Microbiology of the food chain - Horizontal method for determination of hepatitis A virus and norovirus using real-time RT-PCR - Part 2: Method for detection (ISO 15216-2:2019)

This document specifies a method for detection of hepatitis A virus (HAV) and norovirus genogroups I (GI) and II (GII), from test samples of foodstuffs [(soft fruit, leaf, stem and bulb vegetables, bottled water, bivalve molluscan shellfish (BMS)] or surfaces using real-time RT-PCR.
This method is not validated for detection of the target viruses in other foodstuffs (including multi-component foodstuffs), or any other matrices, nor for the detection of other viruses in foodstuffs, surfaces or other matrices.

Mikrobiologie der Lebensmittelkette - Horizontales Verfahren zur Bestimmung von Hepatitis-A-Virus und Norovirus in Lebensmitteln mittels Real-time-RT-PCR - Teil 2: Nachweisverfahren (ISO 15216-2:2019)

Dieses Dokument legt ein Verfahren für den Nachweis von Hepatitis-A-Viren (HAV) und Noroviren der Genogruppen I (GI) und II (GII) in Untersuchungsproben von Lebensmitteln [weiches Obst, Blatt-, Stängel- und Zwiebelgemüse, in Flaschen abgefülltes Trinkwasser, zweischalige Weichtiere (BMS, en: bivalve molluscan shellfish)] oder auf Oberflächen mittels Real-time-RT-PCR fest.
Dieses Verfahren ist weder für den Nachweis der Zielviren in anderen Lebensmitteln (einschließlich zusammengesetzter Lebensmittel) oder anderen Matrices noch für den Nachweis anderer Viren in Lebensmitteln, auf Oberflächen oder anderen Matrices validiert.

Microbiologie dans la chaine alimentaire - Méthode horizontale pour la recherche des virus de l'hépatite A et norovirus par la technique RT-PCR en temps réel - Partie 2: Méthode de détection (ISO 15216-2:2019)

Le présent document spécifie une méthode de détection du virus de l'hépatite A (VHA) et des norovirus des génogroupes I (GI) et II (GII) dans des échantillons pour essai d'aliments (baies, légumes feuilles, tiges et bulbes, eau embouteillée, mollusques bivalves) ou sur des surfaces par RT-PCR en temps réel.
Cette méthode n'est pas validée pour la détection des virus cibles dans d'autres aliments (y compris les aliments à plusieurs composants) ou d'autres matrices, ni pour la détection d'autres virus dans les aliments, sur les surfaces ou dans d'autres matrices.

Mikrobiologija v prehranski verigi - Horizontalna metoda za ugotavljanje virusa hepatitisa A in norovirusov z RT-PCR v realnem času - 2. del: Metoda za ugotavljanje (ISO 15216-2:2019)

Standard EN-ISO 15216-2 določa metodo za ugotavljanje virusa hepatitisa A (HAV) in norovirusov I (GI) in II (GII) iz preskusnih vzorcev živil (mehko sadje, listna, stebelna in gomoljna zelenjava, ustekleničena voda, mehkužci-školjke (BMS)) ali površin z uporabo RT-PCR v realnem času. Ta metoda ni potrjena za odkrivanje ciljnih virusov v drugih živilih (vključno s sestavljenimi živili) ali kateri koli drugih zmeseh, niti za odkrivanje drugih virusov v živilih, površinah ali drugih zmeseh.

General Information

Status
Published
Publication Date
17-Sep-2019
Current Stage
6060 - Definitive text made available (DAV) - Publishing
Due Date
18-Sep-2019
Completion Date
18-Sep-2019

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SLOVENSKI STANDARD
SIST EN ISO 15216-2:2019
01-december-2019
Nadomešča:
SIST-TS CEN ISO/TS 15216-2:2013
Mikrobiologija v prehranski verigi - Horizontalna metoda za ugotavljanje virusa
hepatitisa A in norovirusov z RT-PCR v realnem času - 2. del: Metoda za
ugotavljanje (ISO 15216-2:2019)

Microbiology of the food chain - Horizontal method for determination of hepatitis A virus

and norovirus using real-time RT-PCR - Part 2: Method for detection (ISO 15216-2:2019)

Mikrobiologie der Lebensmittelkette - Horizontales Verfahren zur Bestimmung von

Hepatitis A-Virus und Norovirus in Lebensmitteln mittels Real-time-RT-PCR - Teil 2:

Nachweisverfahren (ISO 15216-2:2019)

Microbiologie dans la chaine alimentaire - Méthode horizontale pour la recherche des

virus de l'hépatite A et norovirus par la technique RT-PCR en temps réel - Partie 2:

Méthode de détection (ISO 15216-2:2019)
Ta slovenski standard je istoveten z: EN ISO 15216-2:2019
ICS:
07.100.30 Mikrobiologija živil Food microbiology
SIST EN ISO 15216-2:2019 en

2003-01.Slovenski inštitut za standardizacijo. Razmnoževanje celote ali delov tega standarda ni dovoljeno.

---------------------- Page: 1 ----------------------
SIST EN ISO 15216-2:2019
---------------------- Page: 2 ----------------------
SIST EN ISO 15216-2:2019
EN ISO 15216-2
EUROPEAN STANDARD
NORME EUROPÉENNE
September 2019
EUROPÄISCHE NORM
ICS 07.100.30 Supersedes CEN ISO/TS 15216-2:2013
English Version
Microbiology of the food chain - Horizontal method for
determination of hepatitis A virus and norovirus using
real-time RT-PCR - Part 2: Method for detection (ISO
15216-2:2019)

Microbiologie dans la chaine alimentaire - Méthode Mikrobiologie der Lebensmittelkette - Horizontales

horizontale pour la recherche des virus de l'hépatite A Verfahren zur Bestimmung von Hepatitis A-Virus und

et norovirus par la technique RT-PCR en temps réel - Norovirus in Lebensmitteln mittels Real-time-RT-PCR -

Partie 2: Méthode de détection (ISO 15216-2:2019) Teil 2: Nachweisverfahren (ISO 15216-2:2019)

This European Standard was approved by CEN on 27 July 2019.

