Exogenous re-infection and the dynamics of tuberculosis epidemics: local effects in a network model of transmission

Infection with Mycobacterium tuberculosis leads to tuberculosis (TB) disease by one of the three possible routes: primary progression after a recent infection; re-activation of a latent infection; or exogenous re-infection of a previously infected individual. Recent studies show that optimal TB control strategies may vary depending on the predominant route to disease in a specific population. It is therefore important for public health policy makers to understand the relative frequency of each type of TB within specific epidemiological scenarios. Although molecular epidemiologic tools have been used to estimate the relative contribution of recent transmission and re-activation to the burden of TB disease, it is not possible to use these techniques to distinguish between primary disease and re-infection on a population level. Current estimates of the contribution of re-infection therefore rely on mathematical models which identify the parameters most consistent with epidemiological data; these studies find that exogenous re-infection is important only when TB incidence is high. A basic assumption of these models is that people in a population are all equally likely to come into contact with an infectious case. However, theoretical studies demonstrate that the social and spatial structure can strongly influence the dynamics of infectious disease transmission. Here, we use a network model of TB transmission to evaluate the impact of non-homogeneous mixing on the relative contribution of re-infection over realistic epidemic trajectories. In contrast to the findings of previous models, our results suggest that re-infection may be important in communities where the average disease incidence is moderate or low as the force of infection can be unevenly distributed in the population. These results have important implications for the development of TB control strategies.

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Estimating asymptomatic, undetected and total cases for the COVID-19 outbreak in Wuhan: a mathematical modeling study

BMC Infectious Diseases ◽

10.1186/s12879-021-06078-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Xi Huo ◽

Jing Chen ◽

Shigui Ruan

Keyword(s):

Disease Transmission ◽

Large Scale ◽

Transmission Rate ◽

Control Strategies ◽

Herd Immunity ◽

Antibody Prevalence ◽

Screening Process ◽

Vaccination Programs ◽

Prevalence Level ◽

The Impact

Abstract Background The COVID-19 outbreak in Wuhan started in December 2019 and was under control by the end of March 2020 with a total of 50,006 confirmed cases by the implementation of a series of nonpharmaceutical interventions (NPIs) including unprecedented lockdown of the city. This study analyzes the complete outbreak data from Wuhan, assesses the impact of these public health interventions, and estimates the asymptomatic, undetected and total cases for the COVID-19 outbreak in Wuhan. Methods By taking different stages of the outbreak into account, we developed a time-dependent compartmental model to describe the dynamics of disease transmission and case detection and reporting. Model coefficients were parameterized by using the reported cases and following key events and escalated control strategies. Then the model was used to calibrate the complete outbreak data by using the Monte Carlo Markov Chain (MCMC) method. Finally we used the model to estimate asymptomatic and undetected cases and approximate the overall antibody prevalence level. Results We found that the transmission rate between Jan 24 and Feb 1, 2020, was twice as large as that before the lockdown on Jan 23 and 67.6% (95% CI [0.584,0.759]) of detectable infections occurred during this period. Based on the reported estimates that around 20% of infections were asymptomatic and their transmission ability was about 70% of symptomatic ones, we estimated that there were about 14,448 asymptomatic and undetected cases (95% CI [12,364,23,254]), which yields an estimate of a total of 64,454 infected cases (95% CI [62,370,73,260]), and the overall antibody prevalence level in the population of Wuhan was 0.745% (95% CI [0.693%,0.814%]) by March 31, 2020. Conclusions We conclude that the control of the COVID-19 outbreak in Wuhan was achieved via the enforcement of a combination of multiple NPIs: the lockdown on Jan 23, the stay-at-home order on Feb 2, the massive isolation of all symptomatic individuals via newly constructed special shelter hospitals on Feb 6, and the large scale screening process on Feb 18. Our results indicate that the population in Wuhan is far away from establishing herd immunity and provide insights for other affected countries and regions in designing control strategies and planing vaccination programs.

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Modeling the impact of school reopening and contact tracing strategies on Covid-19 dynamics in different epidemiologic settings in Brazil

10.1101/2021.10.22.21264706 ◽

2021 ◽

Author(s):

Marcelo Eduardo Borges ◽

Leonardo Souto Ferreira ◽

Silas Poloni ◽

Ângela Maria Bagattini ◽

Caroline Franco ◽

...

