scholarly journals Reconstructing the emergence of a lethal infectious disease of wildlife supports a key role for spread through translocations by humans

2016 ◽  
Vol 283 (1839) ◽  
pp. 20160952 ◽  
Author(s):  
Stephen J. Price ◽  
Trenton W. J. Garner ◽  
Andrew A. Cunningham ◽  
Tom E. S. Langton ◽  
Richard A. Nichols
Keyword(s):  
Phylogenetic Analyses ◽  
Control Measures ◽  
Spatial Spread ◽  
Potential Control ◽  
Temporal Models ◽  
Spatio Temporal ◽  
Using Data ◽  
Impact On Biodiversity ◽  
The Uk ◽  
Citizen Science Project

There have been few reconstructions of wildlife disease emergences, despite their extensive impact on biodiversity and human health. This is in large part attributable to the lack of structured and robust spatio-temporal datasets. We overcame logistical problems of obtaining suitable information by using data from a citizen science project and formulating spatio-temporal models of the spread of a wildlife pathogen (genus Ranavirus , infecting amphibians). We evaluated three main hypotheses for the rapid increase in disease reports in the UK: that outbreaks were being reported more frequently, that climate change had altered the interaction between hosts and a previously widespread pathogen, and that disease was emerging due to spatial spread of a novel pathogen. Our analysis characterized localized spread from nearby ponds, consistent with amphibian dispersal, but also revealed a highly significant trend for elevated rates of additional outbreaks in localities with higher human population density—pointing to human activities in also spreading the virus. Phylogenetic analyses of pathogen genomes support the inference of at least two independent introductions into the UK. Together these results point strongly to humans repeatedly translocating ranaviruses into the UK from other countries and between UK ponds, and therefore suggest potential control measures.

scholarly journals Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Science ◽  
2021 ◽  
pp. eabf2946
Author(s):  
Louis du Plessis ◽  
John T. McCrone ◽  
Alexander E. Zarebski ◽  
Verity Hill ◽  
Christopher Ruis ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Transmission Dynamics ◽  
Genetic Lineage ◽  
Size Dependent ◽  
Spatio Temporal ◽  
The Uk ◽  
Lineage Structure ◽  
And Control ◽  
Lineage Diversity

The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country’s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, while lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

scholarly journals Establishment & lineage dynamics of the SARS-CoV-2 epidemic in the UK

2020 ◽  
Author(s):  
Louis du Plessis ◽  
John T. McCrone ◽  
Alexander E. Zarebski ◽  
Verity Hill ◽  
Christopher Ruis ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Transmission Dynamics ◽  
Genetic Lineage ◽  
Size Dependent ◽  
Spatio Temporal ◽  
The Uk ◽  
Lineage Structure ◽  
And Control ◽  
Lineage Diversity

AbstractThe UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country’s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown were larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whilst lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

scholarly journals Climate drivers of plague epidemiology in British India, 1898–1949

2020 ◽  
Vol 287 (1928) ◽  
pp. 20200538
Author(s):  
Warren S. D. Tennant ◽  
Mike J. Tildesley ◽  
Simon E. F. Spencer ◽  
Matt J. Keeling
Keyword(s):  
Predictive Models ◽  
Control Measures ◽  
Climate Data ◽  
British India ◽  
Middle Income ◽  
Middle Income Countries ◽  
Complex Interactions ◽  
The World ◽  
Spatio Temporal

Plague, caused by Yersinia pestis infection, continues to threaten low- and middle-income countries throughout the world. The complex interactions between rodents and fleas with their respective environments challenge our understanding of human plague epidemiology. Historical long-term datasets of reported plague cases offer a unique opportunity to elucidate the effects of climate on plague outbreaks in detail. Here, we analyse monthly plague deaths and climate data from 25 provinces in British India from 1898 to 1949 to generate insights into the influence of temperature, rainfall and humidity on the occurrence, severity and timing of plague outbreaks. We find that moderate relative humidity levels of between 60% and 80% were strongly associated with outbreaks. Using wavelet analysis, we determine that the nationwide spread of plague was driven by changes in humidity, where, on average, a one-month delay in the onset of rising humidity translated into a one-month delay in the timing of plague outbreaks. This work can inform modern spatio-temporal predictive models for the disease and aid in the development of early-warning strategies for the deployment of prophylactic treatments and other control measures.

