Colin Carlson

• Ph.D.
• Assistant Professor at Yale University

Bacillus anthracis is a spore-forming, Gram-positive bacterium responsible for anthrax, an acute and commonly lethal infection that most significantly affects grazing livestock, wild ungulates and other herbivorous mammals, but also poses a serious threat to human health. The geographic extent of B. anthracis endemism is still poorly understood, de...

Present estimates suggest there are over 1 million virus species found in mammals alone, with about half a million posing a possible threat to human health. Although previous estimates assume linear scaling between host and virus diversity, we show that ecological network theory predicts a non-linear relationship, produced by patterns of host shari...

Despite the global investment in One Health disease surveillance, it remains difficult and costly to identify and monitor the wildlife reservoirs of novel zoonotic viruses. Statistical models can guide sampling target prioritisation, but the predictions from any given model might be highly uncertain; moreover, systematic model validation is rare, a...

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-...

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 r...

Orthopoxviruses (OPVs), including the causative agents of smallpox and mpox have led to devastating outbreaks in human populations worldwide. However, the discontinuation of smallpox vaccination, which also provides cross-protection against related OPVs, has diminished global immunity to OPVs more broadly. We apply machine learning models incorpora...

During the Covid-19 pandemic, the World Health Organization (WHO) was an important public source of information – not only about the pandemic, but also thousands of other potential health emergencies. Here, we examine the 242 reports published in the WHO Disease Outbreak News (DON) during the first four years of the Covid-19 pandemic (2020 to 2023)...

The 2023-24 epidemic of Oropouche fever in the Americas and the associated ongoing outbreak in Cuba suggests a potential state shift in the epidemiology of the disease, raising questions about which vectors are driving transmission. In this study, we conduct a systematic review of vector competence experiments with Oropouche virus (OROV, Orthobunya...

Characterizing host-virus associations is critical due to the rising frequency of emerging infectious diseases originating from wildlife. Past analyses have evaluated zoonotic risk as binary, but virulence and transmissibility can vary dramatically. Recent work suggests bats harbor more viruses with high virulence in humans than other taxa. However...

Although climate change poses a well-established risk to human health, present-day health impacts, particularly those resulting from climate-induced behavioral changes, are under-quantified. Analyzing the U.S. West Coast wildfires of September 2020, we found that poor air quality drives people indoors, increasing the circulation of airborne pathoge...

Despite widespread consensus that climate change poses a serious threat to global public health, very few studies have isolated the specific contributions of human-caused climate change to changes in morbidity and mortality. Here, we systematically review over 3,600 abstracts, and identify a dozen end-to-end impact attribution studies on human heal...

Quantifying how global change impacts wild populations remains challenging, especially for species poorly represented by systematic datasets. Here, we infer climate change effects on masting by Joshua trees (Yucca brevifolia and Y. jaegeriana), keystone perennials of the Mojave Desert, from 15 years of crowdsourced observations. We annotated phenop...

Emerging infectious diseases are increasingly understood as a hallmark of the Anthropocene 1–3 . Most experts agree that anthropogenic ecosystem change and high-risk contact among people, livestock, and wildlife have contributed to the recent emergence of new zoonotic, vector-borne, and environmentally-transmitted pathogens 1,4–6 . However, the ext...

Thousands of scientists and practitioners conduct research on infectious diseases of wildlife. Rapid and comprehensive data sharing is vital to the transparency and actionability of their work, but unfortunately, most efforts designed to publically share these data are focused on pathogen determination and genetic sequence data. Other facets of exi...

During the Covid-19 pandemic, the World Health Organization (WHO) was faced with the task of regular public updating—about both the pandemic itself, and hundreds or potentially thousands of other health emergencies. Here, we examined the 242 reports published in the WHO Disease Outbreak News (DON) during the first four years of the Covid-19 pandemi...

Just like data, models have their own life cycle. By recognizing how one’s model fits within the life cycle of the data (or at least, ensuring that the model life cycle is understood), we can identify opportunities to foster new collaborations, encourage better practices in data analysis, and ultimately accelerate research. In this manuscript, we i...