CEN members are bound to comply with the CEN/CENELEC Internal Regulations which stipulate the conditions for giving this

European Standard the status of a national standard without any alteration. Up-to-date lists and bibliographical references

concerning such national standards may be obtained on application to the CEN-CENELEC Management Centre or to any CEN

member.

This European Standard exists in three official versions (English, French, German). A version in any other language made by

translation under the responsibility of a CEN member into its own language and notified to the CEN-CENELEC Management

Centre has the same status as the official versions.

CEN members are the national standards bodies of Austria, Belgium, Bulgaria, Croatia, Cyprus, Czech Republic, Denmark, Estonia,

Finland, France, Germany, Greece, Hungary, Iceland, Ireland, Italy, Latvia, Lithuania, Luxembourg, Malta, Netherlands, Norway,

Poland, Portugal, Republic of North Macedonia, Romania, Serbia, Slovakia, Slovenia, Spain, Sweden, Switzerland, Turkey and

United Kingdom.
EUROPEAN COMMITTEE FOR STANDARDIZATION
COMITÉ EUROPÉEN DE NORMALISATION
EUROPÄISCHES KOMITEE FÜR NORMUNG
CEN-CENELEC Management Centre: Rue de la Science 23, B-1040 Brussels

© 2019 CEN All rights of exploitation in any form and by any means reserved Ref. No. EN ISO 15216-2:2019 E

worldwide for CEN national Members.
---------------------- Page: 3 ----------------------
SIST EN ISO 15216-2:2019
EN ISO 15216-2:2019 (E)
Contents Page

European foreword ....................................................................................................................................................... 3

---------------------- Page: 4 ----------------------
SIST EN ISO 15216-2:2019
EN ISO 15216-2:2019 (E)
European foreword

This document (EN ISO 15216-2:2019) has been prepared by Technical Committee ISO/TC 34 "Food

products" in collaboration with Technical Committee CEN/TC 275 “Food analysis - Horizontal methods”

the secretariat of which is held by DIN.

This European Standard shall be given the status of a national standard, either by publication of an

identical text or by endorsement, at the latest by March 2020, and conflicting national standards shall

be withdrawn at the latest by March 2020.

Attention is drawn to the possibility that some of the elements of this document may be the subject of

patent rights. CEN shall not be held responsible for identifying any or all such patent rights.

This document supersedes CEN ISO/TS 15216-2:2013.

According to the CEN-CENELEC Internal Regulations, the national standards organizations of the

following countries are bound to implement this European Standard: Austria, Belgium, Bulgaria,

Croatia, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Iceland,

Ireland, Italy, Latvia, Lithuania, Luxembourg, Malta, Netherlands, Norway, Poland, Portugal, Republic of

North Macedonia, Romania, Serbia, Slovakia, Slovenia, Spain, Sweden, Switzerland, Turkey and the

United Kingdom.
Endorsement notice

The text of ISO 15216-2:2019 has been approved by CEN as EN ISO 15216-2:2019 without any

modification.
---------------------- Page: 5 ----------------------
SIST EN ISO 15216-2:2019
---------------------- Page: 6 ----------------------
SIST EN ISO 15216-2:2019
INTERNATIONAL ISO
STANDARD 15216-2
First edition
2019-07
Microbiology of the food chain —
Horizontal method for determination
of hepatitis A virus and norovirus
using real-time RT-PCR —
Part 2:
Method for detection
Microbiologie dans la chaine alimentaire — Méthode horizontale
pour la recherche des virus de l'hépatite A et norovirus par la
technique RT-PCR en temps réel —
Partie 2: Méthode de détection
Reference number
ISO 15216-2:2019(E)
ISO 2019
---------------------- Page: 7 ----------------------
SIST EN ISO 15216-2:2019
ISO 15216-2:2019(E)
COPYRIGHT PROTECTED DOCUMENT
© ISO 2019

All rights reserved. Unless otherwise specified, or required in the context of its implementation, no part of this publication may

be reproduced or utilized otherwise in any form or by any means, electronic or mechanical, including photocopying, or posting

on the internet or an intranet, without prior written permission. Permission can be requested from either ISO at the address

below or ISO’s member body in the country of the requester.
ISO copyright office
CP 401 • Ch. de Blandonnet 8
CH-1214 Vernier, Geneva
Phone: +41 22 749 01 11
Fax: +41 22 749 09 47
Email: copyright@iso.org
Website: www.iso.org
Published in Switzerland
ii © ISO 2019 – All rights reserved
---------------------- Page: 8 ----------------------
SIST EN ISO 15216-2:2019
ISO 15216-2:2019(E)
Contents Page

Foreword ..........................................................................................................................................................................................................................................v

Introduction ................................................................................................................................................................................................................................vi

1 Scope ................................................................................................................................................................................................................................. 1

2 Normative references ...................................................................................................................................................................................... 1

3 Terms and definitions ..................................................................................................................................................................................... 1

4 Principle ........................................................................................................................................................................................................................ 3

4.1 Virus extraction ...................................................................................................................................................................................... 3

4.2 RNA extraction ........................................................................................................................................................................................ 3

4.3 Real-time RT-PCR .................................................................................................................................................................................. 3

4.4 Control materials .................................................................................................................................................................................. 4

4.4.1 Process control virus .................................................................................................................................................... 4

4.4.2 EC RNA control .................................................................................................................................................................. 4

4.5 Test results.................................................................................................................................................................................................. 4

5 Reagents ........................................................................................................................................................................................................................ 4

5.1 General ........................................................................................................................................................................................................... 4

5.2 Reagents used as supplied ............................................................................................................................................................ 4

5.3 Reagents requiring preparation ............................................................................................................................................... 6

6 Equipment and consumables .................................................................................................................................................................. 7

