Transmission of and susceptibility to seasonal influenza in Switzerland from 2003 to 2015
The objective of this study was to obtain a detailed picture of the transmission dynamics of seasonal influenza in Switzerland from 2003 to 2015. To this end, we developed a compartmental influenza transmission model taking into account social mixing between different age groups and seasonal forcing. We applied a Bayesian approach using Markov chain Monte Carlo (MCMC) methods to fit the model to the reported incidence of influenza-like-illness (ILI) and virological data from Sentinella, the Swiss Sentinel Surveillance Network. The maximal basic reproduction number, R0, ranged from 1.46 to 1.81 (median). Median estimates of...
Source: Epidemics - October 11, 2019 Category: Epidemiology Source Type: research

Contemporary statistical inference for infectious disease models using Stan
We describe the fitting of a class of epidemic models using Hamiltonian Monte Carlo and variational inference as implemented in the freely available Stan software. We apply the two methods to real data from outbreaks as well as routinely collected observations. Our results suggest that both inference methods are computationally feasible in this context, and show a trade-off between statistical efficiency versus computational speed. The latter appears particularly relevant for real-time applications. (Source: Epidemics)
Source: Epidemics - October 5, 2019 Category: Epidemiology Source Type: research

Game theory of vaccination and depopulation for managing livestock diseases and zoonoses on small-scale farms
The objective of this theoretical study was to elucidate how these behavioral adaptations may affect the epidemiology of highly-pathogenic avian influenza in domestic poultry and the outcome of the implemented control policies. We studied a symmetric population game where the players are broiler poultry farmers at risk of infection and where the between-farms disease transmission is both environmental and mediated by poultry trade. Three types of farmer behaviors were modelled: vaccination, depopulation, and cessation of poultry farming. We found that the transmission level of the disease through trade networks has strong ...
Source: Epidemics - October 4, 2019 Category: Epidemiology Source Type: research

Introduction to particle Markov-chain Monte Carlo for disease dynamics modellers
Publication date: Available online 3 October 2019Source: EpidemicsAuthor(s): Akira Endo, Edwin van Leeuwen, Marc BaguelinAbstractThe particle Markov-chain Monte Carlo (PMCMC) method is a powerful tool to efficiently explore high-dimensional parameter space using time-series data. We illustrate an overall picture of PMCMC with minimal but sufficient theoretical background to support the readers in the field of biomedical/health science to apply PMCMC to their studies. Some working examples of PMCMC applied to infectious disease dynamic models are presented with R code. (Source: Epidemics)
Source: Epidemics - October 4, 2019 Category: Epidemiology Source Type: research

Approximate Bayesian Computation for infectious disease modelling
We present a tutorial on coding practice for ABC in R and three case studies to illustrate the application of ABC to infectious disease models. (Source: Epidemics)
Source: Epidemics - September 26, 2019 Category: Epidemiology Source Type: research

Ensemble Forecast and Parameter Inference of Childhood Diarrhea in Chobe District, Botswana
Publication date: Available online 16 September 2019Source: EpidemicsAuthor(s): Alexandra Heaney, Kathleen A. Alexander, Jeffrey ShamanAbstractDiarrheal disease is the second largest cause of mortality in children younger than 5, yet our ability to anticipate and prepare for outbreaks remains limited. Here, we develop and test an epidemiological forecast model for childhood diarrheal disease in Chobe District, Botswana. Our prediction system uses a compartmental susceptible-infected-recovered-susceptible (SIRS) model coupled with Bayesian data assimilation to infer relevant epidemiological parameter values and generate ret...
Source: Epidemics - September 18, 2019 Category: Epidemiology Source Type: research

Accurate forecasts of the effectiveness of interventions against Ebola may require models that account for variations in symptoms during infection
Publication date: Available online 11 September 2019Source: EpidemicsAuthor(s): W.S. Hart, L.F.R. Hochfilzer, N.J. Cunniffe, H. Lee, H. Nishiura, R.N. ThompsonAbstractEpidemiological models are routinely used to predict the effects of interventions aimed at reducing the impacts of Ebola epidemics. Most models of interventions targeting symptomatic hosts, such as isolation or treatment, assume that all symptomatic hosts are equally likely to be detected. In other words, following an incubation period, the level of symptoms displayed by an individual host is assumed to remain constant throughout an infection. In reality, how...
Source: Epidemics - September 12, 2019 Category: Epidemiology Source Type: research

