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The Zika virus (ZIKV) is a serious global public health crisis. A major control challenge is its multiple transmission modes. This paper aims to simulate the transmission patterns of ZIKV using a dynamic process-based epidemiological model written in ordinary differential equations, which incorporates the human-to-mosquito infection by bites and sewage, mosquito-to-human infection by bites, and human-to-human infection by sex. Mathematical analyses are carried out to calculate the basic reproduction number and backward bifurcation, and prove the existence and stability of the equilibria. The model is validated with infection data by applying it to the 2015–2016 ZIKV epidemic in Brazil. The results indicate that the reproduction number is estimated to be 2.13, in which the contributions by mosquito bite, sex and sewage account for 85.7%, 3.5% and 10.8%, respectively. This number and the morbidity rate are most sensitive to parameters related to mosquito ecology, rather than asymptomatic or human-to-human transmission. Multiple transmission routes and suitable temperature exacerbate ZIKV infection in Brazil, and the vast majority of human infection cases were prevented by the intervention implemented. These findings may provide new insights to improve the risk assessment of ZIKV infection. [ABSTRACT FROM AUTHOR]

The Zika virus (ZIKV) is a serious global public health crisis. A major control challenge is its multiple transmission modes. This paper aims to simulate the transmission patterns of ZIKV using a dynamic process-based epidemiological model written in ordinary differential equations, which incorporates the human-to-mosquito infection by bites and sewage, mosquito-to-human infection by bites, and human-to-human infection by sex. Mathematical analyses are carried out to calculate the basic reproduction number and backward bifurcation, and prove the existence and stability of the equilibria. The model is validated with infection data by applying it to the 2015–2016 ZIKV epidemic in Brazil. The results indicate that the reproduction number is estimated to be 2.13, in which the contributions by mosquito bite, sex and sewage account for 85.7%, 3.5% and 10.8%, respectively. This number and the morbidity rate are most sensitive to parameters related to mosquito ecology, rather than asymptomatic or human-to-human transmission. Multiple transmission routes and suitable temperature exacerbate ZIKV infection in Brazil, and the vast majority of human infection cases were prevented by the intervention implemented. These findings may provide new insights to improve the risk assessment of ZIKV infection. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has caused significant disruptions to the daily lives of individuals worldwide, with many losing their lives to the virus. Vaccination has been identified as a crucial strategy to combat the spread of a disease, but with a limited supply of vaccines, targeted blocking is becoming increasingly necessary. One such approach is to block a select group of individuals in the community to control the spread of the disease in its early stages. Therefore, in this paper, a method is proposed for solving this problem, based on the similarity between this issue and the problem of identifying super-spreader nodes. The proposed method attempts to select the minimum set of network nodes that, when removed, no large component remains in the network. To this end, the network is partitioned into various communities, and a method for limiting the spread of the disease to communities is proposed by blocking connecting nodes. Four real networks and four synthetics networks created using the LFR algorithm were used to evaluate the control of the disease by the selected set of nodes using each method, and the results obtained indicate better performance of the proposed method compared to other methods. [ABSTRACT FROM AUTHOR]

A dramatic increase in the number of outbreaks of dengue has recently been reported, and climate change is likely to extend the geographical spread of the disease. In this context, this paper shows how a neural network approach can incorporate dengue and COVID-19 data as well as external factors (such as social behaviour or climate variables), to develop predictive models that could improve our knowledge and provide useful tools for health policy makers. Through the use of neural networks with different social and natural parameters, in this paper we define a Correlation Model through which we show that the number of cases of COVID-19 and dengue have very similar trends. We then illustrate the relevance of our model by extending it to a Long short-term memory model (LSTM) that incorporates both diseases, and using this to estimate dengue infections via COVID-19 data in countries that lack sufficient dengue data. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has caused significant disruptions to the daily lives of individuals worldwide, with many losing their lives to the virus. Vaccination has been identified as a crucial strategy to combat the spread of a disease, but with a limited supply of vaccines, targeted blocking is becoming increasingly necessary. One such approach is to block a select group of individuals in the community to control the spread of the disease in its early stages. Therefore, in this paper, a method is proposed for solving this problem, based on the similarity between this issue and the problem of identifying super-spreader nodes. The proposed method attempts to select the minimum set of network nodes that, when removed, no large component remains in the network. To this end, the network is partitioned into various communities, and a method for limiting the spread of the disease to communities is proposed by blocking connecting nodes. Four real networks and four synthetics networks created using the LFR algorithm were used to evaluate the control of the disease by the selected set of nodes using each method, and the results obtained indicate better performance of the proposed method compared to other methods. [ABSTRACT FROM AUTHOR]

