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. 2017 Aug:93:25-29.
doi: 10.1016/j.jcv.2017.05.016. Epub 2017 Jun 3.

Effect of genomic drift of influenza PCR tests

Kathleen A Stellrecht  1 , Seela M Nattanmai  2 , Jumshan Butt  2 , Vincente P Maceira  2 , Alvin A Espino  2 , Allan J Castro  2 , Allen Landes  2 , Nicolas Dresser  2 , Shafiq A Butt  2
Affiliations

Effect of genomic drift of influenza PCR tests

Kathleen A Stellrecht et al. J Clin Virol. 2017 Aug.

Abstract

Background: Nucleic acid amplification assays have become the method of choice for influenza (Flu) testing due to superior accuracy and faster turnaround time. Although assays are designed to detect highly conserved genomic targets, mutations can influence test sensitivity. Most of the circulating viruses in the United States during the 2014-2015 season were associated with significant genetic drift; however, the effect on testing was unknown.

Objectives and study design: We compared the performance of Prodesse ProFlu+/ProFAST+ (PFlu/PFAST), FilmArray Respiratory Panel (RP), cobas® Influenza A/B test (cIAB), and Xpert® Flu (Xpt) in a retrospective analysis of consecutive nasopharyngeal specimens received for a two-week period during the winter of 2015. Furthermore, limits of detection (LOD) were determined with six isolates of Flu.

Results: Of the 275 specimens, 63 were positive for FluA by PFAST, 60 were positive by RP, 58 were positive by cIAB and 52 were positive by Xpt. Only a subset of 135 specimens was tested by PFlu, of which 32 were positive. The sensitivity/specificity for PFAST, RP, cIAB, Xpt and PFlu was 100/99.1%, 96.7/99.5%, 91.8/99.1%, 85.2%/100%, and 75.6%/98.9%, respectively. LOD analyses demonstrated assay performance variations were strain associated. Specifically, PFlu's and cIAB's LODs were higher with A/Texas/50/2012-like and A/Switzerland/9715293/2013-like strains, while Xpt's highest LOD was with the Swiss strain.

Conclusions: Strain-associated assay performance variation is known to occur with other Flu test methods; hence, it is not surprising that such variation would be observed with molecular tests. Careful monitoring and reporting for strain-associated variances are warranted for all test methods.

Keywords: Clades; Diagnostic PCR; Genetic drift; Influenza; Respiratory viruses.

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Figures

Fig. 1
Fig. 1
Virus titers in H3N2 positive samples by test result. Box-and-whisker plot of the FluA viral load in either FN or TP samples by assay. Boxes represent the inter-quartile ranges (25th–75th percentile), and whiskers indicate the minimums and maximums. The medians are represented by horizontal line at the middle of the box. – – LOD with Texas - - - LOD with Swiss.
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