Tackling hepatitis E virus spread and persistence on farrow-to-finish pig farms: insights from a stochastic individual-based multi-pathogen model
The objective of this study was to develop a multi-pathogen modelling approach to understand the conditions under which HEV spreads and persists on a farrow-to-finish pig farm taking into account the fact that pigs may be co-infected with an intercurrent pathogen. A stochastic individual-based model was therefore designed that combines a population dynamics model, which enables us to take different batch rearing systems into account, with a multi-pathogen model representing at the same time the dynamics of both HEV and the intercurrent pathogen. Based on experimental and field data, the epidemiological parameters of the HE...
Source: Epidemics - September 1, 2019 Category: Epidemiology Source Type: research

Publisher's Note
Publication date: Available online 28 August 2019Source: EpidemicsAuthor(s): (Source: Epidemics)
Source: Epidemics - August 29, 2019 Category: Epidemiology Source Type: research

Improved inference of time-varying reproduction numbers during infectious disease outbreaks
We present a tool for estimating the reproduction number in real-time during infectious disease outbreaks accurately, which is available as an R software package (EpiEstim 2.2). It is also accessible as an interactive, user-friendly online interface (EpiEstim App), permitting its use by non-specialists. Our tool is easy to apply for assessing the transmission potential, and hence informing control, during future outbreaks of a wide range of invading pathogens. (Source: Epidemics)
Source: Epidemics - August 28, 2019 Category: Epidemiology Source Type: research

Spatial Analysis Made Easy with Linear Regression and Kernels
Publication date: Available online 21 August 2019Source: EpidemicsAuthor(s): Philip Milton, Helen Coupland, Emanuele Giorgi, Samir BhattAbstractKernel methods are a popular technique for extending linear models to handle non-linear spatial problems via a mapping to an implicit, high-dimensional feature space. While kernel methods are computationally cheaper than an explicit feature mapping, they are still subject to cubic cost on the number of points. Given only a few thousand locations, this computational cost rapidly outstrips the currently available computational power. This paper aims to provide an overview of kernel m...
Source: Epidemics - August 22, 2019 Category: Epidemiology Source Type: research

Predicting the impact of clustered risk and testing behaviour patterns on the population-level effectiveness of pre-exposure prophylaxis against HIV among gay, bisexual and other men who have sex with men in Greater Vancouver, Canada
Publication date: Available online 19 August 2019Source: EpidemicsAuthor(s): Michael A. Irvine, Travis Salway, Troy Grennan, Jason Wong, Mark Gilbert, Daniel CoombsAbstractPre-exposure prophylaxis (PrEP) has the potential to greatly reduce transmission of HIV. However, significant questions remain around how behavioural factors may influence its impact within target populations. We used a 2014 sexual behaviour survey to modify and recalibrate a mathematical model of HIV infection dynamics within the population of gay, bisexual and other men who have sex with men (GBMSM) in the Greater Vancouver area of British Columbia, Ca...
Source: Epidemics - August 20, 2019 Category: Epidemiology Source Type: research

Real-time predictions of the 2018–2019 Ebola virus disease outbreak in the Democratic Republic of the Congo using Hawkes point process models
Publication date: Available online 23 July 2019Source: EpidemicsAuthor(s): J. Daniel Kelly, Junhyung Park, Ryan J. Harrigan, Nicole A. Hoff, Sarita D. Lee, Rae Wannier, Bernice Selo, Mathias Mossoko, Bathe Njoloko, Emile Okitolonda-Wemakoy, Placide Mbala-Kingebeni, George W. Rutherford, Thomas B. Smith, Steve Ahuka-Mundeke, Jean Jacques Muyembe-Tamfum, Anne W. Rimoin, Frederic Paik SchoenbergAbstractAs of June 16, 2019, an Ebola virus disease (EVD) outbreak has led to 2136 reported cases in the northeastern region of the Democratic Republic of the Congo (DRC). As this outbreak continues to threaten the lives and livelihood...
Source: Epidemics - August 7, 2019 Category: Epidemiology Source Type: research

