Rapid differentiation of mixed influenza A/H1N1/infections with seasonal and pandemic variants by multi-temperature single-stranded conformational polymorphism.

J Clin Microbiol. 2011 Apr 6;

Authors: Pajak B, Stefanska I, Lepek K, Donevski S, Romanowska M, Szeliga M, Brydak LB, Szewczyk B, Kucharczyk K

Mixed infections of a single host with different variants of influenza a virus are the main source of reassortants which may have unpredictable properties when they establish themselves in the human population. In this report we describe a method for rapid detection of mixed influenza infections with seasonal A/H1N1/human strain and the pandemic A/H1N1/v strain which emerged in 2009 in Mexico and the United States. The influenza A/H1N1/variants were characterized by the multi-temperature single-stranded conformational polymorphism (MSSCP) method. The MSSCP gel patterns of hemagglutinin gene fragments of pandemic A/H1N1/v and different seasonal A/H1N1/strains were easily distinguishable two hours after completion of RT-PCR. Using the MSSCP based genotyping approach co-infections with seasonal and pandemic variants of the A/H1N1/subtype were identified in four out of 23 primary samples obtained from patients that were presented with influenza-like symptoms to hospitals across Poland during the epidemic season 2009/10. Pandemic influenza strain presence was confirmed in all these primary samples by real-time RT-PCR. The sensitivity level of the MSSCP based minor genetic variant detection was 0.1 % as determined on a mixture of DNA fragments obtained from amplification of the hemagglutinin gene of seasonal and pandemic strains. The high sensitivity of the method suggests its applicability for characterization of new viral variants long before they become dominant.

PMID: 21471335 [PubMed - as supplied by publisher]

Tags: avian flu, h1n1, h1n5, porcine flu, pork flu, swine flu

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