Multinational epidemics of emerging infectious diseases are increasingly common, due to anthropogenic pressure on ecosystems and the growing connectivity of human populations. Early and efficient vaccination can contain outbreaks and prevent mass mortality, but optimal vaccine stockpiling strategies are dependent on pathogen characteristics, reserv...

Climate change can cause outbreaks of infectious diseases in unfamiliar locations — but how do we know which unusual outbreaks are the result of climate change? Scientists often hesitate to guess, leaving the task to journalists or the public. All of these audiences would benefit from a clear and consistent framework for thinking about causality, e...

Impact attribution is an emerging transdisciplinary sub-discipline of detection and attribution, focused on the social, economic, and ecological impacts of climate change. Here, we provide an overview of common end-to-end frameworks in impact attribution, focusing on examples relating to the human health impacts of climate change. We propose a typo...

Pathogen evolution is one of the least predictable components of disease emergence, particularly in nature. Here, building on principles established by the geographic mosaic theory of coevolution, we develop a quantitative, spatially-explicit framework for mapping the evolutionary risk of viral emergence. Driven by interest in diseases like SARS, M...

Orthopoxviruses (OPVs), including the causative agents of smallpox and mpox have led to devastating outbreaks in human populations worldwide. However, the discontinuation of smallpox vaccination, which also provides cross-protection against related OPVs, has diminished global immunity to OPVs more broadly. We apply machine learning models incorpora...

Species distribution modeling (SDM) has become an increasingly common approach to explore questions about ecology, geography, outbreak risk, and global change as they relate to infectious disease vectors. Here, we conducted a systematic review of the scientific literature, screening 563 abstracts and identifying 204 studies that used SDMs to produc...

As the COVID-19 pandemic unfolded in the spring of 2020, governments around the world began to implement policies to mitigate and manage the outbreak. Significant research efforts were deployed to track and analyse these policies in real-time to better inform the response. While much of the policy analysis focused narrowly on social distancing meas...

The dataset provides a uniquely broad capture of the governance strategies for pandemic response, serving as a critical data source for future work in legal epidemiology and political science.

The health burden of anthropogenic climate change is growing exponentially, but present-day impacts remain difficult to measure. Here, we leverage a recently-published comprehensive dataset of 50,425 population surveys to investigate whether human-caused climate change has increased the burden of childhood malaria across sub-Saharan Africa. In hist...

Outbreak response, as a technical and specialized field of practice, is struggling to keep pace with the evolving dynamics of modern public health emergencies. Extensive scholarship across disciplines and epidemics has highlighted the importance of early action, the costs associated with delayed mobilization, the necessity of effective preparedness...

Beginning December 2016, sylvatic yellow fever (YF) outbreaks spread into southeastern Brazil, and Minas Gerais state experienced two sylvatic YF waves (2017 and 2018). Following these massive YF waves, we screened 187 free-living non-human primate (NHPs) carcasses collected throughout the state between January 2019 and June 2021 for YF virus (YFV)...

The Working Group II contribution to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC) provides a comprehensive assessment of the scientific literature relevant to climate change impacts, adaptation and vulnerability. The report recognizes the interactions of climate, ecosystems and biodiversity, and human societie...

The emergence of SARS-CoV-2 highlights a need for evidence-based strategies to monitor bat viruses. We performed a systematic review of coronavirus sampling (testing for RNA positivity) in bats globally. We identified 110 studies published between 2005 and 2020 that collectively reported positivity from 89,752 bat samples. We compiled 2,274 records...

As the COVID-19 pandemic unfolded in the spring of 2020, governments around the world began to implement policies to mitigate and manage the outbreak. Significant research efforts were deployed to track and analyse these policies in real-time to better inform the response. While much of the policy analysis focused narrowly on social distancing meas...

Arboviruses receive heightened research attention during major outbreaks or when they cause unusual or severe clinical disease, but they are otherwise undercharacterized. Global change is also accelerating the emergence and spread of arboviral diseases, leading to time-sensitive questions about potential interactions between viruses and novel vecto...

Predicting host-virus interactions is fundamentally a network science problem. We develop a method for bipartite network prediction that combines a recommender system (linear filtering) with an imputation algorithm based on low-rank graph embedding. We test this method by applying it to a global database of mammal-virus interactions and thus show t...