Human mobility is a key driver of infectious disease spread. Recent literature has uncovered a clear pattern underlying the complexity of human mobility in cities: r · f , the product of distance traveled r and frequency of return f per user to a given location, is invariant across space. This paper asks whether the invariant r · f also serves as a driver for epidemic spread, so that the risk associated with human movement can be modeled by a unifying variable r · f . We use two large-scale datasets of individual human mobility to show that there is in fact a simple relation between r and f and both speed and spatial dispersion of disease spread. This discovery could assist in modeling spread of disease and inform travel policies in future epidemics—based not only on travel distance r but also on frequency of return f. [ABSTRACT FROM AUTHOR]

In this paper, a new spatio-temporal model is formulated to study the spread of coronavirus infection (COVID-19) in a spatially heterogeneous environment with the impact of vaccination. Initially, a detailed qualitative analysis of the spatio-temporal model is presented. The existence, uniqueness, positivity, and boundedness of the model solution are investigated. Local asymptotical stability of the diffusive COVID-19 model at steady state is carried out using well-known criteria. Moreover, a suitable nonlinear Lyapunov functional is constructed for the global asymptotical stability of the spatio-temporal model. Further, the model is solved numerically based on uniform and non-uniform initial conditions. Two different numerical schemes named: finite difference operator-splitting and mesh-free operator-splitting based on multi-quadratic radial basis functions are implemented in the numerical study. The impact of diffusion as well as some pharmaceutical and non-pharmaceutical control measures, i.e., reducing an effective contact causing infection transmission, vaccination rate and vaccine waning rate on the disease dynamics is presented in a spatially heterogeneous environment. Furthermore, the impact of the aforementioned interventions is investigated with and without diffusion on the incidence of disease. The simulation results conclude that the random motion of individuals has a significant impact on the disease dynamics and helps in setting a better control strategy for disease eradication. [ABSTRACT FROM AUTHOR]

The global COVID-19 pandemic brought considerable public and policy attention to the field of infectious disease modelling. A major hurdle that modellers must overcome, particularly when models are used to develop policy, is quantifying the uncertainty in a model's predictions. By including the most recent available data in a model, the quality of its predictions can be improved and uncertainties reduced. This paper adapts an existing, large-scale, individual-based COVID-19 model to explore the benefits of updating the model in pseudo-real time. We use Approximate Bayesian Computation (ABC) to dynamically recalibrate the model's parameter values as new data emerge. ABC offers advantages over alternative calibration methods by providing information about the uncertainty associated with particular parameter values and the resulting COVID-19 predictions through posterior distributions. Analysing such distributions is crucial in fully understanding a model and its outputs. We find that forecasts of future disease infection rates are improved substantially by incorporating up-to-date observations and that the uncertainty in forecasts drops considerably in later simulation windows (as the model is provided with additional data). This is an important outcome because the uncertainty in model predictions is often overlooked when models are used in policy. [ABSTRACT FROM AUTHOR]

