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Improved Detection of Norovirus and Hepatitis A Virus in Surface Water by Applying Pre-PCR Processing
Natl Food Agcy, Div Sci, Dept Biol, Hamnesplanaden 5, S-75319 Uppsala, Sweden..
Natl Food Agcy, Div Sci, Dept Biol, Hamnesplanaden 5, S-75319 Uppsala, Sweden..
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infection medicine. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Natl Food Agcy, Div Sci, Dept Biol, Hamnesplanaden 5, S-75319 Uppsala, Sweden.
Lund Univ, Appl Microbiol, Naturvetarvagen 14, S-22362 Lund, Sweden..
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2017 (English)In: Food and Environmnetal Virology, ISSN 1867-0334, E-ISSN 1867-0342, Vol. 9, no 4, p. 395-405Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2017. Vol. 9, no 4, p. 395-405
Keywords [en]
Norovirus, Hepatitis A virus, Surface water, Ultrafiltration, RT-qPCR, RT-qPCR inhibition
National Category
Microbiology in the medical area
Identifiers
URN: urn:nbn:se:uu:diva-341985DOI: 10.1007/s12560-017-9295-3ISI: 000414377300003PubMedID: 28401478OAI: oai:DiVA.org:uu-341985DiVA, id: diva2:1183419
Funder
Swedish Civil Contingencies Agency, SOFA-2013-02 SOFA-2013-03 SOFA-2015-04Swedish Research Council, 621-2013-5999Available from: 2018-02-16 Created: 2018-02-16 Last updated: 2018-02-16Bibliographically approved

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