Global shifts in mammalian population trends reveal key predictors of virus spillover risk

Identifying life-history patterns along the fast-slow continuum of mammalian viral carriers

Life-history traits have been identified as major indicators of mammals' susceptibility and exposure to viruses due to evolutionary constraints that link life-history speed with species' ecology and immunity. Nonetheless, it is unclear where along the fast-slow continuum of mammalian life-history lies the greatest diversity of host species. Consequently, life-history patterns that govern host-virus associations remain largely unknown. Here we analyse the virome of 1350 wild mammals and detect the characteristics that drive species' compatibility with different groups of viruses. We highlight that mammals with larger body size and either very rapid or very slow life histories are more likely to carry different groups of viruses, particularly zoonotic ones. While some common life-history patterns emerge across carriers, eco-evolutionary characteristics of viral groups appear to determine association with certain carrier species. Our findings underline the importance of incorporating both mammals' life-history information and viruses' ecological diversity into surveillance strategies to identify potential zoonotic carriers in wildlife.

Zoonotic pathogens in wild Asian primates: a systematic review highlighting research gaps

Introduction

Ongoing global changes, including natural land conversion for agriculture and urbanization, modify the dynamics of human-primate contacts, resulting in increased zoonotic risks. Although Asia shelters high primate diversity and experiences rapid expansion of human-primate contact zones, there remains little documentation regarding zoonotic surveillance in the primates of this region.

Methods

Using the PRISMA guidelines, we conducted a systematic review to compile an inventory of zoonotic pathogens detected in wild Asian primates, while highlighting the coverage of primate species, countries, and pathogen groups surveyed, as well as the diagnostic methods used across the studies. Moreover, we compared the species richness of pathogens harbored by primates across diverse types of habitats classified according to their degree of anthropization (i.e., urban vs. rural vs. forest habitats).

Results and discussion

Searches of Scopus, PubMed, and the Global Mammal Parasite Database yielded 152 articles on 39 primate species. We inventoried 183 pathogens, including 63 helminthic gastrointestinal parasites, two blood-borne parasites, 42 protozoa, 45 viruses, 30 bacteria, and one fungus. Considering each study as a sample, species accumulation curves revealed no significant differences in specific richness between habitat types for any of the pathogen groups analyzed. This is likely due to the insufficient sampling effort (i.e., a limited number of studies), which prevents drawing conclusive findings. This systematic review identified several publication biases, particularly the uneven representation of host species and pathogen groups studied, as well as a lack of use of generic diagnostic methods. Addressing these gaps necessitates a multidisciplinary strategy framed in a One Health approach, which may facilitate a broader inventory of pathogens and ultimately limit the risk of cross-species transmission at the human-primate interface. Strengthening the zoonotic surveillance in primates of this region could be realized notably through the application of more comprehensive diagnostic techniques such as broad-spectrum analyses without a priori selection.

Early-stage loss of ecological integrity drives the risk of zoonotic disease emergence

Anthropogenic pressures have increasingly disrupted the integrity of ecosystems worldwide, jeopardizing their capacity to provide essential contributions to human well-being. Recently, the role of natural ecosystems in reducing disease emergence risk has gained prominence in decision-making processes, as scientific evidence indicates that human-driven pressure, such as habitat destruction and deforestation, can trigger the emergence of zoonotic infectious diseases. However, the intricate relationship between biodiversity and emerging infectious diseases (EIDs) remains only partially understood. Here, we updated the most comprehensive zoonotic EID event database with the latest reported events to analyse the relationship between EIDs of wildlife origin (zoonoses) and various facets of ecological integrity. We found EID risk was strongly predicted by structural integrity metrics such as human footprint and ecoregion intactness, in addition to environmental variables such as tropical rainforest density and mammal species richness. EID events were more likely to occur in areas with intermediate levels of compositional and structural integrity, underscoring the risk posed by human encroachment into pristine, undisturbed lands. Our study highlights the need to identify novel indicators and targets that can effectively address EID risk alongside other pressing global challenges in sustainable development, ultimately informing strategies for preserving both human and environmental health.

Hindrance to sustainable development: Global inequities, non-progressive education and inadequate science-policy dialogue

Social habits and economies driven by profit are opposing efforts to reach a path of sustainable development. In addition, many communities worldwide have diverged away from nature through consumerism and technology. In the context of the escalating risks and consequences related to global challenges such as the climate crisis and ecosystem degradation, education for sustainable development and science-driven decision-making offer tremendous opportunities for improvement.

A scoping review on bovine tuberculosis highlights the need for novel data streams and analytical approaches to curb zoonotic diseases

Zoonotic diseases represent a significant societal challenge in terms of their health and economic impacts. One Health approaches to managing zoonotic diseases are becoming more prevalent, but require novel thinking, tools and cross-disciplinary collaboration. Bovine tuberculosis (bTB) is one example of a costly One Health challenge with a complex epidemiology involving humans, domestic animals, wildlife and environmental factors, which require sophisticated collaborative approaches. We undertook a scoping review of multi-host bTB epidemiology to identify trends in species publication focus, methodologies, and One Health approaches. We aimed to identify knowledge gaps where novel research could provide insights to inform control policy, for bTB and other zoonoses. The review included 532 articles. We found different levels of research attention across episystems, with a significant proportion of the literature focusing on the badger-cattle-TB episystem, with far less attention given to tropical multi-host episystems. We found a limited number of studies focusing on management solutions and their efficacy, with very few studies looking at modelling exit strategies. Only a small number of studies looked at the effect of human disturbances on the spread of bTB involving wildlife hosts. Most of the studies we reviewed focused on the effect of badger vaccination and culling on bTB dynamics with few looking at how roads, human perturbations and habitat change may affect wildlife movement and disease spread. Finally, we observed a lack of studies considering the effect of weather variables on bTB spread, which is particularly relevant when studying zoonoses under climate change scenarios. Significant technological and methodological advances have been applied to bTB episystems, providing explicit insights into its spread and maintenance across populations. We identified a prominent bias towards certain species and locations. Generating more high-quality empirical data on wildlife host distribution and abundance, high-resolution individual behaviours and greater use of mathematical models and simulations are key areas for future research. Integrating data sources across disciplines, and a "virtuous cycle" of well-designed empirical data collection linked with mathematical and simulation modelling could provide additional gains for policy-makers and managers, enabling optimised bTB management with broader insights for other zoonoses.