scholarly journals Spatio-temporal evolution and influencing mechanism of the COVID-19 epidemic in Shandong province, China

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jinlong Shi ◽  
Xing Gao ◽  
Shuyan Xue ◽  
Fengqing Li ◽  
Qifan Nie ◽  
...  
Keyword(s):  
Prevention And Control ◽  
Temporal Evolution ◽  
Geographical Location ◽  
Shandong Province ◽  
Control Measures ◽  
Middle Aged ◽  
Health Crisis ◽  
Aged People ◽  
Spatio Temporal ◽  
And Control

AbstractThe novel coronavirus pneumonia (COVID-19) outbreak that emerged in late 2019 has posed a severe threat to human health and social and economic development, and thus has become a major public health crisis affecting the world. The spread of COVID-19 in population and regions is a typical geographical process, which is worth discussing from the geographical perspective. This paper focuses on Shandong province, which has a high incidence, though the first Chinese confirmed case was reported from Hubei province. Based on the data of reported confirmed cases and the detailed information of cases collected manually, we used text analysis, mathematical statistics and spatial analysis to reveal the demographic characteristics of confirmed cases and the spatio-temporal evolution process of the epidemic, and to explore the comprehensive mechanism of epidemic evolution and prevention and control. The results show that: (1) the incidence rate of COVID-19 in Shandong is 0.76/100,000. The majority of confirmed cases are old and middle-aged people who are infected by the intra-province diffusion, followed by young and middle-aged people who are infected outside the province. (2) Up to February 5, the number of daily confirmed cases shows a trend of “rapid increase before slowing down”, among which, the changes of age and gender are closely related to population migration, epidemic characteristics and intervention measures. (3) Affected by the regional economy and population, the spatial distribution of the confirmed cases is obviously unbalanced, with the cluster pattern of “high–low” and “low–high”. (4) The evolution of the migration pattern, affected by the geographical location of Wuhan and Chinese traditional culture, is dominated by “cross-provincial” and “intra-provincial” direct flow, and generally shows the trend of “southwest → northeast”. Finally, combined with the targeted countermeasures of “source-flow-sink”, the comprehensive mechanism of COVID-19 epidemic evolution and prevention and control in Shandong is revealed. External and internal prevention and control measures are also figured out.

scholarly journals Pyramidal Framework: Guidance for the Next Generation of GIS Spatial-Temporal Models

2021 ◽  
Vol 10 (3) ◽  
pp. 188
Author(s):  
Cyril Carré ◽  
Younes Hamdani
Keyword(s):  
Conceptual Models ◽  
Future Generations ◽  
Temporal Data ◽  
Temporal Modeling ◽  
Temporal Models ◽  
Gis Data ◽  
Spatio Temporal ◽  
New Interpretation ◽  
Conventional Literature

Over the last decade, innovative computer technologies and the multiplication of geospatial data acquisition solutions have transformed the geographic information systems (GIS) landscape and opened up new opportunities to close the gap between GIS and the dynamics of geographic phenomena. There is a demand to further develop spatio-temporal conceptual models to comprehensively represent the nature of the evolution of geographic objects. The latter involves a set of considerations like those related to managing changes and object identities, modeling possible causal relations, and integrating multiple interpretations. While conventional literature generally presents these concepts separately and rarely approaches them from a holistic perspective, they are in fact interrelated. Therefore, we believe that the semantics of modeling would be improved by considering these concepts jointly. In this work, we propose to represent these interrelationships in the form of a hierarchical pyramidal framework and to further explore this set of concepts. The objective of this framework is to provide a guideline to orient the design of future generations of GIS data models, enabling them to achieve a better representation of available spatio-temporal data. In addition, this framework aims at providing keys for a new interpretation and classification of spatio-temporal conceptual models. This work can be beneficial for researchers, students, and developers interested in advanced spatio-temporal modeling.

