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Cicero C, Koo MS, Braker E, Abbott J, Bloom D, Campbell M, Cook JA, Demboski JR, Doll AC, Frederick LM, Linn AJ, Mayfield-Meyer TJ, McDonald DL, Nachman MW, Olson LE, Roberts D, Sikes DS, Witt CC, Wommack EA. Arctos: Community-driven innovations for managing natural and cultural history collections. PLoS One 2024; 19:e0296478. [PMID: 38820381 PMCID: PMC11142579 DOI: 10.1371/journal.pone.0296478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/22/2024] [Indexed: 06/02/2024] Open
Abstract
More than tools for managing physical and digital objects, museum collection management systems (CMS) serve as platforms for structuring, integrating, and making accessible the rich data embodied by natural history collections. Here we describe Arctos, a scalable community solution for managing and publishing global biological, geological, and cultural collections data for research and education. Specific goals are to: (1) Describe the core features and implementation of Arctos for a broad audience with respect to the biodiversity informatics principles that enable high quality research; (2) Highlight the unique aspects of Arctos; (3) Illustrate Arctos as a model for supporting and enhancing the Digital Extended Specimen concept; and (4) Emphasize the role of the Arctos community for improving data discovery and enabling cross-disciplinary, integrative studies within a sustainable governance model. In addition to detailing Arctos as both a community of museum professionals and a collection database platform, we discuss how Arctos achieves its richly annotated data by creating a web of knowledge with deep connections between catalog records and derived or associated data. We also highlight the value of Arctos as an educational resource. Finally, we present the financial model of fiscal sponsorship by a nonprofit organization, implemented in 2022, to ensure the long-term success and sustainability of Arctos.
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Affiliation(s)
- Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Michelle S. Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Emily Braker
- University of Colorado Museum of Natural History, University of Colorado, Boulder, Colorado, United States of America
| | - John Abbott
- Department of Museums Research and Collections and Alabama Museum of Natural History, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - David Bloom
- VertNet, Sebastopol, California, United States of America
| | - Mariel Campbell
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Joseph A. Cook
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - John R. Demboski
- Denver Museum of Nature & Science, Denver, Colorado, United States of America
| | - Andrew C. Doll
- Denver Museum of Nature & Science, Denver, Colorado, United States of America
| | - Lindsey M. Frederick
- New Mexico Museum of Natural History & Science, Albuquerque, New Mexico, United States of America
| | - Angela J. Linn
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | | | | | - Michael W. Nachman
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Link E. Olson
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Dawn Roberts
- Chicago Academy of Sciences, Chicago, Illinois, United States of America
| | - Derek S. Sikes
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
- Department of Biology & Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Christopher C. Witt
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Elizabeth A. Wommack
- University of Wyoming Museum of Vertebrates, University of Wyoming, Laramie, Wyoming, United States of America
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Lendino A, Castellanos AA, Pigott DM, Han BA. A review of emerging health threats from zoonotic New World mammarenaviruses. BMC Microbiol 2024; 24:115. [PMID: 38575867 PMCID: PMC10993514 DOI: 10.1186/s12866-024-03257-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/12/2024] [Indexed: 04/06/2024] Open
Abstract
Despite repeated spillover transmission and their potential to cause significant morbidity and mortality in human hosts, the New World mammarenaviruses remain largely understudied. These viruses are endemic to South America, with animal reservoir hosts covering large geographic areas and whose transmission ecology and spillover potential are driven in part by land use change and agriculture that put humans in regular contact with zoonotic hosts.We compiled published studies about Guanarito virus, Junin virus, Machupo virus, Chapare virus, Sabia virus, and Lymphocytic Choriomeningitis virus to review the state of knowledge about the viral hemorrhagic fevers caused by New World mammarenaviruses. We summarize what is known about rodent reservoirs, the conditions of spillover transmission for each of these pathogens, and the characteristics of human populations at greatest risk for hemorrhagic fever diseases. We also review the implications of repeated outbreaks and biosecurity concerns where these diseases are endemic, and steps that countries can take to strengthen surveillance and increase capacity of local healthcare systems. While there are unique risks posed by each of these six viruses, their ecological and epidemiological similarities suggest common steps to mitigate spillover transmission and better contain future outbreaks.
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Affiliation(s)
- Arianna Lendino
- The George Washington University, Milken Institute for Public Health, Washington, DC, 20052, USA
| | | | - David M Pigott
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle, WA, 98121, USA
| | - Barbara A Han
- Cary Institute of Ecosystem Studies, Millbrook, NY, 12545, USA.
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Miller MJ, Perinet L, Alter HJ, Conry-Cantilena K, De Giorgi V. Natural History Studies, a Natural Next Step to Study Emerging Transfusion-Transmitted Infections. Transfus Med Rev 2024; 38:150820. [PMID: 38364616 DOI: 10.1016/j.tmrv.2024.150820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/18/2024]
Affiliation(s)
- Maureen J Miller
- Infectious Diseases Section, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA.
| | - Lara Perinet
- Infectious Diseases Section, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Harvey J Alter
- Infectious Diseases Section, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Kathleen Conry-Cantilena
- Infectious Diseases Section, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Valeria De Giorgi
- Infectious Diseases Section, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
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4
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Clark EC, Neumann S, Hopkins S, Kostopoulos A, Hagerman L, Dobbins M. Changes to Public Health Surveillance Methods Due to the COVID-19 Pandemic: Scoping Review. JMIR Public Health Surveill 2024; 10:e49185. [PMID: 38241067 PMCID: PMC10837764 DOI: 10.2196/49185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/06/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND Public health surveillance plays a vital role in informing public health decision-making. The onset of the COVID-19 pandemic in early 2020 caused a widespread shift in public health priorities. Global efforts focused on COVID-19 monitoring and contact tracing. Existing public health programs were interrupted due to physical distancing measures and reallocation of resources. The onset of the COVID-19 pandemic intersected with advancements in technologies that have the potential to support public health surveillance efforts. OBJECTIVE This scoping review aims to explore emergent public health surveillance methods during the early COVID-19 pandemic to characterize the impact of the pandemic on surveillance methods. METHODS A scoping search was conducted in multiple databases and by scanning key government and public health organization websites from March 2020 to January 2022. Published papers and gray literature that described the application of new or revised approaches to public health surveillance were included. Papers that discussed the implications of novel public health surveillance approaches from ethical, legal, security, and equity perspectives were also included. The surveillance subject, method, location, and setting were extracted from each paper to identify trends in surveillance practices. Two public health epidemiologists were invited to provide their perspectives as peer reviewers. RESULTS Of the 14,238 unique papers, a total of 241 papers describing novel surveillance methods and changes to surveillance methods are included. Eighty papers were review papers and 161 were single studies. Overall, the literature heavily featured papers detailing surveillance of COVID-19 transmission (n=187). Surveillance of other infectious diseases was also described, including other pathogens (n=12). Other public health topics included vaccines (n=9), mental health (n=11), substance use (n=4), healthy nutrition (n=1), maternal and child health (n=3), antimicrobial resistance (n=2), and misinformation (n=6). The literature was dominated by applications of digital surveillance, for example, by using big data through mobility tracking and infodemiology (n=163). Wastewater surveillance was also heavily represented (n=48). Other papers described adaptations to programs or methods that existed prior to the COVID-19 pandemic (n=9). The scoping search also found 109 papers that discuss the ethical, legal, security, and equity implications of emerging surveillance methods. The peer reviewer public health epidemiologists noted that additional changes likely exist, beyond what has been reported and available for evidence syntheses. CONCLUSIONS The COVID-19 pandemic accelerated advancements in surveillance and the adoption of new technologies, especially for digital and wastewater surveillance methods. Given the investments in these systems, further applications for public health surveillance are likely. The literature for surveillance methods was dominated by surveillance of infectious diseases, particularly COVID-19. A substantial amount of literature on the ethical, legal, security, and equity implications of these emerging surveillance methods also points to a need for cautious consideration of potential harm.
