Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) detection of waterborne RNA viruses generally requires concentration of large water volumes due to low virus levels. A common approach is to use dead-end ultrafiltration followed by precipitation with polyethylene glycol. However, this procedure often leads to the co-concentration of PCR inhibitors that impairs the limit of detection and causes false-negative results. Here, we applied the concept of pre-PCR processing to optimize RT-qPCR detection of norovirus genogroup I (GI), genogroup II (GII), and hepatitis A virus (HAV) in challenging water matrices. The RT-qPCR assay was improved by screening for an inhibitor-tolerant master mix and modifying the primers with twisted intercalating nucleic acid molecules. Additionally, a modified protocol based on chaotropic lysis buffer and magnetic silica bead nucleic acid extraction was developed for complex water matrices. A validation of the modified extraction protocol on surface and drinking waters was performed. At least a 26-fold improvement was seen in the most complex surface water studied. The modified protocol resulted in average recoveries of 33, 13, 8, and 4% for mengovirus, norovirus GI, GII, and HAV, respectively. The modified protocol also improved the limit of detection for norovirus GI and HAV. RT-qPCR inhibition with C q shifts of 1.6, 2.8, and 3.5 for norovirus GI, GII, and HAV, respectively, obtained for the standard nucleic acid extraction were completely eliminated by the modified protocol. The standard nucleic acid extraction method worked well on drinking water with no RT-qPCR inhibition observed and average recoveries of 80, 124, 89, and 32% for mengovirus, norovirus GI, GII, and HAV, respectively.
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Thanks are due to colleagues at the National Food Agency; Rikard Dryselius for collecting water from Görväln, Karin Jacobsson for valuable comments, Melle Säve-Söderbergh for help with statistical analyses, and Sofia Lindström for standard curve and EC RNA preparations. Finally, we thank Almunge and Görväln water treatment plants for surface water samples.
This study was funded by the Swedish Civil Contingencies Agency, project “Stärkt beredskapskapacitet via rationell laboratoriediagnostik samt förenklad provberedning, pre-PCR processing”, Grants SOFÄ-2013-02, SOFÄ-2013-03, SOFÄ-2015-04, the Swedish Research Council (Grant 621-2013-5999) and Sweden’s innovation agency, UDI SEAL Grant.
Conflict of interest
The authors declare no conflict of interest.
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Borgmästars, E., Jazi, M.M., Persson, S. et al. Improved Detection of Norovirus and Hepatitis A Virus in Surface Water by Applying Pre-PCR Processing. Food Environ Virol 9, 395–405 (2017). https://doi.org/10.1007/s12560-017-9295-3
- Hepatitis A virus
- Surface water
- RT-qPCR inhibition