A comparative study of digital RT-PCR and RT-qPCR for quantification of Hepatitis A virus and Norovirus in lettuce and water samples.
Sensitive and quantitative detection of foodborne enteric viruses is classically achieved by quantitative RT-PCR (RT-qPCR). Recently, digital PCR (dPCR) was described as a novel approach to genome quantification without need for a standard curve. The performance of microfluidic digital RT-PCR (RT-dPCR) was compared to RT-qPCR for detecting the main viruses responsible for foodborne outbreaks (human Noroviruses (NoV) and Hepatitis A virus (HAV)) in spiked lettuce and bottled water. Two process controls (Mengovirus and Murine Norovirus) were used and external amplification controls (EAC) were added to examine inhibition of RT-qPCR and RT-dPCR. For detecting viral RNA and cDNA, the sensitivity of the RT-dPCR assays was either comparable to that of RT-qPCR (RNA of HAV, NoV GI, Mengovirus) or slightly (around 1 log10) decreased (NoV GII and MNV-1 RNA and of HAV, NoV GI, NoV GII cDNA). The number of genomic copies determined by dPCR was always from 0.4 to 1.7 log10 lower than the expected numbers of copies calculated by using the standard qPCR curve. Viral recoveries calculated by RT-dPCR were found to be significantly higher than by RT-qPCR for NoV GI, HAV and Mengovirus in water, and for NoV GII and HAV in lettuce samples. The RT-dPCR assay proved to be more tolerant to inhibitory substances present in lettuce samples. This absolute quantitation approach may be useful to standardize quantification of enteric viruses in bottled water and lettuce samples and may be extended to quantifying other human pathogens in food samples.
Université Paris-Est, ANSES, Food Safety Laboratory, Enteric Viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort cedex, France.
Coralie
C
Coudray-Meunier
Université Paris-Est, ANSES, Food Safety Laboratory, Enteric Viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort cedex, France.
Audrey
A
Fraisse
Université Paris-Est, ANSES, Food Safety Laboratory, Enteric Viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort cedex, France.
Sandra
S
Martin-Latil
Université Paris-Est, ANSES, Food Safety Laboratory, Modelling of Bacterial Behaviour Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort cedex, France.
Laurent
L
Guillier
Université Paris-Est, ANSES, Food Safety Laboratory, IdentyPath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort cedex, France.
Sabine
S
Delannoy
Université Paris-Est, ANSES, Food Safety Laboratory, IdentyPath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort cedex, France.
Patrick
P
Fach
Université Paris-Est, ANSES, Food Safety Laboratory, Enteric Viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort cedex, France. Electronic address: sylvie.perelle@anses.fr.
Sylvie
S
Perelle
D060766:Drinking Water / Q000821:virology*; D005516:Food Microbiology / Q000379:methods*; D030041:Hepatitis A virus / Q000235:genetics / Q000502:physiology*; D018545:Lactuca / Q000821:virology*; D029322:Norovirus / Q000235:genetics / Q000502:physiology*; D012367:RNA, Viral / Q000032:analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000592:standards*
D060766:Drinking Water; D012367:RNA, Viral
HAV; Lettuce; NoV; RT-dPCR; RT-qPCR; Water