Discovery and genetic characterization of novel paramyxoviruses from small mammals in Hubei Province, Central China

Paramyxoviruses are a group of single-stranded, negative-sense RNA viruses, some of which are responsible for acute human disease, including parainfluenza virus, measles virus, Nipah virus and Hendra virus. In recent years, a large number of novel paramyxoviruses, particularly members of the genus Jeilongvirus, have been discovered in wild mammals, suggesting that the diversity of paramyxoviruses may be underestimated. Here we used hemi-nested reverse transcription PCR to obtain 190 paramyxovirus sequences from 969 small mammals in Hubei Province, Central China. These newly identified paramyxoviruses were classified into four clades: genera Jeilongvirus, Morbillivirus, Henipavirus and Narmovirus, with most of them belonging to the genus Jeilongvirus. Using Illumina sequencing and Sanger sequencing, we successfully recovered six near-full-length genomes with different genomic organizations, revealing the more complex genome content of paramyxoviruses. Co-divergence analysis of jeilongviruses and their known hosts indicates that host-switching occurred more frequently in the evolutionary histories of the genus Jeilongvirus. Together, our findings demonstrate the high prevalence of paramyxoviruses in small mammals, especially jeilongviruses, and highlight the diversity of paramyxoviruses and their genome content, as well as the evolution of jeilongviruses.

Bat species assemblage predicts coronavirus prevalence

Anthropogenic disturbances and the subsequent loss of biodiversity are altering species abundances and communities. Since species vary in their pathogen competence, spatio-temporal changes in host assemblages may lead to changes in disease dynamics. We explore how longitudinal changes in bat species assemblages affect the disease dynamics of coronaviruses (CoVs) in more than 2300 cave-dwelling bats captured over two years from five caves in Ghana. This reveals uneven CoV infection patterns between closely related species, with the alpha-CoV 229E-like and SARS-related beta-CoV 2b emerging as multi-host pathogens. Prevalence and infection likelihood for both phylogenetically distinct CoVs is influenced by the abundance of competent species and naïve subadults. Broadly, bat species vary in CoV competence, and highly competent species are more common in less diverse communities, leading to increased CoV prevalence in less diverse bat assemblages. In line with the One Health framework, our work supports the notion that biodiversity conservation may be the most proactive measure to prevent the spread of pathogens with zoonotic potential.

The PHERCC Matrix. An Ethical Framework for Planning, Governing, and Evaluating Risk and Crisis Communication in the Context of Public Health Emergencies

Risk and crisis communication (RCC) is a current ethical issue subject to controversy, mainly due to the tension between individual liberty (a core component of fairness) and effectiveness. In this paper we propose a consistent definition of the RCC process in public health emergencies (PHERCC), which comprises six key elements: evidence, initiator, channel, publics, message, and feedback. Based on these elements and on a detailed analysis of their role in PHERCC, we present an ethical framework to help design, govern and evaluate PHERCC strategies. The framework aims to facilitate RCC, incorporating effectiveness, autonomy, and fairness. It comprises five operational ethical principles: openness, transparency, inclusivity, understandability, and privacy. The resulting matrix helps understanding the interplay between the PHERCC process and the principles of the framework. The paper includes suggestions and recommendations for the implementation of the PHERCC matrix.

FSC-certified forest management benefits large mammals compared to non-FSC

More than a quarter of the world's tropical forests are exploited for timber1. Logging impacts biodiversity in these ecosystems, primarily through the creation of forest roads that facilitate hunting for wildlife over extensive areas. Forest management certification schemes such as the Forest Stewardship Council (FSC) are expected to mitigate impacts on biodiversity, but so far very little is known about the effectiveness of FSC certification because of research design challenges, predominantly limited sample sizes2,3. Here we provide this evidence by using 1.3 million camera-trap photos of 55 mammal species in 14 logging concessions in western equatorial Africa. We observed higher mammal encounter rates in FSC-certified than in non-FSC logging concessions. The effect was most pronounced for species weighing more than 10 kg and for species of high conservation priority such as the critically endangered forest elephant and western lowland gorilla. Across the whole mammal community, non-FSC concessions contained proportionally more rodents and other small species than did FSC-certified concessions. The first priority for species protection should be to maintain unlogged forests with effective law enforcement, but for logged forests our findings provide convincing data that FSC-certified forest management is less damaging to the mammal community than is non-FSC forest management. This study provides strong evidence that FSC-certified forest management or equivalently stringent requirements and controlling mechanisms should become the norm for timber extraction to avoid half-empty forests dominated by rodents and other small species.

"Long COVID" and Its Impact on The Environment: Emerging Concerns and Perspectives

The COVID-19 pandemic has caused unprecedented global health and economic crises. The emergence of long COVID-19 has raised concerns about the interplay between SARS-CoV-2 infections, climate change, and the environment. In this context, a concise analysis of the potential long-term effects of the COVID-19 epidemic along with the awareness aboutenvironmental issues are realized. While COVID-19 effects in the short-term have reduced environmental air pollutants and pressures, CO2 emissions are projected to increase as the economy recovers and growth rates return to pre-COVID-19 levels. This review discusses the systematic effects of both the short-term and long-term effects of the pandemic on the clean energy revolution and environmental issues. This article also discusses opportunities to achieve long-term environmental benefits and emphasizes the importance of future policies in promoting global environmental sustainability. Future directions for growth and recovery are presented to cope with long COVID-19 epidemic along with the critical findings focussing on various aspects: waste management, air quality improvement.

Immunogenetic-pathogen networks shrink in Tome's spiny rat, a generalist rodent inhabiting disturbed landscapes

Anthropogenic disturbance may increase the emergence of zoonoses. Especially generalists that cope with disturbance and live in close contact with humans and livestock may become reservoirs of zoonotic pathogens. Yet, whether anthropogenic disturbance modifies host-pathogen co-evolutionary relationships in generalists is unknown. We assessed pathogen diversity, neutral genome-wide diversity (SNPs) and adaptive MHC class II diversity in a rodent generalist inhabiting three lowland rainforest landscapes with varying anthropogenic disturbance, and determined which MHC alleles co-occurred more frequently with 13 gastrointestinal nematodes, blood trypanosomes, and four viruses. Pathogen-specific selection pressures varied between landscapes. Genome-wide diversity declined with the degree of disturbance, while MHC diversity was only reduced in the most disturbed landscape. Furthermore, pristine forest landscapes had more functional important MHC-pathogen associations when compared to disturbed forests. We show co-evolutionary links between host and pathogens impoverished in human-disturbed landscapes. This underscores that parasite-mediated selection might change even in generalist species following human disturbance which in turn may facilitate host switching and the emergence of zoonoses.

Small mammal community composition impacts bank vole (Clethrionomys glareolus) population dynamics and associated seroprevalence of Puumala orthohantavirus

Rodents are important reservoirs for zoonotic pathogens that cause diseases in humans. Biodiversity is hypothesized to be closely related to pathogen prevalence through multiple direct and indirect pathways. For example, the presence of non-host species can reduce contact rates of the main reservoir host and thus reduce the risk of transmission ("dilution effect"). In addition, an overlap in ecological niches between two species could lead to increased interspecific competition, potentially limiting host densities and reducing density-dependent pathogen transmission processes. In this study, we investigated the relative impact of population-level regulation of direct and indirect drivers of the prevalence of Puumala orthohantavirus (PUUV) in bank voles (Clethrionomys glareolus) during years with high abundance. We compiled data on small mammal community composition from four regions in Germany between 2010 and 2013. Structural equation modeling revealed a strong seasonality in PUUV control mechanisms in bank voles. The abundance of shrews tended to have a negative relationship with host abundance, and host abundance positively influenced PUUV seroprevalence, while at the same time increasing the abundance of competing non-hosts like the wood mouse (Apodemus sylvaticus) and the yellow-necked field mouse (Apodemus flavicollis) were associated with reduced PUUV seroprevalence in the host. These results indicate that for PUUV in bank voles, dilution is associated with increased interspecific competition. Anthropogenic pressures leading to the decline of Apodemus spp. in a specific habitat could lead to the amplification of mechanisms promoting PUUV transmission within the host populations.