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Affiliation(s)
- Emily C Clark
- National Collaborating Centre for Methods and Tools, Hamilton, ON, Canada
| | - Sophie Neumann
- National Collaborating Centre for Methods and Tools, Hamilton, ON, Canada
| | - Stephanie Hopkins
- National Collaborating Centre for Methods and Tools, Hamilton, ON, Canada
| | - Alyssa Kostopoulos
- National Collaborating Centre for Methods and Tools, Hamilton, ON, Canada
| | - Leah Hagerman
- National Collaborating Centre for Methods and Tools, Hamilton, ON, Canada
| | - Maureen Dobbins
- National Collaborating Centre for Methods and Tools, Hamilton, ON, Canada
- School of Nursing, McMaster University, Hamilton, ON, Canada
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5
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Rayfield KM, Mychajliw AM, Singleton RR, Sholts SB, Hofman CA. Uncovering the Holocene roots of contemporary disease-scapes: bringing archaeology into One Health. Proc Biol Sci 2023; 290:20230525. [PMID: 38052246 DOI: 10.1098/rspb.2023.0525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
The accelerating pace of emerging zoonotic diseases in the twenty-first century has motivated cross-disciplinary collaboration on One Health approaches, combining microbiology, veterinary and environmental sciences, and epidemiology for outbreak prevention and mitigation. Such outbreaks are often caused by spillovers attributed to human activities that encroach on wildlife habitats and ecosystems, such as land use change, industrialized food production, urbanization and animal trade. While the origin of anthropogenic effects on animal ecology and biogeography can be traced to the Late Pleistocene, the archaeological record-a long-term archive of human-animal-environmental interactions-has largely been untapped in these One Health approaches, thus limiting our understanding of these dynamics over time. In this review, we examine how humans, as niche constructors, have facilitated new host species and 'disease-scapes' from the Late Pleistocene to the Anthropocene, by viewing zooarchaeological, bioarchaeological and palaeoecological data with a One Health perspective. We also highlight how new biomolecular tools and advances in the '-omics' can be holistically coupled with archaeological and palaeoecological reconstructions in the service of studying zoonotic disease emergence and re-emergence.
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Affiliation(s)
- Kristen M Rayfield
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Alexis M Mychajliw
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Biology & Program in Environmental Studies, Middlebury College, Middlebury, VT 05753-6203, USA
| | - Robin R Singleton
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
| | - Sabrina B Sholts
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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6
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Nachman MW, Beckman EJ, Bowie RCK, Cicero C, Conroy CJ, Dudley R, Hayes TB, Koo MS, Lacey EA, Martin CH, McGuire JA, Patton JL, Spencer CL, Tarvin RD, Wake MH, Wang IJ, Achmadi A, Álvarez-Castañeda ST, Andersen MJ, Arroyave J, Austin CC, Barker FK, Barrow LN, Barrowclough GF, Bates J, Bauer AM, Bell KC, Bell RC, Bronson AW, Brown RM, Burbrink FT, Burns KJ, Cadena CD, Cannatella DC, Castoe TA, Chakrabarty P, Colella JP, Cook JA, Cracraft JL, Davis DR, Davis Rabosky AR, D’Elía G, Dumbacher JP, Dunnum JL, Edwards SV, Esselstyn JA, Faivovich J, Fjeldså J, Flores-Villela OA, Ford K, Fuchs J, Fujita MK, Good JM, Greenbaum E, Greene HW, Hackett S, Hamidy A, Hanken J, Haryoko T, Hawkins MTR, Heaney LR, Hillis DM, Hollingsworth BD, Hornsby AD, Hosner PA, Irham M, Jansa S, Jiménez RA, Joseph L, Kirchman JJ, LaDuc TJ, Leaché AD, Lessa EP, López-Fernández H, Mason NA, McCormack JE, McMahan CD, Moyle RG, Ojeda RA, Olson LE, Kin Onn C, Parenti LR, Parra-Olea G, Patterson BD, Pauly GB, Pavan SE, Peterson AT, Poe S, Rabosky DL, Raxworthy CJ, Reddy S, Rico-Guevara A, Riyanto A, Rocha LA, Ron SR, Rovito SM, Rowe KC, Rowley J, Ruane S, Salazar-Valenzuela D, Shultz AJ, Sidlauskas B, Sikes DS, Simmons NB, Stiassny MLJ, Streicher JW, Stuart BL, Summers AP, Tavera J, Teta P, Thompson CW, Timm RM, Torres-Carvajal O, Voelker G, Voss RS, Winker K, Witt C, Wommack EA, Zink RM. Specimen collection is essential for modern science. PLoS Biol 2023; 21:e3002318. [PMID: 37992027 PMCID: PMC10664955 DOI: 10.1371/journal.pbio.3002318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/30/2023] [Indexed: 11/24/2023] Open
Abstract
Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.
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Affiliation(s)
- Michael W. Nachman
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Elizabeth J. Beckman
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Rauri CK Bowie
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Carla Cicero
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Chris J. Conroy
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Robert Dudley
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Tyrone B. Hayes
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Michelle S. Koo
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Eileen A. Lacey
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Christopher H. Martin
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - James L. Patton
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Carol L. Spencer
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Rebecca D. Tarvin
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Marvalee H. Wake
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Ian J. Wang
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Anang Achmadi
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | | | - Michael J. Andersen
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Christopher C. Austin
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - F Keith Barker
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Lisa N. Barrow
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | | | - John Bates
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Aaron M. Bauer
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Kayce C. Bell
- Natural History Museum of Los Angeles County, Los Angeles, California, United States of America
| | - Rayna C. Bell
- California Academy of Sciences, San Francisco, California, United States of America
| | - Allison W. Bronson
- Biological Sciences, California State Polytechnic University, Humboldt, Arcata, California, United States of America
| | - Rafe M. Brown
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Frank T. Burbrink
- American Museum of Natural History, New York, New York, United States of America
| | - Kevin J. Burns
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | | | - David C. Cannatella
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Todd A. Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Prosanta Chakrabarty
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jocelyn P. Colella
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Joseph A. Cook
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Joel L. Cracraft
- American Museum of Natural History, New York, New York, United States of America
| | - Drew R. Davis
- Natural History Museum and Dept. of Biology, Eastern New Mexico University, Portales, New Mexico, United States of America
| | | | - Guillermo D’Elía
- Instituto de Cs. Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - John P. Dumbacher
- California Academy of Sciences, San Francisco, California, United States of America
| | - Jonathan L. Dunnum
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Scott V. Edwards
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Julián Faivovich
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia", Buenos Aires, Argentina
| | - Jon Fjeldså
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Kassandra Ford
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jérôme Fuchs
- ISYEB, Muséum national d’Histoire naturelle, Paris, France
| | - Matthew K. Fujita
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Jeffrey M. Good
- Philip L. Wright Zoological Museum, University of Montana, Missoula, Montana, United States of America
| | - Eli Greenbaum
- Biodiversity Collections and Dept. of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - Harry W. Greene
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Shannon Hackett
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Amir Hamidy
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Melissa TR Hawkins
- Smithsonian Institution, National Museum of Natural History, Washington, DC, United States of America
| | - Lawrence R. Heaney
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - David M. Hillis
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | | | - Angela D. Hornsby
- Philip L. Wright Zoological Museum, University of Montana, Missoula, Montana, United States of America
| | - Peter A. Hosner
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mohammad Irham
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Sharon Jansa
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Rosa Alicia Jiménez
- Escuela de Biología, Universidad de San Carlos de Guatemala, Ciudad de Guatemala, Guatemala
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO, Canberra, Australia
| | | | - Travis J. LaDuc
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Adam D. Leaché
- Burke Museum, University of Washington, Seattle, Washington, United States of America
| | - Enrique P. Lessa
- Departamento de Ecología y Evolución, Universidad de la República, Montevideo, Uruguay
| | - Hernán López-Fernández
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nicholas A. Mason
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - John E. McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California, United States of America
| | - Caleb D. McMahan
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Robert G. Moyle
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Ricardo A. Ojeda
- CONICET, Centro de Ciencia y Técnica Mendoza, Mendoza, Argentina
| | - Link E. Olson
- University of Alaska Museum, Fairbanks, Alaska, United States of America
| | | | - Lynne R. Parenti
- Smithsonian Institution, National Museum of Natural History, Washington, DC, United States of America
| | - Gabriela Parra-Olea
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Bruce D. Patterson
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Gregory B. Pauly
- Natural History Museum of Los Angeles County, Los Angeles, California, United States of America
| | - Silvia E. Pavan
- Biological Sciences, California State Polytechnic University, Humboldt, Arcata, California, United States of America
| | - A Townsend Peterson
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Steven Poe
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Daniel L. Rabosky
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Sushma Reddy
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | | | - Awal Riyanto
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Luiz A. Rocha
- California Academy of Sciences, San Francisco, California, United States of America
| | - Santiago R. Ron
- Museo de Zoología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | | | - Kevin C. Rowe
- Museums Victoria Research Institute, Melbourne, Australia
| | - Jodi Rowley
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
| | - Sara Ruane
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | | | - Allison J. Shultz
- Natural History Museum of Los Angeles County, Los Angeles, California, United States of America
| | - Brian Sidlauskas
- Dept. of Fisheries, Wildlife & Conservation Sciences, Oregon State University, Corvallis, Oregon, United States of America
| | - Derek S. Sikes
- University of Alaska Museum, Fairbanks, Alaska, United States of America
| | - Nancy B. Simmons
- American Museum of Natural History, New York, New York, United States of America
| | | | | | - Bryan L. Stuart
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, United States of America
| | - Adam P. Summers
- Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington, United States of America
| | | | - Pablo Teta
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia", Buenos Aires, Argentina
| | - Cody W. Thompson
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Robert M. Timm
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | | | - Gary Voelker
- Dept. Ecology and Conservation Biology, Texas A&M University, College Station, Texas, United States of America
| | - Robert S. Voss
- American Museum of Natural History, New York, New York, United States of America
| | - Kevin Winker
- University of Alaska Museum, Fairbanks, Alaska, United States of America
| | - Christopher Witt
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Elizabeth A. Wommack
- University of Wyoming Museum of Vertebrates, University of Wyoming, Laramie, Wyoming, United States of America
| | - Robert M. Zink
- University of Nebraska State Museum, Lincoln, Nebraska, United States of America
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7
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Giri J, Pezzi L, Cachay R, Gèlvez Ramirez RM, Tami A, Bethencourt S, Lozano A, Gotuzzo Herencia JE, Poje J, Jaenisch T, Chu M. Specimen sharing for epidemic preparedness: Building a virtual biorepository system from local governance to global partnerships. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001568. [PMID: 37819913 PMCID: PMC10566708 DOI: 10.1371/journal.pgph.0001568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 09/03/2023] [Indexed: 10/13/2023]
Abstract
We present a framework for a federated, virtual biorepository system (VBS) with locally collected and managed specimens, as a 'global public good' model based on principles of equitable access and benefit sharing. The VBS is intended to facilitate timely access to biological specimens and associated data for outbreak-prone infectious diseases to accelerate the development and evaluation of diagnostics, assess vaccine efficacy, and to support surveillance and research needs. The VBS is aimed to be aligned with the WHO BioHub and other specimen sharing efforts as a force multiplier to meet the needs of strengthening global tools for countering epidemics. The purpose of our initial research is to lay the basis of the collaboration, management and principles of equitable sharing focused on low- and middle-income country partners. Here we report on surveys and interviews undertaken with biorepository-interested parties to better understand needs and barriers for specimen access and share examples from the ZIKAlliance partnership on the governance and operations of locally organized biorepositories.