A framework for evaluating the effects of observational type and quality on vector-borne disease forecast
Publication date: Available online 5 August 2019Source: EpidemicsAuthor(s): Teresa K. Yamana, Jeffrey ShamanAbstractRecent research has advanced infectious disease forecasting from an aspiration to an operational reality. The accuracy of such operational forecasting depends on the quantity and quality of observations available for system optimization. In particular, for forecasting systems that use combined mechanistic model-inference approaches, a broad suite of epidemiological observations could be utilized, if these data were available in near real time. In cases where such data are limited, an in silica, synthetic fram...
Source: Epidemics - August 6, 2019 Category: Epidemiology Source Type: research

Estimating the impact of violent events on transmission in Ebola virus disease outbreak, Democratic Republic of the Congo, 2018–2019
ConclusionThe difference in the estimated transmission rates between zones affected by recent violent events suggests that violent events are contributing to increased transmission and the ongoing nature of this outbreak. (Source: Epidemics)
Source: Epidemics - July 27, 2019 Category: Epidemiology Source Type: research

Real-time predictions of the 2018-2019 Ebola virus disease outbreak in the Democratic Republic of the Congo using Hawkes point process models
Publication date: Available online 23 July 2019Source: EpidemicsAuthor(s): J. Daniel Kelly, Junhyung Park, Ryan J. Harrigan, Nicole A. Hoff, Sarita D. Lee, Rae Wannier, Bernice Selo, Mathias Mossoko, Bathe Njoloko, Emile Okitolonda-Wemakoy, Placide Mbala-Kingebeni, George W. Rutherford, Thomas B. Smith, Steve Ahuka-Mundeke, Jean Jacques Muyembe-Tamfum, Anne W. Rimoin, Frederic Paik SchoenbergAbstractAs of June 16, 2019, an Ebola virus disease (EVD) outbreak has led to 2136 reported cases in the northeastern region of the Democratic Republic of the Congo (DRC). As this outbreak continues to threaten the lives and livelihood...
Source: Epidemics - July 25, 2019 Category: Epidemiology Source Type: research

Analyzing Influenza Outbreaks in Russia Using an Age-structured Dynamic Transmission Model
In this study, we addressed the ability of a minimalistic SEIR model to satisfactorily describe influenza outbreak dynamics in Russian settings. For that purpose, we calibrated an age-specific influenza dynamics model to Russian acute respiratory infection (ARI) incidence data over 2009-2016 and assessed the variability of proportion of non-immune individuals in the population depending on the regarded city, the non-epidemic indicence baseline, the contact structure considered and the used calibration method. The experiments demonstrated the importance of distinguishing characteristics of different age groups, such as cont...
Source: Epidemics - July 23, 2019 Category: Epidemiology Source Type: research

Heterogeneous local dynamics revealed by classification analysis of spatially disaggregated time series data
Publication date: Available online 22 July 2019Source: EpidemicsAuthor(s): T. Alex Perkins, Isabel Rodriguez-Barraquer, Carrie Manore, Amir S. Siraj, Guido España, Christopher M. Barker, Michael A. Johansson, Robert C. ReinerAbstractTime series data provide a crucial window into infectious disease dynamics, yet their utility is often limited by the spatially aggregated form in which they are presented. When working with time series data, violating the implicit assumption of homogeneous dynamics below the scale of spatial aggregation could bias inferences about underlying processes. We tested this assumption in the c...
Source: Epidemics - July 23, 2019 Category: Epidemiology Source Type: research

The drivers of squirrelpox virus dynamics in its grey squirrel reservoir host
Publication date: Available online 15 July 2019Source: EpidemicsAuthor(s): Julian Chantrey, Timothy Dale, David Jones, Michael Begon, Andy FentonAbstractMany pathogens of conservation concern circulate endemically within natural wildlife reservoir hosts and it is imperative to understand the individual and ecological drivers of natural transmission dynamics, if any threat to a related endangered species is to be assessed. Our study highlights the key drivers of infection and shedding dynamics of squirrelpox virus (SQPV) in its reservoir grey squirrel (Sciurus carolinensis) population. To clarify SQPV dynamics in this popul...
Source: Epidemics - July 16, 2019 Category: Epidemiology Source Type: research

