, it concerns the hemagglutinin gene that carries determinants responsible for forma- tion of the virus-neutralizing immunity (Suzuki, 2008). Specific changes were shown to occur in other influenza virus genes, particularly in genes of non-structural proteins and polymerase. Very important mechanisms of the agents mutability are the processes of intragenic recombination or reassortment of the fragments in the virus genome that includes eight independent genes encoding relevant proteins, two of them (hemagglutinin and neuraminidase) being located in the surface envelope of the virus. The other six fragments include three genes of the polymerase complex (PB1, PB2, PA), the gene encoding nucleoprotein (NP), M-gene encoding two matrix proteins—M1 (inner protein) and M2 built into the virus envelope, and NS gene encoding two functionally important proteins (NS1 and NS2). The smallest, 8th segment of the RNA of the influenza A virus encodes two proteins that are found only in infected cells. The segment consists of 890 nucleotides. Downstream the non-coding region of 5′ nucleotides, there is an open reading frame encoding NS1 protein consisting of 230–237 amino acids (aa) depending on the virus strain with molecular weight 23.0–26.0 kDa. Another reading frame was found at 5′-end of the 8th segment of the virion RNA. The frame encodes NS2 protein consisting of 121 aa with molecular weight 14.0 kDa (Choi et al., 2002; Beklemishev et al., 1993; Suarez and Perdue, 1998; Offringa et al., 2000). NS1 protein is important in the replicative cycle of influenza A viruses (Fouchier et al., 2007; De Jong and Hien, 2006). Cellular processes such as cellular mRNA synthesis, splicing, protein kinase activity, apoptosis induction are associated with multiple functions of this protein. During recent years the evidences have been accumu- lated that the influenza A virus NS1 protein plays a key role in inhibition of synthesis of type 1 interferons that are responsible for non-specific immunity. Glutaminic acid in NS1 protein molecule (position 92) makes influenza H5N1 viruses resistant to interferons and tumor necrosis factor (TNFα)(Seo et al., 2002). The objective of the research described here was to detect nucleotide sequences of NS gene of highly pathogenic influenza virus strains isolated from birds on the territory of Kazakhstan and to study their peculiar features. 2. Materials and methods 2.1. Viruses The following influenza H5N1 virus strains were used: A/ domestic goose/Pavlodar/1/2005, A/chicken/Astana/6/2005 and A/ swan/Mangystau/3/2006. Gene 476 (2011) 15–19 ⁎ Corresponding author at: 7/5, Gvardeiskiy, Kordaiskiy rayon, Zhambylskaya oblast, 080409, Republic of Kazakhstan. Fax: + 7 727 2731069/+7 764 6600113. E-mail addresses: chervyakova@srai.kz, ovch@mail.ru (O.V. Chervyakova), vstrochkov@srai.kz, vstrochkov@gmail.com (V.M. Strochkov), Sultankul70@mail.ru (K.T. Sultankulova), nurlans@srai.kz (N.T. Sandybayev), Zaitsev@srai.kz (V.L. Zaitsev), ribs@srai.kz (S.M. Mamadaliyev). 0378-1119/$ – see front matter © 2011 Elsevier B.V. All rights reserved. doi:10.1016/j.gene.2011.02.003 Contents lists available at ScienceDirect Gene journal homepage: www.elsevier.com/locate/gene