Comparison of nucleic acid extraction and reverse transcription-qPCR approaches for detection of GI and GII noroviruses in drinking water.
The objective of this study was to compare three nucleic acid extraction and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) approaches for norovirus (NoV) detection in drinking water with respect to performance, costs, and analysis time. The approaches evaluated were: (A) an approach that utilizes the QIAamp DNA Blood Mini Kit and multiplex primers and probes for detection; (B) a procedure which includes the NucliSENS Magnetic Extraction Kit and other components of a proposed European Union standard method for NoV detection in foods; and (C) a commercialized assay which uses NucliSENS extraction and Cepheid SmartCycler® technologies. Each approach was evaluated by most probable number (MPN) analysis for detection of GI.1 and GII.4 NoVs from human stool. Furthermore, recoveries of spiked primary effluent in tap water concentrates were compared for each approach. Few significant differences were observed between approaches with regard to performance. However, Approach C was the most time consuming and expensive to perform. This research presents a case study of how molecular-based approaches for detection of NoVs can be compared and how various factors may play a role in which approach laboratories choose to employ.
U.S. Environmental Protection Agency, National Exposure Research Laboratory, 26W. Martin Luther King Dr., Cincinnati, OH 45268, USA. Electronic address: griffin.shannon@epa.gov.
Shannon M
SM
Griffin
U.S. Environmental Protection Agency, National Exposure Research Laboratory, 26W. Martin Luther King Dr., Cincinnati, OH 45268, USA.
Nichole E
NE
Brinkman
U.S. Environmental Protection Agency, Office of Water, Water Security Division, 26W. Martin Luther King Dr., Cincinnati, OH 45268, USA.
Elizabeth J
EJ
Hedrick
U.S. Environmental Protection Agency, National Exposure Research Laboratory, 26W. Martin Luther King Dr., Cincinnati, OH 45268, USA.
Eric R
ER
Rhodes
U.S. Environmental Protection Agency, National Exposure Research Laboratory, 26W. Martin Luther King Dr., Cincinnati, OH 45268, USA.
G Shay
GS
Fout
D060766:Drinking Water / Q000821:virology*; D005243:Feces / Q000821:virology; D006801:Humans; D029322:Norovirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D012367:RNA, Viral / Q000235:genetics* / Q000302:isolation & purification*; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D014773:Virology / Q000379:methods
D060766:Drinking Water; D012367:RNA, Viral
Molecular detection; Norovirus; Water; qPCR