scholarly journals Validation of the BATT score for prehospital risk stratification of traumatic haemorrhagic death: usefulness for tranexamic acid treatment criteria

2021 ◽  
Vol 29 (1) ◽  
Author(s):  
Francois-Xavier Ageron ◽  
Timothy J. Coats ◽  
Vincent Darioli ◽  
Ian Roberts
Keyword(s):  
Tranexamic Acid ◽  
Acid Treatment ◽  
Injury Severity ◽  
External Validation ◽  
Research Network ◽  
Brier Score ◽  
Trauma Patients ◽  
Using Data ◽  
The Uk ◽  
The Impact

Abstract Background Tranexamic acid reduces surgical blood loss and reduces deaths from bleeding in trauma patients. Tranexamic acid must be given urgently, preferably by paramedics at the scene of the injury or in the ambulance. We developed a simple score (Bleeding Audit Triage Trauma score) to predict death from bleeding. Methods We conducted an external validation of the BATT score using data from the UK Trauma Audit Research Network (TARN) from 1st January 2017 to 31st December 2018. We evaluated the impact of tranexamic acid treatment thresholds in trauma patients. Results We included 104,862 trauma patients with an injury severity score of 9 or above. Tranexamic acid was administered to 9915 (9%) patients. Of these 5185 (52%) received prehospital tranexamic acid. The BATT score had good accuracy (Brier score = 6%) and good discrimination (C-statistic 0.90; 95% CI 0.89–0.91). Calibration in the large showed no substantial difference between predicted and observed death due to bleeding (1.15% versus 1.16%, P = 0.81). Pre-hospital tranexamic acid treatment of trauma patients with a BATT score of 2 or more would avoid 210 bleeding deaths by treating 61,598 patients instead of avoiding 55 deaths by treating 9915 as currently. Conclusion The BATT score identifies trauma patient at risk of significant haemorrhage. A score of 2 or more would be an appropriate threshold for pre-hospital tranexamic acid treatment.

scholarly journals Lockdown, slow down: impact of the COVID-19 pandemic on physical activity—an observational study

Open Heart ◽  
2021 ◽  
Vol 8 (1) ◽  
pp. e001600
Author(s):  
Joanne Kathryn Taylor ◽  
Haarith Ndiaye ◽  
Matthew Daniels ◽  
Fozia Ahmed
Keyword(s):  
Physical Activity ◽  
New York ◽  
Heart Association ◽  
Evaluation Study ◽  
Activity Data ◽  
Cardiac Devices ◽  
Significant Difference ◽  
New York Heart Association ◽  
Using Data ◽  
The Uk

AimsIn response to the COVID-19 pandemic, the UK was placed under strict lockdown measures on 23 March 2020. The aim of this study was to quantify the effects on physical activity (PA) levels using data from the prospective Triage-HF Plus Evaluation study.MethodsThis study represents a cohort of adult patients with implanted cardiac devices capable of measuring activity by embedded accelerometery via a remote monitoring platform. Activity data were available for the 4 weeks pre-implementation and post implementation of ‘stay at home’ lockdown measures in the form of ‘minutes active per day’ (min/day).ResultsData were analysed for 311 patients (77.2% men, mean age 68.8, frailty 55.9%. 92.2% established heart failure (HF) diagnosis, of these 51.2% New York Heart Association II), with comorbidities representative of a real-world cohort.Post-lockdown, a significant reduction in median PA equating to 20.8 active min/day was seen. The reduction was uniform with a slightly more pronounced drop in PA for women, but no statistically significant difference with respect to age, body mass index, frailty or device type. Activity dropped in the immediate 2-week period post-lockdown, but steadily returned thereafter. Median activity week 4 weeks post-lockdown remained significantly lower than 4 weeks pre-lockdown (p≤0.001).ConclusionsIn a population of predominantly HF patients with cardiac devices, activity reduced by approximately 20 min active per day in the immediate aftermath of strict COVID-19 lockdown measures.Trial registration numberNCT04177199.