There are numerous contagious diseases caused by pathogenic microorganisms, including bacteria, viruses, fungi, and parasites, that have the propensity to culminate in fatal consequences. A communicable disease is an illness caused by a contagion agent or its toxins and spread directly or indirectly to a susceptible animal or human host by an infected person, animal, vector, or immaterial environment. Human immunodeficiency virus (HIV) infection, hepatitis A, B, and C, and measles are all examples of communicable diseases. Acquired immunodeficiency syndrome (AIDS) is a communicable disease caused by HIV infection that has become the most severe issue facing humanity. The research work in this paper is to numerically explore a mathematical model and demonstrate the dynamics of HIV/AIDS disease transmission using a continuous Galerkin–Petrov time discretization of a higher-order scheme, specifically the cGP(2)-scheme. Depict a graphical and tabular comparison between the outcomes of the mentioned scheme and those obtained through other classical schemes that exist in the literature. Further, a comparison is performed relative to the well-known fourth-order Ruge–Kutta (RK4) method with different step sizes. By contrast, the suggested approach provided more accurate results with a larger step size than RK4 with a smaller step size. After validation and confirmation of the suggested scheme and code, we implement the method to the extended model by introducing a treatment rate and show the impact of various non-linear source terms for the generation of new cells. We also determined the basic reproduction number and use the Routh-Hurwitz criterion to assess the stability of disease-free and unique endemic equilibrium states of the HIV model. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic raised public awareness about airborne particulate matter (PM) due to the spread of infectious diseases via the respiratory route. The persistence of potentially infectious aerosols in public spaces and the spread of nosocomial infections in medical settings deserve careful investigation; however, a systematic approach characterizing the fate of aerosols in clinical environments has not been reported. This paper presents a methodology for mapping aerosol propagation using a low-cost PM sensor network in ICU and adjacent environments and the subsequent development of the data-driven zonal model. Mimicking aerosol generation by a patient, we generated trace NaCl aerosols and monitored their propagation in the environment. In positive (closed door) and neutral-pressure (open door) ICUs, up to 6% or 19%, respectively, of all PM escaped through the door gaps; however, the outside sensors did not register an aerosol spike in negative-pressure ICUs. The K-means clustering analysis of temporospatial aerosol concentration data suggests that ICU can be represented by three distinct zones: (1) near the aerosol source, (2) room periphery, and (3) outside the room. The data suggests two-phase plume behavior: dispersion of the original aerosol spike throughout the room, followed by an evacuation phase where "well-mixed" aerosol concentration decayed uniformly. Decay rates were calculated for positive, neutral, and negative pressure operations, with negative-pressure rooms clearing out nearly twice as fast. These decay trends closely followed the air exchange rates. This research demonstrates the methodology for aerosol monitoring in medical settings. This study is limited by a relatively small data set and is specific to single-occupancy ICU rooms. Future work needs to evaluate medical settings with high risks of infectious disease transmission. [ABSTRACT FROM AUTHOR]

The risk of epidemic spread of diseases in livestock poses a threat to animal and often also human health. Important for the assessment of the effect of control measures is a statistical model quantification of between-farm transmission during epidemics. In particular, quantification of the between-farm transmission kernel has proven its importance for a range of different diseases in livestock. In this paper we explore if a comparison of the different transmission kernels yields further insight. Our comparison identifies common features that connect across the different pathogen-host combinations analyzed. We conjecture that these features are universal and thereby provide generic insights. Comparison of the shape of the spatial transmission kernel suggests that, in absence of animal movement bans, the distance dependence of transmission has a universal shape analogous to Lévy-walk model descriptions of human movement patterns. Also, our analysis suggests that interventions such as movement bans and zoning, through their impact on these movement patterns, change the shape of the kernel in a universal fashion. We discuss how the generic insights suggested can be of practical use for assessing risks of spread and optimizing control measures, in particular when outbreak data is scarce. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has called for swift action from local governments, which have instated non-pharmaceutical interventions (NPIs) to curb the spread of the disease. The swift implementation of social distancing policies has raised questions about the costs and benefits of strategies that either aim to keep cases as low as possible (suppression) or aim to reach herd immunity quickly (mitigation) to tackle the COVID-19 pandemic. While curbing COVID-19 required blunt instruments, it is unclear whether a less-transmissible and less-deadly emerging pathogen would justify the same response. This paper illuminates this question using a parsimonious transmission model by formulating the social distancing lives vs. livelihoods dilemma as a boundary value problem using calculus of variations. In this setup, society balances the costs and benefits of social distancing contingent on the costs of reducing transmission relative to the burden imposed by the disease. We consider both single-objective and multi-objective formulations of the problem. To the best of our knowledge, our approach is distinct in the sense that strategies emerge from the problem structure rather than being imposed a priori. We find that the relative time-horizon of the pandemic (i.e., the time it takes to develop effective vaccines and treatments) and the relative cost of social distancing influence the choice of the optimal policy. Unsurprisingly, we find that the appropriate policy response depends on these two factors. We discuss the conditions under which each policy archetype (suppression vs. mitigation) appears to be the most appropriate. [ABSTRACT FROM AUTHOR]