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Affiliation(s)
- Judith Giri
- Center for Global Health, Colorado School of Public Health, Anschutz Medical Center, Aurora, Colorado, United States of America
| | - Laura Pezzi
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Rodrigo Cachay
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, San Martín de Porres, Lima, Peru
| | | | - Adriana Tami
- Facultad de Ciencias de la Salud, Departamento de Parasitología, Universidad de Carabobo, Valencia, Venezuela
| | - Sarah Bethencourt
- Departamento de Estudios Clínicos-Department of Clinical Studies, Universidad de Carabobo, Valencia, Venezuela
| | - Anyela Lozano
- Centro de Investigaciones Epidemiológicas, Universidad Industrial de Santander, Bucamaranga, Colombia
| | - José Eduardo Gotuzzo Herencia
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, San Martín de Porres, Lima, Peru
| | - Julia Poje
- Center for Global Health, Colorado School of Public Health, Anschutz Medical Center, Aurora, Colorado, United States of America
| | - Thomas Jaenisch
- Center for Global Health, Colorado School of Public Health, Anschutz Medical Center, Aurora, Colorado, United States of America
| | - May Chu
- Center for Global Health, Colorado School of Public Health, Anschutz Medical Center, Aurora, Colorado, United States of America
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8
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Enabulele EE, Le Clec'h W, Roberts EK, Thompson CW, McDonough MM, Ferguson AW, Bradley RD, Anderson TJC, Platt RN. Prospecting for Zoonotic Pathogens by Using Targeted DNA Enrichment. Emerg Infect Dis 2023; 29:1566-1579. [PMID: 37486179 PMCID: PMC10370864 DOI: 10.3201/eid2908.221818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
More than 60 zoonoses are linked to small mammals, including some of the most devastating pathogens in human history. Millions of museum-archived tissues are available to understand natural history of those pathogens. Our goal was to maximize the value of museum collections for pathogen-based research by using targeted sequence capture. We generated a probe panel that includes 39,916 80-bp RNA probes targeting 32 pathogen groups, including bacteria, helminths, fungi, and protozoans. Laboratory-generated, mock-control samples showed that we are capable of enriching targeted loci from pathogen DNA 2,882‒6,746-fold. We identified bacterial species in museum-archived samples, including Bartonella, a known human zoonosis. These results showed that probe-based enrichment of pathogens is a highly customizable and efficient method for identifying pathogens from museum-archived tissues.
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9
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Green TA, Hutchings PA, Scarff FR, Tweedley JR, Calver MC. Research publications of Australia's natural history museums, 1981-2020: Enduring relevance in a changing world. PLoS One 2023; 18:e0287659. [PMID: 37352318 PMCID: PMC10289469 DOI: 10.1371/journal.pone.0287659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 06/12/2023] [Indexed: 06/25/2023] Open
Abstract
As a case study of the responses of natural history museums to changing scientific and funding environments, we analysed research publications of Australia's Natural History Museums (ANHMs) 1981-2020. Using Scopus, 9,923 relevant documents 1981-2020 were identified, mainly research papers but with a growing proportion of reviews. The number of documents published increased over tenfold from 39 (1981) to 553 (2020), likely driven by collaborations (rising from 28.5% of documents 1981-1985 to 87.2% of documents 2016-2020), contributions from retired staff, and volunteer support. The mean length of documents (pages) ranged from a low of 15.3 in 2001-2005 to a high of 17.4 in 1991-1995, but this statistically significant result was trivial in practical terms. The sources (i.e., journals, book titles, conference proceedings) in which ANHM authors published changed over time, with growing proportions of publications in journals covering molecular ecology/phylogenetics and biological conservation. We identified the major areas of study canvassed within the corpus of publications by developing structural topic models based on patterns of word use in document titles, abstracts and keyword lists. The topics discovered included study subjects traditional for natural history museums (new taxa, phylogeny, systematics, animal morphology, palaeontology, minerals), new directions (molecular genetics, ecology, biological conservation) and marine biology (probably reflecting Australia's large coastline). Most citations came from Australia, USA and UK, although in 2016-2020 only 27.9% of citing documents included an Australian author. Growth in numbers of documents and collaborations, as well as use of documents internationally over a period of great change in scientific and funding environments, indicate an enduring legacy of ANHM research, grounded on the intrinsic value of the collections.
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Affiliation(s)
- Tayla A. Green
- Environmental and Conservation Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - Pat A. Hutchings
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
- Department of Biological Sciences, Macquarie University, North Ryde, Australia
| | - Fiona R. Scarff
- Environmental and Conservation Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - James R. Tweedley
- Environmental and Conservation Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - Michael C. Calver
- Environmental and Conservation Sciences, Murdoch University, Murdoch, Western Australia, Australia
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10
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Gonzalez P, Salazar JR, Salinas TP, Avila M, Colella JP, Dunnum JL, Glass GE, Gonzalez G, Juarez E, Lindblade K, Pile E, Mendoza Y, Pascale JM, Armien AG, Cook JA, Armien B. Two Decades of Wildlife Pathogen Surveillance: Case Study of Choclo orthohantavirus and Its Wild Reservoir Oligoryzomys costaricensis. Viruses 2023; 15:1390. [PMID: 37376689 DOI: 10.3390/v15061390] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/04/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The Costa Rican pygmy rice rat (Oligoryzomys costaricensis) is the primary reservoir of Choclo orthohantavirus (CHOV), the causal agent of hantavirus disease, pulmonary syndrome, and fever in humans in Panama. Since the emergence of CHOV in early 2000, we have systematically sampled and archived rodents from >150 sites across Panama to establish a baseline understanding of the host and virus, producing a permanent archive of holistic specimens that we are now probing in greater detail. We summarize these collections and explore preliminary habitat/virus associations to guide future wildlife surveillance and public health efforts related to CHOV and other zoonotic pathogens. Host sequences of the mitochondrial cytochrome b gene form a single monophyletic clade in Panama, despite wide distribution across Panama. Seropositive samples were concentrated in the central region of western Panama, consistent with the ecology of this agricultural commensal and the higher incidence of CHOV in humans in that region. Hantavirus seroprevalence in the pygmy rice rat was >15% overall, with the highest prevalence in agricultural areas (21%) and the lowest prevalence in shrublands (11%). Host-pathogen distribution, transmission dynamics, genomic evolution, and habitat affinities can be derived from the preserved samples, which include frozen tissues, and now provide a foundation for expanded investigations of orthohantaviruses in Panama.
