scholarly journals Bayesian Estimation of real-time Epidemic Growth Rates using Gaussian Processes: local dynamics of SARS-CoV-2 in England

2022 ◽  
Author(s):  
Laura Marcela Guzman Rincon ◽  
Edward M Hill ◽  
Louise Dyson ◽  
Michael J Tildesley ◽  
Matt J Keeling
Keyword(s):  
Regional Growth ◽  
Epidemiological Data ◽  
Control Measures ◽  
Reproductive Number ◽  
Bayesian Hierarchical ◽  
Spatio Temporal ◽  
Epidemiological Trends ◽  
Near Future ◽  
Quantitative Assessments

Quantitative assessments of the recent state of an epidemic and short-term projections into the near future are key public health tools that have substantial policy impacts, helping to determine if existing control measures are sufficient or need to be strengthened. Key to these quantitative assessments is the ability to rapidly and robustly measure the speed with which the epidemic is growing or decaying. Frequently, epidemiological trends are addressed in terms of the (time-varying) reproductive number R. Here, we take a more parsimonious approach and calculate the exponential growth rate, r, using a Bayesian hierarchical model to fit a Gaussian process to the epidemiological data. We show how the method can be employed when only case data from positive tests are available, and the improvement gained by including the total number of tests as a measure of heterogeneous testing effort. Although the methods are generic, we apply them to SARS-CoV-2 cases and testing in England, making use of the available high-resolution spatio-temporal data to determine long-term patterns of national growth, highlight regional growth and spatial heterogeneity.

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 Assessing the Spatial and Spatio-Temporal Distribution of Forest Species via Bayesian Hierarchical Modeling

Forests ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 573 ◽  
Author(s):  
Óscar Rodríguez de Rivera ◽  
Antonio López-Quílez ◽  
Marta Blangiardo
Keyword(s):  
Hierarchical Modeling ◽  
Temporal Distribution ◽  
Short Term ◽  
Distribution Models ◽  
Address Climate Change ◽  
Bayesian Hierarchical ◽  
Temporal Models ◽  
Spatio Temporal ◽  
The Relationship

Climatic change is expected to affect forest development in the short term, as well as the spatial distribution of species in the long term. Species distribution models are potentially useful tools for guiding species choices in reforestation and forest management prescriptions to address climate change. The aim of this study is to build spatial and spatio-temporal models to predict the distribution of four different species present in the Spanish Forest Inventory. We have compared the different models and showed how accounting for dependencies in space and time affect the relationship between species and environmental variables.

scholarly journals 1249Trends and disparities in adult body mass index across 47 prefectures in Japan, 1975–2018

2021 ◽  
Vol 50 (Supplement_1) ◽  
Author(s):  
Nayu Ikeda ◽  
Tomoki Nakaya ◽  
James Bennett ◽  
Majid Ezzati ◽  
Nobuo Nishi
Keyword(s):  
Body Mass Index ◽  
Body Mass ◽  
Temporal Trends ◽  
Poor Performance ◽  
Bayesian Hierarchical ◽  
Adult Body Mass ◽  
Adult Body ◽  
Adult Body Mass Index ◽  
Spatio Temporal

Abstract Background Consistent and comparable health information across prefectures is necessary for monitoring progress in improving population health and reducing geographic health disparities in Japan. We aimed to examine long-term trends and variations in adult body mass index (BMI) by prefecture. Methods We obtained a total sample of 233,988 males and 261,086 females aged 20–79 years with anthropometric measurements from National Health and Nutrition Surveys conducted annually during 1975–2018. We applied a spatio-temporal Bayesian hierarchical model to estimate the annual time series of prefectural mean BMI by 20-year age group and sex. Results Prefectural mean BMI consistently increased in males regardless of age but decreased in younger females. It increased in older females until starting to decrease in the early 2000s. Mean BMI was noticeably higher in Okinawa, the southernmost prefecture, than in other prefectures from 1975 in males and from the 1990s in females. The interquartile range of mean BMI across prefectures was consistently higher in females than in males. It decreased over time to plateau during the 2000s in both sexes. Conclusions Mean BMI increased in males across prefectures and there is a need for stimulating a further reduction in geographic disparities particularly for females. Okinawa once ranked first in longevity but has shown relatively poor performance in recent years, which may be partly attributable to the distinctive trends in adult BMI. Key messages Bayesian hierarchical modelling is useful for reconstructing long-term spatio-temporal trends of mean BMI by integrating small-size survey samples.

