Integrating Biodiversity Infrastructure into Pathogen Discovery and Mitigation of Emerging Infectious Diseases

Cook, Joseph A.; Arai, Satoru; Armién, Blas; Bates, John M.; Bonilla, Carlos Carrion; Cortez, Maria Beatriz de Souza; Dunnum, Jonathan L.; Ferguson, Adam W.; Johnson, Karl M.; Khan, Faisal Ali Anwarali; Paul, Deborah; Reeder, DeeAnn M.; Revelez, Marcia A.; Simmons, Nancy B.; Thiers, Barbara M.; Thompson, Cody W.; Upham, Nathan S.; Vanhove, Maarten Pieterjan; Webala, Paul W.; Weksler, Marcelo; Yanagihara, Richard; Soltis, Pamela S.

doi:10.1093/biosci/biaa064

Cited by 57 publications

(42 citation statements)

References 15 publications

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“…The MDB project developed new field-based protocols for preserving holistic specimens that would facilitate research that integrated across studies of hosts and parasites (Gardner 1996;Gardner and Jiménez-Ruiz 2009). These field techniques have been subsequently expanded and refined through other large sampling efforts worldwide with new cohorts of mammalogists and parasitologists (e. g., Beringian Coevolution Project, Cook et al 2017). From those efforts, best practices in holistic sampling of mammal and parasite faunas (Galbreath et al 2019) now codify the concept of the holistic mammal specimen.…”

Section: Resultsmentioning

confidence: 99%

“…The traditional voucher (skin and skeleton-- Hafner et al 1984, or fluid preserved specimen) was supplemented by an array of ultrafrozen tissues, chromosome cell suspensions, fecal samples, and endo and ectoparasites. Now termed the "Holistic Specimen" (Cook et al 2016;Galbreath et al 2019), but also known as the "Extended Specimen" (Webster 2017), these specimens provide a breadth of materials to address not only traditional systematic and taxonomic questions, but now facilitate and integrate questions in environmental change (e. g., climate change, habitat conversion, pollutants and toxicants, biodiversity loss, introduction of exotics), and other novel and evolving contemporary research areas (e. g., pathogen emergence and discovery, genomics, microbiomes, isotopic and molecular ecology, metagenomics, transcriptomics, and proteomics; Cook et al 2017;Dunnum et al 2017;Greiman et al 2018;Schindel and Cook 2018).…”

Section: Methodsmentioning

confidence: 99%

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Sustained impact of holistic specimens for mammalogy and parasitology in South America: Sydney Anderson’s legacy

Dunnum¹,

Malaney

Cook

2020

Therya

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and the "Mammalian Diversity in Bolivia" (MDB) project (1984-1993) established a highly productive model for integrated specimen-based field expeditions. We assess the extended impact of that decade-long series of holistic surveys of mammalian diversity as a productive model for building enduring and highly integrated infrastructure for biodiversity research. We point to specific examples of impact, but more generally make a case for Sydney Anderson's prescient view that collections, over time, become ever more powerful and essential scientific tools for understanding mammalian diversity and our rapidly changing planet. To assess the number of specimens held in collections and their availability for spatial analyses, we queried the Global Biodiversity Information Facility (GBIF) for Bolivian specimens. Results were downloaded and non-georeferenced specimens were georeferenced in GeoLocate. Publications utilizing specimens or data from the MDB project were identified in Google Scholar, these were used to build a citation profile to analyze impact and breadth of research. Over the course of the decade-long MDB project ca. 10,000 new "holistic" specimens were added to natural history collections in Bolivia and the United States. These specimens and data were used in over 500 papers across a broad range of research areas, including new records for the country, and many descriptions of mammals (nine) and parasites (34) new to science. The Google Scholar profile generated for these publications has more than 20,000 citations and a citation H-index = 68 and an i-10 = 340. Sydney Anderson's legacy will endure through the exceptional collections he helped to build and the wide array of students he helped to inspire. As societal concerns related to environmental change (e. g., biological annihilation, climate change, emerging zoonotic pathogens) become more pressing, scientific questions evolve, and technology continues to develop, these critical resources will be called upon more and more frequently. Thus we can confidently predict that the value and use of the Bolivian mammal specimens archived under Syd Anderson's leadership will continue to increase in the future. Sydney Anderson y el proyecto "Diversidad de mamíferos en Bolivia" (MDB; 1984-1993) establecieron un modelo altamente productivo para expediciones integrales de campo basadas en muestras. Evaluamos el impacto extendido de esa serie de estudios holísticos de la década de la diversidad de mamíferos como modelo productivo para construir una infraestructura duradera y altamente integrada para la investigación de la biodiversidad. Se señalan ejemplos específicos del impacto, pero en general exponemos la visión premonitoria de Sydney Anderson respecto a que las colecciones, con el tiempo, se convertirán en herramientas científicas cada vez más poderosas y esenciales para comprender la diversidad de mamíferos y a nuestro planeta que cambia rápidamente. Para evaluar el número de especímenes almacenados en colecciones y su disponibilidad para análisis espaciales, cons...

