Virome characterization of game animals in China reveals a spectrum of emerging pathogens.

Game animals are wildlife species traded and consumed as food and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of 1,941 game animals, representing 18 species and five mammalian orders, sampled across China. From this, we identified 102 mammalian-infecting viruses, with 65 described for the first time. Twenty-one viruses were considered as potentially high risk to humans and domestic animals. Civets (Paguma larvata) carried the highest number of potentially high-risk viruses. We inferred the transmission of bat-associated coronavirus from bats to civets, as well as cross-species jumps of coronaviruses from bats to hedgehogs, from birds to porcupines, and from dogs to raccoon dogs. Of note, we identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms, as well as cases of likely human-to-wildlife virus transmission. These data highlight the importance of game animals as potential drivers of disease emergence.

Primate hemorrhagic fever-causing arteriviruses are poised for spillover to humans.

Simian arteriviruses are endemic in some African primates and can cause fatal hemorrhagic fevers when they cross into primate hosts of new species. We find that CD163 acts as an intracellular receptor for simian hemorrhagic fever virus (SHFV; a simian arterivirus), a rare mode of virus entry that is shared with other hemorrhagic fever-causing viruses (e.g., Ebola and Lassa viruses). Further, SHFV enters and replicates in human monocytes, indicating full functionality of all of the human cellular proteins required for viral replication. Thus, simian arteriviruses in nature may not require major adaptations to the human host. Given that at least three distinct simian arteriviruses have caused fatal infections in captive macaques after host-switching, and that humans are immunologically naive to this family of viruses, development of serology tests for human surveillance should be a priority.

Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens.

The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation.

Avoiding novel, unwanted interactions among species to decrease risk of zoonoses.

Circumstances that precipitate interactions among species that have never interacted during their evolutionary histories create ideal conditions for the generation of zoonoses. Zoonotic diseases have caused some of the most devastating epidemics in human history. Contact among species that come from different ecosystems or regions creates the risk of zoonoses. In certain situations, humans are generating and promoting conditions that contribute to the creation of infectious diseases and zoonoses. These conditions lead to interactions between wildlife species that have hitherto not interacted under normal circumstances. I call for recognition of the zoonotic potential that novel and unwanted interactions have; identification of these new interactions that are occurring among wild animals, domestic animals, and humans; and efforts to stop these kinds of interactions because they can give rise to zoonotic outbreaks. Live animal markets, the exotic pet trade, illegal wildlife trade, human use and consumption of wild animals, invasive non-native species, releasing of exotic pets, and human encroachment in natural areas are among the activities that cause the most interactions among wild species, domestic species, and humans. These activities should not occur and must be controlled efficiently to prevent future epidemic zoonoses. Society must develop a keen ability to identify these unnatural interactions and prevent them. Controlling these interactions and efficiently addressing their causal factors will benefit human health and, in some cases, lead to positive environmental, ethical, and socioeconomic outcomes. Until these actions are taken, humanity will face future zoonoses and zoonotic pandemic.