The combined effect of bromadiolone and ivermectin (iBr) in controlling both rodents and their fleas

Rodent pests not only cause severe agricultural loss but also spread zoonotic pathogens to human beings. Anticoagulant rodenticides are widely used to decrease the population densities of rodents but often lead to the spillover of ectoparasites because fleas and ticks may gather on surviving rodents. Therefore, it is necessary to kill fleas and ticks before culling rodents to minimize the risk of pathogen transmission. In this study, we used a mixture of ivermectin (an antiparasitic drug) and bromadiolone (an anticoagulant rodenticide) to control both rodent and flea/tick abundances. We found that in a laboratory test, 0.01% ivermectin bait was not lethal for greater long-tailed hamsters after 7 days of treatment, while 0.1% ivermectin bait was lethal for approximately 33% of treated rodents. In a field test, bait containing 0.001%, 0.005%, 0.01%, and 0.05% ivermectin decreased the number of fleas per vole of Brandt's voles to 0.42, 0.22, 0.12, and 0.2, respectively, compared with 0.77 in the control group, indicating that 0.01% ivermectin bait performed best in removing fleas. In another laboratory test, bait containing a 0.01% ivermectin and 0.005% bromadiolone mixture caused the death of all voles within 6-14 days after the intake of the bait. In the field test, the bait containing 0.01% ivermectin and 0.005% bromadiolone reduced the average number of fleas per vole to 0.35, which was significantly lower than the 0.77 of the control group. Our results indicate that a 0.01% ivermectin and 0.005% bromadiolone mixture could be used to control both rodents and fleas to minimize the spillover risk of disease transmission when using traditional rodenticides.

Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies

The agile wallaby (Notamacropus agilis) is one of the most abundant marsupial species in northern Queensland and a competent host for the zoonotic Ross River virus. Despite their increased proximity and interactions with humans, little is known about the viruses carried by these animals, and whether any are of conservation or zoonotic importance. Metagenomics and molecular techniques were used in a complementary manner to identify and characterize novel viruses in the fecal samples of free-ranging agile wallabies. We detected a variety of novel marsupial-related viral species including agile wallaby atadenovirus 1, agile wallaby chaphamaparvovirus 1-2, agile wallaby polyomavirus 1-2, agile wallaby associated picobirnavirus 1-9, and a known macropod gammaherpesvirus 3. Phylogenetic analyses indicate that most of these novel viruses would have co-evolved with their hosts (agile wallabies). Additionally, non-marsupial viruses that infect bacteria (phages), plants, insects, and other eukaryotes were identified. This study highlighted the utility of non-invasive sampling as well as the integration of broad-based molecular assays (consensus PCR and next generation sequencing) for monitoring the emergence of potential pathogenic viruses in wildlife species. Furthermore, the novel marsupial viruses identified in this study will enrich the diversity of knowledge about marsupial viruses, and may be useful for developing diagnostics and vaccines.

Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens

Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.

Incorporating biodiversity responses to land use change scenarios for preventing emerging zoonotic diseases in areas of unknown host-pathogen interactions

The need to reconcile food production, the safeguarding of nature, and the protection of public health is imperative in a world of continuing global change, particularly in the context of risks of emerging zoonotic disease (EZD). In this paper, we explored potential land use strategies to reduce EZD risks using a landscape approach. We focused on strategies for cases where the dynamics of pathogen transmission among species were poorly known and the ideas of "land-use induced spillover" and "landscape immunity" could be used very broadly. We first modeled three different land-use change scenarios in a region of transition between the Cerrado and the Atlantic Forest biodiversity hotspots. The land-use strategies used to build our scenarios reflected different proportions of native vegetation cover, as a proxy of habitat availability. We then evaluated the effects of the proportion of native vegetation cover on the occupancy probability of a group of mammal species and analyzed how the different land-use scenarios might affect the distribution of species in the landscape and thus the risk of EZD. We demonstrate that these approaches can help identify potential future EZD risks, and can thus be used as decision-making tools by stakeholders, with direct implications for improving both environmental and socio-economic outcomes.

Policies to prevent zoonotic spillover: a systematic scoping review of evaluative evidence

BACKGROUND

Emerging infectious diseases of zoonotic origin present a critical threat to global population health. As accelerating globalisation makes epidemics and pandemics more difficult to contain, there is a need for effective preventive interventions that reduce the risk of zoonotic spillover events. Public policies can play a key role in preventing spillover events. The aim of this review is to identify and describe evaluations of public policies that target the determinants of zoonotic spillover. Our approach is informed by a One Health perspective, acknowledging the inter-connectedness of human, animal and environmental health.

METHODS

In this systematic scoping review, we searched Medline, SCOPUS, Web of Science and Global Health in May 2021 using search terms combining animal health and the animal-human interface, public policy, prevention and zoonoses. We screened titles and abstracts, extracted data and reported our process in line with PRISMA-ScR guidelines. We also searched relevant organisations' websites for evaluations published in the grey literature. All evaluations of public policies aiming to prevent zoonotic spillover events were eligible for inclusion. We summarised key data from each study, mapping policies along the spillover pathway.

RESULTS

Our review found 95 publications evaluating 111 policies. We identified 27 unique policy options including habitat protection; trade regulations; border control and quarantine procedures; farm and market biosecurity measures; public information campaigns; and vaccination programmes, as well as multi-component programmes. These were implemented by many sectors, highlighting the cross-sectoral nature of zoonotic spillover prevention. Reports emphasised the importance of surveillance data in both guiding prevention efforts and enabling policy evaluation, as well as the importance of industry and private sector actors in implementing many of these policies. Thoughtful engagement with stakeholders ranging from subsistence hunters and farmers to industrial animal agriculture operations is key for policy success in this area.

CONCLUSION

This review outlines the state of the evaluative evidence around policies to prevent zoonotic spillover in order to guide policy decision-making and focus research efforts. Since we found that most of the existing policy evaluations target 'downstream' determinants, additional research could focus on evaluating policies targeting 'upstream' determinants of zoonotic spillover, such as land use change, and policies impacting infection intensity and pathogen shedding in animal populations, such as those targeting animal welfare.

