Noroviruses are highly infectious but there is strong variation in host susceptibility and virus pathogenicity
Publication date: Available online 17 July 2020Source: EpidemicsAuthor(s): Peter FM Teunis, Françoise S Le Guyader, Pengbo Liu, Joanna Ollivier, Christine L Moe (Source: Epidemics)
Source: Epidemics - July 17, 2020 Category: Epidemiology Source Type: research

Identification and evaluation of epidemic prediction and forecasting reporting guidelines: A systematic review and a call for action
Publication date: Available online 9 July 2020Source: EpidemicsAuthor(s): Simon Pollett, Michael Johansson, Matthew Biggerstaff, Lindsay C. Morton, Sara L. Bazaco, David M. Brett Major, Anna M. Stewart-Ibarra, Julie A. Pavlin, Suzanne Mate, Rachel Sippy, Laurie J. Hartman, Nicholas G. Reich, Irina Maljkovic Berry, Jean-Paul Chretien, Benjamin M. Althouse, Dianne Meyer, Cecile Viboud, Caitlin Rivers (Source: Epidemics)
Source: Epidemics - July 10, 2020 Category: Epidemiology Source Type: research

Bayesian epidemiological modeling over high-resolution network data
Publication date: Available online 2 July 2020Source: EpidemicsAuthor(s): Stefan Engblom, Robin Eriksson, Stefan Widgren (Source: Epidemics)
Source: Epidemics - July 4, 2020 Category: Epidemiology Source Type: research

How mechanistic modelling supports decision making for the control of enzootic infectious diseases
Publication date: Available online 20 June 2020Source: EpidemicsAuthor(s): P. Ezanno, M. Andraud, G. Beaunée, T. Hoch, S. Krebs, A. Rault, S. Touzeau, E. Vergu, S. Widgren (Source: Epidemics)
Source: Epidemics - June 22, 2020 Category: Epidemiology Source Type: research

The effects of border control and quarantine measures on the spread of COVID-19
Publication date: Available online 6 June 2020Source: EpidemicsAuthor(s): M. Pear Hossain, Alvin Junus, Xiaolin Zhu, Pengfei Jia, Tzai-Hung Wen, Dirk Pfeiffer, Hsiang-Yu Yuan (Source: Epidemics)
Source: Epidemics - June 7, 2020 Category: Epidemiology Source Type: research

Influencing public health policy with data-informed mathematical models of infectious diseases: Recent developments and new challenges
Publication date: Available online 17 May 2020Source: EpidemicsAuthor(s): Amani Alahmadi, Sarah Belet, Andrew Black, Deborah Cromer, Jennifer A. Flegg, Thomas House, Pavithra Jayasundara, Jonathan M. Keith, James M. McCaw, Rob Moss, Joshua V. Ross, Freya M. Shearer, Sai Thein Than Tun, James Walker, Lisa White, Jason M. Whyte, W.C. Ada, Alexander E. Zarebski (Source: Epidemics)
Source: Epidemics - May 18, 2020 Category: Epidemiology Source Type: research

Tooling-up for infectious disease transmission modelling
Publication date: Available online 13 May 2020Source: EpidemicsAuthor(s): Marc Baguelin, Graham F. Medley, Emily S. Nightingale, Kathleen M. O’Reilly, Eleanor M. Rees, Naomi R. Waterlow, Moritz Wagner (Source: Epidemics)
Source: Epidemics - May 15, 2020 Category: Epidemiology Source Type: research

The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak
Publication date: Available online 11 May 2020Source: EpidemicsAuthor(s): Sang Woo Park, Daniel M. Cornforth, Jonathan Dushoff, Joshua S. Weitz (Source: Epidemics)
Source: Epidemics - May 12, 2020 Category: Epidemiology Source Type: research

Estimating sea lice infestation pressure on salmon farms: Comparing different methods using multivariate state-space models
Publication date: Available online 11 May 2020Source: EpidemicsAuthor(s): Adel Elghafghuf, Raphael Vanderstichel, Larry Hammell, Henrik Stryhn (Source: Epidemics)
Source: Epidemics - May 11, 2020 Category: Epidemiology Source Type: research

