"Smart markets": harnessing the potential of new technologies for endemic and emerging infectious disease surveillance in traditional food markets.

Emerging and endemic zoonotic diseases continue to threaten human and animal health, our social fabric, and the global economy. Zoonoses frequently emerge from congregate interfaces where multiple animal species and humans coexist, including farms and markets. Traditional food markets are widespread across the globe and create an interface where domestic and wild animals interact among themselves and with humans, increasing the risk of pathogen spillover. Despite decades of evidence linking markets to disease outbreaks across the world, there remains a striking lack of pathogen surveillance programs that can relay timely, cost-effective, and actionable information to decision-makers to protect human and animal health. However, the strategic incorporation of environmental surveillance systems in markets coupled with novel pathogen detection strategies can create an early warning system capable of alerting us to the risk of outbreaks before they happen. Here, we explore the concept of "smart" markets that utilize continuous surveillance systems to monitor the emergence of zoonotic pathogens with spillover potential.IMPORTANCEFast detection and rapid intervention are crucial to mitigate risks of pathogen emergence, spillover and spread-every second counts. However, comprehensive, active, longitudinal surveillance systems at high-risk interfaces that provide real-time data for action remain lacking. This paper proposes "smart market" systems harnessing cutting-edge tools and a range of sampling techniques, including wastewater and air collection, multiplex assays, and metagenomic sequencing. Coupled with robust response pathways, these systems could better enable Early Warning and bolster prevention efforts.

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.

Emergence of Group B Streptococcus Disease in Pigs and Porcupines, Italy.

We describe group B Streptococcus linked to disease in farmed pigs and wild porcupines in Italy. Occurrence in pigs was attributed to transmission from nonpasteurized bovine milk whey. Antimicrobial-resistance profiles in isolates from porcupines suggest no common source of infection. Our findings expand the known host range for group B Streptococcus disease.

Emergence, Evolution, and Pathogenicity of Influenza A(H7N4) Virus in Shorebirds in China.

A 2-year surveillance study of influenza A viruses in migratory birds was conducted to understand the subsequent risk during the migratory seasons in Dandong Yalu River Estuary Coastal Wetland National Nature Reserve, Liaoning Province, China, a major stopover site on the East Asian-Australasian flyway. Overall, we isolated 27 influenza A viruses with multiple subtypes, including H3N8 (n = 2), H4N6 (n = 2), H4N7 (n = 2), H7N4 (n = 9), H7N7 (n = 1), H10N7 (n = 7), and H13N6 (n = 4). Particularly, a novel reassortant influenza A(H7N4) virus was first identified in a woman and her backyard poultry flock in Jiangsu Province, China, posing a serious threat to public health. Here, we describe the genetic characterization and pathogenicity of the nine influenza A(H7N4) isolates. Phylogenetic analysis indicated that complex viral gene flow occurred among Asian countries. We also demonstrated a similar evolutionary trajectory of the surface genes of the A(H7N4) isolates and Jiangsu human-related A(H7N4) viruses. Our A(H7N4) isolates exhibited differing degrees of virulence in mice, suggesting a potential risk to other mammalian species, including humans. We revealed multiple mutations that might affect viral virulence in mice. Our report highlights the importance and need for the long-term surveillance of avian influenza virus in migratory birds combined with domestic poultry surveillance along migratory routes and flyways and, thereby, the development of measures to manage potential health threats. IMPORTANCE The H7 subtype avian influenza viruses, such as H7N2, H7N3, H7N4, H7N7, and H7N9, were documented as being capable of infecting humans, and the H7 subtype low pathogenicity avian influenza viruses are capable of mutating into highly pathogenic avian influenza; therefore, they pose a serious threat to public health. Here, we investigated the evolutionary history, molecular characteristics, and pathogenicity of shorebird-origin influenza A(H7N4) viruses, showing a similar evolutionary trajectory with Jiangsu human A(H7N4) viruses in HA and NA genes. Moreover, our isolates exhibited variable virulence (including moderate virulence) in mice, suggesting a potential risk to other mammalian species, including humans.