The dynamics of human mobility have been known to play a critical role in the spread of infectious diseases like COVID-19. In this paper, we present a simple compact way to model the transmission of infectious disease through transportation networks using widely available aggregate mobility data in the form of a zone-level origin-destination (OD) travel flow matrix. A key feature of our model is that it not only captures the propagation of infection via direct connections between zones (first-order effects) as in most existing studies but also transmission effects that are due to subsequent interactions in the remainder of the system (higher-order effects). We demonstrate the importance of capturing higher-order effects in a simulation study. We then apply our model to study the first wave of COVID-19 infections in (i) Italy, and, (ii) the New York Tri-State area. We use daily data on mobility between Italian provinces (province-level OD data) and between Tri-State Area counties (county-level OD data), and daily reported caseloads at the same geographical levels. Our empirical results indicate substantial predictive power, particularly during the early stages of the outbreak. Our model forecasts at least 85% of the spatial variation in observed weekly COVID-19 cases. Most importantly, our model delivers crucial metrics to identify target areas for intervention. [ABSTRACT FROM AUTHOR]

Controlling the spreading of infectious diseases has been shown crucial in the COVID-19 pandemic. Traditional contact tracing is used to detect newly infected individuals by tracing their previous contacts, and by selectively checking and isolating any individuals likely to have been infected. Digital contact tracing with the utilisation of smartphones was contrived as a technological aid to improve this manual, slow and tedious process. Nevertheless, despite the high hopes raised when smartphone-based contact tracing apps were introduced as a measure to reduce the spread of the COVID-19, their efficiency has been moderately low. In this paper, we propose a methodology for evaluating digital contact tracing apps, based on an epidemic model, which will be used not only to evaluate the deployed Apps against the COVID-19 but also to determine how they can be improved for future pandemics. Firstly, the model confirms the moderate effectiveness of the deployed digital contact tracing, confirming the fact that it could not be used as the unique measure to fight against the COVID-19, and had to be combined with additional measures. Secondly, several improvements are proposed (and evaluated) to increase the efficiency of digital control tracing to become a more useful tool in the future. [ABSTRACT FROM AUTHOR]

In this paper, we study the Covid 19 disease profile in the Algerian territory since February 25, 2020 to February 13, 2021. The idea is to develop a decision support system allowing public health decision and policy-makers to have future statistics (the daily prediction of parameters) of the pandemic; and also encourage citizens for conducting health protocols. Many studies applied traditional epidemic models or machine learning models to forecast the evolution of coronavirus epidemic, but the use of such models alone to make the prediction will be less precise. For this purpose, we assume that the spread of the coronavirus is a moving target described by an epidemic model. On the basis of a SIRD model (Susceptible-Infection-Recovery- Death), we applied the EKF algorithm to predict daily all parameters. These predicted parameters will be much beneficial to hospital managers for updating the available means of hospitalization (beds, oxygen concentrator, etc.) in order to reduce the mortality rate and the infected. Simulations carried out reveal that the EKF seems to be more efficient according to the obtained results. [ABSTRACT FROM AUTHOR]

Controlling the spreading of infectious diseases has been shown crucial in the COVID-19 pandemic. Traditional contact tracing is used to detect newly infected individuals by tracing their previous contacts, and by selectively checking and isolating any individuals likely to have been infected. Digital contact tracing with the utilisation of smartphones was contrived as a technological aid to improve this manual, slow and tedious process. Nevertheless, despite the high hopes raised when smartphone-based contact tracing apps were introduced as a measure to reduce the spread of the COVID-19, their efficiency has been moderately low. In this paper, we propose a methodology for evaluating digital contact tracing apps, based on an epidemic model, which will be used not only to evaluate the deployed Apps against the COVID-19 but also to determine how they can be improved for future pandemics. Firstly, the model confirms the moderate effectiveness of the deployed digital contact tracing, confirming the fact that it could not be used as the unique measure to fight against the COVID-19, and had to be combined with additional measures. Secondly, several improvements are proposed (and evaluated) to increase the efficiency of digital control tracing to become a more useful tool in the future. [ABSTRACT FROM AUTHOR]