Modeling the role of carrier and mobile herds on foot-and-mouth disease virus endemicity in the Far North Region of Cameroon
We present a spatial stochastic model of disease dynamics that incorporates a spatial transmission kernel in a modified Gillespie algorithm, and use it to evaluate two hypothesized drivers of endemicity: asymptomatic carriers and the movement of mobile herds. The model is parameterized using data from the pastoral systems in the Far North Region of Cameroon. Our computational study provides evidence in support of the hypothesis that asymptomatic carriers, but not mobile herds, are a driver of endemicity.Graphical abstract (Source: Epidemics)
Source: Epidemics - July 13, 2019 Category: Epidemiology Source Type: research

Detecting within-host interactions from genotype combination prevalence data
Publication date: Available online 18 June 2019Source: EpidemicsAuthor(s): Samuel Alizon, Carmen Lía Murall, Emma Saulnier, Mircea SofoneaAbstractParasite genetic diversity can provide information on disease transmission dynamics but most mathematical and statistical frameworks ignore the exact combinations of genotypes in infections. We introduce and validate a new method that combines explicit epidemiological modelling of coinfections and regression-Approximate Bayesian Computing (ABC) to detect within-host interactions. Using a susceptible-infected-susceptible (SIS) model, we show that, if sufficiently strong, wi...
Source: Epidemics - June 18, 2019 Category: Epidemiology Source Type: research

Household transmission and disease transmissibility of a large HAV outbreak in Lazio, Italy, 2016–2017
Publication date: Available online 13 June 2019Source: EpidemicsAuthor(s): Giorgio GuzzettaAbstractA major outbreak of Hepatitis A Virus (HAV) has swept through Europe between mid-2016 and 2017, mainly within the community of men who have sex with men (MSM). Over the same period, about 1,000 outbreak-related cases of acute Hepatitis A (AHA) were recorded in Lazio region, Italy.We calibrated a Bayesian model to reconstruct likely transmission events within all 44 households where multiple infections were recorded, representing a total of 103 cases from the HAV outbreak in Lazio. Based on information on the observed times of...
Source: Epidemics - June 15, 2019 Category: Epidemiology Source Type: research

School dismissal as a pandemic influenza response: When, where and for how long?
Publication date: Available online 12 June 2019Source: EpidemicsAuthor(s): Timothy C. Germann, Hongjiang Gao, Manoj Gambhir, Andrew Plummer, Matthew Biggerstaff, Carrie Reed, Amra UzicaninAbstractWe used individual-based computer simulation models at community, regional and national levels to evaluate the likely impact of coordinated pre-emptive school dismissal policies during an influenza pandemic. Such policies involve three key decisions: when, over what geographical scale, and how long to keep schools closed. Our evaluation includes uncertainty and sensitivity analyses, as well as model output uncertainties arising fr...
Source: Epidemics - June 13, 2019 Category: Epidemiology Source Type: research

Complementing the power of deep learning with statistical model fusion: Probabilistic forecasting of influenza in Dallas County, Texas, USA
Publication date: Available online 8 June 2019Source: EpidemicsAuthor(s): Marwah Soliman, Vyacheslav Lyubchich, Yulia R. GelAbstractInfluenza is one of the main causes of death, not only in the USA but worldwide. Its significant economic and public health impacts necessitate development of accurate and efficient algorithms for forecasting of any upcoming influenza outbreaks. Most currently available methods for influenza prediction are based on parametric time series and regression models that impose restrictive and often unverifiable assumptions on the data. In turn, more flexible machine learning models and, particularly...
Source: Epidemics - June 8, 2019 Category: Epidemiology Source Type: research