Evitar interacciones novedosas e indeseadas entre especies para disminuir el riesgo de zoonosis Resumen Las circunstancias que promueven interacciones entre especies que nunca han interactuado durante sus historias evolutivas crean condiciones ideales para la generación de zoonosis. Las enfermedades zoonóticas han causado algunas de las epidemias más devastadoras en la historia de la humanidad. El contacto entre especies que provienen de diferentes ecosistemas o regiones crea el riesgo de zoonosis. En determinadas situaciones, los seres humanos estamos generando y promoviendo condiciones que contribuyen a la creación de enfermedades infecciosas y zoonosis. Estas condiciones conducen a interacciones entre especies silvestres que hasta ahora no habían interactuado en circunstancias normales. Hago un llamado para que se reconozca el potencial zoonótico que tienen las interacciones nuevas y no deseadas; que se identifiquen estas nuevas interacciones que provocamos entre animales silvestres, animales domésticos y humanos; y esforzarnos para detener este tipo de interacciones porque pueden dar lugar a brotes zoonóticos. Los mercados de animales vivos, el comercio de mascotas exóticas, el comercio ilegal de vida silvestre, el uso y consumo humano de animales silvestres, las especies invasoras no nativas, la liberación de mascotas exóticas y la invasión humana en áreas naturales, se encuentran entre las actividades que causan la mayor cantidad de interacciones entre especies silvestres, especies domésticas y humanos. Estas actividades no deberían ocurrir y deben controlarse eficientemente para prevenir futuras zoonosis epidémicas. La sociedad debe desarrollar una gran capacidad para identificar estas interacciones antinaturales y prevenirlas. Controlar estas interacciones y abordar eficientemente sus factores causales beneficiará la salud humana y, en algunos casos, conducirá a resultados ambientales, éticos y socioeconómicos positivos. Mientras estas medidas no se tomen, la humanidad enfrentará futuras zoonosis y pandemias zoonóticas.

The Pandemic Arc: Expanded Narratives in the History of Global Health.

Using the examples of plague, smallpox, and HIV/AIDS, the present essay argues for the benefits of incorporating the evolutionary histories of pathogens, beyond visible epidemic spikes within human populations, into our understanding of what pandemics actually are as epidemiological phenomena. The pandemic arc - which takes the pathogen as the defining "actor" in a pandemic, from emergence to local proliferation to globalization - offers a framework capable of bringing together disparate aspects not only of the manifestations of disease but also of human involvement in the pandemic process. Pathogens may differ, but there are common patterns in disease emergence and proliferation that distinguish those diseases that become pandemic, dispersed through human communities regionally or globally. The same methods of genomic analysis that allow tracking the evolutionary development of a modern pathogen such as SARS-CoV-2 also allow us to trace pandemics into the past. Reconstruction of these pandemic arcs brings new elements of these stories into view, recovering the experiences of regions and populations hitherto overlooked by Eurocentric narratives. This expanded global history of infectious diseases, in turn, lays a groundwork for reconceiving what ambitions a truly global health might aim for.

Local thermal adaptation and local temperature regimes drive the performance of a parasitic helminth under climate change: The case of Marshallagia marshalli from wild ungulates.

Across a species' range, populations are exposed to their local thermal environments, which on an evolutionary scale, may cause adaptative differences among populations. Helminths often have broad geographic ranges and temperature-sensitive life stages but little is known about whether and how local thermal adaptation can influence their response to climate change. We studied the thermal responses of the free-living stages of Marshallagia marshalli, a parasitic nematode of wild ungulates, along a latitudinal gradient. We first determine its distribution in wild sheep species in North America. Then we cultured M. marshalli eggs from different locations at temperatures from 5 to 38°C. We fit performance curves based on the metabolic theory of ecology to determine whether development and mortality showed evidence of local thermal adaptation. We used parameter estimates in life-cycle-based host-parasite models to understand how local thermal responses may influence parasite performance under general and location-specific climate-change projections. We found that M. marshalli has a wide latitudinal and host range, infecting wild sheep species from New Mexico to Yukon. Increases in mortality and development time at higher temperatures were most evident for isolates from northern locations. Accounting for location-specific parasite parameters primarily influenced the magnitude of climate change parasite performance, while accounting for location-specific climates primarily influenced the phenology of parasite performance. Despite differences in development and mortality among M. marshalli populations, when using site-specific climate change projections, there was a similar magnitude of impact on the relative performance of M. marshalli among populations. Climate change is predicted to decrease the expected lifetime reproductive output of M. marshalli in all populations while delaying its seasonal peak by approximately 1 month. Our research suggests that accurate projections of the impacts of climate change on broadly distributed species need to consider local adaptations of organisms together with local temperature profiles and climate projections.

Environmental spillover of emerging viruses: Is it true?

