A. Abbreviations, American type culture collection; CEN: European committee for standardisation; dsRNA: Double-strand RNA; EMA: Ethidium monoazide

, HAV: Hepatitis A virus; LOD: Limit of detection; LOQ: Limit of quantification

, MEM: Minimum essential medium; NCR: Non-coding region

, PBS: Phosphate-buffered saline; PCR: Polymerase chain reaction; PFU: Plaqueforming units; PMA: Propidium monoazide; RT-qPCR: Quantitative reverse transcriptase PCR; RV: Rotavirus; ssRNA: Single-strand RNA

M. Koopmans and E. Duizer, Foodborne viruses: an emerging problem, Int J Food Microbiol, vol.90, pp.23-41, 2004.

D. Rodríguez-lázaro, N. Cook, F. M. Ruggeri, J. Sellwood, A. Nasser et al., FEMS Microbiol Rev, vol.36, pp.786-814, 2012.

B. R. Gulati, P. B. Allwood, C. W. Hedberg, and S. M. Goyal, Efficacy of commonly used disinfectants for the inactivation of calicivirus on strawberry, lettuce, and a food-contact surface, J Food Prot, vol.64, pp.1430-1434, 2001.

K. A. Hirneisen, E. P. Black, J. L. Cascarino, V. R. Fino, D. G. Hoover et al., Viral inactivation in foods: a review of traditional and novel food-processing technologies, CRFSFS, vol.2010, pp.3-20

M. Koopmans, V. Bonsdorff, C. H. Vinjé, J. , D. Medici et al., Foodborne viruses, FEMS Microbiol Rev, vol.2, pp.187-205, 2002.
URL : https://hal.archives-ouvertes.fr/hal-00510661

G. Sánchez, A. Bosch, and R. M. Pintó, Hepatitis A virus detection in food: current and future prospects, Lett Appl Microbiol, vol.45, pp.1-5, 2007.

A. Stals, L. Baert, E. Van-coillie, and M. Uyttendaele, Extraction of food-borne viruses from food samples: a review, Int J Food Microbiol, vol.153, pp.1-9, 2012.

D. Lees, International standardization of a method for detection of human pathogenic viruses in molluscan shellfish, Food Environ Virol, vol.2, pp.146-155, 2010.

I. A. Hamza, L. Jurzik, K. Überla, and M. Wilhelm, Methods to detect infectious human enteric viruses in environmental water samples, Int J Hyg Environ Health, vol.214, pp.424-436, 2011.

S. Lamhoujeb, I. Fliss, S. E. Ngazoa, and J. Jean, Evaluation of the persistence of infectious human noroviruses on food surfaces by using real-time nucleic acid sequence-based amplification, Appl Environ Microbiol, vol.74, pp.3349-3355, 2008.

S. Nuanualsuwan and D. O. Cliver, Pretreatment to avoid positive RT-PCR results with inactivated viruses, J Virol Methods, vol.104, pp.217-225, 2002.

J. R. Topping, H. Schnerr, J. Haines, M. Scott, M. J. Carter et al., Temperature inactivation of Feline calicivirus vaccine strain FCV F-9 in comparison with human noroviruses using an RNA exposure assay and reverse transcribed quantitative real-time polymerase chain reaction-A novel method for predicting virus infectivity, J Virol Methods, vol.156, pp.89-95, 2009.

M. Fittipaldi, A. Nocker, and F. Codony, Progress in understanding preferential detection of live cells using viability dyes in combination with DNA amplification, J Microbiol Methods, vol.91, pp.276-289, 2012.

J. Fujimoto, K. Tanigawa, Y. Kudo, H. Makino, and K. Watanabe, Identification and quantification of viable Bifidobacterium breve strain Yakult in human faeces by using strain-specific primers and propidium monoazide, J Appl Microbiol, vol.110, pp.209-217, 2011.

M. H. Josefsen, C. Löfström, T. B. Hansen, L. S. Christensen, J. E. Olsen et al., Rapid quantification of viable Campylobacter bacteria on chicken carcasses, using real-time PCR and propidium monoazide treatment, as a tool for quantitative risk assessment, Appl Environ Microbiol, vol.76, pp.5097-5104, 2010.

A. Nocker and A. K. Camper, Novel approaches toward preferential detection of viable cells using nucleic acid amplification techniques, FEMS Microbiol Lett, vol.291, pp.137-142, 2009.

M. A. Yáñez, A. Nocker, E. Soria-soria, R. Múrtula, L. Martínez et al., Quantification of viable Legionella pneumophila cells using propidium monoazide combined with quantitative PCR, J Microbiol Methods, vol.85, pp.124-130, 2011.

A. Nocker, C. Y. Cheung, and A. K. Camper, Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells, J Microbiol Methods, vol.67, pp.310-320, 2006.

K. Kim, H. Katayama, M. Kitajima, Y. Tohya, and S. Ohgaki, Development of a realtime RT-PCR assay combined with ethidium monoazide treatment for RNA viruses and its application to detect viral RNA after heat exposure, Water Sci Technol, vol.63, pp.502-507, 2011.

S. Y. Kim and G. Ko, Using propidium monoazide to distinguish between viable and nonviable bacteria, MS2 and murine norovirus, Lett Appl Microbiol, vol.55, pp.182-188, 2012.

S. Parshionikar, I. Laseke, and G. S. Fout, Use of propidium monoazide in reverse transcriptase PCR to distinguish between infectious and noninfectious enteric viruses in water samples, Appl Environ Microbiol, vol.76, pp.4318-4326, 2010.

