Latest revision as of 15:24, 14 February 2024

Date: June 9 2021 7am PDT, 10am EDT, 4pm CET

The Global Genome Biodiversity Network held a short virtual symposium on June 9. The theme of the meeting was "Operating a Biobank During a Pandemic: Facing Challenges During a Period of Heightened Relevance." The meeting was intended for the GGBN community to discuss the challenges, adaptations, and opportunities related to operating a biobank during a pandemic. This two-hour session included:

• Two keynote talks examining the heightened relevancy of biobanks during the pandemic;
• lightning talks illustrating adaptive case studies;
• breakout sessions to discuss common challenges and potential solutions shared by biobanks as a result of the pandemic.

The meeting was held on Zoom with all presentations recorded and shared on the GGBN YouTube Channel. Discussions (including breakouts) were not recorded, but meeting note were compiled so key points could be shared with the membership and to provide GGBN with insight into prioritized areas of focus.

Schedule

Keynote Speakers (10-12 minutes each)

• Dr. Christine Prat, European Virus Archive Global
• Dr. Joseph Cook, Museum of Southwestern Biology

Lightning Talks (5 minutes each)

• Heather Allen, Darwin Tree of Life, NHM London
• Andrew Bentley, University of Kansas
• Manuela Da Silva, FIOCRUZ
• Burton Lim, Royal Ontario Museum
• Kirsty Lloyd, NHM London

5 minute break

Breakout Sessions (40 minutes)

Recorders for each session provide a written summary post-meeting to be included in the symposium report.

• Databasing
  • Chairs: Andrew Bentley, University of Kansas, Biodiversity Institute & Gabi Droege, Botanic Garden and Botanical Museum Berlin
• Physical Care & Shipping
  • Chairs: Heather Allen, Darwin Tree of Life Project, Natural History Museum London & Kirsty Lloyd, CryoArks, Natural History Museum London
• Research Related Aspects
  • Chair: Burton Lim, Department of Natural History, Royal Ontario Museum

Report Back from breakout sessions (15 minutes)

3-5 minutes per breakout group

Abstracts

Biobanking as a preparedness tool against viral emergence PDF

Christine Prat, European Virus Archive GLOBAL (EVA-G)

In the case of a viral emergence, Public Health authorities are faced with the challenge to diagnose the new pathogen as quickly as possible, in order to monitor its spread, the symptoms it is causing, or understand its transmission mode. There is an urgency to gather as much information as possible on it, to develop appropriate counter measures. To fight the new virus in a timely manner, preparedness is key. Diagnostics reagents, and specifically positive controls, are necessary. Viral strains from the emerging pathogen but also from clinically or epidemiologically related viruses constitute also a major need. The distribution logistics of such products can be challenging. Viral biobanks play a crucial role to share those reagents within the scientific community, at times when no industrial partner has any product on the market yet. We describe here the biobanking processes put in place at the European Virus Archive, to allow for efficient sharing of the material needed by public health professional and research scientists in times of viral emergence. We will illustrate our talk with examples of the Zika virus emergence and more recently the SARS-CoV-2 pandemic."

The critical role of frozen biobanks in emerging zoonotic pathogen discovery and mitigation PDF

Joseph A. Cook, Museum of Southwestern Biology and Biology Department, University of New Mexico

At a critical time in human history, biobanks have never been more important as they provide critical scientific infrastructure that emphasizes rigor, sustainability, and diverse options for discovery of zoonotic pathogens and mitigation of emerging diseases. Biobanks can be transformative in emerging pathogen discovery and mitigation as they are especially well positioned to: 1) provide biodiversity libraries for proactive and rapid identification of new pathogens that establish both the range of hosts and probable spatial distributions; 2) facilitate assessment of change through time; 3) become a nexus for diverse perspectives on complexity, from ecosystems to species interactions (including symbioses), phenomes, and genomes; 4) create critical informatics linkages to other data repositories and data streams (GenBank, IsoBank, GBIF, IUCN, ToL, etc); and 5) leverage other stakeholders in human health initiatives (e.g., public health workers, pathobiologists, universities, natural history museums, wildlife agencies) that remain largely disconnected.