Common ground: The foundation of interdisciplinary research on bat disease emergence.

Human perturbation of natural systems is accelerating the emergence of infectious diseases, mandating integration of disease and ecological research. Bats have been associated with recent zoonoses, but our bibliometric analysis of coauthor relationships identified a separation of bat ecologists and infectious disease researchers with few cross-disciplinary relationships. Of 5,645 papers, true interdisciplinary collaborations occurred primarily in research focused on White Nose Syndrome (WNS). This finding is important because it illustrates how research with outcomes favoring both bat conservation and disease mitigation promotes domain integration and network connectivity. We advocate for increased engagement between ecology and infectious researchers to address such common causes and suggest that efforts focus on leveraging existing activities, building interdisciplinary projects, and networking individuals and networks to integrate domains and coordinate resources. We provide specific opportunities for pursuing these strategies through the Bat One Health Research Network (BOHRN).

Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts.

The notion that certain animal groups disproportionately maintain and transmit viruses to humans due to broad-scale differences in ecology, life history, and physiology currently influences global health surveillance and research in disease ecology, virology, and immunology. To directly test whether such "special reservoirs" of zoonoses exist, we used literature searches to construct the largest existing dataset of virus-reservoir relationships, consisting of the avian and mammalian reservoir hosts of 415 RNA and DNA viruses along with their histories of human infection. Reservoir host effects on the propensity of viruses to have been reported as infecting humans were rare and when present were restricted to one or two viral families. The data instead support a largely host-neutral explanation for the distribution of human-infecting viruses across the animal orders studied. After controlling for higher baseline viral richness in mammals versus birds, the observed number of zoonoses per animal order increased as a function of their species richness. Animal orders of established importance as zoonotic reservoirs including bats and rodents were unexceptional, maintaining numbers of zoonoses that closely matched expectations for mammalian groups of their size. Our findings show that variation in the frequency of zoonoses among animal orders can be explained without invoking special ecological or immunological relationships between hosts and viruses, pointing to a need to reconsider current approaches aimed at finding and predicting novel zoonoses.

Surveillance and risk assessment for early detection of emerging infectious diseases in livestock.

Those who work in the area of surveillance and prevention of emerging infectious diseases (EIDs) face a challenge in accurately predicting where infection will occur and who (or what) it will affect. Establishing surveillance and control programmes for EIDs requires substantial and long-term commitment of resources that are limited in nature. This contrasts with the unquantifiable number of possible zoonotic and non-zoonotic infectious diseases that may emerge, even when the focus is restricted to diseases involving livestock. Such diseases may emerge from many combinations of, and changes in, host species, production systems, environments/habitats and pathogen types. Given these multiple elements, risk prioritisation frameworks should be used more widely to support decision-making and resource allocation for surveillance. In this paper, the authors use recent examples of EID events in livestock to review surveillance approaches for the early detection of EIDs, and highlight the need for surveillance programmes to be informed and prioritised by regularly updated risk assessment frameworks. They conclude by discussing some unmet needs in risk assessment practices for EIDs, and the need for improved coordination in global infectious disease surveillance.

