Author
Zoe Grange
Bio: Zoe Grange is an academic researcher from University of California, Davis. The author has contributed to research in topics: Risk assessment & Learning object. The author has an hindex of 2, co-authored 3 publications receiving 29 citations.
Papers
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TL;DR: In this article, a risk ranking framework and interactive web tool, SpillOver, was developed to estimate a risk score for wildlife-origin viruses, creating a comparative risk assessment of viruses with uncharacterized zoonotic spillover potential alongside those already known to be Zoonotic.
Abstract: The death toll and economic loss resulting from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic are stark reminders that we are vulnerable to zoonotic viral threats Strategies are needed to identify and characterize animal viruses that pose the greatest risk of spillover and spread in humans and inform public health interventions Using expert opinion and scientific evidence, we identified host, viral, and environmental risk factors contributing to zoonotic virus spillover and spread in humans We then developed a risk ranking framework and interactive web tool, SpillOver, that estimates a risk score for wildlife-origin viruses, creating a comparative risk assessment of viruses with uncharacterized zoonotic spillover potential alongside those already known to be zoonotic Using data from testing 509,721 samples from 74,635 animals as part of a virus discovery project and public records of virus detections around the world, we ranked the spillover potential of 887 wildlife viruses Validating the risk assessment, the top 12 were known zoonotic viruses, including SARS-CoV-2 Several newly detected wildlife viruses ranked higher than known zoonotic viruses Using a scientifically informed process, we capitalized on the recent wealth of virus discovery data to systematically identify and prioritize targets for investigation The publicly accessible SpillOver platform can be used by policy makers and health scientists to inform research and public health interventions for prevention and rapid control of disease outbreaks SpillOver is a living, interactive database that can be refined over time to continue to improve the quality and public availability of information on viral threats to human health
103 citations
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Georgetown University Medical Center1, University of Toronto2, Institute of Ecosystem Studies3, University of Glasgow4, Georgetown University5, International Livestock Research Institute6, University of Nebraska Medical Center7, Icahn School of Medicine at Mount Sinai8, Louisiana State University9, Pacific Lutheran University10, Colorado State University11, University of Arkansas12, University of London13, Georgetown University Law Center14, University of Cambridge15, University of Manitoba16, Massey University17, Tufts University18, University of Nairobi19, EcoHealth Alliance20, Griffith University21, University of Florida22, Washington State University23, University of Helsinki24, Carnegie Mellon University25, University of Pretoria26, Maasai Mara University27
TL;DR: In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programs will identify hundreds of novel viruses that might someday pose a threat to humans.
Abstract: In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges? This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
33 citations
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07 Apr 2021
TL;DR: This work synthesizes the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions: What are the prerequisites, in terms of open data, equity, and interdisciplinary collaboration, to the development and application of those tools?
Abstract: In light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programs will identify hundreds of novel viruses that might someday pose a threat to humans. Our capacity to identify which viruses are capable of zoonotic emergence depends on the existence of a technology—a machine learning model or other informatic system—that leverages available data on known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions: What are the prerequisites, in terms of open data, equity, and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it, and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges? Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 7 April 2021 doi:10.20944/preprints202104.0200.v1
3 citations
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TL;DR: In this article, the authors demonstrate that the virological data on which these analyses are conducted are incomplete, biased, and rapidly changing with ongoing virus discovery, and suggest that attempts to assess zoonotic risk using available virologogical data are likely to be inaccurate and largely only identify those host taxa that have been studied most extensively.
Abstract: Identifying the animal reservoirs from which zoonotic viruses will likely emerge is central to understanding the determinants of disease emergence. Accordingly, there has been an increase in studies attempting zoonotic "risk assessment." Herein, we demonstrate that the virological data on which these analyses are conducted are incomplete, biased, and rapidly changing with ongoing virus discovery. Together, these shortcomings suggest that attempts to assess zoonotic risk using available virological data are likely to be inaccurate and largely only identify those host taxa that have been studied most extensively. We suggest that virus surveillance at the human-animal interface may be more productive.
42 citations
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TL;DR: In this article, the authors developed machine learning models that identify candidate zoonoses solely using signatures of host range encoded in viral genomes, which outperformed models based on the phylogenetic relatedness of viruses to known human-infecting viruses (area under the receiver operating characteristic curve [AUC] = 0.773).