Integrating databases for spatial analysis of parasite-host associations and the novel Brazilian dataset

Incomplete information on parasites, their associated hosts, and their precise geographical location hampers the ability to predict disease emergence in Brazil, a continental-sized country characterised by significant regional disparities. Here, we demonstrate how the NCBI Nucleotide and GBIF databases can be used as complementary databases to study spatially georeferenced parasite-host associations. We also provide a comprehensive dataset of parasites associated with mammal species that occur in Brazil, the Brazilian Mammal Parasite Occurrence Data (BMPO). This dataset integrates wild mammal species' morphological and life-history traits, zoonotic parasite status, and zoonotic microparasite transmission modes. Through meta-networks, comprising interconnected host species linked by shared zoonotic microparasites, we elucidate patterns of zoonotic microparasite dissemination. This approach contributes to wild animal and zoonoses surveillance, identifying and targeting host species accountable for disproportionate levels of parasite sharing within distinct biomes. Moreover, our novel dataset contributes to the refinement of models concerning disease emergence and parasite distribution among host species.

Effect of epidemic diseases on wild animal conservation

Under the background of global species extinction, the impact of epidemic diseases on wild animal protection is increasingly prominent. Here, we review and synthesize the literature on this topic, and discuss the relationship between diseases and biodiversity. Diseases usually reduce species diversity by decreasing or extinction of species populations, but also accelerate species evolution and promote species diversity. At the same time, species diversity can regulate disease outbreaks through dilution or amplification effects. The synergistic effect of human activities and global change is emphasized, which further aggravates the complex relationship between biodiversity and diseases. Finally, we emphasize the importance of active surveillance of wild animal diseases, which can protect wild animals from potential diseases, maintain population size and genetic variation, and reduce the damage of diseases to the balance of the whole ecosystem and human health. Therefore, we suggest that a background survey of wild animal populations and their pathogens should be carried out to assess the impact of potential outbreaks on the population or species level. The mechanism of dilution and amplification effect between species diversity and diseases of wild animals should be further studied to provide a theoretical basis and technical support for human intervention measures to change biodiversity. Most importantly, we should closely combine the protection of wild animals with the establishment of an active surveillance, prevention, and control system for wild animal epidemics, in an effort to achieve a win-win situation between wild animal protection and disease control.

Mitigating the effects of climate change on human health with vaccines and vaccinations

Climate change represents an unprecedented threat to humanity and will be the ultimate challenge of the 21st century. As a public health consequence, the World Health Organization estimates an additional 250,000 deaths annually by 2030, with resource-poor countries being predominantly affected. Although climate change's direct and indirect consequences on human health are manifold and far from fully explored, a growing body of evidence demonstrates its potential to exacerbate the frequency and spread of transmissible infectious diseases. Effective, high-impact mitigation measures are critical in combating this global crisis. While vaccines and vaccination are among the most cost-effective public health interventions, they have yet to be established as a major strategy in climate change-related health effect mitigation. In this narrative review, we synthesize the available evidence on the effect of climate change on vaccine-preventable diseases. This review examines the direct effect of climate change on water-related diseases such as cholera and other enteropathogens, helminthic infections and leptospirosis. It also explores the effects of rising temperatures on vector-borne diseases like dengue, chikungunya, and malaria, as well as the impact of temperature and humidity on airborne diseases like influenza and respiratory syncytial virus infection. Recent advances in global vaccine development facilitate the use of vaccines and vaccination as a mitigation strategy in the agenda against climate change consequences. A focused evaluation of vaccine research and development, funding, and distribution related to climate change is required.

Vector-Borne Disease in Wild Mammals Impacted by Urban Expansion and Climate Change

Ecologies of zoonotic vector-borne diseases may shift with climate and land use change. As many urban-adapted mammals can host ectoparasites and pathogens of human and animal health concern, our goal was to compare patterns of arthropod-borne disease among medium-sized mammals across gradients of rural to urban landscapes in multiple regions of California. DNA of Anaplasma phagocytophilum was found in 1-5% of raccoons, coyotes, and San Joaquin kit foxes; Borrelia burgdorferi in one coyote, rickettsiae in two desert kit foxes, and Yersinia pestis in two coyotes. There was serological evidence of rickettsiae in 14-37% of coyotes, Virginia opossums, and foxes; and A. phagocytophilum in 6-40% of coyotes, raccoons, Virginia opossums, and foxes. Of six flea species, one Ctenocephalides felis from a raccoon was positive for Y. pestis, and Ct. felis and Pulex simulans fleas tested positive for Rickettsia felis and R. senegalensis. A Dermacentor similis tick off a San Joaquin kit fox was PCR-positive for A. phagocytophilum. There were three statistically significant risk factors: risk of A. phagocytophilum PCR-positivity was threefold greater in fall vs the other three seasons; hosts adjacent to urban areas had sevenfold increased A. phagocytophilum seropositivity compared with urban and rural areas; and there was a significant spatial cluster of rickettsiae within greater Los Angeles. Animals in areas where urban and rural habitats interconnect can serve as sentinels during times of change in disease risk.

Nycteribiid bat flies (Arthropoda, Insecta, Diptera, Nycteribiidae) of Kenya

Bat flies (Diptera: Nycteribiidae and Streblidae) are hematophagous ectoparasites of bats characterized by viviparous pupiparity and generally high host specificity. Nycteribiid bat flies are wingless, morphologically constrained, and are most diverse in the Eastern Hemisphere. Africa hosts approximately 22% of global bat biodiversity and nearly one-third of all African bat species occur in Kenya, one of Africa's most bat-rich countries. However, records of nycteribiid bat fly diversity in Kenya remain sparse and unconsolidated. This paper combines all past species records of nycteribiid bat flies with records from a survey of 4,255 Kenyan bats across 157 localities between 2006 and 2015. A total of seven nycteribiid genera and 17 species are recorded, with seven species from the recent 'Bats of Kenya' surveys representing previously undocumented country records. Host associations and geographic distributions based on all available records are also described. This comprehensive species catalog addresses and further emphasizes the need for similar investigations of nycteribiid biodiversity across Africa.

First Report of Alphacoronavirus Circulating in Cavernicolous Bats from Portugal

The emergence of novel coronaviruses (CoVs) has emphasized the need to understand their diversity and distribution in animal populations. Bats have been identified as crucial reservoirs for CoVs, and they are found in various bat species worldwide. In this study, we investigated the presence of CoVs of four cavernicolous bats in six locations in the centre and south of Portugal. We collected faeces, anal, and buccal swab samples, as well as air samples from the locations using a Coriolis air sampler. Our results indicate that CoVs were more readily detected in faecal samples compared to anal and buccal swab samples. No CoVs were detected in the air samples. Phylogenetic analysis showed that the detected viruses belong to the Alphacoronavirus genus. This study represents the first report of Alphacoronaviruses circulating in bats in Portugal and highlights the importance of continuous surveillance for novel CoVs in bat populations globally. Ongoing surveillance for CoVs in bat populations is essential as they are a vital source of these viruses. It is crucial to understand the ecological relationships between animals, humans, and the environment to prevent and control the emergence and transmission of infectious diseases. Further ecological studies are needed to investigate the factors contributing to the emergence and transmission of zoonotic viruses.

A priority list of environmental health issues for Malaysia

OBJECTIVES

Environmental risk factors contribute to 24% of the global burden of disease from all causes in disability-adjusted life years (DALYs), and to 23% of all global deaths. Malaysia being an advanced developing country, there is a need to prioritise environmental health issues to enable environmental health practitioners to focus on the most significant and urgent environmental health concerns.