Les personnes travaillant dans le domaine de la surveillance et de la prévention des maladies infectieuses émergentes (MIE) sont confrontées à la difficulté de prédire avec exactitude le lieu d'émergence d'une maladie, ainsi que l'espèce, le système ou le site affectés. La mise en place de programmes de surveillance et de lutte contre les MIE exige une mobilisation conséquente et durable de ressources nécessairement limitées. Par contraste, le nombre des maladies infectieuses zoonotiques et non zoonotiques pouvant se déclarer est impossible à quantifier, même si l'on s'en tient aux seules maladies affectant les animaux d'élevage. Ces maladies surviennent à la faveur des nombreuses et diverses configurations, associations ou modifications qui peuvent se produire parmi les espèces hôtes, les systèmes de production, les environnements ou habitats et les types d'agents pathogènes. Compte tenu de la multiplicité de ces éléments, il devrait être fait plus largement appel à des cadres de priorisation du risque afin de soutenir les processus de prise de décision et d'allocation des ressources en matière de surveillance. Les auteurs s'appuient sur des exemples récents d'événements liés à des MIE pour faire le point sur les méthodes de surveillance appliquées pour la détection précoce de ces maladies et soulignent l'importance de documenter et de prioriser les programmes de surveillance en procédant à des mises à jour régulières des cadres utilisés pour l'évaluation du risque. Ils concluent en évoquant certains aspects importants que les pratiques actuelles d'évaluation du risque ne permettent pas de couvrir lorsqu'il s'agit de MIE, ainsi que l'importance d'améliorer la coordination de la surveillance des maladies infectieuses au niveau mondial.

Cuantos trabajan en el ámbito de la vigilancia y la prevención de enfermedades infecciosas emergentes (EIE) tienen dificultades para predecir con precisión dónde va a surgir y a quién (o qué) afectará una infección. La instauración de programas de vigilancia y control de EIE exige una inversión sustancial y duradera de recursos que por definición son escasos, sobre todo teniendo en cuenta el número incalculable de enfermedades infecciosas zoonóticas y no zoonóticas que pueden aparecer, aun considerando solo aquellas que afectan al ganado. Este tipo de enfermedades pueden surgir como resultado de muchas combinaciones distintas de especie hospedadora, sistema productivo, medio/hábitat y tipo de patógeno o por efecto de cambios que se den en cualquiera de estos elementos. En vista de la multiplicidad de factores que concurren, convendría emplear de modo más generalizado un sistema de jerarquización de los riesgos en el cual fundamentar las decisiones de vigilancia y la distribución de los recursos destinados a ella. Los autores, valiéndose de ejemplos recientes de episodios infecciosos emergentes que afectaron al ganado, pasan revista a distintos métodos de vigilancia para la detección temprana de EIE y recalcan que los programas de vigilancia deben reposar en procedimientos de determinación del riesgo periódicamente actualizados y en las prioridades fijadas a partir de estos procedimientos. Por último, los autores se detienen en algunas necesidades desatendidas en la praxis de la determinación del riesgo de EIE y en la necesidad de una mejor coordinación de la vigilancia mundial de las enfermedades infecciosas.

Assessing the quality of data for drivers of disease emergence.

Drivers are factors that have the potential to directly or indirectly influence the likelihood of infectious diseases emerging or re-emerging. It is likely that an emerging infectious disease (EID) rarely occurs as the result of only one driver; rather, a network of sub-drivers (factors that can influence a driver) are likely to provide conditions that allow a pathogen to (re-)emerge and become established. Data on sub-drivers have therefore been used by modellers to identify hotspots where EIDs may next occur, or to estimate which sub-drivers have the greatest influence on the likelihood of their occurrence. To minimise error and bias when modelling how sub-drivers interact, and thus aid in predicting the likelihood of infectious disease emergence, researchers need good-quality data to describe these sub-drivers. This study assesses the quality of the available data on sub-drivers of West Nile virus against various criteria as a case study. The data were found to be of varying quality with regard to fulfilling the criteria. The characteristic with the lowest score was completeness, i.e. where sufficient data are available to fulfil all the requirements for the model. This is an important characteristic as an incomplete data set could lead to erroneous conclusions being drawn from modelling studies. Thus, the availability of good-quality data is essential to reduce uncertainty when estimating the likelihood of where EID outbreaks may occur and identifying the points on the risk pathway where preventive measures may be taken.