Darwin Tree of Life: Pros and cons of starting a project in a pandemic PDF

Heather Allen, Darwin Tree of Life Project, Natural History Museum London

The Darwin Tree of Life project aims to sequence the genomes of all 70,000 species of eukaryotic organisms present in the UK. This ambitious goal is a collaborative effort between ten different research institutions, and many other NGOs, amateur groups, charities, agencies and individuals across Britain and Ireland. The success of the project depends on field collection and identification, and our original plans hinged on BioBlitzes - large scale sampling efforts at specific locations. When the pandemic unfortunately brought this to a halt, collectors adapted by working in their own gardens and local areas, and sending specimens in the post. This meant that there was still a small amount of data trickling in, but by no means the large quantities expected with a project of this scale. This gave the project the unexpected gift of time; time to get workflows and data pipelines in place; time to figure out what works in practice and what does not.

Collections Management from home: Data cleaning, augmentation and integration PDF

Andrew Bentley, University of Kansas, Biodiversity Institute

During the pandemic most tissue collection managers lost the ability to work with physical specimens due to the partial or full closure of their facilities. Collection managers thus had to think of other ways to work with their collections remotely. This typically involved digitization, data augmentation and data cleanup. In my collection here at the University of Kansas, Biodiversity Institute Ichthyology collection and through my involvement in the BCoN Extended Specimen publication, I decided to focus my efforts on creating linkages between tissue samples used for research and the products of that research. Through linking over 17,000 Genbank sequences and over 800 publications to the tissues used I increased advocacy for my collection and highlighted the benefits of Extended Specimens. I will showcase some of this work and discuss some of these benefits.

The Fiocruz COVID-19 Biobank PDF

Manuela da Silva, Fiocruz COVID-19 Biobank

Oswaldo Cruz Foundation - Fiocruz, an Institution of Science and Technology in Health, affiliated to the Brazilian Health Ministry (HM), had dedicated efforts to establish the Biological Resource Center in Health (BRC-Health), constituted by collections of pathogenic microorganisms, related mainly to tropical diseases or those with biotechnological potential, including bacteria, fungi, protozoa, and viruses, diversemicrobiological materials with added value (e.g., taxonomic diversity and/ or biotechnological and/or epidemiological interest), and quality associated information. In the context of the COVID-19 pandemic, Fiocruz, with financial support from the HM, has conducted many important actions against the pandemic, including the building of the Hospital Center and Diagnostic Support Unit for Covid-19. In addition, Fiocruz has several reference laboratories working with Sars-Cov-2 and it has also a Genomic Network that is sequencing new coronavirus samples throughout the national territory. Thus, there is a generation of thousands of human samples related to Covid-19 and many isolates of Sars-Cov-2 and its variants of interest for future research and development that need an adequate repository infrastructure, such as a biobank, that allows safe, reliable, ethical, legal and traceable storage in compliance with national and international regulations. Considering this scenario and the new Biobank ISO (ISO 20387:2018), the Health BRC project was reformulated, following the new concepts and requirements, and with the support of the HM the Fiocruz COVID-19 Biobank was built, initiating its activities with the virus Sars-CoV-2 and its variants, besides human samples related to COVID-19. After the end of the pandemic, the Biobank will increase its scope and will incorporate other viruses, bacteria, fungi and protozoa, as well as samples from other representatives of the Brazilian biodiversity, besides human samples associated to other diseases.

Bats, Coronaviruses, and Vaccines PDF

Burton Lim, Department of Natural History, Royal Ontario Museum'

The mammal frozen tissue collection at the Royal Ontario Museum began in 1989 and now has more than 20,000 samples representing 740 species from about 30 countries in primarily tropical parts of the world. Over these past three decades, we have been preserving tissues in liquid nitrogen, which has made our collection a valuable resource, especially for the newer genomic technologies that require high molecular weight DNA and for recovering less stable RNA. During the pandemic, the importance of our biobank became even more apparent when we were able to contribute to two collaborative research projects. The first is sequencing chromosome-level genomes of horseshoe bats, which are considered the natural reservoir for SARS-like coronaviruses, and the second is screening for coronaviruses to develop ready-made vaccines for the next pandemic.

Enhancing Frozen Collections across the UK PDF (Transcript)

Kirsty Lloyd, Natural History Museum London

The CryoArks project is a UK consortium of zoos, museum, universities, and research institutes that is working to improve access to non-model zoological genetic resources for conservation and research. Our work to consolidate and curate existing collections in freezers across the UK was impacted by access restrictions forcing us to shift the focus of our activities to our digital resources and developing the database. Now that our facilities are opening, we are facing new challenges! How do you conduct an inventory of a frozen collection in a small space with no lone working rules whilst also maintaining social distancing? We have also seen an increase in loan requests from European researchers which are complicated to fulfil in post-Brexit Britain. We are still navigating this new world of contradictions and hope the lessons we have learnt will be helpful to the GGBN community.

Registration

Registration is closed. This event took place on June 9, 2021.