The concept of environmental "spillover" of pathogens to humans is widely used in the scientific literature about emerging diseases with the idea that it is scientifically proven. However, the exact characterization of the mechanism of spillover is simply lacking. A systematic review retrieved 688 articles using this term. The systematic analysis revealed an irreducible polysemy covering ten different definitions. It also demonstrated the absence of explicit definition in most of the articles, and even antinomies. A modeling analysis of the various processes described by these ten definitions showed that none of them corresponded to the complete trajectory leading to the emergence of a disease. There is no article demonstrating a mechanism of spillover. There are only ten articles proposing ideas on how a putative spillover could work but they merely are intellectual constructions. All other articles only reuse the term with no demonstration. It is essential to understand that since there is no scientific concept behind the "spillover", it might be dangerous to base public health and public protection against future pandemics on it.

Is there evidence of sustained human-mosquito-human transmission of the zoonotic malaria Plasmodium knowlesi? A systematic literature review.

BACKGROUND: The zoonotic malaria parasite Plasmodium knowlesi has emerged across Southeast Asia and is now the main cause of malaria in humans in Malaysia. A critical priority for P. knowlesi surveillance and control is understanding whether transmission is entirely zoonotic or is also occurring through human-mosquito-human transmission. METHODS: A systematic literature review was performed to evaluate existing evidence which refutes or supports the occurrence of sustained human-mosquito-human transmission of P. knowlesi. Possible evidence categories and study types which would support or refute non-zoonotic transmission were identified and ranked. A literature search was conducted on Medline, EMBASE and Web of Science using a broad search strategy to identify any possible published literature. Results were synthesized using the Synthesis Without Meta-analysis (SWiM) framework, using vote counting to combine the evidence within specific categories. RESULTS: Of an initial 7,299 studies screened, 131 studies were included within this review: 87 studies of P. knowlesi prevalence in humans, 14 studies in non-human primates, 13 studies in mosquitoes, and 29 studies with direct evidence refuting or supporting non-zoonotic transmission. Overall, the evidence showed that human-mosquito-human transmission is biologically possible, but there is limited evidence of widespread occurrence in endemic areas. Specific areas of research were identified that require further attention, notably quantitative analyses of potential transmission dynamics, epidemiological and entomological surveys, and ecological studies into the sylvatic cycle of the disease. CONCLUSION: There are key questions about P. knowlesi that remain within the areas of research that require more attention. These questions have significant implications for malaria elimination and eradication programs. This paper considers limited but varied research and provides a methodological framework for assessing the likelihood of different transmission patterns for emerging zoonotic diseases.

Resistance Correlations Influence Infection by Foreign Pathogens.

AbstractReciprocal selection promotes the specificity of host-pathogen associations and resistance polymorphisms in response to disease. However, plants and animals also vary in response to pathogen species not previously encountered in nature, with potential effects on new disease emergence. Using anther smut disease, we show that resistance (measured as infection rates) to foreign pathogens can be correlated with standing variation in resistance to an endemic pathogen. In Silene vulgaris, genetic variation in resistance to its endemic anther smut pathogen correlated positively with resistance variation to an anther smut pathogen from another host, but the relationship was negative between anther smut and a necrotrophic pathogen. We present models describing the genetic basis for assessing resistance relationships between endemic and foreign pathogens and for quantifying infection probabilities on foreign pathogen introduction. We show that even when the foreign pathogen has a lower average infection ability than the endemic pathogen, infection outcomes are determined by the sign and strength of the regression of the host's genetic variation in infection rates by a foreign pathogen on variation in infection rates by an endemic pathogen as well as by resistance allele frequencies. Given that preinvasion equilibria of resistance are determined by factors including resistance costs, we show that protection against foreign pathogens afforded by positively correlated resistances can be lessened or even result in elevated infection risk at the population level, depending on local dynamics. Therefore, a pathogen's emergence potential could be influenced not only by its average infection rate but also by resistance variation resulting from prior selection imposed by endemic diseases.

Population Genomics of Bacterial Plant Pathogens.