Les facteurs d'émergence sont des éléments ayant le potentiel direct ou indirect d'influencer la probabilité d'émergence ou de réémergence d'une maladie infectieuse. Il est probablement rare qu'une maladie infectieuse émergente apparaisse en raison d'un seul facteur ; c'est plutôt un faisceau de sous-facteurs (éléments pouvant avoir une influence sur un même facteur) qui contribue à ce que les conditions soient réunies pour qu'un agent pathogène puisse (ré)émerger et s'établir. Les concepteurs de modèles ont donc utilisé les données relatives aux sous-facteurs pour identifier les zones sensibles où les prochaines maladies infectieuses émergentes pourraient survenir, ou pour faire une estimation des sous-facteurs ayant la plus grande influence sur la probabilité de leur occurrence. Les chercheurs ont besoin de données de qualité pour décrire ces sous-facteurs, afin de minimiser le risque d'erreur et de biais lors de la modélisation de l'interaction entre les différents sous-facteurs, et de contribuer ainsi à mieux prédire la probabilité d'apparition d'une maladie infectieuse émergente. Les auteurs présentent une étude de cas qui a consisté à évaluer la qualité des données disponibles relatives aux sous-facteurs d'émergence du virus de la fièvre de West Nile au regard de différents critères. Il est apparu que la qualité des données était variable au regard des critères examinés. Le paramètre dont le score était le plus bas est celui de la complétude - le fait que suffisamment de données soient disponibles pour répondre à toutes les exigences du modèle. Il s'agit pourtant d'un paramètre important car des données incomplètes peuvent inciter à tirer des conclusions erronées des études de modélisation. La disponibilité de données de bonne qualité est essentielle pour réduire l'incertitude lors de l'estimation de la probabilité d'apparition de maladies infectieuses émergentes dans des zones déterminées, ainsi que pour identifier les points critiques de concrétisation du risque où des mesures préventives pourraient être mises en place.

Los inductores o factores de inducción [drivers] son aquellos que, directa o indirectamente, pueden influir en la probabilidad de que surjan o resurjan enfermedades infecciosas. Todo indica que rara vez una enfermedad infecciosa emergente aparece por efecto de un solo factor de inducción, sino que es probable que haya más bien una combinación de "subfactores de influencia" [sub-drivers] (factores que pueden influir en un inductor) que cree condiciones propicias para que un patógeno (re)surja y logre asentarse. Los creadores de modelos, por consiguiente, se han servido de datos sobre estos subfactores de influencia para localizar aquellas zonas donde con mayor probabilidad puedan aparecer próximamente enfermedades infecciosas emergentes o para determinar cuáles son los subfactores que más influyen en la probabilidad de que ello ocurra. Para reducir al mínimo los errores y sesgos al modelizar la interacción entre los subfactores y ayudar así a calcular la probabilidad de que surja una enfermedad infecciosa emergente, los investigadores necesitan datos de buena calidad para caracterizar estos subfactores. En el análisis expuesto por los autores se utilizó el virus del Nilo Occidental como ejemplo de estudio para evaluar, con arreglo a diversos criterios, la calidad de los datos existentes sobre los subfactores que inciden en la aparición de este virus. Lo que se constató, en relación con el grado de cumplimiento de los criterios, es que esos datos eran de calidad variable. La característica o parámetro que deparó la puntuación más baja fue la completud, es decir, la existencia de datos suficientes para aportar al modelo toda la información requerida para que este funcione bien. Se trata de una característica importante, pues un conjunto incompleto de datos podría llevar a extraer conclusiones erróneas de los estudios de modelización. Por ello, para reducir la incertidumbre a la hora de calcular la probabilidad de que en cierto lugar surjan brotes de enfermedades infecciosas emergentes y de determinar, dentro de la cadena de materialización del riesgo, aquellos eslabones en los que cabe adoptar medidas preventivas, es indispensable disponer de datos de buena calidad.

Characterizing Emerging Canine H3 Influenza Viruses.