Species distribution modeling (SDM) has become an increasingly common approach to explore questions about ecology, geography, outbreak risk, and global change as they relate to infectious disease vectors. Here, we conducted a systematic review of the scientific literature, screening 563 abstracts and identifying 204 studies that used SDMs to produc...

Facing a warming climate, many tropical species-including the arthropod vectors of several infectious diseases-will be displaced to higher latitudes and elevations. These shifts are frequently projected for the future, but rarely documented in the present day. Here, we use one of the most comprehensive datasets ever compiled by medical entomologist...

The World Health Organization (WHO) notifies the global community about disease outbreaks through the Disease Outbreak News (DON). These online reports tell important stories about both outbreaks themselves and the high-level decision making that governs information sharing during public health emergencies. However, they have been used only minimal...

Helminthiases are a class of neglected tropical diseases that affect at least 1 billion people worldwide, with a disproportionate impact on resource-poor areas with limited disease surveillance. Geospatial methods can offer valuable insights into the burden of these infections, particularly given that many are subject to strong ecological influence...

Curated databases of species interactions are instrumental to exploring and understanding the spatial distribution of species and their biotic interactions. In the process of conducting such projects, data development and curation efforts may give rise to a data product with utility beyond the scope of the original work, but which becomes inaccessi...

The growing threat of vector-borne diseases, highlighted by recent epidemics, has prompted increased focus on the fundamental biology of vector-virus interactions. To this end, experiments are often the most reliable way to measure vector competence (the potential for arthropod vectors to transmit certain pathogens). Data from these experiments are...

Beginning December 2016, sylvatic yellow fever (YF) outbreaks spread into southeastern Brazil, and Minas Gerais state experienced two sylvatic YF waves (2017 and 2018). Following these massive YF waves, we screened 187 free-living non-human primate (NHPs) carcasses collected throughout the state between January 2019 and June 2021 for YF virus (YFV)...

The sugars that coat the outsides of viruses and host cells are key to successful disease transmission, but they remain understudied compared to other molecular features. Understanding the comparative zoology of glycosylation - and harnessing it for predictive science - could help close the molecular gap in zoonotic risk assessment.

The sugars that coat the outsides of viruses and host cells are key to successful disease transmission, but they remain understudied compared to other molecular features. Understanding the comparative zoology of glycosylation - and harnessing it for predictive science - could help close the molecular gap in zoonotic risk assessment.

An evidence-based treaty must balance prevention, preparedness, response, and repair

Pathogen evolution is one of the least predictable components of disease emergence, particularly in nature. Here, building on principles established by the geographic mosaic theory of coevolution, we develop a quantitative, spatially-explicit framework for mapping the evolutionary risk of viral emergence. Driven by interest in diseases like SARS, M...

Epidemic risk assessment and response relies on rapid information sharing. Using examples from the past decade, we discuss the limitations of the present system for outbreak notifications, which suffers from ambiguous obligations, fragile incentives, and an overly narrow focus on human outbreaks. We examine existing international legal frameworks,...

A growing body of evidence links zoonotic disease risk, including pandemic threats, to biodiversity loss and other upstream anthropogenic impacts on ecosystem health. However, there is little current research assessing viral diversity in endangered species. Here, combining IUCN Red List data on 5,876 mammal species with data on host-virus associati...

The emergence of SARS-CoV-2, and the challenge of pinpointing its ecological and evolutionary context, has highlighted the importance of evidence-based strategies for monitoring viral dynamics in bat reservoir hosts. Here, we compiled the results of 93,877 samples collected from bats across 111 studies between 1996 and 2018, and used these to devel...

The growing threat of vector-borne diseases, highlighted by recent epidemics, has prompted increased focus on the fundamental biology of vector-virus interactions. To this end, experiments are often the most reliable way to measure vector competence (the potential for arthropod vectors to transmit certain pathogens). Data from these experiments are...