Population genomics is transforming our understanding of pathogen biology and evolution, and contributing to the prevention and management of disease in diverse crops. We provide an overview of key methods in bacterial population genomics and describe recent work focusing on three topics of critical importance to plant pathology: (i) resolving pathogen origins and transmission pathways during outbreak events, (ii) identifying the genetic basis of host specificity and virulence, and (iii) understanding how pathogens evolve in response to changing agricultural practices.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Distinct spread of DNA and RNA viruses among mammals amid prominent role of domestic species.

AIM: Emerging infectious diseases arising from pathogen spillover from mammals to humans constitute a substantial health threat. Tracing virus origin and predicting the most likely host species for future spillover events are major objectives in One Health disciplines.We assessed patterns of virus sharing among a large diversity of mammals, including humans and domestic species. LOCATION: Global. TIME PERIOD: Current. MAJOR TAXA STUDIED: Mammals and associated viruses. METHODS: We used network centrality analysis and trait-based Bayesian hierarchical models to explore patterns of virus sharing among mammals. We analysed a global database that compiled the associations between 1,785 virus species and 725 mammalian host species as sourced from automatic screening of meta-data accompanying published nucleotide sequences between 1950 and 2019. RESULTS: We show that based on current evidence, domesticated mammals hold the most central positions in networks of known mammal-virus associations. Among entire host-virus networks, Carnivora and Chiroptera hold central positions for mainly sharing RNA viruses, whereas ungulates hold central positions for sharing both RNA and DNA viruses with other host species. We revealed strong evidence that DNA viruses were phylogenetically more host specific than RNA viruses. RNA viruses exhibited low functional host specificity despite an overall tendency to infect phylogenetically related species, signifying high potential to shift across hosts with different ecological niches. The frequencies of sharing viruses among hosts and the proportion of zoonotic viruses in hosts were larger for RNA than for DNA viruses. MAIN CONCLUSIONS: Acknowledging the role of domestic species in addition to host and virus traits in patterns of virus sharing is necessary to improve our understanding of virus spread and spillover in times of global change. Understanding multi-host virus-sharing pathways adds focus to curtail disease spread.

Knock-on community impacts of a novel vector: spillover of emerging DWV-B from Varroa-infested honeybees to wild bumblebees.

Novel transmission routes can directly impact the evolutionary ecology of infectious diseases, with potentially dramatic effect on host populations and knock-on effects on the wider host community. The invasion of Varroa destructor, an ectoparasitic viral vector in Western honeybees, provides a unique opportunity to examine how a novel vector affects disease epidemiology in a host community. This specialist honeybee mite vectors deformed wing virus (DWV), an important re-emerging honeybee pathogen that also infects wild bumblebees. Comparing island honeybee and wild bumblebee populations with and without V. destructor, we show that V. destructor drives DWV prevalence and titre in honeybees and sympatric bumblebees. Viral genotypes are shared across hosts, with the potentially more virulent DWV-B overtaking DWV-A in prevalence in a current epidemic. This demonstrates disease emergence across a host community driven by the acquisition of a specialist novel transmission route in one host, with dramatic community level knock-on effects.

Climate variation influences host specificity in avian malaria parasites.

Parasites with low host specificity (e.g. infecting a large diversity of host species) are of special interest in disease ecology, as they are likely more capable of circumventing ecological or evolutionary barriers to infect new hosts than are specialist parasites. Yet for many parasites, host specificity is not fixed and can vary in response to environmental conditions. Using data on host associations for avian malaria parasites (Apicomplexa: Haemosporida), we develop a hierarchical model that quantifies this environmental dependency by partitioning host specificity variation into region- and parasite-level effects. Parasites were generally phylogenetic host specialists, infecting phylogenetically clustered subsets of available avian hosts. However, the magnitude of this specialisation varied biogeographically, with parasites exhibiting higher host specificity in regions with more pronounced rainfall seasonality and wetter dry seasons. Recognising the environmental dependency of parasite specialisation can provide useful leverage for improving predictions of infection risk in response to global climate change.