7 Sampling ........................................................................................................................................................................................................................ 8

8 Procedure..................................................................................................................................................................................................................... 8

8.1 General laboratory requirements ........................................................................................................................................... 8

8.2 Virus extraction ...................................................................................................................................................................................... 8

8.2.1 General...................................................................................................................................................................................... 8

8.2.2 Process control virus material ............................................................................................................................. 9

8.2.3 Negative process control ........................................................................................................................................... 9

8.2.4 Surfaces .................................................................................................................................................................................... 9

8.2.5 Soft fruit and leaf, stem and bulb vegetables........................................................................................... 9

8.2.6 Bottled water ...................................................................................................................................................................10

8.2.7 Bivalve molluscan shellfish (BMS) .................................................................................................................10

8.3 RNA extraction .....................................................................................................................................................................................11

8.4 Real-time RT-PCR ...............................................................................................................................................................................11

8.4.1 General requirements ...............................................................................................................................................11

8.4.2 Real-time RT-PCR analysis ....................................................................................................................................12

9 Interpretation of results ............................................................................................................................................................................14

9.1 General ........................................................................................................................................................................................................14

9.2 Construction of process control virus RNA standard curve..........................................................................14

9.3 Control for RT-PCR inhibition..................................................................................................................................................14

9.4 Calculation of extraction efficiency ....................................................................................................................................15

10 Expression of results .....................................................................................................................................................................................15

11 Performance characteristics of the method ..........................................................................................................................16

11.1 Validation study...................................................................................................................................................................................16

11.2 Sensitivity .................................................................................................................................................................................................16

11.3 Specificity .................................................................................................................................................................................................16

11.4 LOD ..........................................................................................................................................................................................................16

12 Test report ................................................................................................................................................................................................................16

Annex A (normative) Diagram of procedure .............................................................................................................................................17

Annex B (normative) Composition and preparation of reagents and buffers ........................................................18

Annex C (informative) Real-time RT-PCR mastermixes and cycling parameters ................................................21

© ISO 2019 – All rights reserved iii
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SIST EN ISO 15216-2:2019
ISO 15216-2:2019(E)

Annex D (informative) Real-time RT-PCR primers and hydrolysis probes for the detection of

HAV, norovirus GI and GII and mengo virus (process control) ..........................................................................22

Annex E (informative) Growth of mengo virus strain MC for use as a process control ..............................25

Annex F (informative) RNA extraction using the BioMerieux NucliSens system .............................................26

Annex G (informative) Generation of external control RNA (EC RNA) stocks .........................................................28

Annex H (informative) Typical optical plate layout ...........................................................................................................................31

Annex I (informative) Method validation studies and performance characteristics ......................................32

Bibliography .............................................................................................................................................................................................................................40

iv © ISO 2019 – All rights reserved
---------------------- Page: 10 ----------------------
SIST EN ISO 15216-2:2019
ISO 15216-2:2019(E)
Foreword

ISO (the International Organization for Standardization) is a worldwide federation of national standards

bodies (ISO member bodies). The work of preparing International Standards is normally carried out

through ISO technical committees. Each member body interested in a subject for which a technical

committee has been established has the right to be represented on that committee. International

organizations, governmental and non-governmental, in liaison with ISO, also take part in the work.

ISO collaborates closely with the International Electrotechnical Commission (IEC) on all matters of

electrotechnical standardization.

The procedures used to develop this document and those intended for its further maintenance are

described in the ISO/IEC Directives, Part 1. In particular, the different approval criteria needed for the

different types of ISO documents should be noted. This document was drafted in accordance with the

editorial rules of the ISO/IEC Directives, Part 2 (see www .iso .org/directives).

Attention is drawn to the possibility that some of the elements of this document may be the subject of

patent rights. ISO shall not be held responsible for identifying any or all such patent rights. Details of

any patent rights identified during the development of the document will be in the Introduction and/or

on the ISO list of patent declarations received (see www .iso .org/patents).

Any trade name used in this document is information given for the convenience of users and does not

constitute an endorsement.

For an explanation of the voluntary nature of standards, the meaning of ISO specific terms and

expressions related to conformity assessment, as well as information about ISO's adherence to the

World Trade Organization (WTO) principles in the Technical Barriers to Trade (TBT) see www .iso

.org/iso/foreword .html.

This document was prepared by the European Committee for Standardization (CEN) Technical

Committee CEN/TC 275, Food analysis — Horizontal methods, in collaboration with ISO Technical

Committee TC 34, Food products, Subcommittee SC 9, Microbiology, in accordance with the agreement

on technical cooperation between ISO and CEN (Vienna Agreement).

This first edition cancels and replaces ISO/TS 15216-2:2013, which has been technically revised with

the following changes:

— a requirement to use a suitable buffer for the dilution of control materials has been added;

— the method for generating process control virus RNA for the standard curve has been changed;

— breakpoints with a defined temperature and time parameters in the extraction methods have

been added;

— the terminology has been changed from amplification efficiency to RT-PCR inhibition;

— extra real-time RT-PCR reactions for sample RNA and negative controls have been added;

— method characteristics and the results of method validation studies have been added.

A list of all parts in the ISO 15216 series can be found on the ISO website.

