Threats to timely sharing of pathogen sequence data

Ribeiro, Carolina dos S.; Koopmans, Marion; Haringhuizen, George B.

doi:10.1126/science.aau5229

Cited by 41 publications

(27 citation statements)

References 2 publications

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“…Because the Nagoya Protocol has only relatively recently entered into force, it is too early to assess its implications for access to and utilization of genetic resources. However, widespread fear exists among users of genetic resources that the Protocol will have negative consequences, which are likely to include high transaction and administrative costs, reduced access to genetic resources, reduced international collaboration and negative impacts on scientific research and public health (Watanabe, 2015;Comizzoli and Holt, 2016;Cressey, 2017;Deplazes-Zemp et al, 2018;Neumann et al, 2018;Ribeiro et al, 2018). Although all countries have national sovereignty over genetic resources, some Parties to the Protocol have opted not to exercise this national sovereignty and not to require prior informed consent and mutually agreed terms for access to their genetic resources.…”

Section: Discussionmentioning

confidence: 99%

Genebank Operation in the Arena of Access and Benefit-Sharing Policies

Brink

Hintum

2020

Front. Plant Sci.

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Since the 1990s, the exchange of genetic resources has been increasingly regulated. The Convention on Biological Diversity (CBD), the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) and the Nagoya Protocol recognize that countries have sovereign rights over their genetic resources and provide a framework for domestic legislations on Access and Benefit-Sharing (ABS). However, within the rules of these international agreements, countries can follow their own interpretations and establish their own rules and regulations, resulting in restricted access to genetic resources and limited benefit-sharing, effects that are contrary to the objectives of these agreements. Although the ITPGRFA's Multilateral System of Access and Benefit-Sharing provides opportunities for easier access to plant genetic resources for food and agriculture (PGRFA), plant genebanks face increasing complexity in their operation. Adding material to genebank collections has become more difficult, not only because collecting missions need to be negotiated with national and local authorities, but also because acquiring material from other collections is only possible if the origin of the material is properly documented and is done in compliance with regulations. Genebanks may only provide access to their own collections if the material that is to be released is distributed in compliance with a) the conditions under which the material was received and b) the national laws of the country where the genebank is located. The only way genebanks can deal with this new complexity, apart from ceasing to add or distribute material, is by setting up proper procedures to document the origin of every accession and the conditions for their use and further distribution. To prevent a further decrease in access to PGRFA, complexity must be fought. Applying the ITPGRFA's Standard Material Transfer Agreement (SMTA) only, even for material that does not fall under the ITPGRFA, would simplify matters. The scope of the ITPGRFA could be expanded to include all crops. Furthermore, certain ambiguities (e.g. regarding in situ material and wild species) could be resolved. Finally, compliance with the ITPGRFA should be improved and better monitored.

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Section: Discussionmentioning

confidence: 99%

Genebank Operation in the Arena of Access and Benefit-Sharing Policies

Brink

Hintum

2020

Front. Plant Sci.

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“…The GSS would incentivize data sharing (including open-source data) by deploying FAIR (findable, accessible, interoperable, and reusable) data principles (14), although accessibility outside the system would be decided on a per-country or regional basis. Although individual countries might want to limit public availability to sensitive crop disease data, and threats to sharing data have been reported (15), the GSS would ensure that norms for sharing information and data usage are established. The GSS, through this network, would work with the plant pathology community and seek support from plant pathology journals, similar to the agreement and support from the International Committee of Medical Journal Editors, by not prejudicing journal publication because of prepublication dissemination of information that is critical to public health emergencies, as when declared by WHO.…”

Section: Department Of Natural Resources Faculty Of Geo-information mentioning

confidence: 99%

A global surveillance system for crop diseases

Carvajal-Yepes

Cardwell

Nelson

et al. 2019

Science

161

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“…Round tables with all involved stakeholders and a maximum of transparency can contribute to a political support for WGS data sharing from both authorities and industry (Jagadeesan et al, 2019). Moreover, clarification of existing regulations on data protection and sharing, such as the Nagoya Protocol (UNEP, 2011), and their application for sharing of genetic resources of pathogens is essential, especially during imminent public health emergencies (Dos et al, 2018). The inclusion in the existing regulation of special exceptions to specific requirements for the sharing of pathogen sequencing data in case of public health emergencies (i.e.…”

Section: Wgs Data Sharingmentioning

confidence: 99%

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

Koutsoumanis¹,

Allende²,

Álvarez‐Ordóñez³

et al. 2019

EFS2

101

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This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne pathogens. WGS offers the highest level of bacterial strain discrimination for food-borne outbreak investigation and sourceattribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial-temporal factors and the detection of multidirectional transmission and pathogenhost interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non-culturable, difficult-to-culture or slow-growing microorganisms, for tracking of hazard-related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin-producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGSbased genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross-border outbreaks and for the development of international standardised risk assessments of food-borne microorganisms.

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Threats to timely sharing of pathogen sequence data

Abstract: The Nagoya Protocol may impose costs and delays

Cited by 41 publications

References 2 publications

Genebank Operation in the Arena of Access and Benefit-Sharing Policies

Genebank Operation in the Arena of Access and Benefit-Sharing Policies

A global surveillance system for crop diseases

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

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