Designing a typhoid environmental surveillance study: a simulation model for optimum sampling site allocation
Publication date: Available online 17 April 2020Source: EpidemicsAuthor(s): Yuke Wang, Christine L. Moe, Shanta Dutta, Ashutosh Wadhwa, Suman Kanungo, Wolfgang Mairinger, Yichuan Zhao, Yi Jiang, Peter FM. Teunis (Source: Epidemics)
Source: Epidemics - April 17, 2020 Category: Epidemiology Source Type: research

Dynamics of Livestock-Associated Methicillin Resistant Staphylococcus aureus in pig movement networks: insight from mathematical modeling and French data
Publication date: Available online 9 February 2020Source: EpidemicsAuthor(s): Jonathan Bastard, Mathieu Andraud, Claire Chauvin, Philippe Glaser, Lulla Opatowski, Laura TemimeAbstractLivestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) colonizes livestock animals worldwide, especially pigs and calves. Although frequently carried asymptomatically, LA-MRSA can cause severe infections in humans. It is therefore important to better understand LA-MRSA spreading dynamics within pig farms and over pig movement networks, and to compare different strategies of control and surveillance. For this purpose, we pro...
Source: Epidemics - February 10, 2020 Category: Epidemiology Source Type: research

Emergence of pertactin-deficient pertussis strains in Australia can be explained by models of vaccine escape
In this study, we considered a deterministic 2-strain compartmental model to characterize the relative fitness of PRN– strains and vaccine efficacy against PRN– infection in comparison to the wild-type pertactin-expressing (PRN+) strains. We first showed that the model’s equilibrium behavior allows for replacement and co-existence, depending on key parameters related to transmission, vaccine efficacy and durations of immunity. We then fitted the model to epidemiological and pathogen PRN data from the state of New South Wales, Australia.Fitted model parameters showed that the changes in pertussis epidemiol...
Source: Epidemics - February 10, 2020 Category: Epidemiology Source Type: research

Spatial and Temporal Clustering of Patients Hospitalized with Laboratory-Confirmed Influenza in the United States
ConclusionsSocioeconomic factors strongly impact local influenza hospitalization burden. Influenza phase synchrony varies by year and by socioeconomics, but is less influenced by socioeconomics than is disease burden. (Source: Epidemics)
Source: Epidemics - February 10, 2020 Category: Epidemiology Source Type: research

Egocentric Sexual Networks of Men Who Have Sex with Men in the United States: Results from the ARTnet Study
Publication date: Available online 24 January 2020Source: EpidemicsAuthor(s): Kevin M. Weiss, Steven M. Goodreau, Martina Morris, Pragati Prasad, Ramya Ramaraju, Travis Sanchez, Samuel M. JennessABSTRACTIn this paper, we present an overview and descriptive results from the first egocentric network study of men who have sex with men (MSM) from across the United States: the ARTnet study. ARTnet was designed to support prevention research for human immunodeficiency virus (HIV) and other sexually transmitted infections (STIs) that are transmitted across partnership networks. ARTnet implemented a population-based egocentric net...
Source: Epidemics - January 26, 2020 Category: Epidemiology Source Type: research

Quantifying the success of measles vaccination campaigns in the Rohingya refugee camps
Publication date: Available online 9 January 2020Source: EpidemicsAuthor(s): Taylor Chin, Caroline O. Buckee, Ayesha S. MahmudAbstractIn the wake of the Rohingya population's mass migration from Myanmar, one of the world's largest refugee settlements was constructed in Cox's Bazar, Bangladesh to accommodate nearly 900,000 new refugees. Refugee populations are particularly vulnerable to infectious disease outbreaks due to many population and environmental factors. A large measles outbreak, with over 1,700 cases, occurred among the Rohingya population between September and November 2017. Here, we estimate key epidemiological...
Source: Epidemics - January 9, 2020 Category: Epidemiology Source Type: research

Small world in the real world: long distance dispersal governs epidemic dynamics in agricultural landscapes
Publication date: Available online 7 January 2020Source: EpidemicsAuthor(s): Giovanni Strona, Claudio Castellano, Simone Fattorini, Luigi Ponti, Andrew Paul Gutierrez, Pieter S.A. BeckAbstractOutbreaks of a plant disease in a landscape can be meaningfully modelled using networks with nodes representing individual crop-fields, and edges representing potential infection pathways between them. Their spatial structure, which resembles that of a regular lattice, makes such networks fairly robust against epidemics. Yet, it is well-known how the addition of a few shortcuts can turn robust regular lattices into vulnerable ‘s...
Source: Epidemics - January 8, 2020 Category: Epidemiology Source Type: research