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Affiliation(s)
- Publio Gonzalez
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
| | - Jacqueline R Salazar
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
| | - Tybbysay P Salinas
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
| | - Mario Avila
- Department of Vector Control-Herrera Health Region, Ministry of Health, Panama City 0843-03441, Panama
| | - Jocelyn P Colella
- Biodiversity Institute & Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Jonathan L Dunnum
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Gregory E Glass
- Department of Geography & Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Gloria Gonzalez
- Department of Genomics and Proteomics, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
| | - Enos Juarez
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
| | - Kimberly Lindblade
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Edwin Pile
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
| | - Yaxelis Mendoza
- Department of Genomics and Proteomics, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
- Sistema Nacional de Investigación (SNI), Secretaria Nacional de Ciencia y Tecnología (SENACYT), Panama City 0816-02852, Panama
| | - Juan Miguel Pascale
- Department of Genomics and Proteomics, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
| | - Anibal G Armien
- California Animal Health & Food Safety Laboratory System (CAHFS), School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Blas Armien
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City 0816-02593, Panama
- Sistema Nacional de Investigación (SNI), Secretaria Nacional de Ciencia y Tecnología (SENACYT), Panama City 0816-02852, Panama
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11
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Colella JP, Cobos ME, Salinas I, Cook JA. Advancing the central role of non-model biorepositories in predictive modeling of emerging pathogens. PLoS Pathog 2023; 19:e1011410. [PMID: 37319170 DOI: 10.1371/journal.ppat.1011410] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Affiliation(s)
- Jocelyn P Colella
- University of Kansas Biodiversity Institute and Department of Ecology & Evolutionary Biology, Lawrence, Kansas, United States of America
| | - Marlon E Cobos
- University of Kansas Biodiversity Institute and Department of Ecology & Evolutionary Biology, Lawrence, Kansas, United States of America
| | - Irene Salinas
- University of New Mexico, Department of Biology, Albuquerque, New Mexico, United States of America
- Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Joseph A Cook
- University of New Mexico, Department of Biology, Albuquerque, New Mexico, United States of America
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
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12
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Szentivanyi T, McKee C, Jones G, Foster JT. Trends in Bacterial Pathogens of Bats: Global Distribution and Knowledge Gaps. Transbound Emerg Dis 2023. [DOI: 10.1155/2023/9285855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Bats have received considerable recent attention for infectious disease research because of their potential to host and transmit viruses, including Ebola, Hendra, Nipah, and multiple coronaviruses. These pathogens are occasionally transmitted from bats to wildlife, livestock, and to humans, directly or through other bridging (intermediate) hosts. Due to their public health relevance, zoonotic viruses are a primary focus of research attention. In contrast, other emerging pathogens of bats, such as bacteria, are vastly understudied despite their ubiquity and diversity. Here, we describe the currently known host ranges and geographic distributional patterns of potentially zoonotic bacterial genera in bats, using published presence-absence data of pathogen occurrence. We identify apparent gaps in our understanding of the distribution of these pathogens on a global scale. The most frequently detected bacterial genera in bats are Bartonella, Leptospira, and Mycoplasma. However, a wide variety of other potentially zoonotic bacterial genera are also occasionally found in bats, such as Anaplasma, Brucella, Borrelia, Coxiella, Ehrlichia, Francisella, Neorickettsia, and Rickettsia. The bat families Phyllostomidae, Vespertilionidae, and Pteropodidae are most frequently reported as hosts of bacterial pathogens; however, the presence of at least one bacterial genus was confirmed in all 15 bat families tested. On a spatial scale, molecular diagnostics of samples from 58 countries and four overseas departments and island states (French Guiana, Mayotte, New Caledonia, and Réunion Island) reported testing for at least one bacterial pathogen in bats. We also identified geographical areas that have been mostly neglected during bacterial pathogen research in bats, such as the Afrotropical region and Southern Asia. Current knowledge on the distribution of potentially zoonotic bacterial genera in bats is strongly biased by research effort towards certain taxonomic groups and geographic regions. Identifying these biases can guide future surveillance efforts, contributing to a better understanding of the ecoepidemiology of zoonotic pathogens in bats.
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13
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Romero-Alvarez D, Garzon-Chavez D, Jackson M, Avanzi C, Peterson AT. Mycobacterium leprae in Armadillo Tissues from Museum Collections, United States. Emerg Infect Dis 2023; 29:622-626. [PMID: 36823763 PMCID: PMC9973711 DOI: 10.3201/eid2903.221636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
We examined armadillos from museum collections in the United States using molecular assays to detect leprosy-causing bacilli. We found Mycobacterium leprae bacilli in samples from the United States, Bolivia, and Paraguay; prevalence was 14.8% in nine-banded armadillos. US isolates belonged to subtype 3I-2, suggesting long-term circulation of this genotype.
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14
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Nguyen HM, Do DT, Greiman SE, Nguyen HV, Hoang HV, Phan TQ, Pham-Duc P, Madsen H. An overview of human helminthioses in Vietnam: Their prevention, control and lessons learnt. Acta Trop 2023; 238:106753. [PMID: 36375522 DOI: 10.1016/j.actatropica.2022.106753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/31/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022]
Abstract
In Vietnam, helminthioses remain a major threat to public health and contribute to the maintenance of poverty in highly endemic regions. Through increased awareness of the damaging effects caused by helminthioses, the Vietnamese government has implemented many national programs over the past 30 years for the prevention and control of the most important helminthioses, such as, lymphatic filariasis, soil transmitted helminths, food borne zoonotic helminths, and others. Various control strategies have been applied to reduce or eliminate these worms, e.g. mass drug administration, economic development, control of vectors or intermediate hosts, public health interventions through education, proper composting procedures for excreta potentially containing helminth eggs, and the expansion of food supply chains and improved technologies for the production and inspection of food products. These control measures have resulted in a significant reduction in the distribution and transmission of helminth infections and have improved the overall living conditions and health outcomes of the Vietnamese citizens. However, the persistence of several helminth diseases continues in some endemic areas, especially where poverty is widespread and local traditions include the consumption of raw foods, especially fish and meats. This manuscript provides an overview of the helminth infection prevention and control programs conducted in Vietnam, their achieved results, learned lessons, and future works.
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Affiliation(s)
- Hung Manh Nguyen
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Street, Hanoi, Viet Nam.
| | - Dung Trung Do
- National Institute of Malariology, Parasitology and Entomology, 34 Trung Van Street, Hanoi, Viet Nam
| | - Stephen E Greiman
- Georgia Southern University, 4324 Old Register Road, Statesboro, GA 30460, USA
| | - Ha Van Nguyen
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Street, Hanoi, Viet Nam
| | - Hien Van Hoang
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Street, Hanoi, Viet Nam
| | - Toan Quoc Phan
- The Center for Entomology and Parasitology Research, College of Medicine and Pharmacy, Duy Tan University, 3 Quang Trung Street, Da Nang, Viet Nam
| | - Phuc Pham-Duc
- Institute of Environmental Health and Sustainable Development, 32/12/3A To Ngoc Van Street, Hanoi, Viet Nam
| | - Henry Madsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Dyrlaegevej 100, Frederiksberg C 1870, Denmark
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15
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Astorga F, Groom Q, Shimabukuro PHF, Manguin S, Noesgaard D, Orrell T, Sinka M, Hirsch T, Schigel D. Biodiversity data supports research on human infectious diseases: Global trends, challenges, and opportunities. One Health 2023; 16:100484. [PMID: 36714536 PMCID: PMC9880238 DOI: 10.1016/j.onehlt.2023.100484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/06/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
The unprecedented generation of large volumes of biodiversity data is consistently contributing to a wide range of disciplines, including disease ecology. Emerging infectious diseases are usually zoonoses caused by multi-host pathogens. Therefore, their understanding may require the access to biodiversity data related to the ecology and the occurrence of the species involved. Nevertheless, despite several data-mobilization initiatives, the usage of biodiversity data for research into disease dynamics has not yet been fully leveraged. To explore current contribution, trends, and to identify limitations, we characterized biodiversity data usage in scientific publications related to human health, contrasting patterns of studies citing the Global Biodiversity Information Facility (GBIF) with those obtaining data from other sources. We found that the studies mainly obtained data from scientific literature and other not aggregated or standardized sources. Most of the studies explored pathogen species and, particularly those with GBIF-mediated data, tended to explore and reuse data of multiple species (>2). Data sources varied according to the taxa and epidemiological roles of the species involved. Biodiversity data repositories were mainly used for species related to hosts, reservoirs, and vectors, and barely used as a source of pathogens data, which was usually obtained from human and animal-health related institutions. While both GBIF- and not GBIF-mediated data studies explored similar diseases and topics, they presented discipline biases and different analytical approaches. Research on emerging infectious diseases may require the access to geographical and ecological data of multiple species. The One Health challenge requires interdisciplinary collaboration and data sharing, which is facilitated by aggregated repositories and platforms. The contribution of biodiversity data to understand infectious disease dynamics should be acknowledged, strengthened, and promoted.