Any feedback or questions on this document should be directed to the user’s national standards body. A

complete listing of these bodies can be found at www .iso .org/members .html.
© ISO 2019 – All rights reserved v
---------------------- Page: 11 ----------------------
SIST EN ISO 15216-2:2019
ISO 15216-2:2019(E)
Introduction

Hepatitis A virus (HAV) and norovirus are important agents of food-borne human viral illness. No

routine methods exist for culture of norovirus, and HAV culture methods are not appropriate for routine

application to food matrices. Detection is therefore reliant on molecular methods using the reverse-

transcriptase polymerase chain reaction (RT-PCR). As many food matrices contain substances that

are inhibitory to RT-PCR, it is necessary to use an extraction method that produces highly clean RNA

preparations that are fit for purpose. For surfaces, viruses are removed by swabbing. For soft fruit and

leaf, stem and bulb vegetables, virus extraction is by elution with agitation followed by precipitation

with PEG/NaCl. For bottled water, adsorption and elution using positively charged membranes followed

by concentration by ultrafiltration is used. For bivalve molluscan shellfish (BMS), viruses are extracted

from the tissues of the digestive glands using treatment with a proteinase K solution. For all matrices

that are not covered by this document, it is necessary to validate this method. All matrices share a

common RNA extraction method based on virus capsid disruption with chaotropic reagents followed

by adsorption of RNA to silica particles. Real-time RT-PCR monitors amplification throughout the real-

time RT-PCR cycle by measuring the excitation of fluorescently labelled molecules. In real-time RT-PCR

with hydrolysis probes, the fluorescent label is attached to a sequence-specific nucleotide probe that

also enables simultaneous confirmation of target template. These modifications increase the sensitivity

and specificity of the real-time RT-PCR method, and obviate the need for additional amplification

product confirmation steps post real-time RT-PCR. Due to the complexity of the method, it is necessary

to include a comprehensive suite of controls. The method described in this document enables detection

of virus RNA in the test sample. A schematic diagram of the testing procedure is shown in Annex A.

The main changes, listed in the Foreword, introduced in this document compared to ISO/TS 15216-2:2013,

are considered as minor (see ISO 17468).
vi © ISO 2019 – All rights reserved
---------------------- Page: 12 ----------------------
SIST EN ISO 15216-2:2019
INTERNATIONAL STANDARD ISO 15216-2:2019(E)
Microbiology of the food chain — Horizontal method for
determination of hepatitis A virus and norovirus using
real-time RT-PCR —
Part 2:
Method for detection
1 Scope

This document specifies a method for detection of hepatitis A virus (HAV) and norovirus genogroups

I (GI) and II (GII), from test samples of foodstuffs [(soft fruit, leaf, stem and bulb vegetables, bottled

water, bivalve molluscan shellfish (BMS)] or surfaces using real-time RT-PCR.

This method is not validated for detection of the target viruses in other foodstuffs (including multi-

component foodstuffs), or any other matrices, nor for the detection of other viruses in foodstuffs,

surfaces or other matrices.
2 Normative references

The following documents are referred to in the text in such a way that some or all of their content

constitutes requirements of this document. For dated references, only the edition cited applies. For

undated references, the latest edition of the referenced document (including any amendments) applies.

ISO 20838, Microbiology of food and animal feeding stuffs — Polymerase chain reaction (PCR) for the

detection of food-borne pathogens — Requirements for amplification and detection for qualitative methods

ISO 22119, Microbiology of food and animal feeding stuffs — Real-time polymerase chain reaction (PCR) for

the detection of food-borne pathogens — General requirements and definitions

ISO 22174, Microbiology of food and animal feeding stuffs — Polymerase chain reaction (PCR) for the

detection of food-borne pathogens — General requirements and definitions
3 Terms and definitions

For the purposes of this document, the terms and definitions given in ISO 20838, ISO 22119, ISO 22174

and the following apply.

ISO and IEC maintain terminological databases for use in standardization at the following addresses:

— ISO Online browsing platform: available at https:/ /www. iso. org/obp
— IEC Electropedia: available at http:/ /www.e lectropedia. org/
3.1
foodstuff
substance used or prepared for use as food

Note 1 to entry: For the purposes of this document, this definition includes bottled water.

3.2
surface
surface of food, food preparation surface or food contact surface
© ISO 2019 – All rights reserved 1
---------------------- Page: 13 ----------------------
SIST EN ISO 15216-2:2019
ISO 15216-2:2019(E)
3.3
soft fruit
small edible stoneless fruit
EXAMPLE Strawberries, raspberries, currants.
3.4
leaf, stem and bulb vegetables
leaves, stems and bulbs of plants, eaten as a vegetable
EXAMPLE Lettuce, green onions.
3.5
hepatitis A virus
HAV
member of the Picornaviridae family responsible for infectious hepatitis

Note 1 to entry: Genetically, HAV can be subdivided into six genotypes on the basis of the VP1/2A region

(genotypes 1, 2 and 3 have been found in humans, while genotypes 4, 5, and 6 are of simian origin). There is only

one serotype.

Note 2 to entry: Transmission occurs via the faecal-oral route by person-to-person contact, through the

consumption of contaminated foodstuffs (3.1), contact with contaminated water or surfaces (3.2), or contact with

contaminated fomites. HAV is classified as a group 2 biological agent by the European Union and as a risk group 2

human aetiological agent by the United States National Institutes of Health.
3.6
norovirus

member of the Caliciviridae family responsible for sporadic cases and outbreaks of acute gastroenteritis

Note 1 to entry: Genetically, norovirus can be subdivided into seven separate genogroups. Three of these

genogroups, GI, GII and GIV have been implicated in human gastrointestinal disease. GI and GII are responsible

for the vast majority of clinical cases.

Note 2 to entry: Transmission occurs via the faecal-oral route by person-to-person contact, through the

consumption of contaminated foodstuffs (3.1), through contact with contaminated water or surfaces (3.2), or

contact with contaminated fomites. GI and GII noroviruses are classified as group 2 biological agents by the

European Union and as risk group 2 human aetiological agents by the United States National Institutes of Health.