The continual emergence of novel influenza A strains from non-human hosts requires constant vigilance and the need for ongoing research to identify strains that may pose a human public health risk. Since 1999, canine H3 influenza A viruses (CIVs) have caused many thousands or millions of respiratory infections in dogs in the United States. While no human infections with CIVs have been reported to date, these viruses could pose a zoonotic risk. In these studies, the National Institutes of Allergy and Infectious Diseases (NIAID) Centers of Excellence for Influenza Research and Surveillance (CEIRS) network collaboratively demonstrated that CIVs replicated in some primary human cells and transmitted effectively in mammalian models. While people born after 1970 had little or no pre-existing humoral immunity against CIVs, the viruses were sensitive to existing antivirals and we identified a panel of H3 cross-reactive human monoclonal antibodies (hmAbs) that could have prophylactic and/or therapeutic value. Our data predict these CIVs posed a low risk to humans. Importantly, we showed that the CEIRS network could work together to provide basic research information important for characterizing emerging influenza viruses, although there were valuable lessons learned.

Strategies for managing marine disease.

The incidence of emerging infectious diseases (EIDs) has increased in wildlife populations in recent years and is expected to continue to increase with global environmental change. Marine diseases are relatively understudied compared with terrestrial diseases but warrant parallel attention as they can disrupt ecosystems, cause economic loss, and threaten human livelihoods. Although there are many existing tools to combat the direct and indirect consequences of EIDs, these management strategies are often insufficient or ineffective in marine habitats compared with their terrestrial counterparts, often due to fundamental differences between marine and terrestrial systems. Here, we first illustrate how the marine environment and marine organism life histories present challenges and opportunities for wildlife disease management. We then assess the application of common disease management strategies to marine versus terrestrial systems to identify those that may be most effective for marine disease outbreak prevention, response, and recovery. Finally, we recommend multiple actions that will enable more successful management of marine wildlife disease emergencies in the future. These include prioritizing marine disease research and understanding its links to climate change, improving marine ecosystem health, forming better monitoring and response networks, developing marine veterinary medicine programs, and enacting policy that addresses marine and other wildlife diseases. Overall, we encourage a more proactive rather than reactive approach to marine wildlife disease management and emphasize that multidisciplinary collaborations are crucial to managing marine wildlife health.

Great ape health watch: Enhancing surveillance for emerging infectious diseases in great apes.

Infectious diseases have the potential to extirpate populations of great apes. As the interface between humans and great apes expands, zoonoses pose an increasingly severe threat to already endangered great ape populations. Despite recognition of the threat posed by human pathogens to great apes, health monitoring is only conducted for a small fraction of the world's wild great apes (and mostly those that are habituated) meaning that outbreaks of disease often go unrecognized and therefore unmitigated. This lack of surveillance (even in sites where capacity to conduct surveillance is present) is the most significant limiting factor in our ability to quickly detect and respond to emerging infectious diseases in great apes when they first appear. Accordingly, we must create a surveillance system that links disease outbreaks in humans and great apes in time and space, and enables veterinarians, clinicians, conservation managers, national decision makers, and the global health community to respond quickly to these events. Here, we review existing great ape health surveillance programs in African range habitats to identify successes, gaps, and challenges. We use these findings to argue that standardization of surveillance across sites and geographic scales, that monitors primate health in real-time and generates early warnings of disease outbreaks, is an efficient, low-cost step to conserve great ape populations. Such a surveillance program, which we call "Great Ape Health Watch" would lead to long-term improvements in outbreak preparedness, prevention, detection, and response, while generating valuable data for epidemiological research and sustainable conservation planning. Standardized monitoring of great apes would also make it easier to integrate with human surveillance activities. This approach would empower local stakeholders to link wildlife and human health, allowing for near real-time, bidirectional surveillance at the great ape-human interface.

Infectious disease threats to amphibians in Greece: new localities positive for Batrachochytrium dendrobatidis.

