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Book: Modeling infectious disease parameters based on serological and social contact data

Hens, Niel

a modern statistical perspective

(Statistics for biology and health)

2012

Author's details	Niel Hens
Series title	Statistics for biology and health
Keywords	Epidemiology--Mathematical models
Language	English
Size	XVI, 298 S. : Ill., zahlr. graph. Darst., 24 cm
Publisher	Springer
Publishing place	New York u.a.
Publishing country	United States
Document type	Book
Accompanying material	Hinweis auf zusätzliches Internetmaterial im Buch
HBZ-ID	HT017399340
ISBN	978-1-4614-4071-0 ; 1-4614-4071-8 ; 9781461440727 ; 1461440726
Database	Catalogue ZB MED Medicine, Health

In stock of ZB MED Cologne/Königswinter

Shelf mark	Loan status	Location
2012 A 3877	order for loan	Magazin

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Article ; Online: Exploring the impact of population ageing on the spread of emerging respiratory infections and the associated burden of mortality.

Møgelmose, Signe / Neels, Karel / Beutels, Philippe / Hens, Niel

BMC infectious diseases

2023 Volume 23, Issue 1, Page(s) 767

Abstract: Background: Increasing life expectancy and persistently low fertility levels have led to old population age structures in most high-income countries, and population ageing is expected to continue or even accelerate in the coming decades. While older ... ...

Abstract	Background: Increasing life expectancy and persistently low fertility levels have led to old population age structures in most high-income countries, and population ageing is expected to continue or even accelerate in the coming decades. While older adults on average have few interactions that potentially could lead to disease transmission, their morbidity and mortality due to infectious diseases, respiratory infections in particular, remain substantial. We aim to explore how population ageing affects the future transmission dynamics and mortality burden of emerging respiratory infections. Methods: Using longitudinal individual-level data from population registers, we model the Belgian population with evolving age and household structures, and explicitly consider long-term care facilities (LTCFs). Three scenarios are presented for the future proportion of older adults living in LTCFs. For each demographic scenario, we simulate outbreaks of SARS-CoV-2 and a novel influenza A virus in 2020, 2030, 2040 and 2050 and distinguish between household and community transmission. We estimate attack rates by age and household size/type, as well as disease-related deaths and the associated quality-adjusted life-years (QALYs) lost. Results: As the population is ageing, small households and LTCFs become more prevalent. Additionally, families with children become smaller (i.e. low fertility, single-parent families). The overall attack rate slightly decreases as the population is ageing, but to a larger degree for influenza than for SARS-CoV-2 due to differential age-specific attack rates. Nevertheless, the number of deaths and QALY losses per 1,000 people is increasing for both infections and at a speed influenced by the share living in LTCFs. Conclusion: Population ageing is associated with smaller outbreaks of COVID-19 and influenza, but at the same time it is causing a substantially larger burden of mortality, even if the proportion of LTCF residents were to decrease. These relationships are influenced by age patterns in epidemiological parameters. Not only the shift in the age distribution, but also the induced changes in the household structures are important to consider when assessing the potential impact of population ageing on the transmission and burden of emerging respiratory infections.
MeSH term(s)	Aged ; Humans ; Aging ; Cause of Death ; Communicable Diseases/epidemiology ; Influenza, Human/epidemiology ; Life Expectancy ; SARS-CoV-2
Language	English
Publishing date	2023-11-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2041550-3
ISSN	1471-2334 ; 1471-2334
ISSN (online)	1471-2334
ISSN	1471-2334
DOI	10.1186/s12879-023-08657-3
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Article: Determinants of life-expectancy and disability-adjusted life years (DALYs) in European and Organisation for Economic Co-operation and Development (OECD) countries: A longitudinal analysis (1990-2019).

Varbanova, Vladimira / Hens, Niel / Beutels, Philippe

SSM - population health

2023 Volume 24, Page(s) 101484

Abstract: We relate 68 factors to population health observed in 61 countries over 30 years.•Using random forests, multiple imputation and generalized estimating equations.•GDP per capita and demographics are key; income inequality is not.•Health and social ... ...

