title: Improved Detection of Norovirus and Hepatitis A Virus in Surface Water by Applying Pre-PCR Processing.
abstract: 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 Cqshifts 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.
authors.affiliation: Science Division, Biology Department, National Food Agency, Hamnesplanaden 5, 75319, Uppsala, Sweden.
authors.forename: Emmy
authors.initials: E
authors.lastname: Borgmästars
authors.affiliation: Science Division, Biology Department, National Food Agency, Hamnesplanaden 5, 75319, Uppsala, Sweden.
authors.forename: Mehrdad Mousavi
authors.initials: MM
authors.lastname: Jazi
authors.affiliation: Science Division, Biology Department, National Food Agency, Hamnesplanaden 5, 75319, Uppsala, Sweden.|Department of Medical Science, Uppsala University, Akademiska sjukhuset, 75185, Uppsala, Sweden.
authors.forename: Sofia
authors.initials: S
authors.lastname: Persson
authors.affiliation: Applied Microbiology, Lund University, Naturvetarvägen 14, 22362, Lund, Sweden.
authors.forename: Linda
authors.initials: L
authors.lastname: Jansson
authors.affiliation: Applied Microbiology, Lund University, Naturvetarvägen 14, 22362, Lund, Sweden.
authors.forename: Peter
authors.initials: P
authors.lastname: Rådström
authors.affiliation: Science Division, Biology Department, National Food Agency, Hamnesplanaden 5, 75319, Uppsala, Sweden.
authors.forename: Magnus
authors.initials: M
authors.lastname: Simonsson
authors.affiliation: Applied Microbiology, Lund University, Naturvetarvägen 14, 22362, Lund, Sweden.|Swedish National Forensic Centre, Brigadgatan 13, 58194, Linköping, Sweden.
authors.forename: Johannes
authors.initials: J
authors.lastname: Hedman
authors.affiliation: Science Division, Biology Department, National Food Agency, Hamnesplanaden 5, 75319, Uppsala, Sweden. Ronnie.Eriksson@slv.se.
authors.forename: Ronnie
authors.initials: R
authors.lastname: Eriksson
mesh_terms: D017931:DNA Primers / Q000235:genetics; D005618:Fresh Water / Q000821:virology*; D030041:Hepatitis A virus / Q000235:genetics / Q000302:isolation & purification*; D029322:Norovirus / Q000235:genetics / Q000302:isolation & purification*; D012367:RNA, Viral / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction / Q000295:instrumentation / Q000379:methods*
chemical_list: D017931:DNA Primers; D012367:RNA, Viral
keywords: Hepatitis A virus; Norovirus; RT-qPCR; RT-qPCR inhibition; Surface water; Ultrafiltration