In the early 2000s, numerous cases of European amphibian population declines and mass die-offs started to emerge. Investigating those events led to the discovery that wild European amphibians were confronted with grave disease threats caused by introduced pathogens, namely the amphibian and the salamander chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal) and ranaviruses. In Greece, Bd was previously documented among wild amphibian populations in 2 different locations and 3 different species. However, no disease-related mass declines or mortality events have been reported. In this work, we build upon previous findings with new, subsequently obtained data, resulting in a 225-sample dataset of 14 species from 17 different locations throughout Greece, in order to examine the occurrence status of all 3 pathogens responsible for emerging infectious diseases in European amphibians. No positive samples for Bsal or ranavirus were recorded in any location. We confirmed the presence of Bd in 4 more localities and in 4 more species, including 1 urodelan (Macedonian crested newt Triturus macedonicus) and 1 introduced anuran (American bullfrog Lithobates catesbeianus). All insular localities were negative for Bd, except for Crete, where Bd was identified in 2 different locations. Again, no mass declines or die-offs were recorded in any Bd-positive area or elsewhere. However, given the persistence of Bd across Greece over the past ~20 yr, monitoring efforts should continue, and ideally be further expanded.

Bovine tuberculosis disturbs parasite functional trait composition in African buffalo.

Novel parasites can have wide-ranging impacts, not only on host populations, but also on the resident parasite community. Historically, impacts of novel parasites have been assessed by examining pairwise interactions between parasite species. However, parasite communities are complex networks of interacting species. Here we used multivariate taxonomic and trait-based approaches to determine how parasite community composition changed when African buffalo (Syncerus caffer) acquired an emerging disease, bovine tuberculosis (BTB). Both taxonomic and functional parasite richness increased significantly in animals that acquired BTB than in those that did not. Thus, the presence of BTB seems to catalyze extraordinary shifts in community composition. There were no differences in overall parasite taxonomic composition between infected and uninfected individuals, however. The trait-based analysis revealed an increase in direct-transmitted, quickly replicating parasites following BTB infection. This study demonstrates that trait-based approaches provide insight into parasite community dynamics in the context of emerging infections.

Synthesizing the connections between environmental disturbances and zoonotic spillover.

Zoonotic spillover is a phenomenon characterized by the transfer of pathogens between different animal species. Most human emerging infectious diseases originate from non-human animals, and human-related environmental disturbances are the driving forces of the emergence of new human pathogens. Synthesizing the sequence of basic events involved in the emergence of new human pathogens is important for guiding the understanding, identification, and description of key aspects of human activities that can be changed to prevent new outbreaks, epidemics, and pandemics. This review synthesizes the connections between environmental disturbances and increased risk of spillover events based on the One Health perspective. Anthropogenic disturbances in the environment (e.g., deforestation, habitat fragmentation, biodiversity loss, wildlife exploitation) lead to changes in ecological niches, reduction of the dilution effect, increased contact between humans and other animals, changes in the incidence and load of pathogens in animal populations, and alterations in the abiotic factors of landscapes. These phenomena can increase the risk of spillover events and, potentially, facilitate new infectious disease outbreaks. Using Brazil as a study model, this review brings a discussion concerning anthropogenic activities in the Amazon region and their potential impacts on spillover risk and spread of emerging diseases in this region.

Emerging infectious diseases may spread across pig trade networks in Thailand once introduced: a network analysis approach.

In Thailand, pork is one of the most consumed meats nationwide. Pig farming is hence an important business in the country. However, 95% of the farms were considered smallholders raising only 50 pigs or less. With limited budgets and resources, the biosecurity level in these farms is relatively low. Pig movements have been previously identified as a risk factor in the spread of infectious diseases. Therefore, the present study aimed to explicitly analyze the pig movement network structure and assess its vulnerability to the spread of emerging diseases in Thailand. We used official electronic records of nationwide pig movements throughout the year 2021 to construct a directed weighted one-mode network. Degree centrality, degree distribution, connected components, network community, and modularity were measured to explore the network architectures and properties. In this network, 484,483 pig movements were captured. In which, 379,948 (78.42%) were moved toward slaughterhouses and hence excluded from further analyses. From the remaining links, we suggested that the pig movement network in Thailand was vulnerable to the spread of emerging infectious diseases. Within the network, we found a strongly connected component (SCC) connecting 1044 subdistricts (38.6% of the nodes), a giant weakly connected component (GWCC) covering 98.2% of the nodes (2654/2704), and inter-regional communities with overall network modularity of 0.68. The disease may rapidly spread throughout the country. A better understanding of the nationwide pig movement networks is helpful in tailoring control interventions to cope with the newly emerged diseases once introduced.