3.7
detection of HAV

detection of HAV (3.5) RNA in a predetermined mass or volume of foodstuff (3.1), or on the area of a

surface (3.2)
3.8
detection of norovirus

detection of norovirus (3.6) RNA in a predetermined mass or volume of foodstuff (3.1), or on the area of

a surface (3.2)
3.9
process control virus

virus added to the sample portion at the earliest opportunity prior to virus extraction to control for

extraction efficiency
3.10
process control virus RNA

RNA extracted from the process control virus (3.9) in order to produce standard curve data for the

estimation of extraction efficiency
3.11
negative RNA extraction control

control free of target RNA carried through all steps of the RNA extraction and detection procedure to

monitor any contamination events
2 © ISO 2019 – All rights reserved
---------------------- Page: 14 ----------------------
SIST EN ISO 15216-2:2019
ISO 15216-2:2019(E)
3.12
negative process control

target pathogen-free sample of the food matrix, or target pathogen-free non-matrix sample, that is run

through all stages of the analytical process
3.13
hydrolysis probe

fluorescent probe coupled with a fluorescent reporter molecule and a quencher molecule, which are

sterically separated by the 5′-3′-exonuclease activity of the enzyme during the amplification process

3.14
negative real-time RT-PCR control

aliquot of highly pure water used in a real-time RT-PCR reaction to assess contamination in the real-

time RT-PCR reagents
3.15
external control RNA
EC RNA

reference RNA that can be used to assess inhibition of amplification for the real-time RT-PCR assay of

relevance by being added in a defined amount to an aliquot of sample RNA in a separate reaction

EXAMPLE RNA synthesized by in vitro transcription from a plasmid carrying a copy of the target gene.

3.16
C value

quantification cycle, which is the cycle at which the target is quantified in a given real-time RT-PCR

reaction

Note 1 to entry: This corresponds to the cycle at which reaction fluorescence rises above a threshold level.

4 Principle
4.1 Virus extraction

The foodstuffs and surfaces covered by this document are often highly complex matrices and the target

viruses can be present at low concentrations. It is therefore necessary to carry out matrix-specific virus

extraction and/or concentration in order to provide a substrate for subsequent common parts of the

process. The choice of method depends upon the matrix.
4.2 RNA extraction
It is necessary
...

SLOVENSKI STANDARD
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01-julij-2018
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Microbiology of the food chain - Horizontal method for determination of hepatitis A virus

and norovirus in food using real-time RT-PCR - Part 2: Method for detection (ISO/DIS

15216-2:2018)
Mikrobiologie der Lebensmittelkette - Horizontales Verfahren zur Bestimmung von

Hepatitis A-Virus und Norovirus in Lebensmitteln mittels Real-time-RT-PCR - Teil 2:

Nachweisverfahren (ISO/DIS 15216-2:2018)

Microbiologie de la chaine alimentaire - Méthode horizontale pour la recherche des virus

de l'hépatite A et norovirus par RT-PCR en temps réel - Partie 2: Méthode de détection

(ISO/DIS 15216-2:2018)
Ta slovenski standard je istoveten z: prEN ISO 15216-2
ICS:
07.100.30 Mikrobiologija živil Food microbiology
oSIST prEN ISO 15216-2:2018 en

2003-01.Slovenski inštitut za standardizacijo. Razmnoževanje celote ali delov tega standarda ni dovoljeno.

---------------------- Page: 1 ----------------------
oSIST prEN ISO 15216-2:2018
---------------------- Page: 2 ----------------------
oSIST prEN ISO 15216-2:2018
DRAFT INTERNATIONAL STANDARD
ISO/DIS 15216-2
ISO/TC 34/SC 9 Secretariat: AFNOR
Voting begins on: Voting terminates on:
2018-04-30 2018-07-23
Microbiology of the food chain — Horizontal method for
determination of hepatitis A virus and norovirus in food
using real-time RT-PCR —
Part 2:
Method for detection

Microbiologie des aliments — Méthode horizontale pour la recherche des virus de l'hépatite A et norovirus

dans les aliments par la technique RT-PCR en temps réel —
Partie 2: Méthode de détection qualitative
ICS: 07.100.30
THIS DOCUMENT IS A DRAFT CIRCULATED
This document is circulated as received from the committee secretariat.
FOR COMMENT AND APPROVAL. IT IS
THEREFORE SUBJECT TO CHANGE AND MAY
NOT BE REFERRED TO AS AN INTERNATIONAL
STANDARD UNTIL PUBLISHED AS SUCH.
IN ADDITION TO THEIR EVALUATION AS
ISO/CEN PARALLEL PROCESSING
BEING ACCEPTABLE FOR INDUSTRIAL,
TECHNOLOGICAL, COMMERCIAL AND
USER PURPOSES, DRAFT INTERNATIONAL
STANDARDS MAY ON OCCASION HAVE TO
BE CONSIDERED IN THE LIGHT OF THEIR
POTENTIAL TO BECOME STANDARDS TO
WHICH REFERENCE MAY BE MADE IN
Reference number
NATIONAL REGULATIONS.
ISO/DIS 15216-2:2018(E)
RECIPIENTS OF THIS DRAFT ARE INVITED
TO SUBMIT, WITH THEIR COMMENTS,
NOTIFICATION OF ANY RELEVANT PATENT
RIGHTS OF WHICH THEY ARE AWARE AND TO
PROVIDE SUPPORTING DOCUMENTATION. ISO 2018
---------------------- Page: 3 ----------------------
oSIST prEN ISO 15216-2:2018
ISO/DIS 15216-2:2018(E)
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oSIST prEN ISO 15216-2:2018
ISO/DIS 15216-2:2018(E)
ISO/DIS 15216-2(E)
Contents

Foreword ........................................................................................................................................................................... v

Introduction ................................................................................................................................................................... vi

1 Scope ....................................................................................................................................................................1

2 Normative references ....................................................................................................................................1

3 Terms and definitions ....................................................................................................................................1

4 Principle ..............................................................................................................................................................3

4.1 Virus extraction ................................................................................................................................................3

4.2 RNA extraction ..................................................................................................................................................3

4.3 Real-time RT-PCR ............................................................................................................................................4

4.4 Control materials .............................................................................................................................................4

4.5 Test results .........................................................................................................................................................4

5 Reagents ..............................................................................................................................................................5

5.1 General ................................................................................................................................................................5

5.2 Reagents used as supplied ............................................................................................................................5

5.3 Prepared reagents ...........................................................................................................................................6