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Affiliation(s)
- Francisca Astorga
- Facultad de Ciencias, Universidad Mayor, Chile,Corresponding author.
| | - Quentin Groom
- Biodiversity Informatics, Meise Botanic Garden, Belgium Nieuwelaan 38, 1860, Meise, Belgium
| | | | - Sylvie Manguin
- HSM, University Montpellier, CNRS, IRD, 911 Av. Agropolis, 34394 Montpellier, France
| | - Daniel Noesgaard
- Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Thomas Orrell
- Smithsonian Institution, National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA
| | | | - Tim Hirsch
- Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Dmitry Schigel
- Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
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16
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Poczai P, Karvalics LZ. The little-known history of cleanliness and the forgotten pioneers of handwashing. Front Public Health 2022; 10:979464. [PMID: 36339162 PMCID: PMC9632745 DOI: 10.3389/fpubh.2022.979464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/28/2022] [Indexed: 01/25/2023] Open
Abstract
Handwashing is a simple method for preventing the spread of pathogens. It is now common practice, but this was not always the case. Advocating for it often costed a doctor his career in the 1840s. Hospitals in the early 1800s had little idea of the significance of hygiene; thus, they were often mocked as disease-producing incubators or as "houses of death." Many of the ill and dying were kept on wards with no ventilation or access to clean water; hospitals were found to offer only the most basic care. The mortality rate for patients admitted to hospital was three to five times greater than that for individuals cared for at home. Doctors did not routinely wash their hands until the mid-1800s, and they would proceed straight from dissecting a corpse to delivering a baby, providing the basis for the spread of puerperal fever. Despite advances in modern medicine, healthcare providers still face the issue of infection outbreaks caused by patient care. While the body of scientific data supporting hand hygiene as the key strategy to prevent the spread of pathogens is substantial, we highlight that achieving this crucial, long-awaited breakthrough was a hard task through history.
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Affiliation(s)
- Peter Poczai
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Museomics Research Group, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Institute of Advanced Studies Kőszeg, Kőszeg, Hungary
| | - László Z. Karvalics
- Institute of Advanced Studies Kőszeg, Kőszeg, Hungary
- Department of Cultural Heritage and Human Information Sciences, University of Szeged, Szeged, Hungary
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17
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Drabik GO, Vivar E, Jiménez FA. NEW SPECIES OF ALIPPISTRONGYLUS (TRICHOSTRONGYLINA: NIPPOSTRONGYLINAE) FROM THE ELEGANT RICE RAT, EURYORYZOMYS NITIDUS, OF LA CONVENCIÓN, PERU. J Parasitol 2022; 108:435-440. [PMID: 36197731 DOI: 10.1645/22-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A new species of AlippistrongylusDigiani and Kinsella, 2014, was found in the intestines of the elegant rice rat, Euryoryzomys nitidus, collected in the Amazon rainforest. These mammals were preserved in alcohol and archived in the Colección Científica de Mamíferos del Museo de Historia Natural de la Universidad Mayor de San Marcos and accessed for the observation and investigation for the diversity of their endo-parasites. A total of 857 worms were recovered from the 3 individuals examined. Morphological investigations and comparisons with the only known species of the genus indicate that this is an undescribed species. These nematodes feature the diagnostic characteristic of the genus, being a bifurcated posterior end that consists of a tail and a conical appendage near the level of the vulva and uninterrupted ridges in the synlophe of unequal size. However, the orientation of this conical appendage on the female tail, features of the synlophe, and shape of the copulatory bursa warrant the proposal of an amended diagnosis to include character variability detected in the new species.
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Affiliation(s)
- Guinevere O Drabik
- School of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, Illinois 62901-6501
| | - Elena Vivar
- Colección Científica de Mamíferos del Museo de Historia Natural de la Universidad Mayor de San Marcos Av. Gral. Antonio Alvarez de Arenales 1256, Jesús María 15072, Lima, Peru
| | - F Agustín Jiménez
- School of Biological Sciences, Southern Illinois University, 1125 Lincoln Drive, Carbondale, Illinois 62901-6501
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18
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Hawkins MTR, Flores MFC, McGowen M, Hinckley A. A comparative analysis of extraction protocol performance on degraded mammalian museum specimens. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.984056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The extraction of nucleic acids is one of the most routine procedures used in molecular biology laboratories, yet kit performance may influence the downstream processing of samples, particularly for samples which are degraded, and in low concentrations. Here we tested several commercial kits for specific use on commonly sampled mammalian museum specimens to evaluate the yield, size distribution, and endogenous content. Samples were weighed and had approximately equal input material for each extraction. These sample types are typical of natural history repositories ranged from 53 to 130 years old. The tested protocols spanned spin-column based extractions, magnetic bead purification, phenol/chloroform isolation, and specific modifications for ancient DNA. Diverse types of mammalian specimens were tested including adherent osteological material, bone and teeth, skin, and baleen. The concentration of DNA was quantified via fluorometry, and the size distributions of extracts visualized on an Agilent TapeStation. Overall, when DNA isolation was successful, all methods had quantifiable concentrations, albeit with variation across extracts. The length distributions varied based on the extraction protocol used. Shotgun sequencing was performed to evaluate if the extraction methods influenced the amount of endogenous versus exogenous content. The DNA content was similar across extraction methods indicating no obvious biases for DNA derived from different sources. Qiagen kits and phenol/chloroform isolation outperformed the Zymo magnetic bead isolations in these types of samples. Statistical analyses revealed that extraction method only explained 5% of the observed variation, and that specimen age explained variation (29%) more effectively.
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19
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Hardisty AR, Ellwood ER, Nelson G, Zimkus B, Buschbom J, Addink W, Rabeler RK, Bates J, Bentley A, Fortes JAB, Hansen S, Macklin JA, Mast AR, Miller JT, Monfils AK, Paul DL, Wallis E, Webster M. Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet. Bioscience 2022; 72:978-987. [PMID: 36196222 PMCID: PMC9525127 DOI: 10.1093/biosci/biac060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information. In the present article, we propose a new interconnected network of digital objects on the Internet—the Digital Extended Specimen (DES) network—that transcends existing aggregator technology, augments the DES with third-party data through machine algorithms, and provides a platform for more efficient research and robust interdisciplinary discovery.
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Affiliation(s)
| | | | - Gil Nelson
- Florida Museum of Natural History , Gainesville, Florida, United States
| | - Breda Zimkus
- Museum of Comparative Zoology , Cambridge, Massachusetts, United States
| | | | | | - Richard K Rabeler
- University of Michigan Herbarium , Ann Arbor, Michigan, United States
| | - John Bates
- Field Museum of Natural History , Chicago, Illinois, United States
| | - Andrew Bentley
- Biodiversity Institute, University of Kansas , Lawrence, Kansas, United States
| | | | - Sara Hansen
- Central Michigan University Herbarium, Central Michigan University , Mt. Pleasant, Michigan, United States
| | | | - Austin R Mast
- Department of Biological Science, Florida State University , Tallahassee, Florida, United States
| | - Joseph T Miller
- Global Biodiversity Information Facility Secretariat , Copenhagen, Denmark
| | - Anna K Monfils
- Central Michigan University Herbarium, Central Michigan University , Mt. Pleasant, Michigan, United States
| | - Deborah L Paul
- University of Illinois Urbana Champaign , Champaign, Illinois, United States
| | - Elycia Wallis
- Atlas of Living Australia, CSIRO , Melbourne, Australia
| | - Michael Webster
- Macaulay Library, Cornell Lab of Ornithology , Ithaca, New York, United States
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20
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Speer KA, Hawkins MTR, Flores MFC, McGowen MR, Fleischer RC, Maldonado JE, Campana MG, Muletz-Wolz CR. A comparative study of RNA yields from museum specimens, including an optimized protocol for extracting RNA from formalin-fixed specimens. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.953131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Animal specimens in natural history collections are invaluable resources in examining the historical context of pathogen dynamics in wildlife and spillovers to humans. For example, natural history specimens may reveal new associations between bat species and coronaviruses. However, RNA viruses are difficult to study in historical specimens because protocols for extracting RNA from these specimens have not been optimized. Advances have been made in our ability to recover nucleic acids from formalin-fixed paraffin-embedded samples (FFPE) commonly used in human clinical studies, yet other types of formalin preserved samples have received less attention. Here, we optimize the recovery of RNA from formalin-fixed ethanol-preserved museum specimens in order to improve the usability of these specimens in surveys for zoonotic diseases. We provide RNA quality and quantity measures for replicate tissues subsamples of 22 bat specimens from five bat genera (Rhinolophus, Hipposideros, Megareops, Cynopterus, and Nyctalus) collected in China and Myanmar from 1886 to 2003. As tissues from a single bat specimen were preserved in a variety of ways, including formalin-fixed (8 bats), ethanol-preserved and frozen (13 bats), and flash frozen (2 bats), we were able to compare RNA quality and yield across different preservation methods. RNA extracted from historical museum specimens is highly fragmented, but usable for short-read sequencing and targeted amplification. Incubation of formalin-fixed samples with Proteinase-K following thorough homogenization improves RNA yield. This optimized protocol extends the types of data that can be derived from existing museum specimens and facilitates future examinations of host and pathogen RNA from specimens.