Geographical and host species barriers differentially affect generalist and specialist parasite community structure in a tropical sky-island archipelago.

Understanding why some parasites emerge in novel host communities while others do not has broad implications for human and wildlife health. In the case of haemosporidian blood parasites, epidemic wild bird mortalities on oceanic islands have been linked to Plasmodium spp., but not genera like Haemoproteus. Indeed, Haemoproteus is absent from many oceanic islands. By contrast, birds on continental islands share long coevolutionary histories with both Plasmodium and Haemoproteus, and are thus ideal model systems to elucidate eco-evolutionary endpoints associated with these parasites in oceanic islands. Here, we examine eco-evolutionary dynamics of avian haemosporidian in the Shola sky-island archipelago of the Western Ghats, India. Our analyses reveal that compared to Plasmodium, Haemoproteus lineages were highly host-specific and diversified via co-speciation with their hosts. We show that community structure of host-generalist Plasmodium was primarily driven by geographical factors (e.g. biogeographic barriers), while that of host-specialist Haemoproteus was driven by host species barriers (e.g. phylogenetic distance). Consequently, a few host species can harbour a high diversity of Plasmodium lineages which, in turn, are capable of infecting multiple host species. These two mechanisms can act in concert to increase the risk of introduction, establishment, and emergence of novel Plasmodium lineages in island systems.

Forest disturbance and vector transmitted diseases in the lowland tropical rainforest of central Panama.

OBJECTIVE: To explore possible changes in the community attributes of haematophagous insects as a function of forest disturbance. We compare the patterns of diversity and abundance, plus the behavioural responses of three epidemiologically distinct vector assemblages across sites depicting various levels of forest cover. METHODS: Over a 3-year period, we sampled mosquitoes, sandflies and biting-midges in forested habitats of central Panama. We placed CDC light traps in the forest canopy and in the understorey to gather blood-seeking females. RESULTS: We collected 168 405 adult haematophagous dipterans in total, including 26 genera and 86 species. Pristine forest settings were always more taxonomically diverse than the disturbed forest sites, confirming that disturbance has a negative impact on species richness. Species of Phlebotominae and Culicoides were mainly classified as climax (i.e. forest specialist) or disturbance-generalist, which tend to decrease in abundance along with rising levels of disturbance. In contrast, a significant portion of mosquito species, including primary and secondary disease vectors, was classified as colonists (i.e. disturbed-areas specialists), which tend to increase in numbers towards more disturbed forest habitats. At pristine forest, the most prevalent species of Phlebotominae and Culicoides partitioned the vertical niche by being active at the forest canopy or in the understorey; yet this pattern was less clear in disturbed habitats. Most mosquito species were not vertically stratified in their habitat preference. CONCLUSION: We posit that entomological risk and related pathogen exposure to humans is higher in pristine forest scenarios for Culicoides and Phlebotominae transmitted diseases, whereas forest disturbance poses a higher entomological risk for mosquito-borne infections. This suggests that the Dilution Effect Hypothesis (DEH) does not apply in tropical rainforests where highly abundant, yet unrecognised insect vectors and neglected zoonotic diseases occur. Comprehensive, community level entomological surveillance is, therefore, the key for predicting potential disease spill over in scenarios of pristine forest intermixed with anthropogenic habitats. We suggest that changes in forest quality should also be considered when assessing arthropod-borne disease transmission risk.