A systematic review of MERS-CoV seroprevalence and RNA prevalence in dromedary camels: implications for animal vaccination
Publication date: Available online 5 June 2019Source: EpidemicsAuthor(s): Amy Dighe, Thibaut Jombart, Maria D. Van Kerkhove, Neil FergusonAbstractHuman infection with Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is driven by recurring dromedary-to-human spill-over events, leading decision-makers to consider dromedary vaccination. Dromedary vaccine candidates in the development pipeline are showing hopeful results, but gaps in our understanding of the epidemiology of MERS-CoV in dromedaries must be addressed to design and evaluate potential vaccination strategies. We aim to bring together existing measures of MER...
Source: Epidemics - June 6, 2019 Category: Epidemiology Source Type: research

Temperature impacts on dengue emergence in the United States: Investigating the role of seasonality and climate change
In this study, we use a deterministic ordinary differential equations model to investigate how seasonal and diurnal temperature fluctuations affect the potential for dengue transmission in six U.S. cities. We specifically consider temperature-dependent mosquito larval development, adult mosquito mortality, and the extrinsic incubation period of the virus. We show that the ability of introductions to lead to outbreaks depends upon the relationship between a city's temperature profile and the time of year at which the initial case is introduced. We also investigate how the potential for outbreaks changes with predicted futur...
Source: Epidemics - June 6, 2019 Category: Epidemiology Source Type: research

Variation and Trends in Transmission Dynamics of Methicillin-Resistant Staphylococcus Aureus in Veterans Affairs Hospitals and Nursing Homes
Publication date: Available online 29 May 2019Source: EpidemicsAuthor(s): Karim Khader, Alun Thomas, Makoto Jones, Damon Toth, Vanessa Stevens, Matthew H. Samore, CDC Modeling Infectious Diseases in Healthcare Program (MInD-Healthcare)AbstractVariation and differences of MRSA transmission within and between healthcare settings are not well understood. This variability is critical for understanding the potential impact of infection control interventions and could aid in the evaluation of future intervention strategies. We fit a Bayesian transmission model to detailed individual-level MRSA surveillance data from over 230 Vet...
Source: Epidemics - May 30, 2019 Category: Epidemiology Source Type: research

Phylogeography of rubella virus in Asia: vaccination and demography shape synchronous outbreaks
Publication date: Available online 28 May 2019Source: EpidemicsAuthor(s): Brooke A. Bozick, Colin J. Worby, C. Jessica E. MetcalfAbstractRubella virus causes mild disease in children but for women in the early stages of pregnancy, it can cause spontaneous abortion, congenital rubella syndrome (CRS) and associated birth defects. Despite the availability of an effective vaccine, rubella virus continues to circulate endemically in several regions of the world. This is particularly true in East and Southeast (E/SE) Asia, where control efforts vary widely among countries that are well connected through travel and immigration. I...
Source: Epidemics - May 30, 2019 Category: Epidemiology Source Type: research

The Contact Structure of Great Britain’s Salmon and Trout Aquaculture Industry
Publication date: Available online 7 May 2019Source: EpidemicsAuthor(s): A.E. Jones, L.A. Munro, D.M. Green, K.L. Morgan, A.G. Murray, R. Norman, D. Ryder, N.K.G. Salama, N.G.H. Taylor, M.A. Thrush, I.S. Wallace, K.J. SharkeyAbstractWe analyse the network structure of the British salmonid aquaculture industry from the perspective of infectious disease control. We combine for the first time live fish transport (or movement) data covering England and Wales with data covering Scotland and include network layers representing potential transmission by rivers, sea water and local transmission via human or animal vectors in the i...
Source: Epidemics - May 8, 2019 Category: Epidemiology Source Type: research

Analyzing and forecasting the Ebola incidence in North Kivu, the Democratic Republic of the Congo from 2018-19 in real time
Publication date: Available online 3 May 2019Source: EpidemicsAuthor(s): Andrei R. Akhmetzhanov, Hyojung Lee, Sung-mok Jung, Taishi Kayano, Baoyin Yuan, Hiroshi NishiuraAbstractDuring an Ebola virus disease (EVD) outbreak, the analysis and forecasting of the incidence in real time is challenged by reporting of cases, especially the reporting delay. It should be remembered that the latest count of cases is likely underestimated in real time, and moreover, the effective reproduction number, i.e. the average number of secondary cases generated by a single primary case at a given point in time, is also underestimated without p...
Source: Epidemics - May 5, 2019 Category: Epidemiology Source Type: research