Keyword(s):

Disease Transmission ◽

Transmission Rate ◽

Disease Incidence ◽

Demographic Data ◽

School Closure ◽

Mitigation Measures ◽

Contact Tracing ◽

School Closures ◽

Infection Transmission ◽

The Impact

Among the various non–pharmaceutical interventions implemented in response to the Covid–19 pandemic during 2020, school closures have been in place in several countries to reduce infection transmission. Nonetheless, the significant short and long–term impacts of prolonged suspension of in–person classes is a major concern. There is still considerable debate around the best timing for school closure and reopening, its impact on the dynamics of disease transmission, and its effectiveness when considered in association with other mitigation measures. Despite the erratic implementation of mitigation measures in Brazil, school closures were among the first measures taken early in the pandemic in most of the 27 states in the country. Further, Brazil delayed the reopening of schools and stands among the countries in which schools remained closed for the most prolonged period in 2020. To assess the impact of school reopening and the effect of contact tracing strategies in rates of Covid–19 cases and deaths, we model the epidemiological dynamics of disease transmission in 3 large urban centers in Brazil under different epidemiological contexts. We implement an extended SEIR model stratified by age and considering contact networks in different settings – school, home, work, and elsewhere, in which the infection transmission rate is affected by various intervention measures. After fitting epidemiological and demographic data, we simulate scenarios with increasing school transmission due to school reopening. Our model shows that reopening schools results in a non–linear increase of reported Covid-19 cases and deaths, which is highly dependent on infection and disease incidence at the time of reopening. While low rates of within[&ndash]school transmission resulted in small effects on disease incidence (cases/100,000 pop), intermediate or high rates can severely impact disease trends resulting in escalating rates of new cases even if other interventions remain unchanged. When contact tracing and quarantining are restricted to school and home settings, a large number of daily tests is required to produce significant effects of reducing the total number of hospitalizations and deaths. Our results suggest that policymakers should carefully consider the epidemiological context and timing regarding the implementation of school closure and return of in-person school activities. Also, although contact tracing strategies are essential to prevent new infections and outbreaks within school environments, our data suggest that they are alone not sufficient to avoid significant impacts on community transmission in the context of school reopening in settings with high and sustained transmission rates.

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Assessing the impact of low-technology emanators alongside long-lasting insecticidal nets to control malaria

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0817 ◽

2020 ◽

Vol 376 (1818) ◽

pp. 20190817 ◽

Cited By ~ 1

Author(s):

Joel Hellewell ◽

Ellie Sherrard-Smith ◽

Sheila Ogoma ◽

Thomas S. Churcher

Keyword(s):

Disease Transmission ◽

Pyrethroid Resistance ◽

Control Strategies ◽

Indoor Residual Spraying ◽

Additional Benefit ◽

Sub Saharan Africa ◽

Outdoor Biting ◽

Mosquito Mortality ◽

The Impact ◽

Long Lasting Insecticidal Nets

Malaria control in sub-Saharan Africa relies on the widespread use of long-lasting insecticidal nets (LLINs) or the indoor residual spraying of insecticide. Disease transmission may be maintained even when these indoor interventions are universally used as some mosquitoes will bite in the early morning and evening when people are outside. As countries seek to eliminate malaria, they can target outdoor biting using new vector control tools such as spatial repellent emanators, which emit airborne insecticide to form a protective area around the user. Field data are used to incorporate a low-technology emanator into a mathematical model of malaria transmission to predict its public health impact across a range of scenarios. Targeting outdoor biting by repeatedly distributing emanators alongside LLINs increases the chance of elimination, but the additional benefit depends on the level of anthropophagy in the local mosquito population, emanator effectiveness and the pre-intervention proportion of mosquitoes biting outdoors. High proportions of pyrethroid-resistant mosquitoes diminish LLIN impact because of reduced mosquito mortality. When mosquitoes are highly anthropophagic, this reduced mortality leads to more outdoor biting and a reduced additional benefit of emanators, even if emanators are assumed to retain their effectiveness in the presence of pyrethroid resistance. Different target product profiles are examined, which show the extra epidemiological benefits of spatial repellents that induce mosquito mortality. This article is part of the theme issue ‘Novel control strategies for mosquito-borne diseases’.

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Vaccinating Adolescents and Children Significantly Reduces COVID-19 Morbidity and Mortality across All Ages: A Popula-Tion-Based Modeling Study Using the UK as an Example

Vaccines ◽

10.3390/vaccines9101180 ◽

2021 ◽

Vol 9 (10) ◽

pp. 1180

Author(s):

Tinevimbo Shiri ◽

Marc Evans ◽

Carla A. Talarico ◽

Angharad R. Morgan ◽

Maaz Mussad ◽

...