Abstract: Determining which animal viruses may be capable of infecting humans is currently intractable at the time of their discovery, precluding prioritization of high-risk viruses for early investigation and outbreak preparedness. Given the increasing use of genomics in virus discovery and the otherwise sparse knowledge of the biology of newly discovered viruses, we developed machine learning models that identify candidate zoonoses solely using signatures of host range encoded in viral genomes. Within a dataset of 861 viral species with known zoonotic status, our approach outperformed models based on the phylogenetic relatedness of viruses to known human-infecting viruses (area under the receiver operating characteristic curve [AUC] = 0.773), distinguishing high-risk viruses within families that contain a minority of human-infecting species and identifying putatively undetected or so far unrealized zoonoses. Analyses of the underpinnings of model predictions suggested the existence of generalizable features of viral genomes that are independent of virus taxonomic relationships and that may preadapt viruses to infect humans. Our model reduced a second set of 645 animal-associated viruses that were excluded from training to 272 high and 41 very high-risk candidate zoonoses and showed significantly elevated predicted zoonotic risk in viruses from nonhuman primates, but not other mammalian or avian host groups. A second application showed that our models could have identified Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a relatively high-risk coronavirus strain and that this prediction required no prior knowledge of zoonotic Severe Acute Respiratory Syndrome (SARS)-related coronaviruses. Genome-based zoonotic risk assessment provides a rapid, low-cost approach to enable evidence-driven virus surveillance and increases the feasibility of downstream biological and ecological characterization of viruses.
40 citations
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Georgetown University1, University of Oklahoma2, University of Liverpool3, University of California, Berkeley4, Louisiana State University5, Icahn School of Medicine at Mount Sinai6, University of South Carolina7, Pacific Lutheran University8, Colorado State University9, University of Toronto10, University of Cambridge11, University of Colorado Boulder12, University of Glasgow13, National Institute of Standards and Technology14, Université de Montréal15, University of Saskatchewan16, Vaccine and Infectious Disease Organization17, University of Florida18, University of KwaZulu-Natal19, Washington State University20, University of Idaho21, Georgetown University Medical Center22
TL;DR: In this article, a network science framework for understanding and predicting human and animal susceptibility to viral infections is proposed to identify basic biological rules that govern cross-species transmission and structure the global virome.
Abstract: Better methods to predict and prevent the emergence of zoonotic viruses could support future efforts to reduce the risk of epidemics. We propose a network science framework for understanding and predicting human and animal susceptibility to viral infections. Related approaches have so far helped to identify basic biological rules that govern cross-species transmission and structure the global virome. We highlight ways to make modelling both accurate and actionable, and discuss the barriers that prevent researchers from translating viral ecology into public health policies that could prevent future pandemics.
37 citations
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TL;DR: Genome-based risk assessment allows identification of high-risk viruses immediately upon discovery, increasing both the feasibility and likelihood of downstream virological and ecological characterization and allowing for evidence-driven virus surveillance.
Abstract: Rapid assessment of which animal viruses may be capable of infecting humans is currently intractable, but would allow their prioritization for further investigation and pandemic preparedness. We developed machine learning algorithms that identify candidate zoonoses using evolutionary signals of host range encoded in viral genomes. This reduces lists of hundreds of viruses with uncertain human infectivity to tractable numbers for prioritized research, generalizes to virus families excluded from model training, can distinguish high risk viruses within families that contain a minority of zoonotic species, and could have identified the exceptional risk of SARS-CoV-2 prior to its emergence. Genome-based risk assessment allows identification of high-risk viruses immediately upon discovery, increasing both the feasibility and likelihood of downstream virological and ecological characterization and allowing for evidence-driven virus surveillance.
37 citations
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Georgetown University Medical Center1, University of Toronto2, Institute of Ecosystem Studies3, University of Glasgow4, Georgetown University5, International Livestock Research Institute6, University of Nebraska Medical Center7, Icahn School of Medicine at Mount Sinai8, Louisiana State University9, Pacific Lutheran University10, Colorado State University11, University of Arkansas12, University of London13, Georgetown University Law Center14, University of Cambridge15, University of Manitoba16, Massey University17, Tufts University18, University of Nairobi19, EcoHealth Alliance20, Griffith University21, University of Florida22, Washington State University23, University of Helsinki24, Carnegie Mellon University25, University of Pretoria26, Maasai Mara University27
TL;DR: In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programs will identify hundreds of novel viruses that might someday pose a threat to humans.
Abstract: In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges? This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
33 citations