Network analyses of transhumance movements and simulations of foot-and-mouth disease virus transmission among mobile livestock in Cameroon
Publication date: Available online 25 April 2019Source: EpidemicsAuthor(s): Laura W. Pomeroy, Mark Moritz, Rebecca GarabedAbstractFoot-and-mouth disease (FMD) affects cloven-hoofed livestock and agricultural economies worldwide. Analyses of the 2001 FMD outbreak in the United Kingdom informed how livestock movement contributed to disease spread. However, livestock reared in other locations use different production systems that might also influence disease dynamics. Here, we investigate a livestock production system known as transhumance, which is the practice of moving livestock between seasonal grazing areas. We built mec...
Source: Epidemics - April 26, 2019 Category: Epidemiology Source Type: research

Real-time prediction of influenza outbreaks in Belgium
Publication date: Available online 18 April 2019Source: EpidemicsAuthor(s): Gisele H.B. Miranda, Jan M. Baetens, Nathalie Bossuyt, Odemir M. Bruno, Bernard De BaetsAbstractSeasonal influenza is a worldwide public health concern. Forecasting its dynamics can improve the management of public health regulations, resources and infrastructure, and eventually reduce mortality and the costs induced by influenza-related absenteism. In Belgium, a network of Sentinel General Practitioners (SGPs) is in place for the early detection of the seasonal influenza epidemic. This surveillance network reports the weekly incidence of influenza...
Source: Epidemics - April 19, 2019 Category: Epidemiology Source Type: research

Acknowledgement to reviewers of Epidemics - The Journal on Infectious Disease Dynamics
Publication date: March 2019Source: Epidemics, Volume 26Author(s): (Source: Epidemics)
Source: Epidemics - April 3, 2019 Category: Epidemiology Source Type: research

Highly pathogenic avian influenza H5N8 in south-west France 2016–2017: A modeling study of control strategies
This study showcases the possible contribution of modeling to inform and optimize control strategies during an outbreak. (Source: Epidemics)
Source: Epidemics - April 3, 2019 Category: Epidemiology Source Type: research

Highly Pathogenic Avian Influenza H5N8 in South-West France 2016-2017: A Modeling Study of Control Strategies
This study showcases the possible contribution of modeling to inform and optimize control strategies during an outbreak. (Source: Epidemics)
Source: Epidemics - March 29, 2019 Category: Epidemiology Source Type: research

Systematic biases in disease forecasting – The role of behavior change
Publication date: Available online 28 February 2019Source: EpidemicsAuthor(s): Ceyhun Eksin, Keith Paarporn, Joshua S. WeitzAbstractIn a simple susceptible-infected-recovered (SIR) model, the initial speed at which infected cases increase is indicative of the long-term trajectory of the outbreak. Yet during real-world outbreaks, individuals may modify their behavior and take preventative steps to reduce infection risk. As a consequence, the relationship between the initial rate of spread and the final case count may become tenuous. Here, we evaluate this hypothesis by comparing the dynamics arising from a simple SIR epidem...
Source: Epidemics - March 27, 2019 Category: Epidemiology Source Type: research

Estimating age-mixing patterns relevant for the transmission of airborne infections
ConclusionsPatterns of age-mixing can be estimated for all contacts using data that can be easily collected as part of social contact surveys or time-use surveys, and may differ from patterns between close contacts. (Source: Epidemics)
Source: Epidemics - March 21, 2019 Category: Epidemiology Source Type: research

Patterns of seasonal influenza activity in U.S. core-based statistical areas, described using prescriptions of oseltamivir in Medicare claims data
Publication date: Available online 29 August 2018Source: EpidemicsAuthor(s): F. Scott Dahlgren, David K. Shay, Hector S. Izurieta, Richard A. Forshee, Michael Wernecke, Yoganand Chillarige, Yun Lu, Jeffrey A. Kelman, Carrie ReedAbstractUsing Medicare claims data on prescriptions of oseltamivir dispensed to people 65 years old and older, we present a descriptive analysis of patterns of influenza activity in the United States for 579 core-based statistical areas (CBSAs) from the 2010–2011 through the 2015–2016 influenza seasons. During this time, 1,010,819 beneficiaries received a prescription of oseltamivir, ran...
Source: Epidemics - March 21, 2019 Category: Epidemiology Source Type: research

