Etiopathogenesis and diagnostic laboratory methods in pandemic influenza infections

Association of influenza viruses (InfVs) with pandemics during the history due to the antigenic changes leads the maintaining of their importance until to date. InfVs belong to Orthomyxoviridae family, are enveloped and spheric/pleomorphic viruses with helical nucleocapsids. The 8-fragmented genome of single-stranded negative-sense RNA encodes 10 structural and one non-structural proteins. InfVs exhibit three types (type A, B, and C) according to the differences of nucleoprotein (NP) and matrix (M) proteins. Influenza A viruses also exhibit subtypes according to the differences of two major cell surface glycoproteins; hemagglutinin (HA) and neuraminidase (NA). Antigenic variations in influenza A viruses arise through antigenic drift (via point mutations) and antigenic shift (via genetic reassortment). Antigenic shift refers to the introduction of a novel influenza A virus subtype to which all or most of the population has no preexisting immunity. The natural reservoir for all influenza A subtypes is wild waterfowl, with certain subtypes transmissible among humans, pigs, horses, sea and other mammals. The epithelial cells of swine express suitable receptors in which both human and avian subtypes can bind and infect these cells, making swine a mixing vessel for coinfection and reassortment. The first pandemic of the 21st century in April 2009 is caused by a newly emerged influenza A (H1N1) virus originated from swine (swine-origin influenza A virus; SOIV). This virus contain a combination of gene segments from four different subtypes (quadruple assortant). Its PB2 and PA genes originate from North American avian virus; PB1 originates from the human H3N2 virus; HA (H1), NP, and NS genes come from classical swine virus (closely related to the 1918 human influenza A virus); NA and M genes are from the Eurasian avian-like swine virus. The pathogenicity and virulence of S-OIV appears to be similar to the other seasonal influenza A (H1N1) viruses, however it shoud be kept in mind that the virulence may change as the number of adaptive mutations increases. The laboratory diagnosis of 2009 pandemic influenza infections is mainly based on real-time reverse transcriptase-polymerase chain reaction performed in the nasopharyngeal aspirate/ swab, nasal aspirate/swab together with oropharyngeal swab, endotracheal aspirate or bronchoalveolar lavage samples, as recommended by Centers for Disease Control and Prevention (CDC). In this review article, general properties of influenza viruses and genetic origin, pathogenesis and laboratory diagnosis of S-OIV have been discussed under the light of recent literature.