6 Equipment and consumables ......................................................................................................................7

7 Sampling .............................................................................................................................................................8

8 Procedure ...........................................................................................................................................................8

8.1 General laboratory requirements .............................................................................................................8

8.2 Virus extraction ................................................................................................................................................8

8.3 RNA extraction ............................................................................................................................................... 11

8.4 Real-time RT-PCR ......................................................................................................................................... 12

9 Interpretation of results ............................................................................................................................ 14

9.1 General ............................................................................................................................................................. 14

9.2 Construction of process control virus RNA standard curve .......................................................... 14

9.3 Control for RT-PCR inhibition .................................................................................................................. 14

9.4 Calculation of extraction efficiency ........................................................................................................ 15

10 Expression of results ................................................................................................................................... 16

11 Performance characteristics of the method........................................................................................ 16

11.1 Validation study ............................................................................................................................................ 16

11.2 Sensitivity ........................................................................................................................................................ 16

11.3 Specificity ........................................................................................................................................................ 16

11.4 LOD ................................................................................................................................................................. 16

12 Test report ...................................................................................................................................................... 16

Annex A (normative) Diagram of procedure ................................................................................................... 18

Annex B (normative) Composition and preparation of reagents and buffers ..................................... 19

Annex C (informative) Real-time RT-PCR mastermixes and cycling parameters .............................. 22

Annex D (informative) Real-time RT-PCR primers and hydrolysis probes for the detection

of HAV, norovirus GI and GII and mengo virus (process control) ............................................... 23

Annex E (informative) Growth of mengo virus strain MC for use as a process control .................. 25

Annex F (informative) RNA extraction using the BioMerieux NucliSens system ............................. 26

Annex G (informative) Generation of external control RNA (EC RNA) stocks ..................................... 28

iii
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Annex H (informative) Typical optical plate layout...................................................................................... 31

Annex I (informative) Method validation studies and performance characteristics ....................... 32

Bibliography ................................................................................................................................................................. 44

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oSIST prEN ISO 15216-2:2018
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ISO/DIS 15216-2(E)
Foreword

ISO (the International Organization for Standardization) is a worldwide federation of national

standards bodies (ISO member bodies). The work of preparing International Standards is normally

carried out through ISO technical committees. Each member body interested in a subject for which a

technical committee has been established has the right to be represented on that committee.

International organizations, governmental and non-governmental, in liaison with ISO, also take part in

the work. ISO collaborates closely with the International Electrotechnical Commission (IEC) on all

matters of electrotechnical standardization.

The procedures used to develop this document and those intended for its further maintenance are

described in the ISO/IEC Directives, Part 1. In particular the different approval criteria needed for the

different types of ISO documents should be noted. This document was drafted in accordance with the

editorial rules of the ISO/IEC Directives, Part 2 (see www.iso.org/directives).

Attention is drawn to the possibility that some of the elements of this document may be the subject of

patent rights. ISO shall not be held responsible for identifying any or all such patent rights. Details of

any patent rights identified during the development of the document will be in the Introduction and/or

on the ISO list of patent declarations received (see www.iso.org/patents).

Any trade name used in this document is information given for the convenience of users and does not

constitute an endorsement.

For an explanation on the voluntary nature of standards, the meaning of ISO specific terms and

expressions related to conformity assessment, as well as information about ISO's adherence to the

World Trade Organization (WTO) principles in the Technical Barriers to Trade (TBT) see the following

URL: www.iso.org/iso/foreword.html.

This document was prepared by Technical Committee ISO/TC 34, Food products, Subcommittee SC 9,

Microbiology.

This first edition cancels and replaces ISO/TS 15216-2:2013, which has been technically revised with

the following changes:
- use of a suitable buffer for dilution of control materials prescribed;

- change to the method for generating process control virus RNA for the standard curve;

- addition of breakpoints with defined temperature and time parameters in the extraction methods;

- change in terminology from amplification efficiency to RT-PCR inhibition;

- addition of extra real-time RT-PCR reactions for sample RNA and negative controls;

- addition of method characteristics and results of method validation studies.
A list of all parts in the ISO 15216 series can be found on the ISO website.
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Introduction

Hepatitis A virus (HAV) and norovirus are important agents of food-borne human viral illness. No

routine methods exist for culture of norovirus, and HAV culture methods are not appropriate for

routine application to food matrices. Detection is therefore reliant on molecular methods using the

reverse-transcriptase polymerase chain reaction (RT-PCR). As many food matrices contain substances

that are inhibitory to RT-PCR, it is necessary to use an extraction method that produces highly clean

RNA preparations that are fit for purpose. For food surfaces, viruses are removed by swabbing. For soft

fruit, leaf, stem and bulb vegetables, virus extraction is by elution with agitation followed by

precipitation with PEG/NaCl. For bottled water, adsorption and elution using positively charged

membranes followed by concentration by ultrafiltration is used and for bivalve molluscan shellfish

(BMS), viruses are extracted from the tissues of the digestive glands using treatment with a proteinase

K solution. For all matrices that are not covered by this International Standard, it is necessary to

validate this method. All matrices share a common RNA extraction method based on virus capsid

disruption with chaotropic reagents followed by adsorption of RNA to silica particles. Real-time RT-PCR

monitors amplification throughout the real-time RT-PCR cycle by measuring the excitation of

fluorescently labelled molecules. In real-time RT-PCR with hydrolysis probes, the fluorescent label is

attached to a sequence-specific nucleotide probe that also enables simultaneous confirmation of target

template. These modifications increase the sensitivity and specificity of the real-time RT-PCR method,

and obviate the need for additional amplification product confirmation steps post real-time RT-PCR.

Due to the complexity of the method, it is necessary to include a comprehensive suite of controls. The

method described in this part of ISO 15216 enables detection of virus RNA in the test sample. A

schematic diagram of the testing procedure is shown in Annex A.