scholarly journals The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing

2020 ◽  
Author(s):  
Joilson Xavier ◽  
Marta Giovanetti ◽  
Talita Adelino ◽  
Vagner Fonseca ◽  
Alana Vitor Barbosa da Costa ◽  
...  
Keyword(s):  
Epidemiological Data ◽  
Minas Gerais ◽  
Reproductive Number ◽  
Viral Pathogens ◽  
Transmission Potential ◽  
First Case ◽  
Recent Emergence ◽  
Rapid Dissemination ◽  
Genome Analyses ◽  
Near Future

AbstractThe recent emergence of a previously unknown coronavirus (SARS-CoV-2), first confirmed in the city of Wuhan in China in December 2019, has caused serious public health and economic issues due to its rapid dissemination worldwide. Although 61,888 confirmed cases had been reported in Brazil by 28 April 2020, little was known about the SARS-CoV-2 epidemic in the country. To better understand the recent epidemic in the second most populous state in southeast Brazil (Minas Gerais, MG), we looked at existing epidemiological data from 3 states and sequenced 40 complete genomes from MG cases using Nanopore. We found evidence of multiple independent introductions from outside MG, both from genome analyses and the overly dispersed distribution of reported cases and deaths. Epidemiological estimates of the reproductive number using different data sources and theoretical assumptions all suggest a reduction in transmission potential since the first reported case, but potential for sustained transmission in the near future. The estimated date of introduction in Brazil was consistent with epidemiological data from the first case of a returning-traveler from Lombardy, Italy. These findings highlight the unique reality of MG’s epidemic and reinforce the need for real-time and continued genomic surveillance strategies as a way of understanding and therefore preparing against the epidemic spread of emerging viral pathogens.

scholarly journals Living with COVID-19: The road ahead

2021 ◽  
Vol 50 (8) ◽  
pp. 619-628
Author(s):  
Wycliffe Enli Wei ◽  
Wei Keat Tan ◽  
Alex Richard Cook ◽  
Li Yang Hsu ◽  
Yik Ying Teo ◽  
...  
Keyword(s):  
Epidemiological Data ◽  
Control Measures ◽  
Pandemic Preparedness ◽  
The Road ◽  
Mild Disease ◽  
The World ◽  
Response Measures ◽  
Pharmaceutical Interventions ◽  
Endemic State

ABSTRACT Introduction: The COVID-19 pandemic has affected the world for more than a year, with multiple waves of infections resulting in morbidity, mortality and disruption to the economy and society. Response measures employed to control it have generally been effective but are unlikely to be sustainable over the long term. Methods: We examined the evidence for a vaccine-driven COVID-19 exit strategy including academic papers, governmental reports and epidemiological data, and discuss the shift from the current pandemic footing to an endemic approach similar to influenza and other re spiratory infectious diseases. Results: A desired endemic state is characterised by a baseline prevalence of infections with a generally mild disease profile that can be sustainably managed by the healthcare system, together with the resumption of near normalcy in human activities. Such an endemic state is attainable for COVID-19 given the promising data around vaccine efficacy, although uncertainty remains around vaccine immunity escape in emergent variants of concern. Maintenance of non-pharmaceutical interventions remains crucial until high vaccination coverage is attained to avoid runaway outbreaks. It may also be worthwhile to de-escalate measures in phases, before standing down most measures for an endemic state. If a variant that substantially evades immunity emerges, it will need to be managed akin to a new disease threat, with pandemic preparedness and response plans. Conclusion: An endemic state for COVID-19, characterised by sustainable disease control measures, is likely attainable through vaccination. Keywords: COVID-19, endemic, non-pharmaceutical interventions, transition, vaccination

scholarly journals The coverage and frequency of mass drug administration required to eliminate persistent transmission of soil-transmitted helminths

