Molecular diagnostics and genetic characteristics of influenza A/H1N1 virus circulating in the territory of the West Kazakhstan in 2012–2014

Abstract

No: 1437 Presentation at ESCV 2015: Poster 1 Molecular diagnostics and genetic characteristics of influenza A/H1N1 virus circulating in the territory of the West Kazakhstan in 2012–2014 N.G. Klivleoeva1,∗, G.V. Lukmanova1, T.I. Glebova1, M.G. Shamenova1, N.T. Saktaganov1, K.V. Duysenova2 1 Institute of Microbiology and Virology of the Ministry of Education and Science of the Republic of Kazakhstan, Kazakhstan 2 Atyrau Regional Center of Sanitary – Epidemiological Expertise, Kazakhstan Background: The purpose of this study was to analyze the molecular characteristics of influenza A/H1N1virus circulating in the territory of the West Kazakhstan in 2012–2014. Methods: Samples of clinicalmaterials (nasopharyngeal swabs) were collected in polyclinics and infectious diseases hospitals of the Atyrau oblast (West Kazakhstan) from people with symptoms ofARVI andpneumonia in the2012–2014period. The sampleswere tested by RT-PCR considering the results in the real-time mode and using AmliSens reagent kit produced by the Central Research Institute of Epidemiology (Moscow). Nucleotide sequences of HA andNA geneswere analyzed using the BlAST software (http://blast. ncbi.nlm.nih.gov), which allowed to determine the percentage of identity with the influenza virus isolates and strains available in the GenBank. PCR diagnostics of 337 clinical samples showed that the genetic material of influenza viruses was detected in 118 swabs (35% of the total number of samples tested). Influenza A/H1 viral RNA was detected in 27 samples (23.0% of the total number of positive samples), A/H3 viral RNA in 13 samples (11%). RNA of simultaneously both subtypes of influenza A virus (H1N1+H3N2) was also detected in six samples (5.0%). Influenza B viruses were not detected. These data suggest the influenza A epidemic of the mixed etiology with a predominance of influenza A/H1N1 virus. Molecular genetic characterization of the six A/H1N1 strains, isolated in the Atyrau region in 2012 and 2013, showed that these viruses by the hemagglutinin gene are similar to the reference strain A/swine/Guangdong/L3/2009 (H1N1) by 98-99%. When studying the NA gene sequence, it was established that isolates exhibited 99% identity with A/swine/Changhua/1993/2000 (H1N1), A/swine/USA/1976-M/1931 (H1N1) and A/swine/Guangdong/L3/2009 (H1N1), and 98% homology with A/swine/Iowa/1973 (H1N1). Two strains (A/Atyrau/880/12 and A/Atyrau/901/13), in addition to this, showed 99% identity with the classical swine viruses A/swine/Jamesburg/1942 (H1N1), A/swine/1931 (H1N1) and A/swine/Iowa/1973 (H1N1). The study of mutational changes in NA and M genes and comparative analysis of amino acid sequences in NA genes in comparison with a pandemic strain A/California/04/2009 (H1N1)v of American line and A/England/195/2009 (H1N1) of Eurasian line indicated that the Kazakhstan strains have more than 70 differences from the reference ones. Phylogenetic analysis showed that closely related strains of influenza virus belonging to the same cluster with the virus A/swine/Guandong/L3/2009 (H1N1), isolated in 2009 from swine in China, are circulating in the territory of the West Kazakhstan; the changes in HA gene do not lead to the changes in the antigen properties. In this way, the molecular biological analysis showed that the population of A/H1N1 strains of theWest Kazakhstan is genetically homogeneous, and within two epidemic seasons of the circulation has not undergone significant changes. http://dx.doi.org/10.1016/j.jcv.2015.07.057