Abstract	•We relate 68 factors to population health observed in 61 countries over 30 years.•Using random forests, multiple imputation and generalized estimating equations.•GDP per capita and demographics are key; income inequality is not.•Health and social expenditure are more influential than freedom and corruption.•On the macro-level, life-style effects appear to be mediated by cultural context.
Language	English
Publishing date	2023-08-10
Publishing country	England
Document type	Journal Article
ISSN	2352-8273
ISSN	2352-8273
DOI	10.1016/j.ssmph.2023.101484
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Article ; Online: An approximate Bayesian approach for estimation of the instantaneous reproduction number under misreported epidemic data.

Gressani, Oswaldo / Faes, Christel / Hens, Niel

Biometrical journal. Biometrische Zeitschrift

2023 Volume 65, Issue 6, Page(s) e2200024

Abstract: In epidemic models, the effective reproduction number is of central importance to assess the transmission dynamics of an infectious disease and to orient health intervention strategies. Publicly shared data during an outbreak often suffers from two ... ...

Abstract	In epidemic models, the effective reproduction number is of central importance to assess the transmission dynamics of an infectious disease and to orient health intervention strategies. Publicly shared data during an outbreak often suffers from two sources of misreporting (underreporting and delay in reporting) that should not be overlooked when estimating epidemiological parameters. The main statistical challenge in models that intrinsically account for a misreporting process lies in the joint estimation of the time-varying reproduction number and the delay/underreporting parameters. Existing Bayesian approaches typically rely on Markov chain Monte Carlo algorithms that are extremely costly from a computational perspective. We propose a much faster alternative based on Laplacian-P-splines (LPS) that combines Bayesian penalized B-splines for flexible and smooth estimation of the instantaneous reproduction number and Laplace approximations to selected posterior distributions for fast computation. Assuming a known generation interval distribution, the incidence at a given calendar time is governed by the epidemic renewal equation and the delay structure is specified through a composite link framework. Laplace approximations to the conditional posterior of the spline vector are obtained from analytical versions of the gradient and Hessian of the log-likelihood, implying a drastic speed-up in the computation of posterior estimates. Furthermore, the proposed LPS approach can be used to obtain point estimates and approximate credible intervals for the delay and reporting probabilities. Simulation of epidemics with different combinations for the underreporting rate and delay structure (one-day, two-day, and weekend delays) show that the proposed LPS methodology delivers fast and accurate estimates outperforming existing methods that do not take into account underreporting and delay patterns. Finally, LPS is illustrated in two real case studies of epidemic outbreaks.
MeSH term(s)	Humans ; Bayes Theorem ; Lipopolysaccharides ; Computer Simulation ; Communicable Diseases/epidemiology ; Epidemics ; Monte Carlo Method
Chemical Substances	Lipopolysaccharides
Language	English
Publishing date	2023-01-13
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	131640-0
ISSN	1521-4036 ; 0323-3847 ; 0006-3452
ISSN (online)	1521-4036
ISSN	0323-3847 ; 0006-3452
DOI	10.1002/bimj.202200024
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Article: Rethinking Screening Intensity in Terms of Reducing Prevalence or Increasing Selection Pressure for the Emergence of Resistant Gonorrhea: A Modeling Study of Men Who Have Sex With Men in Belgium.

Tsoumanis, Achilleas / Van Dijck, Christophe / Hens, Niel / Kenyon, Chris

Open forum infectious diseases

2023 Volume 10, Issue 4, Page(s) ofad165

Abstract: Background: Neisseria gonorrhoeae: Methods: We built a network-based model of NG transmission dynamics among MSM in Belgium to estimate the prevalence of NG in the population and the risk of AMR. The model simulates daily transmission of NG among 3 ... ...

