MSSCP applications


RNA viruses demonstrate high genetic variation rate during the genomic material replication and this feature it's the source of their fitness. One of the observed phenotype of this feature is viral antigenic drift which overcome the host immunological response and very important one is a drug resistance developed during the antiviral therapies.

The MSSCP genotyping method assist in the discovery and detection of the presence in the clinical material of the minor genetic viral variants long before their phonotype will be observed on the clinical level. We propose MSSCP genotyping method for the sensitive and rapid discovery and the detection of minor viral genetic variants, which could be missed by the conventional diagnostics.

Example 1.   Detection of the influenza A/H1N1 pandemic and seasonal strains co-infection of humans by the MSSCP method

Figure 1. Simultaneous detection of seasonal and pandemic A/H1N1 strains in specimens collected in 2009. Products of hemagglutinin gene amplification obtained for pandemic A/H1N1/v and reference seasonal strains of influenza virus A/H1N1 were denatured and ssDNA was separated in 9% polyacrylamide gel using MSSCP method under optimal electrophoretic conditions. The presence of both pandemic and seasonal H1N1 virus strains in four samples indicated co-infection (marked with arrows). Clinical specimens are indicated by numbers (1-23), seasonal reference strains: S1 – A/Brisbane/59/2007, S2 – A/Fukushima/141/2006, S3 – A/Fukushima/97/2006, S4 – A/Hong Kong/2652/2006, S5 – A/New Caledonia/20/1999, S6 – A/St. Petersburg/10/2007, S7 – A/Solomon Islands/3/2006, S8 – A/Taiwan/1/1986; pandemic viruses: P1 – A/Gdansk/037/2009(H1N1), P2 – A/Gdansk/036/2009 (H1N1).

Example 2. Minor genetic variants in A/H5N1 virus sequence

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Figure 2. MSSCP genotyping of A/H5N1 virus haemagglutinin gene. Minor genetic variants present among different clones of HA amplicones are indicated by arrows.

MSSCP method has been sucessfully applied for HBV, HCV, A/H1N1, A/H5N1 and A/H7N7 viruses minor genetic variants detection.