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21
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Alnaqeb H, Galbreath KE, Koehler AV, Campbell ML, Jiménez FA. Citellinema (Nematoda: Heligmosomidae) from North America with descriptions of 2 new species from the red squirrel Tamiasciurus hudsonicus and 1 from the Canadian woodchuck, Marmota monax. Parasitology 2022; 149:1199-1218. [PMID: 35621015 PMCID: PMC11010518 DOI: 10.1017/s0031182022000737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/06/2022]
Abstract
Citellinema Hall, 1918 includes 6 valid species of gastrointestinal nematodes of sciurids. Two species occur in the Palearctic and 4 in the Nearctic, 3 of which occur minimally across Colorado, Idaho and Oregon and 1, Citellinema bifurcatum, has a wide distribution across North America. Members of the genus are didelphic, possess a cephalic vesicle, a terminal spine-like process in females and feature robust spicules, consisting of a proximal end fused and semicylindrical shaft connected to a lamina supported by 2 terminal filiform processes. Typically, the size of the spicules is used to differentiate species. As part of the Beringian Coevolution Project, specimens provisionally identified as C. bifurcatum were collected through intensive field sampling of mammals and associated parasites from across localities spanning the Holarctic. These specimens revealed considerable genetic variability at both mitochondrial and nuclear loci, supporting the identification of deeply divergent clades. Examination of these new specimens, along with the holotypes of C. bifurcatum and Citellinema quadrivittati indicates that Citellinema monacis (previously synonymized with C. bifurcatum) should be resurrected and 3 additional species described. We suggest that the apparent bifurcated nature of the spicule should be considered a generic diagnostic trait, while the proportional length of the lamina relative to that of the spicule is used as a specific character. We demonstrate the critical need for continued inventory of often poorly known assemblages of hosts and parasites, contributing to a growing baseline of archival specimens, collections and information that make explorations of faunal structure and diversity possible.
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Affiliation(s)
- Haitham Alnaqeb
- School of Biological Sciences, Southern Illinois University, Carbondale, Illinois 62901-6501, USA
| | - Kurt E. Galbreath
- Department of Biology, Northern Michigan University, Marquette, Michigan 49855, USA
| | - Anson V. Koehler
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mariel L. Campbell
- Division of Genomic Resources, Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - F. Agustín Jiménez
- School of Biological Sciences, Southern Illinois University, Carbondale, Illinois 62901-6501, USA
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22
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Verocai GG, Kafle P, Sulliotti V, Lejeune M, Hoberg EP, Kutz SJ. Morphometry of First-Stage Larvae of Orthostrongylus macrotis (Nematoda: Protostrongylidae), Lungworm of Wild Ungulates from Western North America. J Parasitol 2022; 108:322-329. [DOI: 10.1645/22-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Guilherme G. Verocai
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843
| | - Pratap Kafle
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine Long Island University, Brookville, New York 11548
| | - Valerio Sulliotti
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843
| | - Manigandan Lejeune
- Animal Health Diagnostic Center, Department of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, New York 14850
| | - Eric P. Hoberg
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Susan J. Kutz
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary. 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada
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23
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Andreone F, Boero F, Bologna MA, Carpaneto GM, Castiglia R, Gippoliti S, Massa B, Minelli A. Reconnecting research and natural history museums in Italy and the need of a national collection biorepository. Zookeys 2022; 1104:55-68. [PMID: 36761931 PMCID: PMC9848790 DOI: 10.3897/zookeys.1104.79823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/18/2022] [Indexed: 11/12/2022] Open
Abstract
In Italy, differently from other countries, a national museum of natural history is not present. This absence is due, among other reasons, to its historical political fragmentation up to 1870, which led to the establishment of medium-sized museums, mostly managed by local administrations or universities. Moreover, a change of paradigm in biological research, at the beginning of the 20th century, contributed to privilege experimental studies in universities and facilitated the dismissal of descriptive and exploratory biology, which formed the basis of the taxonomic research carried out by natural history museums. Consequently, only a few museums have a provision of curatorial staff, space and material resources adequate to maintain their original mission of discovering the natural world, by conducting a regular research activity accompanied by field campaigns. The creation of a national research centre for the study of biodiversity, facilitating interconnections among the existing natural history museums could be a solution and is here supported, together with a centralised biorepository to host collections and vouchers, to the benefit of current and future taxonomic research and environmental conservation. Such an institution should find place and realisation within the recently proposed National Biodiversity Future Center (NBFC) planned within the National Plan of Recovery and Resilience (PNRR). Pending upon the creation of this new national centre, a network among the existing museums should coordinate their activities.
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Affiliation(s)
- Franco Andreone
- Museo Regionale di Scienze Naturali, Via G. Giolitti, 36, I-10123 Torino, ItalyMuseo Regionale di Scienze NaturaliTorinoItaly
| | - Ferdinando Boero
- Università di Napoli Federico II, CNR-IAS, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, ItalyUniversità di Napoli Federico IINapoliItaly
| | - Marco A. Bologna
- Dipartimento di Scienze, Università Roma Tre, Viale G. Marconi, 446, I-00146 Roma, ItalyUniversità Roma TreRomaItaly
| | - Giuseppe M. Carpaneto
- Dipartimento di Scienze, Università Roma Tre, Viale G. Marconi, 446, I-00146 Roma, ItalyUniversità Roma TreRomaItaly
| | - Riccardo Castiglia
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Università “La Sapienza” di Roma, Via A. Borelli, 50, I-00161 Roma, ItalyUniversità “La Sapienza” di RomaRomaItaly
| | - Spartaco Gippoliti
- Società Italiana per la Storia della Fauna “Giuseppe Altobello”, Viale Liegi, 48A, I-00198 Roma, ItalySocietà Italiana per la Storia della Fauna “Giuseppe Altobello”RomeItaly
| | - Bruno Massa
- Dipartimento di Scienze agrarie, alimentari e forestali, Università di Palermo, Viale Scienze, 13, I-90128 Palermo, ItalyUniversità di PalermoPalermoItaly
| | - Alessandro Minelli
- Dipartimento di Biologia, Università di Padova, Via Ugo Bassi, 58B, I-35131 Padova, ItalyUniversità di PadovaPadovaItaly
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24
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Boeger WA, Brooks DR, Trivellone V, Agosta SJ, Hoberg EP. Ecological super-spreaders drive host-range oscillations: Omicron and risk-space for emerging infectious disease. Transbound Emerg Dis 2022; 69:e1280-e1288. [PMID: 35411706 PMCID: PMC9115439 DOI: 10.1111/tbed.14557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/16/2022] [Accepted: 04/07/2022] [Indexed: 11/28/2022]
Abstract
The unusual genetic diversity of the Omicron strain has led to speculation about its origin. The mathematical modelling platform developed for the Stockholm Paradigm (SP) indicates strongly that it has retro‐colonized humans from an unidentified nonhuman mammal, likely originally infected by humans. The relationship between Omicron and all other SARS‐CoV‐2 variants indicates oscillations among hosts, a core part of the SP. Such oscillations result from the emergence of novel variants following colonization of new hosts, replenishing and expanding the risk space for disease emergence. The SP predicts that pathogens colonize new hosts using pre‐existing capacities. Those events are thus predictable to a certain extent. Novel variants emerge after a colonization and are not predictable. This makes it imperative to take proactive measures for anticipating emerging infectious diseases (EID) and mitigating their impact. The SP suggests a policy protocol, DAMA, to accomplish this goal. DAMA comprises: DOCUMENT to detect pathogens before they emerge in new places or colonize new hosts; ASSESS to determine risk; MONITOR to detect changes in pathogen populations that increase the risk of outbreaks and ACT to prevent outbreaks when possible and minimize their impact when they occur.
