Download Forum Summary FOR E-DECISION

International Plant Protection Convention
Forum Summary for SC E-decision
2016_eSC_May_15_Forum Summary
FORUM SUMMARY FOR E-DECISION
(2016_eSC_May_15)
TITLE: APPROVAL OF TECHNICAL REVISION OF ADOPTED DIAGNOSTIC
PROTOCOL 07: POTATO SPINDLE TUBER VIROID
21 April 2016
Background
[1]
[2]
The diagnostic protocol (DP) 07 for Potato spindle tuber viroid1 was adopted by the Standards
Committee (SC) on behalf of the Commission on Phytosanitary Measures (CPM) in January 2015. The
lead author2 of this DP contacted the Secretariat enquiring about the possibility of a technical revision
as a discrepancy was identified in the sequence of the internal primer COX F. This discrepancy was
based on a three base pair sequence according to the referenced literature, Weller et al. 20003. However,
it was acknowledged that while both sequences do work, the results using the sequence as described by
Weller et al. 2000 are more efficient and also match the COX sequences in GenBank. The discrepancy
was as follows (in bold and underlined), under section “3.3.4.2 Real-time RT-PCR using the primers of
Boonham et al. (2004)” in the adopted DP:

IPPC DP 07: COX-F: 5´-CGT GCG ATT CCA GAT TAT CCA-3´

Weller et al. 2000: COX-F: 5´-CGT CGC ATT CCA GAT TAT CCA-3´
The SC in May 2013 established criteria for revising DPs such as a technical revision that should be
carried out by the Technical Panel on Diagnostic Protocols (TPDP), noting that other revisions would
need to be subject to the normal DP adoption process (i.e. member consultation, redrafting, SC approval,
formal objection period, SC adoption). The agreed criteria by the SC is presented in the IPPC Standard
Setting Procedure Manual4 and it is as follows:
The SC May 2013 defined the criteria for DPs revision as a technical revision that should be done by
the TPDP as follow:
-
Editorials;
-
Taxonomic changes that do not affects the identification of the pest (and do not change the
diagnosis);
-
Addition of validation data relating to the methods already on the DP;
-
Improved specification of method, e.g. additional descriptors such as amount of DNA;
-
Pest information;
-
New information on distribution of official notification;
-
New host that may help the diagnosis reported in an official notification and does not affect the
diagnosis.
1
DP 07: Potato spindle tuber viroid: https://www.ippc.int/en/publications/8073/
IPPC Diagnostic Protocols (DPs) drafting groups: https://www.ippc.int/en/publications/2582/
3
Weller, S.A., Elphinstone, J.G., Smith, N.C., Boonham, N. & Stead, D.E. 2000. Detection of Ralstonia
solanacearum strains with a quantitative multiplex, real-time, fluorogenic PCR (TaqMan) assay. Applied and
Environmental Microbiology, 66: 2853–2858. (http://aem.asm.org/content/66/7/2853.full.pdf+html)
4
IPPC Standard Setting Procedure Manual: https://www.ippc.int/en/core-activities/ippc-standard-settingprocedure-manual/
2
International Plant Protection Convention
Page 1 of 2
2015_eSC_Nov_15_ForumSummary
Forum Summary for SC E-decision
Other revisions different from the above, would need to be subject to the normal DP adoption process
(i.e. member consultation, redrafting, SC approval, formal objection period, SC adoption).
[3]
The TPDP in its March 2016 virtual meeting5 discussed this point and the TPDP agreed to invite the
SC to approve this technical revision to the adopted DP 07: Potato spindle tuber viroid. It was pointed
out by the panel that this technical revision lies under “editorials” in the list of technical revisions
approved by the SC, as is a typographical error in the primer sequence and thus falls under the
jurisdiction of the TPDP. The TPDP suggested that the erratum be accompanied by an explanation with
the information that both sequences of the primer COX-F work by the time the Secretariat re-publishes
the DP.
[4]
For easier reference, the proposed changes to the adopted DP 07: Potato spindle tuber viroid are as
follows (in track changes):
3.3.4.2 Real-time RT-PCR using the primers of Boonham et al. (2004)
(…)
Primers
(…)
The internal control COX primers amplify the cytochrome oxidase 1 gene found in plant mitochondria
(Weller et al., 2000).
COX-F: 5´-CGT CGC ATT CCA GAT TAT CCA-3´
The SC provided responses to the forum question:
(1)
Do you Approve the technical revision to the adopted DP 07: Potato spindle tuber viroid, based
on “editorials” to adjust the sequence of the internal control primer COX-F from “5´-CGT GCG
ATT CCA GAT TAT CCA-3´” to “5´-CGT CGC ATT CCA GAT TAT CCA-3´”, in accordance
with the literature referenced Weller et al. 2000.
Conclusion of the forum discussion:
The forum was open from 12 to 26 April.
The Secretariat reviewed SC member’s responses. Nine members commented and approved the
technical revision to the adopted DP 07: Potato spindle tuber viroid
5
TPDP March 2016 virtual meeting report: not available yet.
Page 2 of 2
Convention
International Plant Protection