In order to slow the spread of the CoViD-19 pandemic, governments around the world have enacted a wide set of policies limiting the transmission of the disease. Initially, these focused on non-pharmaceutical interventions; more recently, vaccinations and large-scale rapid testing have started to play a major role. The objective of this study is to explain the quantitative effects of these policies on determining the course of the pandemic, allowing for factors like seasonality or virus strains with different transmission profiles. To do so, the study develops an agent-based simulation model, which explicitly takes into account test demand and behavioral changes following positive tests. The model is estimated using data for the second and the third wave of the CoViD-19 pandemic in Germany. The paper finds that during a period where vaccination rates rose from 5 to 40%, seasonality and rapid testing had the largest effect on reducing infection numbers. Frequent large-scale rapid testing should remain part of strategies to contain CoViD-19; it can substitute for many non-pharmaceutical interventions that come at a much larger cost to individuals, society, and the economy. [ABSTRACT FROM AUTHOR]

Identifying influential spreaders is an important task in controlling the spread of information and epidemic diseases in complex networks. Many recent studies have indicated that the identification of influential spreaders is dependent on the spreading dynamics. Finding a general optimal order of node importance ranking is difficult because of the complexity of network structures and the physical background of dynamics. In this paper, we use four metrics, namely, betweenness, degree, H-index, and coreness, to measure the central attributes of nodes for constructing the disease spreading models and target immunization strategies. Numerical simulations show that spreading processes based on betweenness centrality lead to the widest range of propagation and the smallest epidemic threshold for all six networks (including four real networks and two BA scale-free networks generated according to Barabasi–Albert algorithm). The target immunization strategy based on the betweenness centrality of nodes is the most effective for BA scale-free networks but displays poor immune effect for real networks in identifying the most important spreaders for disease control. The immunization strategy based on node degrees is the most effective for the four real networks. Findings show that the target immune strategy based on the betweenness centrality of nodes works best for standard scale-free networks, whereas that based on node degrees works best for other nonstandard scale-free networks. The results can provide insights into understanding the different metrics of measuring node importance in disease transmission and control. [ABSTRACT FROM AUTHOR]

Social distancing measures are effective in reducing overall community transmission but much remains unknown about how they have impacted finer-scale dynamics. In particular, much is unknown about how changes of contact patterns and other behaviors including adherence to social distancing, induced by these measures, may have impacted finer-scale transmission dynamics among different age groups. In this paper, we build a stochastic age-specific transmission model to systematically characterize the degree and variation of age-specific transmission dynamics, before and after lifting the lockdown in Georgia, USA. We perform Bayesian (missing-)data-augmentation model inference, leveraging reported age-specific case, seroprevalence and mortality data. We estimate that overall population-level transmissibility was reduced to 41.2% with 95% CI [39%, 43.8%] of the pre-lockdown level in about a week of the announcement of the shelter-in-place order. Although it subsequently increased after the lockdown was lifted, it only bounced back to 62% [58%, 67.2%] of the pre-lockdown level after about a month. We also find that during the lockdown susceptibility to infection increases with age. Specifically, relative to the oldest age group (> 65+), susceptibility for the youngest age group (0–17 years) is 0.13 [0.09, 0.18], and it increases to 0.53 [0.49, 0.59] for 18–44 and 0.75 [0.68, 0.82] for 45–64. More importantly, our results reveal clear changes of age-specific susceptibility (defined as average risk of getting infected during an infectious contact incorporating age-dependent behavioral factors) after the lockdown was lifted, with a trend largely consistent with reported age-specific adherence levels to social distancing and preventive measures. Specifically, the older groups (> 45) (with the highest levels of adherence) appear to have the most significant reductions of susceptibility (e.g., post-lockdown susceptibility reduced to 31.6% [29.3%, 34%] of the estimate before lifting the lockdown for the 6+ group). Finally, we find heterogeneity in case reporting among different age groups, with the lowest rate occurring among the 0–17 group (9.7% [6.4%, 19%]). Our results provide a more fundamental understanding of the impacts of stringent lockdown measures, and finer evidence that other social distancing and preventive measures may be effective in reducing SARS-CoV-2 transmission. These results may be exploited to guide more effective implementations of these measures in many current settings (with low vaccination rate globally and emerging variants) and in future potential outbreaks of novel pathogens. [ABSTRACT FROM AUTHOR]