Abstract	Background: Neisseria gonorrhoeae Methods: We built a network-based model of NG transmission dynamics among MSM in Belgium to estimate the prevalence of NG in the population and the risk of AMR. The model simulates daily transmission of NG among 3 anatomical sites in a population of 10 000 MSM, grouped as low risk or high risk, over 10 years. The effect of group-wise variation in treatment efficacy levels and screening intensities on NG prevalence and cumulative risk of AMR emergence was evaluated. Results: Increasing screening intensity in the low-risk MSM had little effect on NG prevalence. An inverse correlation between screening intensity in the high-risk group and both NG prevalence and the risk for azithromycin resistance was observed, irrespective of the screening intensity in the low-risk group. High-risk MSM were at higher risk for azithromycin-resistant NG in all screening intensity and treatment efficacy scenarios, compared to low-risk MSM. Conclusions: Our results suggest that intensive screening in the low-risk population has little impact on prevalence but may increase the probability of AMR emerging. In contrast, intensive screening in the high-risk population reduces both the prevalence of NG and macrolide resistance.
Language	English
Publishing date	2023-03-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2757767-3
ISSN	2328-8957
ISSN	2328-8957
DOI	10.1093/ofid/ofad165
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Article ; Online: Impact of the COVID-19 pandemic on community antibiotic consumption in the EU/European Economic Area: a changepoint analysis.

Vermeulen, Helene / Hens, Niel / Catteau, Lucy / Catry, Boudewijn / Coenen, Samuel

The Journal of antimicrobial chemotherapy

2023 Volume 78, Issue 10, Page(s) 2572–2580

Abstract: Objectives: A decrease in community antibiotic consumption in Europe has been observed during the COVID-19 pandemic. The magnitude of this decrease, how fast after the outbreak it occurred, whether it was sustained during the pandemic and whether the ... ...

Abstract	Objectives: A decrease in community antibiotic consumption in Europe has been observed during the COVID-19 pandemic. The magnitude of this decrease, how fast after the outbreak it occurred, whether it was sustained during the pandemic and whether the seasonal variation in antibiotic consumption was affected, have not yet been evaluated in detail. Methods: Data on community antibiotic consumption were available from the European Surveillance of Antimicrobial Consumption Network for 28 EU/European Economic Area (EEA) countries between 2010 and 2021. Antibiotic consumption was expressed as DDDs per 1000 inhabitants per day (DID). The impact of the pandemic on antibiotic consumption was investigated using descriptive statistics and non-linear mixed changepoint models for quarterly and yearly data. Results: The decrease in overall antibiotic consumption between 2019 and 2020 (-3.4 DID; -18.6%) was mainly due to a decrease in the consumption of penicillins [Anatomical Therapeutic Chemical (ATC) code J01C] (-1.9 DID; -23.0%), other β-lactam antibacterials (J01D) (-0.6 DID; -25.8%) and macrolides, lincosamides and streptogramins (J01F) (-0.5 DID; -17.4%) and was sustained during 2021. The changepoint analysis of yearly data (28 countries) estimated a decrease of 3.3 DID in overall antibiotic consumption (J01) between 2019 and 2020. The analysis of quarterly data (16 countries) estimated a decrease in overall antibiotic consumption (J01) of 4.0 DID and a decrease in seasonal variation of 1.2 DID between the first and second quarters of 2020. Conclusions: The changepoint analysis indicated a significant, sudden and steep decrease in community antibiotic consumption in the EU/EEA immediately after the start of the COVID-19 outbreak in Europe, as well as a decrease in its seasonal variation.
MeSH term(s)	Humans ; Anti-Bacterial Agents/therapeutic use ; Pandemics ; Drug Utilization ; COVID-19/epidemiology ; Streptogramins ; Europe/epidemiology
Chemical Substances	Anti-Bacterial Agents ; Streptogramins
Language	English
Publishing date	2023-10-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	191709-2
ISSN	1460-2091 ; 0305-7453
ISSN (online)	1460-2091
ISSN	0305-7453
DOI	10.1093/jac/dkad273
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Article ; Online: Determinants of basic childhood vaccination coverage in European and OECD countries.