Keyword(s):

Disease Transmission ◽

Age Groups ◽

Population Level ◽

Vital Role ◽

Morbidity And Mortality ◽

Transmission Model ◽

Base Case ◽

Global Public Health ◽

The Uk ◽

The Impact

Debate persists around the risk–benefit balance of vaccinating adolescents and children against COVID-19. Central to this debate is quantifying the contribution of adolescents and children to the transmission of SARS-CoV-2, and the potential impact of vaccinating these age groups. In this study, we present a novel SEIR mathematical disease transmission model that quantifies the impact of different vaccination strategies on population-level SARS-CoV-2 infections and clinical outcomes. The model employs both age- and time-dependent social mixing patterns to capture the impact of changes in restrictions. The model was used to assess the impact of vaccinating adolescents and children on the natural history of the COVID-19 pandemic across all age groups, using the UK as an example. The base case model demonstrates significant increases in COVID-19 disease burden in the UK following a relaxation of restrictions, if vaccines are limited to those ≥18 years and vulnerable adolescents (≥12 years). Including adolescents and children in the vaccination program could reduce overall COVID-related mortality by 57%, and reduce cases of long COVID by 75%. This study demonstrates that vaccinating adolescents and children has the potential to play a vital role in reducing SARS-CoV-2 infections, and subsequent COVID-19 morbidity and mortality, across all ages. Our results have major global public health implications and provide valuable information to inform a potential pandemic exit strategy.

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Moving towards a reliable HIV incidence test – current status, resources available, future directions and challenges ahead

Epidemiology and Infection ◽

10.1017/s0950268816002910 ◽

2016 ◽

Vol 145 (5) ◽

pp. 925-941 ◽

Cited By ~ 19

Author(s):

G. MURPHY ◽

C. D. PILCHER ◽

S. M. KEATING ◽

R. KASSANJEE ◽

S. N. FACENTE ◽

...

Keyword(s):

Performance Metrics ◽

Critical Path ◽

Population Level ◽

Current Status ◽

Hiv Incidence ◽

Recent Infection ◽

Novel Approach ◽

Product Profile ◽

And Performance ◽

The Impact

SUMMARYIn 2011 the Incidence Assay Critical Path Working Group reviewed the current state of HIV incidence assays and helped to determine a critical path to the introduction of an HIV incidence assay. At that time the Consortium for Evaluation and Performance of HIV Incidence Assays (CEPHIA) was formed to spur progress and raise standards among assay developers, scientists and laboratories involved in HIV incidence measurement and to structure and conduct a direct independent comparative evaluation of the performance of 10 existing HIV incidence assays, to be considered singly and in combinations as recent infection test algorithms. In this paper we report on a new framework for HIV incidence assay evaluation that has emerged from this effort over the past 5 years, which includes a preliminary target product profile for an incidence assay, a consensus around key performance metrics along with analytical tools and deployment of a standardized approach for incidence assay evaluation. The specimen panels for this evaluation have been collected in large volumes, characterized using a novel approach for infection dating rules and assembled into panels designed to assess the impact of important sources of measurement error with incidence assays such as viral subtype, elite host control of viraemia and antiretroviral treatment. We present the specific rationale for several of these innovations, and discuss important resources for assay developers and researchers that have recently become available. Finally, we summarize the key remaining steps on the path to development and implementation of reliable assays for monitoring HIV incidence at a population level.

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Introduction to pertussis transmission and epidemiological dynamics

Pertussis ◽

10.1093/oso/9780198811879.003.0001 ◽

2018 ◽

pp. 6-25

Author(s):

Pejman Rohani ◽

Samuel V. Scarpino

Keyword(s):

Control Strategies ◽

Age Distribution ◽

Population Level ◽

Vaccine Uptake ◽

Effective Control ◽

Transmission Potential ◽

Epidemic Period ◽

The Impact ◽

Pertussis Epidemiology

Resolving the long-term, population-level consequences of changes in pertussis epidemiology, arising from bacterial evolution, shifts in vaccine-induced immunity, or changes in surveillance, are key challenges for devising effective control strategies. This chapter reviews some of the key features of pertussis epidemiology, together with the underlying epidemiological principles that set the context for their interpretation. These include the relationship between the age distribution of cases and pertussis transmission potential, the impact of vaccine uptake on incidence, periodicity and age incidence, as well as spatially explicit recurrent pertussis epidemics and associated extinction frequency. This review highlights some of the predictable and consistent aspects of pertussis epidemiology (e.g. the systematic increase in the inter-epidemic period with the introduction of whole-cell vaccines) and a number of important heterogeneities, including variations in contemporary patterns of incidence and geographic spread.