Social distancing measures are effective in reducing overall community transmission but much remains unknown about how they have impacted finer-scale dynamics. In particular, much is unknown about how changes of contact patterns and other behaviors including adherence to social distancing, induced by these measures, may have impacted finer-scale transmission dynamics among different age groups. In this paper, we build a stochastic age-specific transmission model to systematically characterize the degree and variation of age-specific transmission dynamics, before and after lifting the lockdown in Georgia, USA. We perform Bayesian (missing-)data-augmentation model inference, leveraging reported age-specific case, seroprevalence and mortality data. We estimate that overall population-level transmissibility was reduced to 41.2% with 95% CI [39%, 43.8%] of the pre-lockdown level in about a week of the announcement of the shelter-in-place order. Although it subsequently increased after the lockdown was lifted, it only bounced back to 62% [58%, 67.2%] of the pre-lockdown level after about a month. We also find that during the lockdown susceptibility to infection increases with age. Specifically, relative to the oldest age group (> 65+), susceptibility for the youngest age group (0–17 years) is 0.13 [0.09, 0.18], and it increases to 0.53 [0.49, 0.59] for 18–44 and 0.75 [0.68, 0.82] for 45–64. More importantly, our results reveal clear changes of age-specific susceptibility (defined as average risk of getting infected during an infectious contact incorporating age-dependent behavioral factors) after the lockdown was lifted, with a trend largely consistent with reported age-specific adherence levels to social distancing and preventive measures. Specifically, the older groups (> 45) (with the highest levels of adherence) appear to have the most significant reductions of susceptibility (e.g., post-lockdown susceptibility reduced to 31.6% [29.3%, 34%] of the estimate before lifting the lockdown for the 6+ group). Finally, we find heterogeneity in case reporting among different age groups, with the lowest rate occurring among the 0–17 group (9.7% [6.4%, 19%]). Our results provide a more fundamental understanding of the impacts of stringent lockdown measures, and finer evidence that other social distancing and preventive measures may be effective in reducing SARS-CoV-2 transmission. These results may be exploited to guide more effective implementations of these measures in many current settings (with low vaccination rate globally and emerging variants) and in future potential outbreaks of novel pathogens. [ABSTRACT FROM AUTHOR]

European countries struggled to fight against the second and the third waves of the COVID-19 pandemic, as the Test-Trace-Isolate (TTI) strategy widely adopted over the summer and early fall 2020 failed to contain the spread of the disease effectively. This paper sheds light on the effectiveness of such a strategy in two European countries (Spain and Italy) by analysing data from June to December 2020, collected via a large-scale online citizen survey with 95,251 and 43,393 answers in Spain and Italy, respectively. Our analysis describes several weaknesses in each of the three pillars of the TTI strategy: Test, Trace, and Isolate. We find that 40% of respondents had to wait more than 48 hours to obtain coronavirus tests results, while literature has shown that a delay of more than one day might make tracing all cases inefficient. We also identify limitations in the manual contact tracing capabilities in both countries, as only 29% of respondents in close contact with a confirmed infected individual reported having been contact traced. Moreover, our analysis shows that more than 45% of respondents report being unable to self-isolate if needed. We also analyse the mitigation strategies deployed to contain the second wave of coronavirus. We find that these interventions were particularly effective in Italy, where close contacts were reduced by more than 20% in the general population. Finally, we analyse the participants' perceptions about the coronavirus risk associated with different daily activities. We observe that they are often gender- and age-dependent, and not aligned with the actual risk identified by the literature. This finding emphasises the importance of deploying public-health communication campaigns to debunk misconceptions about SARS-CoV-2. Overall, our work illustrates the value of online citizen surveys to quickly and efficiently collect large-scale population data to support and evaluate policy decisions to combat the spread of infectious diseases, such as coronavirus. [ABSTRACT FROM AUTHOR]