OBJECTIF: Explorer les changements possibles dans les attributs communautaires des insectes hématophages en fonction de la perturbation des forêts. Nous comparons les modèles de diversité et d'abondance, ainsi que les réponses comportementales de trois assemblages de vecteurs épidémiologiquement distincts sur des sites illustrant divers niveaux de couverture forestière. MÉTHODES: Au cours d'une période de trois ans, nous avons échantillonné des moustiques, des phlébotomes et des moucherons piqueurs dans les habitats forestiers du centre de Panama. Nous avons placé des pièges à lumière CDC dans la canopée de la forêt et dans le sous-étage pour recueillir les femelles en quête de sang. RÉSULTATS: Nous avons collecté un total de 168.405 diptères hématophages adultes, dont 26 genres et 86 espèces. Les environnements de forêt intacts étaient toujours plus diversifiés du point de vue taxonomique que les sites forestiers perturbés, confirmant que les perturbations avaient un impact négatif sur la richesse en espèces. Les espèces de phlébotome et Culicoïdes étaient principalement classés comme climax (spécialiste de la forêt) ou généralistes de perturbation, qui ont tendance à diminuer en abondance parallèlement aux niveaux croissants de perturbation. En revanche, une partie importante des espèces de moustiques, y compris les vecteurs primaires et secondaires de maladies, a été classée dans la catégorie des colons (c'est-à-dire spécialistes des zones perturbées), qui ont tendance à se multiplier vers des habitats forestiers plus perturbés. Dans la forêt vierge, les espèces de phlébotomes et Culicoïdes les plus répandues cloisonnaient la niche verticale en étant actives dans la canopée de la forêt ou dans le sous-étage; pourtant, cette tendance était moins nette dans les habitats perturbés. La plupart des espèces de moustiques n'étaient pas stratifiées verticalement dans leur préférence d'habitat. CONCLUSION: Nous estimons que le risque entomologique et l'exposition associée des agents pathogènes à l'homme est plus élevé dans les scénarios de forêt vierge pour les maladies transmises par les phlébotomes et Culicoïdes, alors que la perturbation des forêts pose un risque entomologique plus élevé pour les infections transmises par les moustiques. Cela suggère que l'hypothèse de l'effet de dilution ne s'applique pas dans les forêts tropicales humides où se reproduisent très abondamment les insectes vecteurs, mais non reconnus, et où des maladies zoonotiques négligées surviennent. Une surveillance entomologique approfondie au niveau de la communauté est donc la clé pour prédire le potentiel de propagation des maladies dans des scénarios de forêt vierge mélangée à des habitats anthropiques. Nous suggérons que les changements dans la qualité des forêts soient également pris en compte lors de l'évaluation du risque de propagation de maladies transmises par les arthropodes.

Bacterial Pathogen Emergence Requires More than Direct Contact with a Novel Passerine Host.

While direct contact may sometimes be sufficient to allow a pathogen to jump into a new host species, in other cases, fortuitously adaptive mutations that arise in the original donor host are also necessary. Viruses have been the focus of most host shift studies, so less is known about the importance of ecological versus evolutionary processes to successful bacterial host shifts. Here we tested whether direct contact with the novel host was sufficient to enable the mid-1990s jump of the bacterium Mycoplasma gallisepticum from domestic poultry to house finches (Haemorhous mexicanus). We experimentally inoculated house finches with two genetically distinct M. gallisepticum strains obtained either from poultry (Rlow) or from house finches (HF1995) during an epizootic outbreak. All 15 house finches inoculated with HF1995 became infected, whereas Rlow successfully infected 12 of 15 (80%) inoculated house finches. Comparisons among infected birds showed that, relative to HF1995, Rlow achieved substantially lower bacterial loads in the host respiratory mucosa and was cleared faster. Furthermore, Rlow-infected finches were less likely to develop clinical symptoms than HF1995-infected birds and, when they did, displayed milder conjunctivitis. The lower infection success of Rlow relative to HF1995 was not, however, due to a heightened host antibody response to Rlow. Taken together, our results indicate that contact between infected poultry and house finches was not, by itself, sufficient to explain the jump of M. gallisepticum to house finches. Instead, mutations arising in the original poultry host would have been necessary for successful pathogen emergence in the novel finch host.

Population structure of Venturia inaequalis, a causal agent of apple scab, in response to heterogeneous apple tree cultivation.