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The effects of non-pharmaceutical interventions on SARS-CoV-2 transmission in different socioeconomic populations in Kuwait: A modelling study

University of Toronto Journal of Public Health ◽

10.33137/utjph.v2i2.36995 ◽

2021 ◽

Vol 2 (2) ◽

Author(s):

Fatima Khadadah ◽

Abdullah A. Al-Shammari ◽

Ahmad Alhashemi ◽

Dari Alhuwail ◽

Bader Al-Saif ◽

...

Keyword(s):

Disease Transmission ◽

Reproduction Number ◽

Public Health Intervention ◽

Population Level ◽

Socioeconomic Groups ◽

Before And After ◽

Cross Transmission ◽

Community Transmission ◽

The Impact ◽

Pharmaceutical Interventions

Background: Aggressive non-pharmaceutical interventions (NPIs) may reduce transmission of SARS-CoV2. The extent to which these interventions are successful in stopping the spread have not been characterized in countries with distinct socioeconomic groups. We compared the effects of a partial lockdown on disease transmission among Kuwaitis (P1) and non-Kuwaitis (P2) living in Kuwait. Methods: We fit a metapopulation Susceptible-Exposed-Infectious-Recovered (SEIR) model to reported cases stratified by two groups to estimate the impact of a lockdown on the effective reproduction number (Re). We estimated the basic reproduction number (R0) for the transmission in each group and simulated the potential trajectories of an outbreak from the first recorded case of community transmission until 12 days after the lockdown. We estimated Re values of both groups before and after the lockdown, simulated the effect of these values on epidemic curves and explored a range of cross-transmission scenarios. Results: We estimate R0 at 1·06 (95% CI: 1·05-1·28) for P1 and 1·83 (1·58-2·33) for P2. On March 22nd, Re for P1 and P2 are estimated at 1·13 (1·07-1·17) and 1·38 (1·25-1·63) respectively. After the curfew had taken effect, Re for P1 dropped modestly to 1·04 (1·02-1·06) but almost doubled for P2 to 2·47 (1·98-3·45). Our simulated epidemic trajectories show that the partial curfew measure modestly reduced and delayed the height of the peak in P1, yet significantly elevated and hastened the peak in P2. Modest cross-transmission from P2 to P1 elevated the height of the peak in P1 and brought it forward in time closer to the peak of P2. Conclusion: Our results demonstrate that a lockdown can reduce SARS-CoV2 transmission in one subpopulation but accelerate it in another. At the population level, the consequences of lockdowns may vary across the socioeconomic spectrum. Any public health intervention needs to be sensitive to disparities within populations.

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Impact of non-pharmaceutical interventions against COVID-19 in Europe in 2020: a quasi-experimental non-equivalent group and time series design study

Eurosurveillance ◽

10.2807/1560-7917.es.2021.26.28.2001401 ◽

2021 ◽

Vol 26 (28) ◽

Author(s):

Paul R Hunter ◽

Felipe J Colón-González ◽

Julii Brainard ◽

Steven Rushton

Keyword(s):

Social Life ◽

Control Strategies ◽

Disease Incidence ◽

Disease Spread ◽

Social Distancing ◽

Mass Gatherings ◽

Quasi Experimental ◽

The Impact ◽

Pharmaceutical Interventions ◽

At Home

Introduction The current pandemic of coronavirus disease (COVID-19) is unparalleled in recent history as are the social distancing interventions that have led to a considerable halt on the economic and social life of so many countries. Aim We aimed to generate empirical evidence about which social distancing measures had the most impact in reducing case counts and mortality. Methods We report a quasi-experimental (observational) study of the impact of various interventions for control of the outbreak through 24 April 2020. Chronological data on case numbers and deaths were taken from the daily published figures by the European Centre for Disease Prevention and Control and dates of initiation of various control strategies from the Institute of Health Metrics and Evaluation website and published sources. Our complementary analyses were modelled in R using Bayesian generalised additive mixed models and in STATA using multilevel mixed-effects regression models. Results From both sets of modelling, we found that closure of education facilities, prohibiting mass gatherings and closure of some non-essential businesses were associated with reduced incidence whereas stay-at-home orders and closure of additional non-essential businesses was not associated with any independent additional impact. Conclusions Our findings are that schools and some non-essential businesses operating ‘as normal’ as well as allowing mass gatherings were incompatible with suppressing disease spread. Closure of all businesses and stay at home orders are less likely to be required to keep disease incidence low. Our results help identify what were the most effective non-pharmaceutical interventions in this period.