Varbanova, Vladimira / Verelst, Frederik / Hens, Niel / Beutels, Philippe

Human vaccines & immunotherapeutics

2022 Volume 18, Issue 6, Page(s) 2123883

Abstract: Vaccination coverage varies between countries and over time. Using official databases, we extracted data on 50 national-level immunization, socio-economic, demographic, healthcare, and cultural factors, and the uptake of the third dose of diphtheria ... ...

Abstract	Vaccination coverage varies between countries and over time. Using official databases, we extracted data on 50 national-level immunization, socio-economic, demographic, healthcare, and cultural factors, and the uptake of the third dose of diphtheria toxoid, tetanus toxoid, and pertussis vaccines (DTP3) and the first dose of measles-containing vaccines (MCV1) for 61 countries between 1990 and 2019. The main branch of the analysis included all covariates, while a secondary branch excluded life-expectancy and child mortality. The statistical analysis was completed in three stages: a variable-selection stage via random forests; multilevel multiple imputation for missing data in the reduced dataset; and generalized estimating equations (GEE) over all imputed datasets with pooled results. Less than 20 covariates were retained after variable-selection. Among a relatively small number of statistically significant (
Language	English
Publishing date	2022-09-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2664176-8
ISSN	2164-554X ; 2164-5515
ISSN (online)	2164-554X
ISSN	2164-5515
DOI	10.1080/21645515.2022.2123883
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Article ; Online: Incorporating human dynamic populations in models of infectious disease transmission: a systematic review.

Møgelmose, Signe / Neels, Karel / Hens, Niel

BMC infectious diseases

2022 Volume 22, Issue 1, Page(s) 862

Abstract: Background: An increasing number of infectious disease models consider demographic change in the host population, but the demographic methods and assumptions vary considerably. We carry out a systematic review of the methods and assumptions used to ... ...

Abstract	Background: An increasing number of infectious disease models consider demographic change in the host population, but the demographic methods and assumptions vary considerably. We carry out a systematic review of the methods and assumptions used to incorporate dynamic populations in infectious disease models. Methods: We systematically searched PubMed and Web of Science for articles on infectious disease transmission in dynamic host populations. We screened the articles and extracted data in accordance with the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Results: We identified 46 articles containing 53 infectious disease models with dynamic populations. Population dynamics were modelled explicitly in 71% of the disease transmission models using cohort-component-based models (CCBMs) or individual-based models (IBMs), while 29% used population prospects as an external input. Fertility and mortality were in most cases age- or age-sex-specific, but several models used crude fertility rates (40%). Households were incorporated in 15% of the models, which were IBMs except for one model using external population prospects. Finally, 17% of the infectious disease models included demographic sensitivity analyses. Conclusions: We find that most studies model fertility, mortality and migration explicitly. Moreover, population-level modelling was more common than IBMs. Demographic characteristics beyond age and sex are cumbersome to implement in population-level models and were for that reason only incorporated in IBMs. Several IBMs included households and networks, but the granularity of the underlying demographic processes was often similar to that of CCBMs. We describe the implications of the most common assumptions and discuss possible extensions.
MeSH term(s)	Humans ; Male ; Female ; Communicable Diseases/epidemiology ; Family Characteristics ; Research Design
Language	English
Publishing date	2022-11-18
Publishing country	England
Document type	Systematic Review ; Journal Article
ZDB-ID	2041550-3
ISSN	1471-2334 ; 1471-2334
ISSN (online)	1471-2334
ISSN	1471-2334
DOI	10.1186/s12879-022-07842-0
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Article ; Online: Laplacian-P-splines for Bayesian inference in the mixture cure model.

Gressani, Oswaldo / Faes, Christel / Hens, Niel

Statistics in medicine

2022 Volume 41, Issue 14, Page(s) 2602–2626

Abstract: The mixture cure model for analyzing survival data is characterized by the assumption that the population under study is divided into a group of subjects who will experience the event of interest over some finite time horizon and another group of cured ... ...