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Sustained impact of holistic specimens for mammalogy and parasitology in South America: Sydney Anderson’s legacy

Dunnum¹,

Malaney

Cook

2020

Therya

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“…The high level of research complementarity among Panamanian institutions can be used to enable an information system for the prediction and mitigation of future zoonotic spillover events, including enhanced voucher collections of wildlife, domestic animal and human tissues plus associated pathogens and vectors [70].…”

Section: Targets and Bene Ts From Implementing A One Health Researchmentioning

confidence: 99%

The Bibliometric Landscape of Infectious Disease Research in Panama (1990 - 2019): An Evaluation of the Country’s Capability on One Health

Loaiza

Zapata

Kosagisharaf

et al. 2020

Preprint

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Background: This work aims to analyze the landscape of scientific publications on subjects related to One Health and infectious diseases in Panama. We asked the following specific questions: How does the One Health research landscape look like in Panama? Are historical research efforts aligned with the One Health concept? What infectious diseases have received more attention from the local scientific community since 1990?Methods: Boolean searches on the Web of Science, SCOPUS and PubMed were undertaken to evaluate the main trends of publications related to One Health and infectious disease research in the country of Panama, between 1990 and 2019. Results: 4,547 publications were identified since 1990, including 3,564 peer-reviewed articles interconnected with One Health related descriptors, and 211 articles focused particularly on infectious diseases. There was a pattern of exponential growth in the number of publications with various contributions from Panamanian institutions. The rates of multidisciplinary, inter-institutional and inter-sectoral research ranged from moderate to low, to very low, respectively. Research efforts have centered largely on protozoan, neglected and arthropod-borne diseases with a strong emphasis on malaria, Chagas and leishmaniasis. Conclusion: Panama has scientific capabilities on One Health to tackle future infectious disease threats, but the official collaboration schemes and strategic investment to develop further competencies need to be considered. Through future collaborative efforts, Panama can reduce the risk of pandemics by developing surveillance strategies to improve the prediction of disease spillover, spread and persistence while helping to mitigate the impact on public health and the economy, regionally.

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“…Efforts since March 2020 have promoted collaboration across disciplines, international boundaries, and continents. At iDigBio, staff updated information about genetic/genomic resources available in US mammal collections; 24 records were added and information enhanced (Cortez and Soltis 2020). The Distributed System of Scientific Collections (DiSSCo) and the Consortium of European Taxonomic Facilities ( CETAF) formed a worldwide COVID-19 Task Force (TaF).…”

mentioning

confidence: 99%

“…Members of the ViralMuse group worked to raise awareness of the critical value of and need for museum experts, collections data, and samples in any analyses of zoonotic events. ViralMuse members (Cook et al 2020) stressed the need for collaborative action to:…”

mentioning

confidence: 99%

Progress Out of a Pandemic: Global collections, data sharing, and changing standards of practice

