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. 2015 Oct;53(10):3353-4.
doi: 10.1128/JCM.01044-15. Epub 2015 Jul 22.

A Single Nucleotide Polymorphism at the TaqMan Probe-Binding Site Impedes Real-Time Reverse Transcription-PCR-Based Detection of Norovirus GII.4 Sydney

Ran Zhuo  1 , Maria Eloisa Hasing  1 ; Team of Molecular Diagnostics; Xiaoli Pang  2
Affiliations

A Single Nucleotide Polymorphism at the TaqMan Probe-Binding Site Impedes Real-Time Reverse Transcription-PCR-Based Detection of Norovirus GII.4 Sydney

Ran Zhuo et al. J Clin Microbiol. 2015 Oct.

Abstract

A single nucleotide polymorphism (SNP) in the TaqMan probe-binding site resulted in decreased sensitivity of real-time reverse transcription-PCR (RT-rtPCR) for detection of norovirus genogroup II genotype 4 (GII.4) Sydney. A new degenerate probe was designed that improved the sensitivity of the detection while not interfering with the detection of other GII and GI strains.

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Figures

FIG 1
FIG 1
Newly designed degenerate probe improved detection of GII.4 Sydney carrying SNP in clinical specimens. (A) An SNP in the sequences of a published TaqMan probe-binding site in some of the GII.4 Sydney strains resulted in mutation-like flat amplification curves of the RT-rtPCR assay. (B) RT-rtPCR assay with degenerate probe improved detection of GII.4 Sydney carrying SNP, while remaining accurate in detection of GII.4 Sydney without SNP.
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