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44 results for “disease outbreak”
How does parasite environmental transmission stage concentration change before, during, and after disease outbreaks?
<p>Outbreaks of environmentally transmitted parasites require that susceptible hosts encounter transmission stages in the environment and become infected, but we also know that transmission stages can be in the environment without triggering disease outbreaks. One challenge for understanding the relationship between environmental transmission stages and disease outbreaks is that the distribution and abundance of transmission stages outside of their hosts have been difficult to quantify. Thus, we have limited data about how changes in transmission stage abundance influence disease dynamics; moreover, we do not know whether the relationship between transmission stages and outbreaks differs among parasite species. We used digital PCR to quantify environmental transmission stages of five parasites in six lakes in southeastern Michigan every two weeks from June to November 2021. At the same time, we quantified infection prevalence in hosts and host density. Our study focused on eight zooplankton host species (<em>Daphnia</em> spp. and <em>Ceriodaphnia</em> <em>dubia</em>) and five of their parasites from diverse taxonomic groups (bacteria, yeast, microsporidia, and oomycete) with different infection mechanisms. We found that parasite transmission stage concentration increased prior to disease outbreaks for all parasites. However, parasites differed significantly in the relative timing of peaks in transmission stage concentration and infection outbreaks. The 'continuous shedder' parasites had transmission stage peaks at the same time as or slightly after the outbreak peaks. In contrast, parasites relying on host death for transmission ('obligate killers') had transmission stage peaks before outbreak peaks. For most parasites, lakes with outbreaks had higher spore concentrations than those without outbreaks, especially once an outbreak began; the exception was for a parasite, <em>Pasteuria</em> <em>ramosa</em>, with very strong genotypic specificity of infection. Overall, our results show that disease outbreaks are tightly linked to transmission stage concentration; outbreaks were preceded by increases in transmission stage concentration in the environment and then were fueled by the production of more transmission stages during the outbreak itself, with concentrations decreasing to pre-outbreak levels as outbreaks waned. Thus, tracking transmission stages in the environment improves our understanding of the drivers of disease outbreaks and reveals how parasite traits may affect these dynamics.</p>
Supplementary Material: Climate-sensitive disease outbreaks in the aftermath of extreme climatic events: a scoping review
<p><strong>Supplemental experimental procedures</strong></p> <p><em>General Information</em></p> <p>Here we provide the data extraction of the studies retrieved for the scoping review "Climate-sensitive disease outbreaks in the aftermath of extreme climatic events" following PRISMA-ScR guidelines. Data were extracted for the following variables: title, first author, year of publication, country/region studied, extreme climate event, extreme climate event name (tropical cyclones are often named e.g. Typhoon Haiyan), Index used to measure climate anomaly, extreme climate event definition, text description of extreme climate event, disease, outbreak definition, time period of the study, data source, baseline/reference period, study design, statistics, outcome, outcome quantification, outbreak risk, qualitative description of extreme climate event and outbreak risk, time lag. Outcome was defined as either disease cases or incidence. </p>
Mysterious microsporidians: springtime outbreaks of disease in Daphnia communities in shallow pond ecosystems
<p>Parasites can play key roles in ecosystems, especially when they infect common hosts that play important ecological roles. <em>Daphnia</em> are critical grazers in many lentic freshwater ecosystems and typically reach peak densities in early spring. <em>Daphnia</em> have also become prominent model host organisms for the field of disease ecology, although most well-studied parasites infect them in summer or fall. Here, we report field patterns of virulent microsporidian parasites that consistently infect <em>Daphnia</em> in springtime, in a set of seven shallow ponds in Georgia, USA, sampled every 3–4 weeks for 18 months. We detected two distinct parasite taxa, closely matching sequences of <em>Pseudoberwaldia</em> <em>daphniae</em> and <em>Conglomerata</em> <em>obtusa</em>, both infecting all three resident species of <em>Daphnia</em>: <em>D. ambigua, D. laevis, </em>and<em> D. parvula</em>. To our knowledge, neither parasite has been previously reported in any of these host species or anywhere in North America. Infection prevalence peaked consistently in February-May, but the severity of these outbreaks differed substantially among ponds. Moreover, host species differed markedly in terms of their maximum infection prevalence (5% [<em>D. parvula</em>] to 72% [<em>D. laevis</em>]), mean reduction of fecundity when infected (70.6% [<em>D. ambigua</em>] to 99.8% [<em>D. laevis</em>]), mean spore yield (62,000 [<em>D. parvula</em>] to 377,000 [<em>D. laevis</em>] per host), and likelihood of being infected by each parasite. The timing and severity of the outbreaks suggest that these parasites could be impactful members of these shallow freshwater ecosystems and that the strength of their effects is likely to hinge on the composition of ponds' zooplankton communities.</p>
Data and code for: Disease outbreaks select for mate choice and coat color in wolves
<p><span>We know much about pathogen evolution and the emergence of new disease strains but less about host resistance and how it is signaled to other individuals and subsequently maintained. The cline in frequency of black-coated wolves across North America is hypothesized to result from a relationship with canine distemper virus (CDV) outbreaks. We test this hypothesis using cross-sectional data from wolf populations across North America that vary in the prevalence of CDV and the allele that makes coats black, longitudinal data from Yellowstone National Park, and modeling. The frequency of CDV outbreaks generates fluctuating selection that results in heterozygote advantage that in turn impacts the frequency of the black allele, the optimal mating behavior, and the black wolf cline across the continent.</span></p>
Data and code for: Disease outbreaks select for mate choice and coat color in wolves
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Indirect pathogen transmission underlies an emerging infectious fungal disease outbreak in a wild reptile population
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How does parasite environmental transmission stage concentration change before, during, and after disease outbreaks?