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Affiliation(s)
- Walter A Boeger
- Biological Interactions, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Daniel R Brooks
- Eötvös Loránd Research Network, Centre for Ecological Research, Institute of Evolution, 1121 Budapest, Konkoly-Thege Miklós út 29-33, Budapest, Hungary.,Stellenbosch Institute for Advanced Study, Stellenbosch, South Africa.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Valeria Trivellone
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, 61821, USA
| | - Salvatore J Agosta
- Stellenbosch Institute for Advanced Study, Stellenbosch, South Africa.,Center for Environmental Studies, VCU Life Sciences, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Eric P Hoberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53716, USA.,Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, 87138, USA
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25
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Sett S, Dos Santos Ribeiro C, Prat C, Haringhuizen G, Scholz AH. Access and benefit-sharing by the European Virus Archive in response to COVID-19. THE LANCET. MICROBE 2022; 3:e316-e323. [PMID: 34806057 PMCID: PMC8594928 DOI: 10.1016/s2666-5247(21)00211-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Biobanking infrastructures, which are crucial for responding early to new viral outbreaks, share pathogen genetic resources in an affordable, safe, and impartial manner and can provide expertise to address access and benefit-sharing issues. The European Virus Archive has had a crucial role in the global response to the COVID-19 pandemic by distributing EU-subsidised (free of charge) viral resources to users worldwide, providing non-monetary benefit sharing, implementing access and benefit-sharing compliance, and raising access and benefit-sharing awareness among members and users. All currently available SARS-CoV-2 material in the European Virus Archive catalogue, including variants of concern, are not access and benefit-sharing cases per se, but multilateral benefit-sharing has nevertheless occurred. We propose and discuss how a multilateral system enabling access and benefit-sharing from pathogen genetic resources, based on the European Virus Archive operational model, could help bridge the discrepancies between the current bilateral legal framework for pathogen genetic resources and actual pandemic response practices.
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Affiliation(s)
- Scarlett Sett
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Carolina Dos Santos Ribeiro
- National Institute for Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, Netherlands
| | - Christine Prat
- Unité des Virus Émergents, UVE: Aix-Marseille University, IRD 190, Inserm 1207, Marseille, France
| | - George Haringhuizen
- National Institute for Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, Netherlands
| | - Amber Hartman Scholz
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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26
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Worsley-Tonks KEL, Bender JB, Deem SL, Ferguson AW, Fèvre EM, Martins DJ, Muloi DM, Murray S, Mutinda M, Ogada D, Omondi GP, Prasad S, Wild H, Zimmerman DM, Hassell JM. Strengthening global health security by improving disease surveillance in remote rural areas of low-income and middle-income countries. Lancet Glob Health 2022; 10:e579-e584. [PMID: 35303467 PMCID: PMC8923676 DOI: 10.1016/s2214-109x(22)00031-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/20/2022] [Indexed: 01/19/2023]
Abstract
The COVID-19 pandemic has underscored the need to strengthen national surveillance systems to protect a globally connected world. In low-income and middle-income countries, zoonotic disease surveillance has advanced considerably in the past two decades. However, surveillance efforts often prioritise urban and adjacent rural communities. Communities in remote rural areas have had far less support despite having routine exposure to zoonotic diseases due to frequent contact with domestic and wild animals, and restricted access to health care. Limited disease surveillance in remote rural areas is a crucial gap in global health security. Although this point has been made in the past, practical solutions on how to implement surveillance efficiently in these resource-limited and logistically challenging settings have yet to be discussed. We highlight why investing in disease surveillance in remote rural areas of low-income and middle-income countries will benefit the global community and review current approaches. Using semi-arid regions in Kenya as a case study, we provide a practical approach by which surveillance in remote rural areas can be strengthened and integrated into existing systems. This Viewpoint represents a transition from simply highlighting the need for a more holistic approach to disease surveillance to a solid plan for how this outcome might be achieved.
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Affiliation(s)
| | - Jeff B Bender
- School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Sharon L Deem
- Institute for Conservation Medicine, Saint Louis Zoo, Saint Louis, MO, USA
| | - Adam W Ferguson
- Gantz Family Collection Center, Field Museum of Natural History, Chicago, IL, USA
| | - Eric M Fèvre
- International Livestock Research Institute, Nairobi, Kenya; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Dino J Martins
- Mpala Research Centre, Nanyuki, Kenya; Department of Ecology and Evolution, Princeton University, Princeton, NJ, USA
| | - Dishon M Muloi
- International Livestock Research Institute, Nairobi, Kenya; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Suzan Murray
- Global Health Program, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Mathew Mutinda
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | - Darcy Ogada
- The Peregrine Fund, Boise, ID, USA; National Museums of Kenya, Nairobi, Kenya
| | - George P Omondi
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA; Ahadi Veterinary Resource Center, Nairobi, Kenya
| | - Shailendra Prasad
- Center for Global Health and Social Responsibility, University of Minnesota, Minneapolis, MN, USA
| | - Hannah Wild
- Department of Surgery, University of Washington, Seattle, WA, USA
| | - Dawn M Zimmerman
- Department of Clinical Studies, University of Nairobi, Nairobi, Kenya; Department of Epidemiology of Microbial Disease, Yale School of Public Health, New Haven, CT, USA
| | - James M Hassell
- Global Health Program, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA; Department of Epidemiology of Microbial Disease, Yale School of Public Health, New Haven, CT, USA
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27
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Trivellone V, Hoberg EP, Boeger WA, Brooks DR. Food security and emerging infectious disease: risk assessment and risk management. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211687. [PMID: 35223062 PMCID: PMC8847898 DOI: 10.1098/rsos.211687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/20/2022] [Indexed: 05/03/2023]
Abstract
Climate change, emerging infectious diseases (EIDs) and food security create a dangerous nexus. Habitat interfaces, assumed to be efficient buffers, are being disrupted by human activities which in turn accelerate the movement of pathogens. EIDs threaten directly and indirectly availability and access to nutritious food, affecting global security and human health. In the next 70 years, food-secure and food-insecure countries will face EIDs driving increasingly unsustainable costs of production, predicted to exceed national and global gross domestic products. Our modern challenge is to transform this business as usual and embrace an alternative vision of the biosphere formalized in the Stockholm paradigm (SP). First, a pathogen-centric focus shifts our vision of risk space, determining how pathogens circulate in realized and potential fitness space. Risk space and pathogen exchange are always heightened at habitat interfaces. Second, apply the document-assess-monitor-act (DAMA) protocol developing strategic data for EID risk, to be translated, synthesized and broadcast as actionable information. Risk management is realized through targeted interventions focused around information exchanged among a community of scientists, policy practitioners of food and public health security and local populations. Ultimately, SP and DAMA protect human rights, supporting food security, access to nutritious food, health interventions and environmental integrity.
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Affiliation(s)
- Valeria Trivellone
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana Champaign, 1816 South Oak Street, Champaign, IL 61820, USA
| | - Eric P. Hoberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, WI 53716, USA
- Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Walter A. Boeger
- Biological Interactions, Universidade Federal do Paraná, Cx Postal 19073, Curitiba, Brazil
| | - Daniel R. Brooks
- Department of Ecology and Evolutionary Biology, University of Toronto (emeritus), Toronto, ON, Canada
- Harold W. Manter Laboratory of Parasitology, University of Nebraska-Lincoln, NE 68588-0514, USA
- Institute for Evolution, Centre for Ecological Research, Karolina ut 29, Budapest, Hungary H-1113
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28
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Poo S, Whitfield SM, Shepack A, Watkins-Colwell GJ, Nelson G, Goodwin J, Bogisich A, Brennan PLR, D'Agostino J, Koo MS, Mendelson JR, Snyder R, Wilson S, Aronsen GP, Bentley AC, Blackburn DC, Borths MR, Campbell ML, Conde DA, Cook JA, Daza JD, Dembiec DP, Dunnum JL, Early CM, Ferguson AW, Greene A, Guralnick R, Janney C, Johnson D, Knightly F, Poulin S, Rocha L, Soltis PS, Thiers B, Chakrabarty P. OUP accepted manuscript. Bioscience 2022; 72:449-460. [PMID: 35592056 PMCID: PMC9113241 DOI: 10.1093/biosci/biac022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Zoos and natural history museums are both collections-based institutions with important missions in biodiversity research and education. Animals in zoos are a repository and living record of the world's biodiversity, whereas natural history museums are a permanent historical record of snapshots of biodiversity in time. Surprisingly, despite significant overlap in institutional missions, formal partnerships between these institution types are infrequent. Life history information, pedigrees, and medical records maintained at zoos should be seen as complementary to historical records of morphology, genetics, and distribution kept at museums. Through examining both institution types, we synthesize the benefits and challenges of cross-institutional exchanges and propose actions to increase the dialog between zoos and museums. With a growing recognition of the importance of collections to the advancement of scientific research and discovery, a transformational impact could be made with long-term investments in connecting the institutions that are caretakers of living and preserved animals.