BACKGROUND: Tracking newly emergent virulent populations in agroecosystems provides an opportunity to increase our understanding of the co-evolution dynamics of pathogens and their hosts. On the one hand host plants exert selective pressure on pathogen populations, thus dividing them into subpopulations of different virulence, while on the other hand they create an opportunity for secondary contact between the two divergent populations on one tree. The main objectives of the study were to explore whether the previously reported structure between two Venturia inaequalis population types, virulent or avirulent towards Malus x domestica cultivars carrying Rvi6 gene, is maintained or broken several years after the first emergence of new virulent strains in Poland, and to investigate the relationship between 'new' and 'native' populations derived from the same commercial orchards. For this purpose, we investigated the genetic structure of populations of the apple scab fungus, occurring on apple tree cultivars containing Rvi6, Rvi1 or Rvi17 resistance gene or no resistance at all, based on microsatellite data obtained from 606 strains sampled in 10 orchards composed of various host cultivars. RESULTS: Application of genetic distance inferring and clustering methods allowed us to observe clear genetic distinctness of the populations virulent towards cultivars carrying Rvi6 gene from the Rvi6-avirulent populations and substructures within the Rvi6-group as a consequence of independent immigration events followed by rare, long-distance dispersals. We did not observe such a structuring effect of other genes determining apple scab resistance on any other populations, which in turn were genetically homogenous. However, in two orchards the co-occurrence of strains of different virulence pattern on the same trees was detected, blurring the genetic boundaries between populations. CONCLUSIONS: Among several resistance genes studied, only Rvi6 exerted selective pressure on pathogens populations: those virulent toward Rvi6 hosts show unique and clear genetic and virulence pattern. For the first time in commercial Malus x domestica orchards, we reported secondary contacts between populations virulent and avirulent toward Rvi6 hosts. These two populations, first diverged in allopatry, second came into contact and subsequently began interbreeding, in such way that they show unambiguous footprints of gene flow today.

Genomic sequencing, evolution and molecular epidemiology of rabies virus.

Advances in sequencing techniques, improved computational methods of sequence interrogation and more accurate collection of epidemiological data through Global Positioning System (GPS) technology are improving our ability to monitor rabies outbreaks and better understand the processes that affect viral spread, evolution and host restriction. Whole-genome sequencing of rabies viruses (RABVs), using a range of different methodological approaches, is becoming more widespread and permits evolutionary and epidemiological studies at an unprecedented rate. Such studies are yielding insights into the fundamental processes of viral evolution, including molecular mechanisms of host adaptation and viral emergence in novel hosts. In addition, sequence data are revealing the importance of both landscape features and anthropomorphic activities as drivers of rabies spread; knowledge that is crucial for disease control efforts. This review summarises the state of the RABV genomics field and suggests how the above-mentioned approaches can be used to further understand and develop intervention strategies for rabies in the future.

Les avancées enregistrées dans les techniques de séquençage, l'amélioration des logiciels d'interrogation des banques de séquences et la collecte plus précise de données épidémiologiques grâce aux systèmes de géolocalisation par satellite (GPS) renforcent nos capacités de surveillance des foyers de rage et nous aident à mieux comprendre les processus qui influent sur la propagation du virus, sur son évolution et sur les contraintes liées aux hôtes. Le séquençage du génome entier des virus de la rage au moyen d'approches méthodologiques diverses se généralise de plus en plus, permettant d'étudier à un rythme jamais atteint auparavant l'évolution et l'épidémiologie de ces virus. Ces études apportent de nouveaux éclairages sur les processus fondamentaux de l'évolution des virus, y compris les mécanismes moléculaires sous-jacents à l'adaptation des hôtes et à l'émergence virale chez de nouveaux hôtes. En outre, les données de séquençage mettent en lumière le rôle de l'environnement et des activités humaines sur la propagation de la rage, rôle dont la connaissance est déterminante pour lutter efficacement contre la maladie. Les auteurs font le point sur l'état des connaissances dans le domaine de la génomique des virus de la rage et proposent quelques pistes afin d'utiliser ces approches pour approfondir et développer davantage les futures stratégies d'intervention contre la rage.