The world is rapidly urbanizing, inviting mounting concern that urban environments will experience increased zoonotic disease risk. Urban animals could have more frequent contact with humans, therefore transmitting more zoonotic parasites; however, this relationship is complicated by sampling bias and phenotypic confounders. Here we test whether ur...

Global changes in response to human encroachment into natural habitats and carbon emissions are driving the biodiversity extinction crisis and increasing disease emergence risk. Host distributions are one critical component to identify areas at risk of viral spillover, and bats act as reservoirs of diverse viruses. We developed a reproducible ecolo...

Arboviruses receive heightened research attention during major outbreaks, or when they cause unusual or severe clinical disease, but are otherwise under-characterized. Global change is also accelerating the emergence and spread of arboviral diseases, leading to time sensitive questions about potential interactions between viruses and novel vectors....

The sugars that coat the outsides of viruses and host cells are key to successful disease transmission, but they remain understudied compared to other molecular features. Understanding the comparative zoology of glycosylation - and harnessing it for predictive science - could help close the molecular gap in zoonotic risk assessment.

At least 10,000 virus species have the capacity to infect humans, but at present, the vast majority are circulating silently in wild mammals1,2. However, climate and land use change will produce novel opportunities for viral sharing among previously geographically-isolated species of wildlife3,4. In some cases, this will facilitate zoonotic spillov...

Solar geoengineering is often framed as a stopgap measure to decrease the magnitude, impacts, and injustice of climate change. However, the benefits or costs of geoengineering for human health are largely unknown. We project how geoengineering could impact malaria risk by comparing current transmission suitability and populations-at-risk under mode...

The sugars that coat the outsides of viruses and host cells are key to successful disease transmission, but they remain understudied compared to other molecular features. Understanding the comparative zoology of glycosylation - and harnessing it for predictive science - could help close the molecular gap in zoonotic risk assessment.

Identifying reservoir host species is crucial for understanding the ecology of multi‐host pathogens and predicting risks of pathogen spillover from wildlife to people. Predictive models are increasingly used for identifying ecological traits and prioritizing surveillance of likely zoonotic reservoirs, but these often employ different types of evide...

The World Health Organization (WHO) notifies the global community about disease outbreaks through the Disease Outbreak News (DON). These online reports tell important stories about both outbreaks themselves and the high-level decision making that governs information sharing during public health emergencies. However, they have been used only minimal...

The SARS‐CoV‐2 pandemic has led to increased concern over transmission of pathogens from humans to animals, and its potential to threaten conservation and public health. To assess this threat, we reviewed published evidence of human‐to‐wildlife transmission events, with a focus on how such events could threaten animal and human health. We identifie...

Data that catalogue viral diversity on Earth have been fragmented across sources, disciplines, formats, and various degrees of open sharing, posing challenges for research on macroecology, evolution, and public health. Here, we solve this problem by establishing a dynamically maintained database of vertebrate-virus associations, called The Global V...

Host-virus association data underpin research into the distribution and eco-evolutionary correlates of viral diversity and zoonotic risk across host species. However, current knowledge of the wildlife virome is inherently constrained by historical discovery effort, and there are concerns that the reliability of ecological inference from host-virus...

Global changes in response to human encroachment into natural habitats and carbon emissions are driving the biodiversity extinction crisis and increasing disease emergence risk. Host distributions are one critical component to identify areas at risk of spillover, and bats act as reservoirs of diverse viruses. We developed a reproducible ecological...

Understanding possible climate futures that include carbon dioxide removal (CDR) and solar radiation modification (SRM) requires thinking not just about staying within the remaining carbon budget, but also about politics and people. However, despite growing interest in CDR and SRM, scenarios focused on these potential responses to climate change te...

The potential for a pathogen to infect a host is mediated by traits of both the host and pathogen, as well as the complex interactions between them. Arthropod-borne viruses (arboviruses) require an intermediate vector, introducing an additional compatibility layer. Existing predictive models of host-virus networks rarely incorporate the unique aspe...

After several pandemics over the last two millennia, the wildlife reservoirs of plague (Yersinia pestis) now persist around the world, including in the western United States. Routine surveillance in this region has generated comprehensive records of human cases and animal seroprevalence, creating a unique opportunity to test how plague reservoirs a...