The main changes, listed in the Foreword, introduced in this document compared to ISO/TS 15216-

[2]
2:2013, are considered as minor (see ISO 17468 ).
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ISO/DIS 15216-2:2018(E)
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Microbiology of the food chain — Horizontal method for
determination of hepatitis A virus and norovirus using real-time
RT-PCR — Part 2: Method for detection
1 Scope

This document specifies a method for detection of HAV and norovirus genogroups I (GI) and II (GII),

from test samples of foodstuffs (soft fruit, leaf, stem and bulb vegetables, bottled water, BMS) or food

surfaces. Following liberation of viruses from the test sample, viral RNA is then extracted by lysis with

guanidine thiocyanate and adsorption on silica. Target sequences within the viral RNA are amplified

and detected by real-time RT-PCR.

This method is not validated for detection of the target viruses in other foodstuffs (including multi-

component foodstuffs), or any other matrices, nor for the detection of other viruses in foodstuffs, food

surfaces or other matrices.
2 Normative references

The following documents are referred to in the text in such a way that some or all of their content

constitutes requirements of this document. For dated references, only the edition cited applies. For

undated references, the latest edition of the referenced document (including any amendments) applies.

ISO 22174, Microbiology of food and animal feeding stuffs — Polymerase chain reaction (PCR) for the

detection of food-borne pathogens — General requirements and definitions

ISO 22119, Microbiology of food and animal feeding stuffs — Real time polymerase chain reaction (PCR)

for the detection of food borne pathogens — General requirements and definitions

ISO 20838, Microbiology of food and animal feeding stuffs — Polymerase chain reaction (PCR) for the

detection of food-borne pathogens — Requirements for amplification and detection for qualitative

methods
3 Terms and definitions

For the purposes of this document, the terms and definitions given in ISO 22174, ISO 22119 and ISO

20838 and the following apply.

ISO and IEC maintain terminological databases for use in standardization at the following addresses:

— IEC Electropedia: available at http://www.electropedia.org/
— ISO Online browsing platform: available at http://www.iso.org/obp
3.1
foodstuff
substance used or prepared for use as food

Note 1 to entry: For the purposes of this part of ISO 15216, this definition includes bottled water.

3.2
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food surface
surface of food, food preparation surface or food contact surface
3.3
soft fruit
small edible stoneless fruit
EXAMPLE Strawberries, raspberries or currants
3.4
leaf, stem and bulb vegetables
leaves, stems and bulbs of plants, eaten as a vegetable
EXAMPLE Lettuce or green onions
3.5hepatitis A virus
HAV
member of the Picornaviridae family responsible for infectious hepatitis

Note 1 to entry: Genetically, HAV can be subdivided into six genotypes on the basis of the VP1/2A region

(genotypes 1, 2, and 3 have been found in humans, while genotypes 4, 5, and 6 are of simian origin). There is only

one serotype.

Note 2 to entry: Transmission occurs via the faecal-oral route by person-to-person contact, through the

consumption of contaminated foodstuffs, contact with contaminated water or food surfaces, or contact with

contaminated fomites. HAV is classified as a group 2 biological agent by the European Union and as a risk group 2

human aetiological agent by the United States National Institutes of Health.
3.6
norovirus

member of the Caliciviridae family responsible for sporadic cases and outbreaks of acute gastroenteritis

Note 1 to entry: Genetically, norovirus can be subdivided into seven separate genogroups. Three of these

genogroups, GI, GII and GIV have been implicated in human gastrointestinal disease. GI and GII are responsible for

the vast majority of clinical cases.

Note 2 to entry: Transmission occurs via the faecal-oral route by person-to-person contact, through the

consumption of contaminated foodstuffs or through contact with contaminated water or food surfaces or contact

with contaminated fomites. GI and GII noroviruses are classified as group 2 biological agents by the European

Union and as risk group 2 human aetiological agents by the United States National Institutes of Health.

3.7
detection of HAV

detection of HAV RNA in a predetermined mass or volume of foodstuff, or area of food surface

3.8
detection of norovirus

detection of norovirus RNA in a predetermined mass or volume of foodstuff, or area of food surface

3.9
process control virus

virus added to the sample portion at the earliest opportunity prior to virus extraction to control for

extraction efficiency
3.10
process control virus RNA
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RNA extracted from the process control virus in order to produce standard curve data for the

estimation of extraction efficiency
3.11
negative RNA extraction control

control free of target RNA carried through all steps of the RNA extraction and detection procedure to

monitor any contamination events
3.12
negative process control

target pathogen-free sample of the food matrix, or target pathogen-free non-matrix sample, that is run

through all stages of the analytical process
3.13
hydrolysis probe

fluorescent probe coupled with a fluorescent reporter molecule and a quencher molecule, which are

sterically separated by the 5′-3′-exonuclease activity of the enzyme during the amplification process

3.14
negative real-time RT-PCR control

aliquot of highly pure water used in a real-time RT-PCR reaction to control for contamination in the

real-time RT-PCR reagents
3.15
external control RNA
EC RNA

reference RNA that can be used to assess inhibition of amplification for the real-time RT-PCR assay of

relevance by being added in a defined amount to an aliquot of sample RNA in a separate reaction

EXAMPLE RNA synthesized by in-vitro transcription from a plasmid carrying a copy of the target gene

3.16
C value

quantification cycle; the cycle at which the target is quantified in a given real-time RT-PCR reaction

Note 1 to entry: This corresponds to the point at which reaction fluorescence rises above a threshold level.

4 Principle
4.1 Virus extraction

The foodstuffs and food surfaces covered by this part of ISO 15216 are often highly complex matrices

and the target viruses can be present at low concentrations. It is therefore necessary to carry out

matrix-specific virus extraction and/or concentration in order to provide a substrate for subsequent

common parts of the process. The choice of method depends upon the matrix.
4.2 RNA extraction

It is necessary to extract RNA using a method that yields RNA preparations of suitable purity to reduce

the effect of RT-PCR inhibitors. In this part of ISO 15216 the chaotropic agent guanidine thiocyanate is

used to disrupt the viral capsid. RNA is then adsorbed to silica to assist purification through several

washing stages. Purified viral RNA is released from the silica into a buffer prior to real-time RT-PCR.