Gracias al progreso de las técnicas de secuenciación, a la mejora de los métodos informáticos para estudiar las secuencias y a una obtención más exacta de datos epidemiológicos mediante la tecnología del sistema de posicionamiento mundial (GPS), hoy estamos en mejores condiciones para seguir de cerca los brotes de rabia y conocer más a fondo los procesos que inciden en la propagación y evolución del virus y en los factores de restricción de los anfitriones. La secuenciación del genoma entero de virus rábicos con muy diversos enfoques metodológicos, cada vez más extendida, permite hoy realizar estudios evolutivos y epidemiológicos a un ritmo sin precedentes. Estos estudios están arrojando luz sobre los procesos fundamentales de la evolución vírica, incluidos los mecanismos moleculares de la adaptación al anfitrión y la aparición del virus en nuevos anfitriones. Además, los datos de secuenciación están revelando la importancia de las características del paisaje y de las actividades antrópicas como factores de propagación de la rabia, un conocimiento crucial para la labor de lucha contra la enfermedad. Los autores resumen la situación de la genómica aplicada a los virus rábicos y explican cómo utilizar estos métodos para entender mejor la enfermedad y perfeccionar las estrategias de intervención contra ella en el futuro.

Expansion of spatial and host range of Puumala virus in Sweden: an increasing threat for humans?

Hantaviruses are globally distributed and cause severe human disease. Puumala hantavirus (PUUV) is the most common species in Northern Europe, and the only hantavirus confirmed to circulate in Sweden, restricted to the northern regions of the country. In this study, we aimed to further add to the natural ecology of PUUV in Sweden by investigating prevalence, and spatial and host species infection patterns. Specifically, we wanted to ascertain whether PUUV was present in the natural reservoir, the bank vole (Myodes glareolus) further south than Dalälven river, in south-central Sweden, and whether PUUV can be detected in other rodent species in addition to the natural reservoir. In total, 559 animals were collected at Grimsö (59°43'N; 15°28'E), Sala (59°55'N; 16°36'E) and Bogesund (59°24'N; 18°14'E) in south-central Sweden between May 2013 and November 2014. PUUV ELISA-reactive antibodies were found both in 2013 (22/295) and in 2014 (18/264), and nine samples were confirmed as PUUV-specific by focus reduction neutralization test. Most of the PUUV-specific samples were from the natural host, the bank vole, but also from other rodent hosts, indicating viral spill-over. Finally, we showed that PUUV is present in more highly populated central Sweden.

The Genetic Signature of Range Expansion in a Disease Vector-The Black-Legged Tick.

Monitoring and predicting the spread of emerging infectious diseases requires that we understand the mechanisms of range expansion by its vectors. Here, we examined spatial and temporal variation of genetic structure among 13 populations of the Lyme disease vector, the black-legged tick, in southern Quebec, where this tick species is currently expanding and Lyme disease is emerging. Our objective was to identify the primary mode of tick movement into Canada based on observed spatial and temporal genetic patterns. Upon genotyping 10 microsatellite loci from 613 tick specimens, we found multiple genetic signatures of frequent long-distance dispersal events, supporting the hypothesis that migratory birds are the primary carriers of black-legged ticks into southern Quebec. When we compared results from analyses of pairwise differences among ticks collected from 8 different sites at different years between 2011 and 2014, we found that genetic variation observed among tick individuals appeared to be better explained by collection year than sampling locality. This suggests that while cohorts of black-legged ticks can rapidly invade large areas across southern Quebec, they also appear to be undergoing frequent turnover. Finally, the amount of genetic variation in tick populations across our study area appeared to be related to their degree of establishment, with established populations displaying a lower amount of temporal genetic variation than adventitious ones. Given that Lyme disease infection risk in a region can be influenced by the relative presence of established and/or adventitious tick populations, our results are useful for understanding both the seasonality and spatial variation of Lyme disease.