NCBITaxonomy.jl is a package designed to facilitate the reconciliation and cleaning of taxonomic names, using a local copy of the NCBI taxonomic backbone (Federhen 2012, Schoch et al. 2020); The basic search functions are coupled with quality-of-life functions including case-insensitive search and custom fuzzy string matching to facilitate the amou...

Curated databases of species interactions are instrumental to exploring and understanding the spatial distribution of species and their biotic interactions. In the process of conducting such projects, data development and curation efforts may give rise to a data product with utility beyond the scope of the original work, but which becomes inaccessi...

Ecologists increasingly recognise coinfection as an important component of emergent epidemiological patterns, connecting aspects of ecoimmunology, behaviour, ecosystem function and even extinction risk. Building on syndemic theory in medical anthropology, we propose the term ‘synzootics’ to describe co‐occurring enzootic or epizootic processes that...

The fields of viral ecology and evolution are rapidly expanding, motivated in part by concerns around emerging zoonoses. One consequence is the proliferation of host–virus association data, which underpin viral macroecology and zoonotic risk prediction but remain fragmented across numerous data portals. In the present article, we propose that synth...

Host-virus association data form the backbone of research into eco-evolutionary drivers of viral diversity and host-level zoonotic risk. However, knowledge of the wildlife virome is inherently constrained by historical discovery effort, and there are concerns that the reliability of ecological inference from host-virus data may be undermined by tax...

Data cataloguing viral diversity on Earth have been fragmented across sources, disciplines, formats, and various degrees of open collation, posing challenges for research on macroecology, evolution, and public health. Here, we solve this problem by establishing a dynamically-maintained database of vertebrate-virus associations, called The Global Vi...

Due to climate change and habitat conversion, estimates of the resulting levels of species extinction over the next century are alarming. Devising conservation solutions will require many different approaches, including examining the extinction processes of recently extinct species. Given that parrots are one of the most threatened groups of birds,...

At most 1-2% of the global virome has been sampled to date. Here, we develop a novel method that combines Linear Filtering (LF) and Singular Value Decomposition (SVD) to infer host-virus associations. Using this method, we recovered highly plausible undiscovered interactions with a strong signal of viral coevolutionary history, and revealed a globa...

Tick-borne diseases are a growing problem in many parts of the world, and their surveillance and control touch on challenging issues in medical entomology, agricultural health, veterinary medicine, and biosecurity. Spatial approaches can be used to synthesize the data generated by integrative One Health surveillance systems, and help stakeholders,...

The SARS-CoV-2 pandemic has led to increased concern over transmission of pathogens from humans to animals (“spillback”) and its potential to threaten conservation and public health. To assess this threat, we reviewed published evidence of spillback events, including instances where spillback could threaten conservation and human health. We identif...

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 m...

Understanding and addressing the complex effects of climate change on planetary health requires a multidisciplinary approach. Here, experts share their experience working at the intersection of health and climate. Their Voices advocate for cooperation, rethinking the concept of sustainability,and urge for immediate action to preserve global health.

After several pandemics over the last two millennia, the wildlife reservoirs of plague (Yersinia pestis) now persist around the world, including in the western United States. Routine surveillance in this region has generated comprehensive records of human cases and animal seroprevalence, creating a unique opportunity to test how plague reservoirs a...

Tick-borne diseases are a growing problem in many parts of the world, and their surveillance and control touches on challenging issues in medical entomology, agricultural health, veterinary medicine, and biosecurity. Spatial approaches can be used to synthesize the data generated by integrative One Health surveillance systems, and help stakeholders...

The fields of viral ecology and evolution have rapidly expanded in the last two decades, driven by technological improvements, and motivated by efforts to discover potentially zoonotic wildlife viruses under the rubric of pandemic prevention. One consequence has been a massive proliferation of host-virus association data, which comprise the backbon...

Mammals that regularly inhabit urban environments may have more frequent contact with humans and therefore host more known zoonotic pathogens. Here, we test this prediction using a consolidated dataset of phenotypic traits, urban affiliate status, and pathogen diversity, across 3004 mammal species. We show that urban-adapted mammals have more docum...