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Mysterious microsporidians: springtime outbreaks of disease in Daphnia communities in shallow pond ecosystems
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Source code and datasets used to link new waves of plague outbreaks in medieval Europe to climate fluctuations affecting the reservoirs of the disease in Asia.
<p>The zipfile contains the project directory which includes the source code and datasets used in the paper on <strong>Climate-driven introduction of the Black Death and successive plague reintroductions into Europe</strong>, as published in <em>Proceedings of the National Academy of Sciences</em> (PNAS). Access the paper at http://www.doi.org/pnas.1412887112</p> <p>If you are not familiar with Clojure, Leiningen, and its project directory format, see http://clojure.org/getting_started for one of the IDE's to run the clojure code in, and use http://leiningen.org/ as the project / dependency manager.</p>
Data from: Cascading effects of a disease outbreak in a remote protected area
<p>Disease outbreaks induced by humans increasingly threaten wildlife communities worldwide. Like predators, pathogens can be key top-down forces in ecosystems, initiating trophic cascades that may alter food webs. An outbreak of mange in a remote Andean protected area caused a dramatic population decline in a mammalian herbivore (the vicuña), creating conditions to test the cascading effects of disease on the ecological community. By comparing a suite of ecological measurements to pre-disease baseline records, we demonstrate that mange restructured tightly-linked trophic interactions previously driven by a mammalian predator (the puma). Following the mange outbreak, scavenger (Andean condor) occurrence in the ecosystem declined sharply and plant biomass and cover increased dramatically in predation refuges where herbivory was historically concentrated. The evidence shows that a disease-induced trophic cascade, mediated by vicuña density, could supplant the predator-induced trophic cascade, mediated by vicuña behavior, thereby transforming the Andean ecosystem. </p>
Data from: Comparing the efficacy of control strategies for infectious disease outbreaks using field and simulation studies
<p>Diseases characterized by long distance inoculum dispersal (LDD) are among the fastest spreading epidemics in both natural and managed landscapes. Management of such epidemics is extremely challenging because of asymptomatic infection extending at large spatial scales and frequent escape from the newly established disease sources. We compared the efficacy of area- and timing-based disease management strategies in artificially initiated field epidemics of wheat stripe rust and complemented with simulations from an updated version of the spatially explicit model EPIMUL, using model parameters relevant to field epidemics. The model was further used to expand the number of epidemic mitigations beyond that feasible to incorporate in the field. The field experiment was conducted for two years in two locations having different climatic conditions. Culling and protection treatments were applied at different times after epidemic initiation and to different spatial extents surrounding the outbreaks. In each experiment, treatments were replicated four times in plots 33.5 m long and 1.52 m wide with a 0.76 x 0.76 m inoculated focus centered within each plot. Disease gradients were assessed along the center lines of the plots at 1.52 m intervals both upwind and downwind from the focus. Both field and simulation results indicated that control measures applied over the entire population were highly effective in suppressing the epidemics by more than 99% but may not always be logistically and economically feasible at large spatial scales. Comparison between the variable sized treatment areas and application timings suggested that implementing contiguous premises (CP) cull at 1 day after first sporulation in the outbreak focus reduced rust by 52 and 60% in Corvallis and Madras, respectively. However, altering the cull size did not significantly affect the disease epidemic development, which suggested that early timing had a greater influence in suppressing the epidemics than did increased area of application. However, sufficiently large, treated areas may compensate for a delay in application timing to some extent. Results from these replicated treatments may help to devise appropriate management strategies for other LDD pathogens. </p>
Mechanical transmission of Dengue Virus by Aedes aegypti may influence disease transmission dynamics during outbreaks data
<strong><span>Summary</span></strong> <p class="MsoNormal"><em><span>Background</span></em><span>: Dengue virus outbreaks are increasing in number and severity worldwide. Viral transmission is assumed to require a minimum time period of viral replication within the mosquito midgut. It is unknown if alternative transmission periods not requiring replication are possible.</span></p> <p class="MsoNormal"><em><span>Methods</span></em><span>: We used a mouse model of dengue virus transmission to investigate the potential of mechanical transmission of dengue virus. We investigated minimal viral titres necessary for development of symptoms in bitten mice and used resulting parameters to inform a new model of dengue virus transmission within a susceptible population.</span></p> <p class="MsoNormal"><em><span>Findings</span></em><span>: Naïve mice bitten by mosquitoes immediately after they took partial blood meals from dengue infected mice showed symptoms of dengue virus, followed by mortality. Incorporation of mechanical transmission into mathematical models of dengue virus transmission suggests that this supplemental transmission route could result in larger outbreaks which peak sooner.</span></p> <p class="MsoNormal"><em><span>Interpretation</span></em><span>: The potential of dengue transmission routes independent of midgut viral replication has implications for vector control strategies that target mosquito lifespan and suggest the possibility of similar mechanical transmission routes in other disease-carrying mosquitoes.</span></p>
Mechanical transmission of Dengue Virus by Aedes aegypti may influence disease transmission dynamics during outbreaks data
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Data from: El Niño drives a widespread ulcerative skin disease outbreak in Galapagos marine fishes
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Data from: Cascading effects of a disease outbreak in a remote protected area
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Data from: Comparing the efficacy of control strategies for infectious disease outbreaks using field and simulation studies
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History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses. According to the current international classification of diseases49, MERS and SARS are classified as 1D64 and 1D65, respectively. in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses. According to the current international classification of diseases49, MERS and SARS are classified as 1D64 and 1D65, respectively.