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COVID-19 effective reproductive ratio determination: An application, and analysis of issues and influential factors

10.1101/2020.07.15.20154039 ◽

2020 ◽

Cited By ~ 1

Author(s):

Luis Alfredo Bautista Balbás ◽

Mario Gil Conesa ◽

Gil Rodríguez Caravaca ◽

Blanca Bautista Balbás

Keyword(s):

Web Application ◽

Control Strategies ◽

Infected Individual ◽

National Level ◽

Open Data ◽

Conclusive Evidence ◽

Influential Factors ◽

Mitigation Strategies ◽

Epidemic Control ◽

The Impact

An essential indicator of COVID-19 transmission is the effective reproduction number (Rt), the number of cases which an infected individual is expected to infect at a particular moment of time; curves of the evolution of Rt over time (transmission curves) reflect the impact of preventive measures and whether an epidemic is controlled. We have created a Shiny/R web application with user-selectable features: open data sources with daily COVID-19 incidences from all countries and many regions, customizable preprocessing options (smoothing, proportional increment, backwards distribution of negative corrections, etc), different MonteCarlo-Markov-Chain estimates of the generation time or serial interval distributions and state-of-the-art Rt estimation frameworks (EpiEstim, R0). We have analyzed the impact of these factors in the obtained transmission curves. We also have obtained curves at the national and sub-national level and analyzed the impact of epidemic control strategies, superspreading events, socioeconomic factors and outbreaks. We conclude that country wealth and, to a lesser extent, mitigation strategies, were associated with poorer epidemic control. Dataset quality was an important factor, and sometimes dictated the necessity of time series smoothing. We couldn't find conclusive evidence regarding the impact of alleged superspreading events. In the reopening phase, outbreaks had an impact on transmission curves. This application could be used interactively as a tool both to obtain transmission estimates and to perform interactive sensitivity analysis.

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Pulmonary tuberculosis incidence, trends and predictions in Monastir, Tunisia (2000-2030)

European Journal of Public Health ◽

10.1093/eurpub/ckaa165.798 ◽

2020 ◽

Vol 30 (Supplement_5) ◽

Author(s):

C Ben Nasrallah ◽

I Zemni ◽

M Kacem ◽

W Dhouib ◽

R Bannour ◽

...

Keyword(s):

Pulmonary Tuberculosis ◽

Incidence Rate ◽

Program Effectiveness ◽

Control Strategies ◽

Control Program ◽

Crude Incidence ◽

Age Cohorts ◽

Tb Control ◽

Incidence Trends ◽

The Impact

Abstract Background Tuberculosis (TB) continues to be one of the infectious diseases with the highest morbidity worldwide. The lung is the most commonly involved organ, but lesions can occur in other body systems. This study aimed to describe incidence and trends of pulmonary tuberculosis (PTB) over a period of 18 years in Monastir and to estimate predictions for 2030. Methods We carried out an observational study from 2000 to 2017. Data were collected by the regional direction of primary health care. Incidence was estimated by the crude incidence rate (CIR) and the age standardized rate (ASR). Poisson regression model was used to calculate the slope 'b' in order to describe trends and was performed to estimate incidence projection for 2030. Data were verified and analyzed using IBM SPSS Statistics version 22.0 software. Results A total of 997 patients were recorded with 486 cases of PTB (48.95%). Sex ratio was 2.85. The median age was 40.5 [IQR 28-56] years old. PTB ASR was 5.71/100,000 inhabitants (inh). CIR was the highest among the eldest cohort aged more than 60 years (12.65/100,000 inh) and the lowest among youth aged less than 19 years (1.01/100,000 inh). We established a negative trend of PTB over 18 years (b= -0.032; p < 10-4) in all age cohorts. PTB would be decreasing by 2030 with an estimate incidence rate of 1.83/100,000 inh. Conclusions The decline of PTB may be a sign of TB control program effectiveness in Monastir. Thus, the challenges for the future are to maintain PTB towards decreasing. Key messages Our study highlighted the impact of TB control strategies in Tunisia. Our findings play a key role in estimating whether the WHO’s End TB strategy targets can be achieved by 2030.

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