Mosquito-borne arboviruses in Uganda: history, transmission and burden.

Mosquito-transmitted arboviruses constitute a large proportion of emerging infectious diseases that are both a public health problem and a threat to animal populations. Many such viruses were identified in East Africa, a region where they remain important and from where new arboviruses may emerge. We set out to describe and review the relevant mosquito-borne viruses that have been identified specifically in Uganda. We focused on the discovery, burden, mode of transmission, animal hosts and clinical manifestation of those previously involved in disease outbreaks. A search for mosquito-borne arboviruses detected in Uganda was conducted using search terms 'Arboviruses in Uganda' and 'Mosquitoes and Viruses in Uganda' in PubMed and Google Scholar in 2020. Twenty-four mosquito-borne viruses from different animal hosts, humans and mosquitoes were documented. The majority of these were from family Peribunyaviridae, followed by Flaviviridae, Togaviridae, Phenuiviridae and only one each from family Rhabdoviridae and Reoviridae. Sixteen (66.7 %) of the viruses were associated with febrile illnesses. Ten (41.7 %) of them were first described locally in Uganda. Six of these are a public threat as they have been previously associated with disease outbreaks either within or outside Uganda. Historically, there is a high burden and endemicity of arboviruses in Uganda. Given the many diverse mosquito species known in the country, there is also a likelihood of many undescribed mosquito-borne viruses. New generation diagnostic platforms have great potential to identify new viruses. Indeed, four novel viruses, two of which were from humans (Ntwetwe and Nyangole viruses) and two from mosquitoes (Kibale and Mburo viruses) including the 2010 yellow fever virus (YFV) outbreak were identified in the last decade using next generation sequencing. Given the unbiased approach of detection of viruses by this technology, its use will undoubtedly be critically important in the characterization of mosquito viromes which in turn will inform other diagnostic efforts.

Mammal assemblage composition predicts global patterns in emerging infectious disease risk.

As a source of emerging infectious diseases, wildlife assemblages (and related spatial patterns) must be quantitatively assessed to help identify high-risk locations. Previous assessments have largely focussed on the distributions of individual species; however, transmission dynamics are expected to depend on assemblage composition. Moreover, disease-diversity relationships have mainly been studied in the context of species loss, but assemblage composition and disease risk (e.g. infection prevalence in wildlife assemblages) can change without extinction. Based on the predicted distributions and abundances of 4466 mammal species, we estimated global patterns of disease risk through the calculation of the community-level basic reproductive ratio R0, an index of invasion potential, persistence, and maximum prevalence of a pathogen in a wildlife assemblage. For density-dependent diseases, we found that, in addition to tropical areas which are commonly viewed as infectious disease hotspots, northern temperate latitudes included high-risk areas. We also forecasted the effects of climate change and habitat loss from 2015 to 2035. Over this period, many local assemblages showed no net loss of species richness, but the assemblage composition (i.e. the mix of species and their abundances) changed considerably. Simultaneously, most areas experienced a decreased risk of density-dependent diseases but an increased risk of frequency-dependent diseases. We further explored the factors driving these changes in disease risk. Our results suggest that biodiversity and changes therein jointly influence disease risk. Understanding these changes and their drivers and ultimately identifying emerging infectious disease hotspots can help health officials prioritize resource distribution.

Emerging infectious diseases of amphibians in Poland: distribution and environmental drivers.