CONTENT

This project was undertaken by a Thematic Working Group on Environmental Health Experts (TWG 10) under the Malaysian National Environmental Health Action Plan. Sixteen pre-selected environmental health issues were presented to a two focus group discussions among 20 environmental health and related professionals who then scored each issue on its magnitude and severity scale.

SUMMARY

The total of these scores generated a list of priority environmental health issues for Malaysia. Children environmental health came out as the environmental health issue of the highest priority.

OUTLOOK

We hope that this list of priority environmental health issues will be used for prioritising academic and professional manpower training, research funding allocation and planning for intervention programmes by various stakeholders.

Exposure to diverse sarbecoviruses indicates frequent zoonotic spillover in human communities interacting with wildlife

BACKGROUND

Sarbecoviruses are a subgenus of Coronaviridae that mostly infect bats with known potential to infect humans (SARS-CoV and SARS-CoV-2). Populations in Southeast Asia, where these viruses are most likely to emerge, have been undersurveyed to date.

METHODS

We surveyed communities engaged in extractive industries and bat guano harvesting from rural areas in Myanmar. Participants were screened for exposure to sarbecoviruses, and their interactions with wildlife were evaluated to determine the factors associated with exposure to sarbecoviruses.

RESULTS

Of 693 people screened between July 2017 and February 2020, 12.1% were seropositive for sarbecoviruses. Individuals were significantly more likely to have been exposed to sarbecoviruses if their main livelihood involved working in extractive industries (logging, hunting, or harvesting of forest products; odds ratio [OR] = 2.71, P = 0.019) or had been hunting/slaughtering bats (OR = 6.09, P = 0.020). Exposure to a range of bat and pangolin sarbecoviruses was identified.

CONCLUSION

Exposure to diverse sarbecoviruses among high-risk human communities provides epidemiologic and immunologic evidence that zoonotic spillover is occurring. These findings inform risk mitigation efforts needed to decrease disease transmission at the bat-human interface, as well as future surveillance efforts warranted to monitor isolated populations for viruses with pandemic potential.

Climate change and infectious disease: a review of evidence and research trends

BACKGROUND

Climate change presents an imminent threat to almost all biological systems across the globe. In recent years there have been a series of studies showing how changes in climate can impact infectious disease transmission. Many of these publications focus on simulations based on in silico data, shadowing empirical research based on field and laboratory data. A synthesis work of empirical climate change and infectious disease research is still lacking.

METHODS

We conducted a systemic review of research from 2015 to 2020 period on climate change and infectious diseases to identify major trends and current gaps of research. Literature was sourced from Web of Science and PubMed literary repositories using a key word search, and was reviewed using a delineated inclusion criteria by a team of reviewers.

RESULTS

Our review revealed that both taxonomic and geographic biases are present in climate and infectious disease research, specifically with regard to types of disease transmission and localities studied. Empirical investigations on vector-borne diseases associated with mosquitoes comprised the majority of research on the climate change and infectious disease literature. Furthermore, demographic trends in the institutions and individuals published revealed research bias towards research conducted across temperate, high-income countries. We also identified key trends in funding sources for most resent literature and a discrepancy in the gender identities of publishing authors which may reflect current systemic inequities in the scientific field.

CONCLUSIONS

Future research lines on climate change and infectious diseases should considered diseases of direct transmission (non-vector-borne) and more research effort in the tropics. Inclusion of local research in low- and middle-income countries was generally neglected. Research on climate change and infectious disease has failed to be socially inclusive, geographically balanced, and broad in terms of the disease systems studied, limiting our capacities to better understand the actual effects of climate change on health.

Wildlife gut microbiomes of sympatric generalist species respond differently to anthropogenic landscape disturbances

BACKGROUND

Human encroachment into nature and the accompanying environmental changes are a big concern for wildlife biodiversity and health. While changes on the macroecological scale, i.e. species community and abundance pattern, are well documented, impacts on the microecological scale, such as the host's microbial community, remain understudied. Particularly, it is unclear if impacts of anthropogenic landscape modification on wildlife gut microbiomes are species-specific. Of special interest are sympatric, generalist species, assumed to be more resilient to environmental changes and which often are well-known pathogen reservoirs and drivers of spill-over events. Here, we analyzed the gut microbiome of three such sympatric, generalist species, one rodent (Proechimys semispinosus) and two marsupials (Didelphis marsupialis and Philander opossum), captured in 28 study sites in four different landscapes in Panama characterized by different degrees of anthropogenic disturbance.

RESULTS

Our results show species-specific gut microbial responses to the same landscape disturbances. The gut microbiome of P. semispinosus was less diverse and more heterogeneous in landscapes with close contact with humans, where it contained bacterial taxa associated with humans, their domesticated animals, and potential pathogens. The gut microbiome of D. marsupialis showed similar patterns, but only in the most disturbed landscape. P. opossum, in contrast, showed little gut microbial changes, however, this species' absence in the most fragmented landscapes indicates its sensitivity to long-term isolation.

CONCLUSION

These results demonstrate that wildlife gut microbiomes even in generalist species with a large ecological plasticity are impacted by human encroachment into nature, but differ in resilience which can have critical implications on conservation efforts and One Health strategies.

Absence of Hepatitis E Virus (HEV) Circulation in the Most Widespread Wild Croatian Canine Species, the Red Fox (Vulpes vulpes) and Jackal (Canis aureus moreoticus)

Hepatitis E virus (HEV) can infect a wide range of domestic and wild animals, and the identification of new host species is reported successively worldwide. Nevertheless, its zoonotic potential and natural transmission, especially in wildlife remains unclear, primarily due to the discrete nature of HEV infections. Since the red fox (Vulpus vulpus) is the most widespread carnivore worldwide, and has been recognized as a potential HEV reservoir, its role as a potent host species is of increasing interest. Another wild canine species, the jackal （Canis aureus moreoticus）, is becoming more important within the same habitat as that of the red fox since its number and geographical distribution have been rapidly growing. Therefore, we have chosen these wild species to determine their potential role in the epidemiology and persistence of HEV in the wilderness. The main reason for this is the finding of HEV and a rather high HEV seroprevalence in wild boars sharing the same ecological niche as the wild canine species, as well as the risk of the spread of HEV through red foxes into the outskirts of cities, where possible indirect and even direct contact with people are not excluded. Therefore, our study aimed to investigate the possibility of natural HEV infection of free-living wild canines, by testing samples for the presence of HEV RNA and anti-HEV antibodies to gain better epidemiological knowledge of the disease. For this purpose, 692 red fox and 171 jackal muscle extracts and feces samples were tested. Neither HEV RNA nor anti-HEV antibodies were detected. Although HEV circulation was not detected in the tested samples, to our knowledge, these are the first results that include jackals as a growing and important omnivore wildlife species for the presence of HEV infection in Europe.

