Molecular characterization and phylogenetic analysis of Middle East 2009 H1N1 pdm isolates

AbstractObjectiveTo study hemagglutinin genetic evolution of some Middle East (ME) 2009 H1N1 pdm isolates and compared them with prototype vaccine strain [A/California/07/2009 (H1N1)], which is used as a vaccine strain in the Northern Hemisphere 2010-2011.MethodsNucleotide and/or amino acid sequences of HA gene of fifty-four ME 2009 H1N1 pdm isolates were retrieved from GenBank Database by using Basic BLAST engine. Phylogenetic trees were established for both nucleotide and amino acid sequences using the muscle algorithm of the computer program CLC free workbench 5.6.1 JRE software. Amino acids alignment was also done to compare sequences HA1 domains of HA genes of ME 2009 H1N1 pdm isolates (n=39) with amino acid sequence of prototype vaccine strain A/California/07/2009 (H1N1).ResultsPhylogenetic analysis of amino acids and nucleotides of the HA gene of the ME 2009 H1N1 pdm isolates confirmed their evolutionary position in cluster with prototype vaccine strain (A/California/07/2009 (H1N1)) which is used as vaccine strain in the Northern Hemisphere 2010-2011. Antigenically, the ME 2009 H1N1 pdm isolates were homogeneous and closely related to prototype vaccine. Only a few amino acid substitutions in the HA among the ME 2009 H1N1 pdm isolates were analyzed.ConclusionsThe current influenza vaccine is expected to provide a good protection against ME 2009 H1N1 pdm because it contains strains with H1 HA [A/California/07/2009 (H1N1)]-like strain