scholarly journals The genetic architecture of structural left–right asymmetry of the human brain

2021 ◽  
Author(s):  
Zhiqiang Sha ◽  
Dick Schijven ◽  
Amaia Carrion-Castillo ◽  
Marc Joliot ◽  
Bernard Mazoyer ◽  
...  
Keyword(s):  
Brain Asymmetry ◽  
Functional Enrichment ◽  
Brain Organization ◽  
Genome Wide ◽  
Brain Expression ◽  
Using Data ◽  
Left Right Asymmetry ◽  
The Uk ◽  
Subcortical Volume

AbstractLeft–right hemispheric asymmetry is an important aspect of healthy brain organization for many functions including language, and it can be altered in cognitive and psychiatric disorders. No mechanism has yet been identified for establishing the human brain’s left–right axis. We performed multivariate genome-wide association scanning of cortical regional surface area and thickness asymmetries, and subcortical volume asymmetries, using data from 32,256 participants from the UK Biobank. There were 21 significant loci associated with different aspects of brain asymmetry, with functional enrichment involving microtubule-related genes and embryonic brain expression. These findings are consistent with a known role of the cytoskeleton in left–right axis determination in other organs of invertebrates and frogs. Genetic variants associated with brain asymmetry overlapped with those associated with autism, educational attainment and schizophrenia. Comparably large datasets will likely be required in future studies, to replicate and further clarify the associations of microtubule-related genes with variation in brain asymmetry, behavioural and psychiatric traits.

scholarly journals Controlling the Spatial Spread of a Xylella Epidemic

2021 ◽  
Vol 83 (4) ◽  
Author(s):  
Sebastian Aniţa ◽  
Vincenzo Capasso ◽  
Simone Scacchi
Keyword(s):  
Spatial Structure ◽  
Numerical Simulations ◽  
Control Strategies ◽  
Xylella Fastidiosa ◽  
Cost Effective ◽  
Olive Tree ◽  
Control Measures ◽  
Weed Biomass ◽  
Spatial Spread ◽  
Olive Trees

AbstractIn a recent paper by one of the authors and collaborators, motivated by the Olive Quick Decline Syndrome (OQDS) outbreak, which has been ongoing in Southern Italy since 2013, a simple epidemiological model describing this epidemic was presented. Beside the bacterium Xylella fastidiosa, the main players considered in the model are its insect vectors, Philaenus spumarius, and the host plants (olive trees and weeds) of the insects and of the bacterium. The model was based on a system of ordinary differential equations, the analysis of which provided interesting results about possible equilibria of the epidemic system and guidelines for its numerical simulations. Although the model presented there was mathematically rather simplified, its analysis has highlighted threshold parameters that could be the target of control strategies within an integrated pest management framework, not requiring the removal of the productive resource represented by the olive trees. Indeed, numerical simulations support the outcomes of the mathematical analysis, according to which the removal of a suitable amount of weed biomass (reservoir of Xylella fastidiosa) from olive orchards and surrounding areas resulted in the most efficient strategy to control the spread of the OQDS. In addition, as expected, the adoption of more resistant olive tree cultivars has been shown to be a good strategy, though less cost-effective, in controlling the pathogen. In this paper for a more realistic description and a clearer interpretation of the proposed control measures, a spatial structure of the epidemic system has been included, but, in order to keep mathematical technicalities to a minimum, only two players have been described in a dynamical way, trees and insects, while the weed biomass is taken to be a given quantity. The control measures have been introduced only on a subregion of the whole habitat, in order to contain costs of intervention. We show that such a practice can lead to the eradication of an epidemic outbreak. Numerical simulations confirm both the results of the previous paper and the theoretical results of the model with a spatial structure, though subject to regional control only.

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