Panarchy theory for convergence

Coping with surprise and uncertainty resulting from the emergence of undesired and unexpected novelty or the sudden reorganization of systems at multiple spatiotemporal scales requires both a scientific process that can incorporate diverse expertise and viewpoints, and a scientific framework that can account for the structure and dynamics of interacting social-ecological systems (SES) and the inherent uncertainty of what might emerge in the future. We argue that combining a convergence scientific process with a panarchy framework provides a pathway for improving our understanding of, and response to, emergence. Emergent phenomena are often unexpected (e.g., pandemics, regime shifts) and can be highly disruptive, so can pose a significant challenge to the development of sustainable and resilient SES. Convergence science is a new approach promoted by the U.S. National Science Foundation for tackling complex problems confronting humanity through the integration of multiple perspectives, expertise, methods, tools, and analytical approaches. Panarchy theory is a framework useful for studying emergence, because it characterizes complex systems of people and nature as dynamically organized and structured within and across scales of space and time. It accounts for the fundamental tenets of complex systems and explicitly grapples with emergence, including the emergence of novelty, and the emergent property of social-ecological resilience. We provide an overview of panarchy, convergence science, and emergence. We discuss the significant data and methodological challenges of using panarchy in a convergence approach to address emergent phenomena, as well as state-of-the-art methods for overcoming them. We present two examples that would benefit from such an approach: climate change and its impacts on social-ecological systems, and the relationships between infectious disease and social-ecological systems.

Climate change and mental health: time for action and advocacy

Climate change poses an existential threat to our planet and our health. We explore the intersections of climate change and mental health which has been under-recognised to date. Climate change can affect mental health directly through the effects of extreme weather events such as heat, drought and flooding, and indirectly through increasing rates of migration and inequality. Vulnerable individuals with neuropsychiatric disorders will be particularly at risk. Emerging evidence is also showing effects of air pollution on brain development. Mitigation efforts related to reducing carbon emissions will have both direct and indirect effects on mental health. A further consideration demonstrated by the COVID-19 pandemic is that the spread of infectious disease can have substantial effects on the mental health of the population. With climate change and biodiversity loss, pandemics could recur in the future with increasing frequency. It is now essential that mental health professionals be equipped as agents for climate action.

Detection and Characterization of an H9N2 Influenza A Virus in the Egyptian Rousette Bat in Limpopo, South Africa

In recent years, bats have been shown to host various novel bat-specific influenza viruses, including H17N10 and H18N11 in the Americas and the H9N2 subtype from Africa. Rousettus aegyptiacus (Egyptian Rousette bat) is recognized as a host species for diverse viral agents. This study focused on the molecular surveillance of a maternal colony in Limpopo, South Africa, between 2017-2018. A pan-influenza hemi-nested RT-PCR assay targeting the PB1 gene was established, and influenza A virus RNA was identified from one fecal sample out of 860 samples. Genome segments were recovered using segment-specific amplification combined with standard Sanger sequencing and Illumina unbiased sequencing. The identified influenza A virus was closely related to the H9N2 bat-influenza virus, confirming the circulation of this subtype among Egyptian fruit bat populations in Southern Africa. This bat H9N2 subtype contained amino acid residues associated with transmission and virulence in either mammalian or avian hosts, though it will likely require additional adaptations before spillover.

Potential Mammalian Vector-Borne Diseases in Live and Wet Markets in Indonesia and Myanmar

Vector-borne diseases spread from wild animals and their associated ectoparasites to humans and domesticated animals. Wildlife markets are recognized as important areas where this transfer can take place. We assessed the potential for spreading vector-borne diseases in two live and wet markets in Myanmar (Mong La, on the Myanmar-China border) and Indonesia (Sukahaji in Bandung on the island of Java) by making an inventory of all live and freshly killed wild mammals for sale. For eight mammal families, we quantified the number of animals on offer, and we used a heatmap cluster analysis to map vector-borne diseases that these families may carry. In Myanmar, we observed large numbers of wild pigs and deer (potentially carrying West Nile and various encephalitis viruses) whereas in Indonesia we observed Old World fruit bats (potentially carrying Chikungunya and encephalitis viruses) and squirrels (potentially carrying West Nile and encephalitis viruses). The trade in Indonesia was dominated by live mammals offered for sale as pets, and only Old World fruit bats and squirrels traded for traditional Asian medicine were killed in the markets. The trade in Myanmar was more geared towards wild meat (e.g., wild pigs, deer, primates) and traditional Asian medicine (squirrels). The combined risks of vector-borne diseases spreading from traded animals to human health highlight the need for an integrated approach protecting public health, economic interests and biodiversity.

The role of invasive alien species in the emergence and spread of zoonoses

The role of invasive alien species in the transmission dynamics of zoonotic pathogens is often overlooked, despite the rapid escalation in biological invasions globally. Here we synthesise available information on the influence of invasive alien species on zoonotic pathogen dynamics in invaded ranges, focussing on Europe, and identify key associated knowledge gaps. We identified 272 documented interactions between alien species and zoonotic pathogens within invaded ranges. The majority of these involved invasive alien mammals followed by birds with only a few occurrences of other taxa documented. A wide range of potential interactions between invasive alien species and zoonotic pathogens were identified but few studies considered transmission to humans and so there was limited evidence of actual impacts on human health. However, there is an urgent need to raise awareness of the potential risks posed to human health by the transmission of zoonotic diseases by invasive alien species; the role of invasive alien species in zoonotic disease transmission may exceed that of native wildlife and occur in a relatively short period following the arrival of an invasive alien species within a new region. Ecological and social mechanisms govern the dynamics of zoonotic disease transmission but wildlife diseases are not consistently included within animal, plant and human policies. Rapid advances in the development of systems frameworks that integrate the ecological, economic and social processes promoting spillover in rapidly changing environments will increase understanding to inform decision-making.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10530-022-02978-1.

Risk of Viral Infectious Diseases from Live Bats, Primates, Rodents and Carnivores for Sale in Indonesian Wildlife Markets

Southeast Asia is considered a global hotspot of emerging zoonotic diseases. There, wildlife is commonly traded under poor sanitary conditions in open markets; these markets have been considered 'the perfect storm' for zoonotic disease transmission. We assessed the potential of wildlife trade in spreading viral diseases by quantifying the number of wild animals of four mammalian orders (Rodentia, Chiroptera, Carnivora and Primates) on sale in 14 Indonesian wildlife markets and identifying zoonotic viruses potentially hosted by these animals. We constructed a network analysis to visualize the animals that are traded alongside each other that may carry similar viruses. We recorded 6725 wild animals of at least 15 species on sale. Cities and markets with larger human population and number of stalls, respectively, offered more individuals for sale. Eight out of 15 animal taxa recorded are hosts of 17 zoonotic virus species, nine of which can infect more than one species as a host. The network analysis showed that long-tailed macaque has the greatest potential for spreading viral diseases, since it is simultaneously the most traded species, sold in 13/14 markets, and a potential host for nine viruses. It is traded alongside pig-tailed macaques in three markets, with which it shares six viruses in common (Cowpox, Dengue, Hepatitis E, Herpes B, Simian foamy, and Simian retrovirus type D). Short-nosed fruit bats and large flying foxes are potential hosts of Nipah virus and are also sold in large quantities in 10/14 markets. This study highlights the need for better surveillance and sanitary conditions to avoid the negative health impacts of unregulated wildlife markets.