Emerging infectious diseases are a threat to biodiversity and have taken a large toll on amphibian populations worldwide. The chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), and the iridovirus Ranavirus (Rv), are of concern as all have contributed to amphibian declines. In central and eastern Europe, their geographical and host distributions and main environmental drivers determining prevalence are poorly known. We screened over 1000 amphibians from natural and captive populations in Poland for the presence of Bd, Bsal and Rv. In wild amphibian populations, we found that Bd is widespread, present in 46 out of 115 sampled localities as well as 2 captive colonies, and relatively common with overall prevalence at 14.4% in 9 species. We found lower prevalence of Rv at 2.4%, present in 11 out of 92 sampling sites, with a taxonomic breadth of 8 different amphibian species. Bsal infection was not detected in any individuals. In natural populations, Pelophylax esculentus and Bombina variegata accounted for 75% of all Bd infections, suggesting a major role for these 2 species as pathogen reservoirs in Central European freshwater habitats. General linear models showed that climatic as well as landscape features are associated with Bd infection in Poland. We found that higher average annual temperature constrains Bd infection, while landscapes with numerous water bodies or artificial elements (a surrogate for urbanization) increase the chances of infection. Our results show that a combination of climatic and landscape variables may drive regional and local pathogen emergence.

Broad receptor engagement of an emerging global coronavirus may potentiate its diverse cross-species transmissibility.

Porcine deltacoronavirus (PDCoV), identified in 2012, is a common enteropathogen of swine with worldwide distribution. The source and evolutionary history of this virus is, however, unknown. PDCoV belongs to the Deltacoronavirus genus that comprises predominantly avian CoV. Phylogenetic analysis suggests that PDCoV originated relatively recently from a host-switching event between birds and mammals. Insight into receptor engagement by PDCoV may shed light into such an exceptional phenomenon. Here we report that PDCoV employs host aminopeptidase N (APN) as an entry receptor and interacts with APN via domain B of its spike (S) protein. Infection of porcine cells with PDCoV was drastically reduced by APN knockout and rescued after reconstitution of APN expression. In addition, we observed that PDCoV efficiently infects cells of unusual broad species range, including human and chicken. Accordingly, PDCoV S was found to target the phylogenetically conserved catalytic domain of APN. Moreover, transient expression of porcine, feline, human, and chicken APN renders cells susceptible to PDCoV infection. Binding of PDCoV to an interspecies conserved site on APN may facilitate direct transmission of PDCoV to nonreservoir species, including humans, potentially reflecting the mechanism that enabled a virus, ancestral to PDCoV, to breach the species barrier between birds and mammals. The APN cell surface protein is also used by several members of the Alphacoronavirus genus. Hence, our data constitute the second identification of CoVs from different genera that use the same receptor, implying that CoV receptor selection is subjected to specific restrictions that are still poorly understood.

Global trends in infectious diseases of swine.

Pork accounts for more than one-third of meat produced worldwide and is an important component of global food security, agricultural economies, and trade. Infectious diseases are among the primary constraints to swine production, and the globalization of the swine industry has contributed to the emergence and spread of pathogens. Despite the importance of infectious diseases to animal health and the stability and productivity of the global swine industry, pathogens of swine have never been reviewed at a global scale. Here, we build a holistic global picture of research on swine pathogens to enhance preparedness and understand patterns of emergence and spread. By conducting a scoping review of more than 57,000 publications across 50 years, we identify priority pathogens globally and regionally, and characterize geographic and temporal trends in research priorities. Of the 40 identified pathogens, publication rates for eight pathogens increased faster than overall trends, suggesting that these pathogens may be emerging or constitute an increasing threat. We also compared regional patterns of pathogen prioritization in the context of policy differences, history of outbreaks, and differing swine health challenges faced in regions where swine production has become more industrialized. We documented a general increasing trend in importance of zoonotic pathogens and show that structural changes in the industry related to intensive swine production shift pathogen prioritization. Multinational collaboration networks were strongly shaped by region, colonial ties, and pig trade networks. This review represents the most comprehensive overview of research on swine infectious diseases to date.