Choices and trade-offs in inference with infectious disease models
Publication date: Available online 20 December 2019Source: EpidemicsAuthor(s): Sebastian Funk, Aaron A. KingAbstractInference using mathematical models of infectious disease dynamics can be an invaluable tool for the interpretation and analysis of epidemiological data. However, researchers wishing to use this tool are faced with a choice of models and model types, simulation methods, inference methods and software packages. Given the multitude of options, it can be challenging to decide on the best approach. Here, we delineate the choices and trade-offs involved in deciding on an approach for inference, and discuss aspects...
Source: Epidemics - December 21, 2019 Category: Epidemiology Source Type: research

Real-time forecasting of epidemic trajectories using computational dynamic ensembles
Publication date: Available online 21 December 2019Source: EpidemicsAuthor(s): G. Chowell, R. Luo, K. Sun, K. Roosa, A. Tariq, C. ViboudAbstractForecasting the trajectory of social dynamic processes, such as the spread of infectious diseases, poses significant challenges that call for methods that account for data and model uncertainty. Here we introduce an ensemble model for sequential forecasting that weights a set of plausible models and use a frequentist computational bootstrap approach to evaluate its uncertainty. We demonstrate the feasibility of our approach using simple dynamic differential-equation models and the ...
Source: Epidemics - December 21, 2019 Category: Epidemiology Source Type: research

Dynamic modeling of hepatitis C transmission among people who inject drugs
Publication date: Available online 11 December 2019Source: EpidemicsAuthor(s): Theresa Stocks, Leah J. Martin, Sharon Kühlmann-Berenzon, Tom BrittonAbstractTo reach the WHO goal of hepatitis C elimination, it is essential to identify the number of people unaware of their hepatitis C virus (HCV) infection and to investigate the effect of interventions on the disease transmission dynamics. In many high-income countries, one of the primary routes of HCV transmission is via contaminated needles shared by people who inject drugs (PWIDs). However, substantial underreporting combined with high uncertainty regarding the size ...
Source: Epidemics - December 11, 2019 Category: Epidemiology Source Type: research

Prospects of toxoplasmosis control by cat vaccination
ConclusionFor attaining elimination of oocyst-originated human infections, only few cats may remain unvaccinated, regardless of the cat-population size, and only a few more cats may remain unvaccinated for reducing infections substantially. Such vaccination coverages can in practice be achieved only when small cat-populations are considered, but in larger cat-populations the large efficacy and vaccination coverage needed are unfeasible. (Source: Epidemics)
Source: Epidemics - December 7, 2019 Category: Epidemiology Source Type: research

Temperature-dependent variation in the extrinsic incubation period elevates the risk of vector-borne disease emergence
Publication date: Available online 6 December 2019Source: EpidemicsAuthor(s): Tsukushi Kamiya, Megan A. Greischar, Kiran Wadhawan, Benjamin Gilbert, Krijn Paaijmans, Nicole MideoAbstractIdentifying ecological drivers of disease transmission is central to understanding disease risks. For vector-borne diseases, temperature is a major determinant of transmission because vital parameters determining the fitness of parasites and vectors are highly temperature-sensitive, including the extrinsic incubation period required for parasites to develop within the vector. Temperature also underlies dramatic differences in the individual...
Source: Epidemics - December 7, 2019 Category: Epidemiology Source Type: research

Epidemiological Impact of Targeted Interventions for People with Diabetes Mellitus on Tuberculosis Transmission in India: Modelling Based Predictions
ConclusionGains can be attained by targeting DM individuals with interventions to reduce TB burden. Most strategies were effective with
Source: Epidemics - December 4, 2019 Category: Epidemiology Source Type: research

