The impact of primer and probe-template mismatches on the sensitivity of pandemic influenza A/H1N1/2009 virus detection by real-time RT-PCR

Klungthong, Chonticha; Chinnawirotpisan, Piyawan; Hussem, Kittinun; Phonpakobsin, Thipwipha; Manasatienkij, Wudtichai; Ajariyakhajorn, Chuanpis; Rungrojcharoenkit, Kamonthip; Gibbons, Robert V.; Jarman, Richard G.

doi:10.1016/j.jcv.2010.03.012

Cited by 73 publications

(68 citation statements)

References 16 publications

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“…Other authors have reported mismatches in the binding regions targeted by CDC primers and swH1probes that affect the sensitivity of the CDC protocol in detecting influenza A (H1N1) 2009. 18,19 Our finding indicates that periodical DNA sequencing can be used to monitor changes in the virus that might affect molecular diagnosis.…”

Section: Discussionmentioning

confidence: 85%

Genotyping of a nosocomial outbreak of pandemic influenza A/H1N1 2009

Rodríguez‐Sánchez

Alonso

Catalán

et al. 2011

Journal of Clinical Virology

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Section: Discussionmentioning

confidence: 85%

Genotyping of a nosocomial outbreak of pandemic influenza A/H1N1 2009

Rodríguez‐Sánchez

Alonso

Catalán

et al. 2011

Journal of Clinical Virology

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“…The performance of quantitative assays for RNA viruses is influenced by their genetic diversity (15,23,43). For the 34 clinical samples, the sequence identity between the different subtypes in the ORF2 region ranged from 83% to 90.4% (data not shown).…”

Section: Discussionmentioning

confidence: 99%

Genotype 3 Diversity and Quantification of Hepatitis E Virus RNA

et al. 2012

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Genotype 3 hepatitis E viruses (HEVs) are distributed across the world and are now considered to be an emerging public health concern in industrialized countries. At least 10 genotype 3 subtypes have been identified in humans and animals worldwide. It was recently reported that the sensitivities of HEV RNA assays differ greatly. We have assessed the influence of genotype 3 diversity on the performances of two HEV RNA assays: one targeting the ORF3 gene and the other targeting the ORF2 gene. We tested a panel of 5 HEV-positive reference samples of genotypes 3a, 3b, 3c, 3e, and 3f at 10-fold serial dilutions. The HEV RNA concentrations obtained with both reverse transcription (RT)-PCRs were correlated, but the RT-PCR based on ORF2 underestimated the HEV RNA concentrations. The mean [ORF3 ؊ ORF2] difference was 1.41 log copies/ml. We also tested 34 clinical specimens of genotypes 3c (n ‫؍‬ 15), 3e (n ‫؍‬ 4), and 3f (n ‫؍‬ 15), representing the most prevalent subtypes in Europe. The mean [ORF3 ؊ ORF2] differences were 1.41 log copies/ml for genotype 3c, 0.96 log copies/ml for genotype 3e, and 0.70 log copies/ml for genotype 3f. The bias between the 2 RT-PCR assays was significantly greater for genotype 3c than for genotype 3f (P ‫؍‬ 0.007). We therefore recommend the use of an RT-PCR protocol based on ORF3 to quantify HEV RNA of genotype 3 strains.

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“…The qPCR transcript pairs appear more robust and resolve into four groups based on the relationships of any two transcripts in normal and DFS samples. [1] The correlation of the following five transcript pairs was disrupted in DFS but stable in the normal samples: SRP54-ACSBG2, SRP54-GRP137, SRP54-TTC7A, SRP54-UBAC1.2 and UBAC1.2-RNF7 ( Table 2). Note that SRP54 anchors all but one of the pairs.…”

Section: Identification Of Potential Biomarkers For Dfsmentioning

confidence: 99%

“…S pecific biomarkers of clinical significance can be identified based on gene expression analysis (1,2). Several spermatozoal RNAs as candidate markers of male fertility status have been identified and tested using microarray-based and other genomic techniques.…”

mentioning

confidence: 99%