Multiplexed rapid antigen tests developed using multicolored nanoparticles and cross-reactive antibody pairs: Implications for pandemic preparedness

Global public health infrastructure is unprepared for emerging pathogen epidemics, in part because diagnostic tests are not developed in advance. The recent Zika, Ebola, and SARS-CoV-2 virus epidemics are cases in point. We demonstrate here that multicolored gold nanoparticles, when coupled to cross-reactive monoclonal antibody pairs generated from a single immunization regimen, can be used to create multiple diagnostics that specifically detect and distinguish related viruses. The multiplex approach for specific detection centers on immunochromatography with pairs of antibody-conjugated red and blue gold nanoparticles, coupled with clustering algorithms to detect and distinguish related pathogens. Cross-reactive antibodies were used to develop rapid tests for i) Dengue virus serotypes 1-4, ii) Zika virus, iii) Ebola and Marburg viruses, and iv) SARS-CoV and SARS-CoV-2 viruses. Multiplexed rapid antigen tests based on multicolored nanoparticles and cross-reactive antibodies and can be developed prospectively at low cost to improve preparedness for epidemic outbreaks.

Spatial and temporal overlap of domestic cats (Felis catus) and native urban wildlife

Free-roaming domestic cats (Felis catus) are known to pose threats to ecosystem health via transmission of zoonotic diseases and predation of native wildlife. Likewise, free-roaming cats are also susceptible to predation or disease transmission from native wildlife. Physical interactions are required for many of these risks to be manifested, necessitating spatial and temporal overlap between cats and wildlife species. Therefore, knowledge of the location and extent of shared habitat and activity periods would benefit management programs. We used data from a 3-year camera trap survey to model species-specific occupancy and identify landscape variables that contribute to the distribution of free-roaming domestic cats and eight native mammal species in Washington, DC. (USA). Our analysis includes five species that are common prey items of domestic cats, and three species that are potential disease vectors or are otherwise known to be a risk to cats. We then predicted the probability of occupancy and estimated the probability of spatial overlap between cats and each native wildlife species at multiple scales. We also used kernel density estimations to calculate temporal overlap between cats and each native wildlife species. Across spatial scales, occupancy for potential disease vector species was generally positively correlated with canopy cover and open water. Prey species were also generally positively correlated with canopy cover, but displayed negative associations with human population density and inconsistent associations with average per capita income. Domestic cat occupancy was negatively correlated with natural habitat characteristics and positively correlated with human population density. Predicted spatial overlap between domestic cats and native wildlife was greatest for potential disease vector species. Temporal overlap was high (>0.50) between cats and all but two native wildlife species, indicating that temporal overlap is probable wherever species overlap spatially. Our findings indicate that the risk to and from domestic cats varies across urban landscapes, but primarily arises from human activities. As such, humans are implicated in the negative outcomes that result from cats interacting with wildlife. Data-driven management to reduce such interactions can aid in cat population management, biodiversity conservation, and public health campaigns.

The one health perspective to improve environmental surveillance of zoonotic viruses: lessons from COVID-19 and outlook beyond

The human population has doubled in the last 50 years from about 3.7 billion to approximately 7.8 billion. With this rapid expansion, more people live in close contact with wildlife, livestock, and pets, which in turn creates increasing opportunities for zoonotic diseases to pass between animals and people. At present an estimated 75% of all emerging virus-associated infectious diseases possess a zoonotic origin, and outbreaks of Zika, Ebola and COVID-19 in the past decade showed their huge disruptive potential on the global economy. Here, we describe how One Health inspired environmental surveillance campaigns have emerged as the preferred tools to monitor human-adjacent environments for known and yet to be discovered infectious diseases, and how they can complement classical clinical diagnostics. We highlight the importance of environmental factors concerning interactions between animals, pathogens and/or humans that drive the emergence of zoonoses, and the methodologies currently proposed to monitor them-the surveillance of wastewater, for example, was identified as one of the main tools to assess the spread of SARS-CoV-2 by public health professionals and policy makers during the COVID-19 pandemic. One-Health driven approaches that facilitate surveillance, thus harbour the potential of preparing humanity for future pandemics caused by aetiological agents with environmental reservoirs. Via the example of COVID-19 and other viral diseases, we propose that wastewater surveillance is a useful complement to clinical diagnosis as it is centralized, robust, cost-effective, and relatively easy to implement.

Pandemic origins and a One Health approach to preparedness and prevention: Solutions based on SARS-CoV-2 and other RNA viruses

COVID-19 is the latest zoonotic RNA virus epidemic of concern. Learning how it began and spread will help to determine how to reduce the risk of future events. We review major RNA virus outbreaks since 1967 to identify common features and opportunities to prevent emergence, including ancestral viral origins in birds, bats, and other mammals; animal reservoirs and intermediate hosts; and pathways for zoonotic spillover and community spread, leading to local, regional, or international outbreaks. The increasing scientific evidence concerning the origins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is most consistent with a zoonotic origin and a spillover pathway from wildlife to people via wildlife farming and the wildlife trade. We apply what we know about these outbreaks to identify relevant, feasible, and implementable interventions. We identify three primary targets for pandemic prevention and preparedness: first, smart surveillance coupled with epidemiological risk assessment across wildlife–livestock–human (One Health) spillover interfaces; second, research to enhance pandemic preparedness and expedite development of vaccines and therapeutics; and third, strategies to reduce underlying drivers of spillover risk and spread and reduce the influence of misinformation. For all three, continued efforts to improve and integrate biosafety and biosecurity with the implementation of a One Health approach are essential. We discuss new models to address the challenges of creating an inclusive and effective governance structure, with the necessary stable funding for cross-disciplinary collaborative research. Finally, we offer recommendations for feasible actions to close the knowledge gaps across the One Health continuum and improve preparedness and response in the future.

Comprehensive role of SARS-CoV-2 spike glycoprotein in regulating host signaling pathway

Since the outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, global public health and the economy have suffered unprecedented damage. Based on the increasing related literature, the characteristics and pathogenic mechanisms of the virus, and epidemiological and clinical features of the disease are being rapidly discovered. The spike glycoprotein (S protein), as a key antigen of SARS-CoV-2 for developing vaccines, antibodies, and drug targets, has been shown to play an important role in viral entry, tissue tropism, and pathogenesis. In this review, we summarize the molecular mechanisms of interaction between S protein and host factors, especially receptor-mediated viral modulation of host signaling pathways, and highlight the progression of potential therapeutic targets, prophylactic and therapeutic agents for prevention and treatment of SARS-CoV-2 infection.