Predicting Ebola virus disease risk and the role of African bat birthing
Publication date: Available online 16 November 2019Source: EpidemicsAuthor(s): C. Reed Hranac, Jonathan C. Marshall, Ara Monadjem, David T.S. HaymanAbstractEbola virus disease (EVD) presents a threat to public health throughout equatorial Africa. Despite numerous ‘spillover’ events into humans and apes, the maintenance reservoirs and mechanism of spillover are poorly understood. Evidence suggests fruit bats play a role in both instances, yet data remain sparse and bats exhibit a wide range of life history traits. Here we pool sparse data and use a mechanistic approach to examine how birthing cycles of African f...
Source: Epidemics - November 18, 2019 Category: Epidemiology Source Type: research

Phylodynamic analysis of HIV-1 subtypes B, C and CRF 02_AG in Senegal
Publication date: Available online 14 November 2019Source: EpidemicsAuthor(s): Fabrícia F. Nascimento, Stefan Baral, Lily Geidelberg, Christinah Mukandavire, Sheree R. Schwartz, Gnilane Turpin, Nguissali Turpin, Daouda Diouf, Nafissatou Leye Diouf, Karleen Coly, Coumba Toure Kane, Cheikh Ndour, Peter Vickerman, Marie-Claude Boily, Erik M. VolzAbstractSurveillance of HIV epidemics in key populations and in developing countries is often challenging due to sparse, incomplete, or low-quality data. Analysis of HIV sequence data can provide an alternative source of information about epidemic history, population structure,...
Source: Epidemics - November 15, 2019 Category: Epidemiology Source Type: research

Measles transmission during a large outbreak in California
Publication date: Available online 10 November 2019Source: EpidemicsAuthor(s): Lee Worden, Sarah F. Ackley, Jennifer Zipprich, Kathleen Harriman, Wayne T.A. Enanoria, Rae Wannier, Travis C. PorcoAbstractA large measles outbreak in 2014–2015, linked to Disneyland theme parks, attracted international attention, and led to changes in California vaccine policy. We use dates of symptom onset and known epidemic links for California cases in this outbreak to estimate time-varying transmission in the outbreak, and to estimate generation membership of cases probabilistically. We find that transmission declined significantly d...
Source: Epidemics - November 12, 2019 Category: Epidemiology Source Type: research

The forecasting of dynamical Ross River virus outbreaks: Victoria, Australia
Publication date: Available online 5 November 2019Source: EpidemicsAuthor(s): Iain S. Koolhof, Katherine B. Gibney, Silvana Bettiol, Michael Charleston, Anke Wiethoelter, Anna-Lena Arnold, Patricia T. Campbell, Peter J. Neville, Phyo. Aung, Tsubasa Shiga, Scott Carver, Simon M. FirestoneAbstractRoss River virus (RRV) is Australia’s most epidemiologically important mosquito-borne disease. During RRV epidemics in the State of Victoria (such as 2010/11 and 2016/17) notifications can account for up to 30% of national RRV notifications. However, little is known about factors which can forecast RRV transmission in Victoria...
Source: Epidemics - November 6, 2019 Category: Epidemiology Source Type: research

Desirable BUGS in models of infectious diseases
Publication date: Available online 17 October 2019Source: EpidemicsAuthor(s): Megan Auzenbergs, Carla Correia-Gomes, Theo Economou, Rachel Lowe, Kathleen M O’ReillyAbstractBayesian inference using Gibbs sampling (BUGS) is a set of statistical software that uses Markov chain Monte Carlo (MCMC) methods to estimate almost any specified model. Originally developed in the late 1980s, the software is an excellent introduction to applied Bayesian statistics without the need to write a MCMC sampler. The software is typically used for regression-based analyses, but any models that can be specified using graphical nodes are po...
Source: Epidemics - October 19, 2019 Category: Epidemiology Source Type: research

Heterogeneous infectiousness in mathematical models of tuberculosis: a systematic review
Publication date: Available online 17 October 2019Source: EpidemicsAuthor(s): Yayehirad A. Melsew, Adeshina I. Adekunle, Allen C. Cheng, Emma S. McBryde, Romain Ragonnet, James M. TrauerAbstractTB mathematical models employ various assumptions and approaches in dealing with the heterogeneous infectiousness of persons with active TB. We reviewed existing approaches and considered the relationship between them and existing epidemiological evidence.We searched the following electronic bibliographic databases from inception to 9 October 2018: MEDLINE, EMBASE, Biosis, Global Health and Scopus. Two investigators extracted data u...
Source: Epidemics - October 19, 2019 Category: Epidemiology Source Type: research

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