A lesson learned from the MERS epidemic in Korea: an essay on MERS.
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ABSTRACT:
SUBMITTER: Meng KH
PROVIDER: S-EPMC4546989 | biostudies-literature | 2015
REPOSITORIES: biostudies-literature
Publications
A lesson learned from the MERS epidemic in Korea: an essay on MERS.
Epidemiology and health 20150730
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Project description:Understanding behavioral responses to epidemics is important in evaluating the broad health consequences of emerging infectious diseases. Building on the economic epidemiology literature, this study investigates individual behavioral responses to the 2015 Middle East Respiratory Syndrome Coronavirus (MERS-CoV) epidemic in Korea using a panel of individuals in a nationally representative survey. Results show that exposure to the epidemic led to lasting impacts on smoking and drinking behaviors, indicating that emerging infectious disease outbreaks are motivations for behavioral changes and opportunities for public policy interventions. In particular, individuals in the hardest-hit regions or socially connected persons were more likely to change their risky behaviors, suggesting that intensity of exposure and social interactions are potential mechanisms.
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Project description:It is well known, but frequently overlooked, that low- and high-throughput molecular data may contain batch effects, i.e., systematic technical variation. Confounding of experimental batches with the variable(s) of interest is especially concerning, as a batch effect may then be interpreted as a biologically significant finding. An integral step towards reducing false discovery in molecular data analysis includes inspection for batch effects and application of computational tools to reduce this signal if present. In a 30-sample pilot Illumina Infinium HumanMethylation450 (450k array) experiment, we identified two sources of batch effects: array row and chip. Here, we demonstrate two approaches taken to process the 450k data in which an R function, ComBat, was applied to adjust for this non-biological signal. In the “initial analysis”, the application of ComBat to an unbalanced study design resulted in 9,683 and 19,192 significant (FDR<0.05) DNA methylation differences, despite none present prior to correction. Suspicious of this dramatic change, a “revised processing” included changes to our analysis as well as a greater number of samples, and successfully reduced batch effects without introducing false signal. Our work supports conclusions made by an article previously published in this journal: though the ultimate antidote to batch effects is thoughtful study design, every DNA methylation microarray analysis should inspect, assess and, if necessary, adjust for batch effects. The analysis experience presented here can serve as a reminder to the broader community to establish research questions a priori, ensure that they match with study design and encourage communication between technicians and analysts.
2018-07-01 | GSE108567 | GEO
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Project description:It is well-known, but frequently overlooked, that low- and high-throughput molecular data may contain batch effects, i.e., systematic technical variation. Confounding of experimental batches with the variable(s) of interest is especially concerning, as a batch effect may then be interpreted as a biologically significant finding. An integral step toward reducing false discovery in molecular data analysis includes inspection for batch effects and accounting for this signal if present. In a 30-sample pilot Illumina Infinium HumanMethylation450 (450k array) experiment, we identified two sources of batch effects: row and chip. Here, we demonstrate two approaches taken to process the 450k data in which an R function, ComBat, was applied to adjust for the non-biological signal. In the "initial analysis," the application of ComBat to an unbalanced study design resulted in 9,612 and 19,214 significant (FDR < 0.05) DNA methylation differences, despite none present prior to correction. Suspicious of this dramatic change, a "revised processing" included changes to our analysis as well as a greater number of samples, and successfully reduced batch effects without introducing false signal. Our work supports conclusions made by an article previously published in this journal: though the ultimate antidote to batch effects is thoughtful study design, every DNA methylation microarray analysis should inspect, assess and, if necessary, account for batch effects. The analysis experience presented here can serve as a reminder to the broader community to establish research questions a priori, ensure that they match with study design and encourage communication between technicians and analysts.