Confronting data sparsity to identify potential sources of Zika virus spillover infection among primates
Publication date: Available online 19 March 2019Source: EpidemicsAuthor(s): Barbara A. Han, Subhabrata Majumdar, Flavio P. Calmon, Benjamin S. Glicksberg, Raya Horesh, Abhishek Kumar, Adam Perer, Elisa B. von Marschall, Dennis Wei, Aleksandra Mojsilović, Kush R. VarshneyAbstractThe recent Zika virus (ZIKV) epidemic in the Americas ranks among the largest outbreaks in modern times. Like other mosquito-borne flaviviruses, ZIKV circulates in sylvatic cycles among primates that can serve as reservoirs of spillover infection to humans. Identifying sylvatic reservoirs is critical to mitigating spillover risk, but relevant surve...
Source: Epidemics - March 21, 2019 Category: Epidemiology Source Type: research

Assessing reporting delays and the effective reproduction number: The Ebola epidemic in DRC, May 2018–January 2019
Publication date: Available online 3 February 2019Source: EpidemicsAuthor(s): A. Tariq, K. Roosa, K. Mizumoto, G. ChowellAbstractOn August 1, 2018, the Democratic Republic of Congo declared its 10th and largest outbreak of Ebola inflicting North Khivu and Ituri provinces. The spread of Ebola to Congolese urban centers along with deliberate attacks on the health care workers has hindered epidemiological surveillance activities, leading to substantial reporting delays. Reporting delays distort the epidemic incidence pattern misrepresenting estimates of epidemic potential and the outbreak trajectory. To assess the impact of r...
Source: Epidemics - March 15, 2019 Category: Epidemiology Source Type: research

Impact of sexual trajectories of men who have sex with men on the reduction in HIV transmission by pre-exposure prophylaxis
In conclusion, our study predicts that sexual trajectories increase the estimated impact of PrEP on reducing HIV prevalence when compared to a population where risk levels do not change. (Source: Epidemics)
Source: Epidemics - March 15, 2019 Category: Epidemiology Source Type: research

Efficient vaccination strategies for epidemic control using network information
ConclusionsUsing even partial network information to prioritize vaccines at either the village or individual level, i.e. determine the optimal order of communities or individuals within each village, substantially improved epidemic outcomes. Such approaches may be feasible and effective in outbreak settings, and full ascertainment of network structure may not be required. (Source: Epidemics)
Source: Epidemics - March 7, 2019 Category: Epidemiology Source Type: research

Control of Ebola virus disease outbreaks: comparison of health care worker-targeted and community vaccination strategies
ConclusionsThe vaccine strategies tested had a different impact depending on the transmission dynamics and previous control measures. Although we will not know the characteristics of a new outbreak, ahead-of-time HCW-targeted vaccination can decrease the total outbreak size, even at low vaccine coverage. (Source: Epidemics)
Source: Epidemics - March 4, 2019 Category: Epidemiology Source Type: research

Systematic biases in disease forecasting - the role of behavior change
Publication date: Available online 28 February 2019Source: EpidemicsAuthor(s): Ceyhun Eksin, Keith Paarporn, Joshua S. WeitzAbstractIn a simple susceptible-infected-recovered (SIR) model, the initial speed at which infected cases increase is indicative of the long-term trajectory of the outbreak. Yet during real-world outbreaks, individuals may modify their behavior and take preventative steps to reduce infection risk. As a consequence, the relationship between the initial rate of spread and the final case count may become tenuous. Here, we evaluate this hypothesis by comparing the dynamics arising from a simple SIR epidem...
Source: Epidemics - March 1, 2019 Category: Epidemiology Source Type: research