Wildlife susceptibility to infectious diseases at global scales

Disease transmission prediction across wildlife is crucial for risk assessment of emerging infectious diseases. Susceptibility of host species to pathogens is influenced by the geographic, environmental, and phylogenetic context of the specific system under study. We used machine learning to analyze how such variables influence pathogen incidence for multihost pathogen assemblages, including one of direct transmission (coronaviruses and bats) and two vector-borne systems (West Nile Virus [WNV] and birds, and malaria and birds). Here we show that this methodology is able to provide reliable global spatial susceptibility predictions for the studied host-pathogen systems, even when using a small amount of incidence information (i.e., [Formula: see text] of information in a database). We found that avian malaria was mostly affected by environmental factors and by an interaction between phylogeny and geography, and WNV susceptibility was mostly influenced by phylogeny and by the interaction between geographic and environmental distances, whereas coronavirus susceptibility was mostly affected by geography. This approach will help to direct surveillance and field efforts providing cost-effective decisions on where to invest limited resources.

The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic

Understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 is critical to preventing future zoonotic outbreaks before they become the next pandemic. The Huanan Seafood Wholesale Market in Wuhan, China, was identified as a likely source of cases in early reports, but later this conclusion became controversial. We show here that the earliest known COVID-19 cases from December 2019, including those without reported direct links, were geographically centered on this market. We report that live SARS-CoV-2-susceptible mammals were sold at the market in late 2019 and that within the market, SARS-CoV-2-positive environmental samples were spatially associated with vendors selling live mammals. Although there is insufficient evidence to define upstream events, and exact circumstances remain obscure, our analyses indicate that the emergence of SARS-CoV-2 occurred through the live wildlife trade in China and show that the Huanan market was the epicenter of the COVID-19 pandemic.

A framework for testing the impact of co-infections on host gut microbiomes

Parasitic infections disturb gut microbial communities beyond their natural range of variation, possibly leading to dysbiosis. Yet it remains underappreciated that most infections are accompanied by one or more co-infections and their collective impact is largely unexplored. Here we developed a framework illustrating changes to the host gut microbiome following single infections, and build on it by describing the neutral, synergistic or antagonistic impacts on microbial α- and ß-diversity expected from co-infections. We tested the framework on microbiome data from a non-human primate population co-infected with helminths and Adenovirus, and matched patterns reported in published studies to the introduced framework. In this case study, α-diversity of co-infected Malagasy mouse lemurs (Microcebus griseorufus) did not differ in comparison with that of singly infected or uninfected individuals, even though community composition captured with ß-diversity metrices changed significantly. Explicitly, we record stochastic changes in dispersion, a sign of dysbiosis, following the Anna-Karenina principle rather than deterministic shifts in the microbial gut community. From the literature review and our case study, neutral and synergistic impacts emerged as common outcomes from co-infections, wherein both shifts and dispersion of microbial communities following co-infections were often more severe than after a single infection alone, but microbial α-diversity was not universally altered. Important functions of the microbiome may also suffer from such heavily altered, though no less species-rich microbial community. Lastly, we pose the hypothesis that the reshuffling of host-associated microbial communities due to the impact of various, often coinciding parasitic infections may become a source of novel or zoonotic diseases.

COVID-19 related policies: The role of environmental concern in understanding citizens' preferences

COVID-19 has led to an unprecedented health and economic crisis worldwide. Many governments of the world have accelerated an adoption of public policies to address this crisis; however, a trade-off between the economy and public health exists. Previous studies in this area have mainly focused on the impact of COVID-19 on human life and the environment. This work adds to the literature by analyzing how individual environmental concern can affect citizens' preferences for public policies that deal with COVID-19. A data set of 26,131 participants from 26 countries was used to test the research model. Results indicate that environmental concern is positively associated with a preference for long-term oriented altruistic policies, and it shapes the relationship between economic and health problems at the country level on our dependent variable. Specifically, as the level of environmental concern increases, the negative effect of COVID-19's economic problems on the preference for long-term altruistic policies is diminished. In turn, in the case of health problems, the impact on the preference for long-term altruistic policies increases as environmental concern increases. Also, both individual-level and country-level characteristics affect citizens' preferences for policies related to the COVID-19 pandemic.

Exceptional diversity and selection pressure on coronavirus host receptors in bats compared to other mammals

Pandemics originating from non-human animals highlight the need to understand how natural hosts have evolved in response to emerging human pathogens and which groups may be susceptible to infection and/or potential reservoirs to mitigate public health and conservation concerns. Multiple zoonotic coronaviruses, such as severe acute respiratory syndrome-associated coronavirus (SARS-CoV), SARS-CoV-2 and Middle Eastern respiratory syndrome-associated coronavirus (MERS-CoV), are hypothesized to have evolved in bats. We investigate angiotensin-converting enzyme 2 (ACE2), the host protein bound by SARS-CoV and SARS-CoV-2, and dipeptidyl-peptidase 4 (DPP4 or CD26), the host protein bound by MERS-CoV, in the largest bat datasets to date. Both the ACE2 and DPP4 genes are under strong selection pressure in bats, more so than in other mammals, and in residues that contact viruses. Additionally, mammalian groups vary in their similarity to humans in residues that contact SARS-CoV, SARS-CoV-2 and MERS-CoV, and increased similarity to humans in binding residues is broadly predictive of susceptibility to SARS-CoV-2. This work augments our understanding of the relationship between coronaviruses and mammals, particularly bats, provides taxonomically diverse data for studies of how host proteins are bound by coronaviruses and can inform surveillance, conservation and public health efforts.

Demographic Expansions and the Emergence of Host Specialization in Genetically Distinct Ecotypes of the Tick-Transmitted Bacterium Anaplasma phagocytophilum

In Europe, genetically distinct ecotypes of the tick-vectored bacterium Anaplasma phagocytophilum circulate among mammals in three discrete enzootic cycles. To date, potential ecological factors that contributed to the emergence of these divergent ecotypes have been poorly studied. Here, we show that the ecotype that predominantly infects roe deer (Capreolus capreolus) is evolutionarily derived. Its divergence from a host generalist ancestor occurred after the last glacial maximum as mammal populations, including roe deer, recolonized the European mainland from southern refugia. We also provide evidence that this host specialist ecotype's effective population size (N_e) has tracked changes in the population of its roe deer host. Specifically, both host and bacterium have undergone substantial increases in N_e over the past 1,500 years. In contrast, we show that while it appears to have undergone a major population expansion starting ~3,500 years ago, in the past 500 years, the contemporary host generalist ecotype has experienced a substantial reduction in genetic diversity levels, possibly as a result of reduced opportunities for transmission between competent hosts. IMPORTANCE The findings of this study reveal specific events important for the evolution of host specialization in a naturally occurring, obligately intracellular bacterial pathogen. Specifically, they show that host range shifts and the emergence of host specialization may occur during periods of population growth in a generalist ancestor. Our results also demonstrate the close correlation between demographic patterns in host and pathogen for a specialist system. These findings have important relevance for understanding the evolution of host range diversity. They may inform future work on host range dynamics, and they provide insights for understanding the emergence of pathogens that have human and veterinary health implications.