D. A. Graiver, S. E. Saunders, C. L. Topliff, C. L. Kelling, and B. Sl, Ethidium monoazide does not inhibit RT-PCR amplification of nonviable avian influenza RNA, J Virol Methods, vol.164, pp.51-54, 2010.

G. Sánchez, P. Elizaquível, and R. Aznar, Discrimination of infectious hepatitis A viruses by propidium monoazide real-time RT-PCR, Food Environ Virol, vol.4, pp.21-25, 2012.

I. Bertrand, J. F. Schijven, G. Sánchez, W. , P. Ottoson et al., The impact of temperature on the inactivation of enteric viruses in food and water: a review, J Appl Microbiol, vol.112, pp.1059-1074, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01803203

N. Deboosere, A. Pinon, A. Delobel, S. Temmam, T. Morin et al., A predictive microbiology approach for thermal inactivation of Hepatitis A Virus in acidified berries, Food Microbiol, vol.27, pp.962-967, 2010.

, Cliver DO: Capsid and infectivity in virus detection, Food Environ Virol, vol.1, pp.123-128, 2009.

A. Stals, E. Van-coillie, and M. Uyttendaele, Viral genes everywhere: public health implications of PCR-based testing of foods, Curr Opin Virol, vol.3, pp.69-73, 2013.

Y. Y. Kusov and V. Gauss-müller, In vitro RNA binding of the hepatitis A virus proteinase 3C (HAV 3Cpro) to secondary structure elements within the 5' terminus of the HAV genome, RNA, vol.3, pp.291-302, 1997.

P. J. Contreras, H. Urrutia, K. Sossa, and A. Nocker, Effect of PCR amplicon length on suppressing signals from membrane-compromised cells by propidium monoazide treatment, J Microbiol Methods, vol.87, pp.89-95, 2011.

T. Soejima, F. Schlitt-dittrich, and S. Yoshida, Polymerase chain reaction amplification length-dependent ethidium monoazide suppression power for heat-killed cells of Enterobacteriaceae, Anal Biochem, vol.418, pp.37-43, 2011.

J. F. Luo, W. T. Lin, and Y. Guo, Method to detect only viable cells in microbial ecology, Appl Microbiol Biotechnol, vol.86, pp.377-384, 2010.

F. B. Hollinger and S. U. Emerson, Hepatitis A virus, Fields Virology, pp.911-947, 2007.

P. K. Mathis, M. Ciarlet, K. M. Campbell, S. Wang, K. E. Owen et al., Separation of rotavirus double-layered particles and triple-layered particles by capillary zone electrophoresis, J Virol Methods, vol.169, pp.13-21, 2010.

M. Estes, B. N. Fields, D. N. Knipe, P. M. Howley, R. M. Chanock et al., Rotaviruses and their replication, Fields Virology, pp.1625-1655, 1996.

S. M. Lemon, P. C. Murphy, P. A. Shields, L. H. Ping, S. M. Feinstone et al., Antigenic and genetic variation in cytopathic hepatitis A virus variants arising during persistent infection: evidence for genetic recombination, J Virol, vol.65, pp.2056-2065, 1991.

T. Cromeans, M. D. Sobsey, and H. A. Fields, Development of a plaque assay for a cytopathic, rapidly replicating isolate of hepatitis A virus, J Med Virol, vol.22, pp.45-56, 1987.

E. Dubois, C. Hennechart, N. Deboosere, G. Merle, O. Legeay et al., Intra-laboratory validation of a concentration method adapted for the enumeration of infectious F-specific RNA coliphage, enterovirus, and hepatitis A virus from inoculated leaves of salad vegetables, Int J Food Microbiol, vol.108, pp.164-171, 2006.

M. I. Costafreda, A. Bosch, and R. M. Pinto, Development, evaluation and standardization of a real time TaqMan reverse transcription-PCR assay for quantification of hepatitis A virus in clinical and shellfish samples, Appl Environ Microbiol, vol.72, pp.3846-3855, 2006.

D. Pasquale, S. Paniconi, M. , D. Medici, D. Suffredini et al., Duplex real time PCR for the detection of hepatitis A virus in shellfish using feline calicivirus as a process control, J Virol Methods, vol.163, pp.96-100, 2010.

D. Pasquale, S. Paniconi, M. Auricchio, B. Orefice, L. Schultz et al., Comparison of different concentration methods for the detection of hepatitis A virus and calicivirus from bottled natural mineral waters, J Virol Methods, vol.165, pp.57-63, 2010.

X. L. Pang, B. Lee, N. Boroumand, B. Leblanc, J. K. Preiksaitis et al., Increased detection of rotavirus using a real time reverse transcription-polymerase chain reaction (RT-PCR) assay in stool specimens from children with diarrhea, J Med Virol, vol.72, pp.496-501, 2004.

A. Tichopad, M. Dilger, G. Schwarz, and M. W. Plaffl, Standardized determination of real-time PCR efficiency from a single reaction set-up, Nucleic Acids Res, vol.31, issue.20, p.6688, 2003.

A. H. Geeraerd, V. P. Valdramidis, and J. F. Van-impe, GInaFiT, a freeware tool to assess non-log-linear microbial survivor curves, Int J Food Microbiol, vol.102, p.297, 2005.

. Coudray-meunier, Submit your next manuscript to BioMed Central and take full advantage of: ? Convenient online submission ? Thorough peer review ? No space constraints or color figure charges ? Immediate publication on acceptance ? Inclusion in PubMed, CAS, Scopus and Google Scholar ? Research which is freely available for redistribution, BMC Microbiology, vol.13, p.216, 2013.