Hepatitis C Transmission in Young People who Inject Drugs: Insights Using a Dynamic Model Informed by State Public Health Surveillance
Publication date: Available online 28 February 2019Source: EpidemicsAuthor(s): Rachel E. Gicquelais, Betsy Foxman, Joseph Coyle, Marisa C. EisenbergAbstractIncreasing injection of heroin and prescription opioids have led to increases in the incidence of hepatitis C Virus (HCV) infections in US young adults since the early 2000s. How best to interrupt transmission and decrease HCV prevalence in young people who inject drugs (PWID) is uncertain.We developed an age-stratified ordinary differential equation HCV transmission model of PWID aged 15-64, which we fit to Michigan HCV surveillance data among young PWID aged 15-29. We...
Source: Epidemics - February 28, 2019 Category: Epidemiology Source Type: research

Estimating HIV incidence from surveillance data indicates a second wave of infections in Brazil
Publication date: Available online 7 February 2019Source: EpidemicsAuthor(s): Tara D. Mangal, Ana Roberta Pati Pascom, Juan Vesga, Mariana Veloso Meireles, Adele Schwartz Benzaken, Timothy B. HallettAbstractEmerging evidence suggests that HIV incidence rates in Brazil, particularly among men, may be rising. Here we use Brazil’s integrated health systems data to develop a mathematical model, reproducing the complex surveillance systems and providing estimates of HIV incidence, number of people living with HIV (PLHIV), reporting rates and ART initiation rates.An age-structured deterministic model with a flexible spline...
Source: Epidemics - February 8, 2019 Category: Epidemiology Source Type: research

A dynamic network model to disentangle the roles of steady and casual partners for HIV transmission among MSM
This study indicates that small reductions in the time to diagnosis, and thereby, beginning of treatment, may substantially reduce HIV prevalence. Moreover, we find that moderate increases in condom use with casual sex partners have greater impact on reducing prevalence than the same increases in condom use with steady sex partners. This result demonstrates the relative importance of casual contacts on the HIV transmission dynamics among MSM in Sweden. Our results highlight the importance of HIV testing and condom-use interventions, and the role that casual and steady partners play in this, in order to turn the epidemiolog...
Source: Epidemics - February 7, 2019 Category: Epidemiology Source Type: research

A dynamic network model to disentangle the roles of steady and casual partnersfor HIV transmission among MSM
This study indicates that small reductions in the time to diagnosis, and thereby, beginning of treatment, may substantially reduce HIV prevalence. Moreover, we find that moderate increases in condom use with casual sex partners have greater impact on reducing prevalence than the same increases in condom use with steady sex partners. This result demonstrates the relative importance of casual contacts on the HIV transmission dynamics among MSM in Sweden. Our results highlight the importance of HIV testing and condom-use interventions, and the role that casual and steady partners play in this, in order to turn the epidemiolog...
Source: Epidemics - February 3, 2019 Category: Epidemiology Source Type: research

Assessing reporting delays and the effective reproduction number: The 2018-19 Ebola epidemic in DRC, May 2018-January 2019
Publication date: Available online 3 February 2019Source: EpidemicsAuthor(s): A. Tariq, K. Roosa, K. Mizumoto, G. ChowellAbstractOn August 1, 2018, the Democratic Republic of Congo declared its 10th and largest outbreak of Ebola inflicting North Khivu and Ituri provinces. The spread of Ebola to Congolese urban centers along with deliberate attacks on the health care workers has hindered epidemiological surveillance activities, leading to substantial reporting delays. Reporting delays distort the epidemic incidence pattern and misrepresenting estimates of epidemic potential and the outbreak trajectory. To assess the impact ...
Source: Epidemics - February 3, 2019 Category: Epidemiology Source Type: research

Managing Marek’s disease in the egg industry
Publication date: Available online 2 February 2019Source: EpidemicsAuthor(s): Carly Rozins, Troy Day, Scott GreenhalghAbstractThe industrialization of farming has had an enormous impact. To most, this impact is viewed solely in the context of productivity, but the denser living conditions and shorter rearing periods of industrial livestock farms provide pathogens with an ideal opportunity to spread and evolve. For example, the industrialization of poultry farms drove the Marek’s disease virus (MDV) to evolve from a mild paralytic syndrome to a highly contagious, globally prevalent, deadly disease. Fortunately, the ec...
Source: Epidemics - February 2, 2019 Category: Epidemiology Source Type: research