Paul¹,

Soltis²

2020

BISS

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The COVID-19 pandemic has disrupted all aspects of our lives, but has also spawned new opportunities. Months of multidisciplinary, global collaboration have explored the connections between natural history collections and COVID-19. Museums have unrivalled (and still largely untapped) potential to contribute data, methods, and expertise to prediction, mitigation, and prevention efforts related to zoonotic disease outbreaks (DiEuliis et al. 2016, Dunnum et al. 2017), and there is a clear need for ongoing collaboration across (at least) microbiology, disease ecology, and natural history collections. In addition, we note that the roadblocks to effective data access and integration related to microbes and their hosts are a microcosm of the larger data landscape; solving these issues in the context of COVID-19—from liberating data from publications to ensuring digital connections between voucher specimens and all derived viral genetic sequences—will improve biodiversity data access and use more broadly. Efforts since March 2020 have promoted collaboration across disciplines, international boundaries, and continents. At iDigBio, staff updated information about genetic/genomic resources available in US mammal collections; 24 records were added and information enhanced (Cortez and Soltis 2020). The Distributed System of Scientific Collections (DiSSCo) and the Consortium of European Taxonomic Facilities (CETAF) formed a worldwide COVID-19 Task Force (TaF). A US-led group formed the ViralMuse Task Force, working in concert with the TaF. Activities of the TaF centered on four areas: building a hub to coalesce knowledge from this group in a central location – including mining mammals-of-the-world literature, improving the metadata shared when publishing sequence data, encouraging virologists to voucher in museum collections, and gathering critical research questions around zoonotic disease from the scientific community. Through an online public event, this TaF shared work to date and critical next steps. Ongoing efforts include further refinement of metadata requirements for deposition of viral genetic data to include host specimen voucher identifiers, development of methods for better integration of bat and pathogen data from the literature and databases, analysis of community surveys, and development of webinars, symposia, and publications to report the work of the TaF. Members of the ViralMuse group worked to raise awareness of the critical value of and need for museum experts, collections data, and samples in any analyses of zoonotic events. ViralMuse members (Cook et al. 2020) stressed the need for collaborative action to: develop guidelines for keeping samples of both pathogens and hosts. develop and implement metadata requirements for physical specimens and samples. expand investment in infrastructure, both cyber and physical, to support archives of biological materials. increase communication and development of new channels of dialogue and collaboration among museum scientists, microbiologists, bioinformaticians, biomedical professionals, and disease ecologists. enhance financial support and realize strong leadership from federal agencies, international partners, and private foundations to develop proactive, multi-disciplinary approaches to future pandemics (see also da Silva et al. 2020). develop guidelines for keeping samples of both pathogens and hosts. develop and implement metadata requirements for physical specimens and samples. expand investment in infrastructure, both cyber and physical, to support archives of biological materials. increase communication and development of new channels of dialogue and collaboration among museum scientists, microbiologists, bioinformaticians, biomedical professionals, and disease ecologists. enhance financial support and realize strong leadership from federal agencies, international partners, and private foundations to develop proactive, multi-disciplinary approaches to future pandemics (see also da Silva et al. 2020). ViralMuse continues to advance these goals. To reach a broader audience, we published an article in The Conversation (Soltis et al. 2020). A new project, funded by the US National Science Foundation (NSF), is aimed at enhancing existing published museum specimen data relevant to one potential reservoir of SARS-CoV-2, horseshoe bats (Mast and Paul 2020). NSF has also provided support to foster continued collaboration, infrastructure development, and integration of communities of practice concerning zoonotic diseases (Soltis and Paul 2020). From a TDWG perspective, issues relating to data access, data standards, and data integration require attention. Methods to liberate data from publications need to be expanded, and proposed metadata requirements for viral genetic sequences need to be implemented by international databases and adopted by the community. A summit on collections management software could help align efforts to both store and share the necessary host-pathogen information in standards-compliant formats that support discovery, access, and citation/attribution. A new and effective communication strategy is needed to develop an integrated research community (comprising the biodiversity, collections, data science, disease ecology, microbiology, and One Health communities) and to support needed changes in standards of practice (emphasizing vouchering, data standards, and data integration).

show abstract

Integrating Biodiversity Infrastructure into Pathogen Discovery and Mitigation of Emerging Infectious Diseases

Cited by 57 publications

References 15 publications

Sustained impact of holistic specimens for mammalogy and parasitology in South America: Sydney Anderson’s legacy

Sustained impact of holistic specimens for mammalogy and parasitology in South America: Sydney Anderson’s legacy

The Bibliometric Landscape of Infectious Disease Research in Panama (1990 - 2019): An Evaluation of the Country’s Capability on One Health

Progress Out of a Pandemic: Global collections, data sharing, and changing standards of practice

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