Abstract	The mixture cure model for analyzing survival data is characterized by the assumption that the population under study is divided into a group of subjects who will experience the event of interest over some finite time horizon and another group of cured subjects who will never experience the event irrespective of the duration of follow-up. When using the Bayesian paradigm for inference in survival models with a cure fraction, it is common practice to rely on Markov chain Monte Carlo (MCMC) methods to sample from posterior distributions. Although computationally feasible, the iterative nature of MCMC often implies long sampling times to explore the target space with chains that may suffer from slow convergence and poor mixing. Furthermore, extra efforts have to be invested in diagnostic checks to monitor the reliability of the generated posterior samples. A sampling-free strategy for fast and flexible Bayesian inference in the mixture cure model is suggested in this article by combining Laplace approximations and penalized B-splines. A logistic regression model is assumed for the cure proportion and a Cox proportional hazards model with a P-spline approximated baseline hazard is used to specify the conditional survival function of susceptible subjects. Laplace approximations to the posterior conditional latent vector are based on analytical formulas for the gradient and Hessian of the log-likelihood, resulting in a substantial speed-up in approximating posterior distributions. The spline specification yields smooth estimates of survival curves and functions of latent variables together with their associated credible interval are estimated in seconds. A fully stochastic algorithm based on a Metropolis-Langevin-within-Gibbs sampler is also suggested as an alternative to the proposed Laplacian-P-splines mixture cure (LPSMC) methodology. The statistical performance and computational efficiency of LPSMC is assessed in a simulation study. Results show that LPSMC is an appealing alternative to MCMC for approximate Bayesian inference in standard mixture cure models. Finally, the novel LPSMC approach is illustrated on three applications involving real survival data.
MeSH term(s)	Algorithms ; Bayes Theorem ; Humans ; Markov Chains ; Monte Carlo Method ; Proportional Hazards Models ; Reproducibility of Results
Language	English
Publishing date	2022-03-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	843037-8
ISSN	1097-0258 ; 0277-6715
ISSN (online)	1097-0258
ISSN	0277-6715
DOI	10.1002/sim.9373
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Article ; Online: Measles epidemic in Southern Vietnam: an age-stratified spatio-temporal model for infectious disease counts.

Nguyen, Thi Huyen Trang / Faes, Christel / Hens, Niel

Epidemiology and infection

2022 Volume 150, Page(s) e169

Abstract: Measles resurged in Vietnam between 2018 and 2020, especially in the Southern region. The proportion of children with measles infection showed quite some variation at the provincial level. We applied a spatio-temporal endemic-epidemic modelling framework ...

Abstract	Measles resurged in Vietnam between 2018 and 2020, especially in the Southern region. The proportion of children with measles infection showed quite some variation at the provincial level. We applied a spatio-temporal endemic-epidemic modelling framework for age-stratified infectious disease counts using measles surveillance data collected in Southern Vietnam between 1 January 2018 and 30 June 2020. We found that disease transmission within age groups was greatest in young children aged 0-4 years whereas a relatively high between-group transmission was observed in older age groups (5-14 years, 15-24 years and 25+ years groups). At the provincial level, spatial transmission followed an age-dependent distance decay with measles spread mainly depending on local and neighbouring transmission. Our study helped to clarify the measles transmission dynamics in a more detailed fashion with respect to age strata, time and space. Findings from this study may help determine proper strategies in measles outbreak control including promotion of age-targeted intervention programmes in specific areas.
MeSH term(s)	Aged ; Child ; Child, Preschool ; Communicable Diseases/epidemiology ; Disease Outbreaks/prevention & control ; Epidemics ; Humans ; Measles/prevention & control ; Vietnam/epidemiology
Language	English
Publishing date	2022-09-12
Publishing country	England
Document type	Journal Article
ZDB-ID	632982-2
ISSN	1469-4409 ; 0950-2688
ISSN (online)	1469-4409
ISSN	0950-2688
DOI	10.1017/S0950268822001431
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