Data and code for changes in contact patterns shape the dynamics of the novel coronavirus disease 2019 outbreak in China
<p>Data and code for the paper "changes in contact patterns shape the dynamics of the novel coronavirus disease 2019 outbreak in China" published in Science.</p>
Impact of coronavirus disease 2019 (COVID-19) outbreak on radiology research: an Italian survey
<p>This article reports the results of a national survey, which had the purpose of understanding how COVID-19 pandemic has changed the scientific activity of Italian radiology researchers. A total of 327 Italian radiologists took part in the survey (mean age: 49±12 years). The majority of participants (245/327, 74.9%) was not working for or in agreement with a University and most of them were hospital staff radiologists (222/327, 67.9%). More than two-thirds of surveyed radiologists (231/327, 71%) was working in a public institution, which mostly was a general hospital (188/327, 57.5%); 86/327 (26.3%) participants declared to work in a university hospital. After national lockdown, the working-flow came back to normal in the vast majority of cases (285/327, 87.2%). Participants reported that a total of 462 radiological trials were recruiting patients at their institutions prior to COVID-19 outbreak, of which 332 (71.9%) were stopped during the emergency. On the other hand, 252 radiological trials have been started during the pandemic, of which 156 were non-COVID-19 trials (61.9%) and 96 were focused on COVID-19 patients (38.2%). Participants reported a significant increase of the number of hours per week spent for research purposes during national lockdown (mean 4.5±8.9 hours during lockdown vs. 3.3±6.8 hours before lockdown; p=.046), followed by a significant drop after lockdown (3.2±6.5 hours per week, p=.035). Notably, 60% of participants reported that they do not spend any time on research. During national lockdown, 15.6% of participants started new review articles and completed old papers, 14.1% completed old works, and 8.9% started new review articles. Ninety-six surveyed radiologists (29.3%) declared to have submitted at least one article during COVID-19 emergency. This study confirms the need to be prepared to future challenging scenarios like COVID-19 emergency in order to support radiology researchers, thereby allowing them to push forward their activity.</p>
Data from: Infection dynamics, dispersal, and adaptation: understanding the lack of recovery in a remnant frog population following a disease outbreak
Emerging infectious diseases can cause dramatic declines in wildlife populations. Sometimes these declines are followed by recovery, but many populations do not recover. Studying differential recovery patterns may yield important information for managing disease-afflicted populations and facilitating population recoveries. In the late1980s, a chytridiomycosis outbreak caused multiple frog species in Australia's Wet Tropics to decline. Populations of some species (e.g., Litoria nannotis) subsequently recovered, while others (e.g., Litoria dayi) did not. We examined the population genetics and current infection status of L. dayi, to test several hypotheses regarding the failure of its populations to recover: 1) a lack of individual dispersal abilities has prevented recolonization of previously occupied locations, 2) a loss of genetic variation has resulted in limited adaptive potential, and 3) L. dayi is currently adapting to chytridiomycosis. We found moderate to hig h levels of gene flow and diversity (Fst range: <0.01–0.15; minor allele frequency: 0.192–0.245), which were similar to previously published levels for recovered L. nannotis populations. This suggests that dispersal ability and genetic diversity do not limit the ability of L dayi to recolonize upland sites. Further, infection intensity and prevalence increased with elevation, suggesting that chytridiomycosis is still limiting the elevational range of L. dayi. Outlier tests comparing infected and uninfected individuals consistently identified 18 markers as putatively under selection, and several of those markers matched genes that were previously implicated in infection. This suggests that L. dayi has genetic variation for genes that affect infection dynamics and may be undergoing adaptation.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.