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Affiliation(s)
| | | | | | | | - Gil Nelson
- Florida Museum of Natural History and with iDigBio, Gainesville, Florida, United States
| | - Jillian Goodwin
- Florida Museum of Natural History and with iDigBio, Gainesville, Florida, United States
| | | | | | | | - Michelle S Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States
| | | | - Rebecca Snyder
- Oklahoma City Zoo, Oklahoma City, Oklahoma, United States
| | | | | | | | - David C Blackburn
- Florida Museum of Natural History and with iDigBio, Gainesville, Florida, United States
| | | | - Mariel L Campbell
- Museum of Southwestern Biology, Albuquerque, New Mexico, United States
| | | | - Joseph A Cook
- Museum of Southwestern Biology, Albuquerque, New Mexico, United States
| | - Juan D Daza
- Sam Houston State University, Huntsville, Texas, United States
| | | | - Jonathan L Dunnum
- Museum of Southwestern Biology, Albuquerque, New Mexico, United States
| | | | | | - Amanda Greene
- Duke Lemur Center, Durham, North Carolina, United States
| | - Robert Guralnick
- Florida Museum of Natural History and with iDigBio, Gainesville, Florida, United States
| | - Courtney Janney
- Memphis Zoological Society, Memphis, Tennessee, United States
| | | | | | - Stephane Poulin
- Arizona-Sonora Desert Museum, Tucson, Arizona, United States
| | - Luiz Rocha
- California Academy of Sciences, San Francisco, United States
| | - Pamela S Soltis
- Florida Museum of Natural History and with iDigBio, Gainesville, Florida, United States
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29
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Adler Miserendino RA, Meyer RS, Zimkus BM, Bates J, Silvestri L, Taylor C, Blumenfield T, Srigyan M, Pandey JL. OUP accepted manuscript. Bioscience 2022; 72:405-408. [PMID: 35592054 PMCID: PMC9113315 DOI: 10.1093/biosci/biac019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Rachel Sarah Meyer
- University of California Santa Cruz, Santa Cruz, California, United States
| | - Breda M Zimkus
- Harvard University, Cambridge, Massachusetts, in the United States
| | - John Bates
- The Field Museum, Chicago, Illinois, United States
| | - Luciana Silvestri
- Instituto de Ciencias Humanas, Sociales y Ambientales of the Consejo Nacional de Investigaciones Científicas y Técnicas, Mendoza, Argentina
| | - Crispin Taylor
- American Society of Plant Biologists, Rockville, Maryland, United States
| | - Tami Blumenfield
- Yunnan University, People's Republic of China, and with the Department of Anthropology, University of New Mexico, United States
| | - Megha Srigyan
- University of California Santa Cruz, Santa Cruz, California, United States
| | - Jyotsna L Pandey
- American Institute of Biological Sciences, Herndon, Virginia, United States
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30
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Ragan EJ, McCallum C, Marathe J, Cole M, Hofman M, Henderson AJ, Flack T, Miller NS, Burks EJ, Zhao GQ, Denis R, Lin NH, Jacobson KR, Andry CD, Pelton SI, Duffy ER, Bhadelia N. Pandemic Response Requires Research Samples: A U.S. Safety-Net Hospital's Experience and Call for National Action. Ann Intern Med 2021; 174:1727-1732. [PMID: 34724402 DOI: 10.7326/m21-2857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Biorepositories provide a critical resource for gaining knowledge of emerging infectious diseases and offer a mechanism to rapidly respond to outbreaks; the emergence of the novel coronavirus, SARS-CoV-2, has proved their importance. During the COVID-19 pandemic, the absence of centralized, national biorepository efforts meant that the onus fell on individual institutions to establish sample repositories. As a safety-net hospital, Boston Medical Center (BMC) recognized the importance of creating a COVID-19 biorepository to both support critical science at BMC and ensure representation in research for its urban patient population, most of whom are from underserved communities. This article offers a realistic overview of the authors' experience in establishing this biorepository at the onset of the COVID-19 pandemic during the height of the first surge of cases in Boston, Massachusetts, with the hope that the challenges and solutions described are useful to other institutions. Going forward, funders, policymakers, and infectious disease and public health communities must support biorepository implementation as an essential element of future pandemic preparedness.
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Affiliation(s)
- Elizabeth J Ragan
- Section of Infectious Diseases and Research Operations, Boston Medical Center, Boston, Massachusetts (E.J.R.)
| | - Caitryn McCallum
- Section of Infectious Diseases, Boston Medical Center, and Center for Emerging Infectious Diseases Policy and Research, Boston University, Boston, Massachusetts (C.M.)
| | - Jai Marathe
- Section of Infectious Diseases, Boston Medical Center, Boston, Massachusetts (J.M., N.H.L., K.R.J.)
| | - Manisha Cole
- Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (M.C., N.S.M., E.J.B., G.Q.Z.)
| | - Melissa Hofman
- Clinical Data Warehouse, Boston Medical Center, Boston, Massachusetts (M.H.)
| | - Andrew J Henderson
- Section of Infectious Diseases, Boston Medical Center, and Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts (A.J.H.)
| | - Tyler Flack
- Research Operations, Boston Medical Center, Boston, Massachusetts (T.F.)
| | - Nancy S Miller
- Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (M.C., N.S.M., E.J.B., G.Q.Z.)
| | - Eric J Burks
- Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (M.C., N.S.M., E.J.B., G.Q.Z.)
| | - Grace Qing Zhao
- Department of Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts (M.C., N.S.M., E.J.B., G.Q.Z.)
| | - Ridiane Denis
- General Clinical Research Unit, Boston University, Boston, Massachusetts (R.D.)
| | - Nina H Lin
- Section of Infectious Diseases, Boston Medical Center, Boston, Massachusetts (J.M., N.H.L., K.R.J.)
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston Medical Center, Boston, Massachusetts (J.M., N.H.L., K.R.J.)
| | - Christopher D Andry
- Department of Pathology and Laboratory Medicine, Boston Medical Center, and Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts (C.D.A., E.R.D.)
| | - Stephen I Pelton
- Section of Pediatric Infectious Diseases, Department of Pediatrics, Boston University Medical Center, Department of Epidemiology, Boston University School of Public Health, and Maxwell Finland Laboratory for Infectious Diseases, Boston, Massachusetts (S.I.P.)
| | - Elizabeth R Duffy
- Department of Pathology and Laboratory Medicine, Boston Medical Center, and Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts (C.D.A., E.R.D.)
| | - Nahid Bhadelia
- Section of Infectious Diseases, Boston Medical Center, and Center for Emerging Infectious Diseases Policy and Research and National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts (N.B.)
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31
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Abstract
Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.
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Affiliation(s)
- Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
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32
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Jacob Machado D, White RA, Kofsky J, Janies DA. Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2021; 1:e60. [PMID: 36168505 PMCID: PMC9495640 DOI: 10.1017/ash.2021.222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 04/19/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic was one of the significant causes of death worldwide in 2020. The disease is caused by severe acute coronavirus syndrome (SARS) coronavirus 2 (SARS-CoV-2), an RNA virus of the subfamily Orthocoronavirinae related to 2 other clinically relevant coronaviruses, SARS-CoV and MERS-CoV. Like other coronaviruses and several other viruses, SARS-CoV-2 originated in bats. However, unlike other coronaviruses, SARS-CoV-2 resulted in a devastating pandemic. The SARS-CoV-2 pandemic rages on due to viral evolution that leads to more transmissible and immune evasive variants. Technology such as genomic sequencing has driven the shift from syndromic to molecular epidemiology and promises better understanding of variants. The COVID-19 pandemic has exposed critical impediments that must be addressed to develop the science of pandemics. Much of the progress is being applied in the developed world. However, barriers to the use of molecular epidemiology in low- and middle-income countries (LMICs) remain, including lack of logistics for equipment and reagents and lack of training in analysis. We review the molecular epidemiology literature to understand its origins from the SARS epidemic (2002-2003) through influenza events and the current COVID-19 pandemic. We advocate for improved genomic surveillance of SARS-CoV and understanding the pathogen diversity in potential zoonotic hosts. This work will require training in phylogenetic and high-performance computing to improve analyses of the origin and spread of pathogens. The overarching goals are to understand and abate zoonosis risk through interdisciplinary collaboration and lowering logistical barriers.
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Affiliation(s)
- Denis Jacob Machado
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- Author for correspondence: Denis Jacob Machado, PhD, Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, BINF 224, Charlotte, NC28223. E-mail:
| | - Richard Allen White
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- University of North Carolina at Charlotte, North Carolina Research Campus (NCRC), Kannapolis, North Carolina
| | - Janice Kofsky
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
| | - Daniel A. Janies
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
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