2014 ◽  
Vol 369 (1645) ◽  
pp. 20130435 ◽  
Author(s):  
Roy Anderson ◽  
James Truscott ◽  
T. Deirdre Hollingsworth
Keyword(s):  
Drug Administration ◽  
Mass Drug Administration ◽  
Cost Effective ◽  
Epidemiological Data ◽  
Basic Reproductive Number ◽  
Reproductive Number ◽  
Soil Transmitted Helminths ◽  
School Aged Children ◽  
Helminth Infections

A combination of methods, including mathematical model construction, demographic plus epidemiological data analysis and parameter estimation, are used to examine whether mass drug administration (MDA) alone can eliminate the transmission of soil-transmitted helminths (STHs). Numerical analyses suggest that in all but low transmission settings (as defined by the magnitude of the basic reproductive number, R 0 ), the treatment of pre-school-aged children (pre-SAC) and school-aged children (SAC) is unlikely to drive transmission to a level where the parasites cannot persist. High levels of coverage (defined as the fraction of an age group effectively treated) are required in pre-SAC, SAC and adults, if MDA is to drive the parasite below the breakpoint under which transmission is eliminated. Long-term solutions to controlling helminth infections lie in concomitantly improving the quality of the water supply, sanitation and hygiene (WASH). MDA, however, is a very cost-effective tool in long-term control given that most drugs are donated free by the pharmaceutical industry for poor regions of the world. WASH interventions, by lowering the basic reproductive number, can facilitate the ability of MDA to interrupt transmission.

scholarly journals Regional COVID-19 spread despite expected declines: how mitigation is hindered by spatio-temporal variation in local control measures.

2020 ◽  
Author(s):  
Nicholas Kortessis ◽  
Margaret W Simon ◽  
Michael Barfield ◽  
Gregory Glass ◽  
Burton H Singer ◽  
...  
Keyword(s):  
Sir Model ◽  
Local Information ◽  
Mitigation Strategies ◽  
Control Measures ◽  
Infectious Individual ◽  
Parrondo’S Paradox ◽  
Targeted Testing ◽  
Spatio Temporal ◽  
Two Populations

Successful public health regimes for COVID-19 push below unity long-term global Rt -- the average number of secondary cases caused by an infectious individual. Most assessments use local information. Populations differ in Rt, amongst themselves and over time. We use a SIR model for two populations to make the conceptual point that even if each locality averages Rt < 1, the overall epidemic can still grow, provided these populations have asynchronous variation in transmission, and are coupled by movement of infectious individuals. This emergent effect in pandemic dynamics instantiates "Parrondo's Paradox," -- an entity comprised of distinct but interacting units can behave qualitatively differently than each part on its own. For effective COVID-19 disease mitigation strategies, it is critical that infectious individuals moving among locations be identified and quarantined. This does not warrant indiscriminate prevention of movement, but rather rational, targeted testing and national coordination.

Demographic gaps between Syrian and the European populations: What do they suggest?

2017 ◽  
Vol 7 (2) ◽  
pp. 207-230 ◽  
Author(s):  
Mustafa Murat Yucesahin ◽  
Ibrahim Sirkeci
Keyword(s):  
Transition Theory ◽  
World Population ◽  
Demographic Analysis ◽  
Demographic Differences ◽  
Syrian Crisis ◽  
The United Kingdom ◽  
Syrian Population ◽  
Displaced People ◽  
Near Future

Syrian crisis resulted in at least 6.1 million externally displaced people 983,876 of whom are in Europe while the rest are in neighbouring countries in the region. Turkey, due to its geographical proximity and substantial land borders with the country, has been the most popular destination for those fleeing Syria since April 2011. Especially after 2012, a sharp increase in the number of Syrian refugees arriving in Turkey was witnessed. This has triggered an exponential growth in academic and public interest in Syrian population. Numerous reports mostly based on non-representative sample surveys have been disseminated whilst authoritative robust analyses remained absent. This study aims to fill this gap by offering a comprehensive demographic analysis of the Syrian population. We focus on the demographic differences (from 1950s to 2015) and demographic trends (from 2015 to 2100) in medium to long term, based on data from World Population Prospects (WPP). We offer a comparative picture to underline potential changes and convergences between populations in Syria, Turkey, Germany, and the United Kingdom. We frame our discussion here with reference to the demographic transition theory to help understanding the implications for movers and non-movers in receiving countries in the near future.

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