| S-EPMC5864890 | biostudies-literature
Project description:We evaluated the nosocomial outbreak of Middle East Respiratory Syndrome (MERS) Coronavirus (CoV) in the Republic of Korea, 2015, from a healthcare operations management perspective. Establishment of healthcare policy in South Korea provides patients' freedom to select and visit multiple hospitals. Current policy enforces hospitals preference for multi-patient rooms to single-patient rooms, to lower financial burden. Existing healthcare systems tragically contributed to 186 MERS outbreak cases, starting from single "index patient" into three generations of secondary infections. By developing a macro-level health system dynamics model, we provide empirical knowledge to examining the case from both operational and financial perspectives. In our simulation, under base infectivity scenario, high emergency room occupancy circumstance contributed to an estimated average of 101 (917%) more infected patients, compared to when in low occupancy circumstance. Economic patient room design showed an estimated 702% increase in the number of infected patients, despite the overall 98% savings in total expected costs compared to optimal room design. This study provides first time, system dynamics model, performance measurements from an operational perspective. Importantly, the intent of this study was to provide evidence to motivate public, private, and government healthcare administrators' recognition of current shortcomings, to optimize performance as a whole system, rather than mere individual aspects.
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Project description:BackgroundEpidemics are a constant threat in the 21st century, particularly disease outbreaks following spillover of an animal virus to humans. Timeliness, a key metric in epidemic response, can be examined to identify critical steps and delays in public health action.AimTo examine timeliness, we analysed the response to the Middle East respiratory syndrome (MERS) epidemic, with a focus on the international and One Health response efforts.MethodsWe performed a historical review of the MERS epidemic between September 2012 and January 2019 in three steps: (i) the construction of a timeline identifying critical events in the global response, (ii) the performance of a critical path analysis to define outbreak milestones and (iii) a time gap analysis to measure timeliness in the execution of these milestones.ResultsWe proposed 14 MERS-specific milestones at different phases of the epidemic, assessing timeliness of the public health response as well as at the animal-human interface, where we identified the most significant delays.ConclusionsWhen comparing timeliness across three coronavirus epidemics, i.e. MERS (2012), SARS (2002) and COVID-19 (2019), we identified clear improvements over time for certain milestones including laboratory confirmation and diagnostics development, while this was not as apparent for others, as the identification of zoonotic hosts. To more efficiently respond to emerging threats, the global health community should widely assess and tackle specific delays in implementing response interventions by addressing challenges in the sharing of information, data and resources, as well as efficiency, quality, transparency and reliability of reporting events.
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Project description:The distinct characteristic of the Middle East Respiratory Syndrome (MERS) outbreak in South Korea is that it not only involves intra-hospital transmission, but it also involves hospital-to-hospital transmission. It has been the largest MERS outbreak outside the Middle East, with 186 confirmed cases and, among them, 36 fatal cases as of July 26, 2015. All confirmed cases are suspected to be hospital-acquired infections except one case of household transmission and two cases still undergoing examination. The Korean health care system has been the major factor shaping the unique characteristics of the outbreak. Taking this as an opportunity, the Korean government should carefully assess the fundamental problems of the vulnerability to hospital infection and make short- as well as long-term plans for countermeasures. In addition, it is hoped that this journal, Epidemiology and Health, becomes a place where various topics regarding MERS can be discussed and shared.
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Project description:The present study provides new insight into suitable microsporidian–host associations. It relates regional and continental-wide host specialization in microsporidians infecting amphipods to degraded and recovering habitats across 2 German river catchments. It provides a unique opportunity to infer the persistence of parasites following anthropogenic disturbance and their establishment in restored rivers. Amphipods were collected in 31 sampling sites with differing degradation and restoration gradients. Specimens were morphologically (hosts) and molecularly identified (host and parasites). Amphipod diversity and abundance, microsporidian diversity, host phylogenetic specificity and continental-wide β-specificity were investigated and related to each other and/or environmental variables. Fourteen microsporidian molecular operational taxonomic units (MOTUs), mainly generalist parasites, infecting 6 amphipod MOTUs were detected, expanding the current knowledge on the host range by 17 interactions. There was no difference in microsporidian diversity and host specificity among restored and near-natural streams (Boye) or between those located in urban and rural areas (Kinzig). Similarly, microsporidian diversity was generally not influenced by water parameters. In the Boye catchment, host densities did not influence microsporidian MOTU richness across restored and near-natural sites. High host turnover across the geographical range suggests that neither environmental conditions nor host diversity plays a significant role in the establishment into restored areas. Host diversity and environmental parameters do not indicate the persistence and dispersal of phylogenetic host generalist microsporidians in environments that experienced anthropogenic disturbance. Instead, these might depend on more complex mechanisms such as the production of resistant spores, host switching and host dispersal acting individually or conjointly.
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