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4.3 Real-time RT-PCR

This part of ISO 15216 uses one-step real-time RT-PCR using hydrolysis probes. In one-step real-time

RT-PCR, reverse transcription and PCR amplification are carried out consecutively in the same tube.

Real-time RT-PCR using hydrolysis probes utilizes a short DNA probe with a fluorescent label and a

fluorescence quencher attached at opposite ends. The assay chemistry ensures that as the quantity of

amplified product increases, the probe is hydrolysed and the fluorescent signal from the label increases

proportionately.

Due to the low levels of virus template often present in foodstuffs or food surfaces and the strain

diversity in the target viruses, selection of fit-for-purpose one step real-time RT-PCR reagents and PCR

primers and hydrolysis probes for the target viruses is important. Guidelines for their selection are

given in 5.2.18 and 5.2.19. Illustrative details of reagents, primers, and probes (used in the development

of this part of ISO 15216) are provided in Annexes C and D.
4.4 Control materials
4.4.1 Process control virus

Losses of target virus can occur at several stages during sample virus extraction and RNA extraction. To

account for these losses, samples are spiked at the earliest opportunity prior to virus extraction with a

defined amount of a process control virus. The level of recovery of the process control virus shall be

determined for each sample.

The virus selected for use as a process control shall be a culturable non-enveloped positive-sense

ssRNA virus of a similar size to the target viruses to provide a good morphological and physicochemical

model. The process control virus shall exhibit similar persistence in the environment to the targets. The

virus shall be sufficiently distinct genetically from the target viruses that real-time RT-PCR assays for

the target and process control viruses do not cross-react, and shall not normally be expected to occur

naturally in the foodstuffs or food surfaces under test.

An example of the preparation of process control virus (used in the development of this part of ISO

15216) is provided in Annex E.
4.4.2 EC RNA control

Many food matrices contain substances inhibitory to RT-PCR, and there is also a possibility of carryover

of further inhibitory substances from upstream processing. In order to control for RT-PCR inhibition in

individual samples, EC RNA (an RNA species carrying the target sequence of interest, 5.3.11) is added to

an aliquot of sample RNA and tested using the real-time RT-PCR method. Comparison of the results of

this with the results of EC RNA in the absence of sample RNA enables determination of the level of RT-

PCR inhibition in each sample under test. In addition, in this method, the EC RNA control acts as a

positive control for real-time RT-PCR for the target viruses.

Alternative approaches for the assessment of inhibition of RT-PCR that can be demonstrated to provide

equivalent performance to the use of EC RNA control are permitted.
4.5 Test results

For food surfaces, this method provides a result expressed either as “virus genome detected” or “virus

genome not detected” followed by “in x cm ” where x is the approximate surface area swabbed; where it

is not possible to record the surface area swabbed, results are expressed either as “virus genome

detected” or “virus genome not detected”. For other sample types, results are expressed as “virus

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genome detected” or “virus genome not detected” followed by "in x ml" or "in x g”, where x is the

amount of sample tested.
5 Reagents
5.1 General
Use only reagents of recognized analytical grade, unless otherwise specified.
[1]
For current laboratory practice, see ISO 7218.
5.2 Reagents used as supplied
5.2.1 Molecular biology grade water.
5.2.2 Polyethylene glycol (PEG), mean relative molecular mass 8 000.
5.2.3 Sodium chloride (NaCl).
5.2.4 Potassium chloride (KCl).
5.2.5 Disodium hydrogenphosphate (Na HPO ).
2 4
5.2.6 Potassium dihydrogenphosphate (KH PO ).
2 4
5.2.7 Tris base.
5.2.8 Glycine.
5.2.9 Beef extract powder.
5.2.10 Proteinase K.
5.2.11 Pectinase from Aspergillus niger or A. aculeatus.
5.2.12 Chloroform.
5.2.13 n-Butanol.
5.2.14 Sodium hydroxide (NaOH) (≥10 mol/l).
5.2.15 Hydrochloric acid (HCl) (≥5 mol/l).
5.2.16 Ethylenediaminetetraacetic acid (EDTA) disodium dihydrate.

5.2.17 Silica, lysis, wash, and elution buffers for extraction of viral RNA. Reagents shall enable

processing of 500 μl of sample extract, using lysis with a chaotropic buffer containing guanidine

thiocyanate (Reference [3]) and using silica as the RNA-binding matrix. Following treatment of silica-

bound RNA with wash buffer(s) to remove impurities, RNA shall be eluted in 100 μl elution buffer.

The RNA preparation shall be of a quality and concentration suitable for the intended purpose. See

Annex F for illustrative details of RNA extraction reagents (used in the development of the method

described in this part of ISO 15216).
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5.2.18 Reagents for one step real-time RT-PCR. Reagents shall allow processing of 5 μl RNA in 25 μl

total volume. They shall be suitable for one step real-time RT-PCR using hydrolysis probes (the DNA

polymerase used shall possess 5'-3' exonuclease activity) and sufficiently sensitive for the detection of

virus RNA as expected in virus-contaminated foodstuffs and food surfaces. See Annex C for illustrative

details of one step real-time RT-PCR reagents (used in the development of this part of ISO 15216).

5.2.19 Primers and hydrolysis probes for detection of HAV and norovirus GI and GII. Primer and

hydrolysis probe sequences shall be published in a peer-reviewed journal and be verified for use

against a broad range of strains of target virus. Primers for detection of HAV shall target the 5’ non-

coding region of the genome. Primers for detection of norovirus GI and GII shall target the ORF1/ORF2

junction of the genome. See Annex D for illustrative details of primers and hydrolysis probes (used in

the development of this part of ISO 15216).
5.2.20 Primer
...

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