In the absence of an effective vaccine or drug therapy, non-pharmaceutical interventions are the only option for control of the outbreak of the coronavirus disease 2019, a pandemic with global implications. Each of the over 200 countries affected has followed its own path in dealing with the crisis, making it difficult to evaluate the effectiveness of measures implemented, either individually, or collectively. In this paper we analyse the case of the south Indian state of Kerala, which received much attention in the international media for its actions in containing the spread of the disease in the early months of the pandemic, but later succumbed to a second wave. We use a model to study the trajectory of the disease in the state during the first four months of the outbreak. We then use the model for a retrospective analysis of measures taken to combat the spread of the disease, to evaluate their impact. Because of the differences in the trajectory of the outbreak in Kerala, we argue that it is a model worthy of a place in the discussion on how the world might best handle this and other, future, pandemics. [ABSTRACT FROM AUTHOR]

COVID-19 outbreaks have had high mortality in low- and middle-income countries such as Ecuador. Human mobility is an important factor influencing the spread of diseases possibly leading to a high burden of disease at the country level. Drastic control measures, such as complete lockdown, are effective epidemic controls, yet in practice one hopes that a partial shutdown would suffice. It is an open problem to determine how much mobility can be allowed while controlling an outbreak. In this paper, we use statistical models to relate human mobility to the excess death in Ecuador while controlling for demographic factors. The mobility index provided by GRANDATA, based on mobile phone users, represents the change of number of out-of-home events with respect to a benchmark date (March 2nd, 2020). The study confirms the global trend that more men are dying than expected compared to women, and that people under 30 show less deaths than expected, particularly individuals younger than 20 with a death rate reduction between 22 and 27%. The weekly median mobility time series shows a sharp decrease in human mobility immediately after a national lockdown was declared on March 17, 2020 and a progressive increase towards the pre-lockdown level within two months. Relating median mobility to excess deaths shows a lag in its effect: first, a decrease in mobility in the previous two to three weeks decreases excess death and, more novel, we found an increase of mobility variability four weeks prior increases the number of excess deaths. [ABSTRACT FROM AUTHOR]

Rising temperature levels during spring and summer are often argued to enable lifting of strict containment measures even in the absence of herd immunity. Despite broad scholarly interest in the relationship between weather and coronavirus spread, previous studies come to very mixed results. To contribute to this puzzle, the paper examines the impact of weather on the COVID-19 pandemic using a unique granular dataset of over 1.2 million daily observations covering over 3700 counties in nine countries for all seasons of 2020. Our results show that temperature and wind speed have a robust negative effect on virus spread after controlling for a range of potential confounding factors. These effects, however, are substantially larger during mealtimes, as well as in periods of high mobility and low containment, suggesting an important role for social behaviour. [ABSTRACT FROM AUTHOR]

To support public health policymakers in Connecticut, we developed a flexible county-structured compartmental SEIR-type model of SARS-CoV-2 transmission and COVID-19 disease progression. Our goals were to provide projections of infections, hospitalizations, and deaths, and estimates of important features of disease transmission and clinical progression. In this paper, we outline the model design, implementation and calibration, and describe how projections and estimates were used to meet the changing requirements of policymakers and officials in Connecticut from March 2020 to February 2021. The approach takes advantage of our unique access to Connecticut public health surveillance and hospital data and our direct connection to state officials and policymakers. We calibrated this model to data on deaths and hospitalizations and developed a novel measure of close interpersonal contact frequency to capture changes in transmission risk over time and used multiple local data sources to infer dynamics of time-varying model inputs. Estimated epidemiologic features of the COVID-19 epidemic in Connecticut include the effective reproduction number, cumulative incidence of infection, infection hospitalization and fatality ratios, and the case detection ratio. We conclude with a discussion of the limitations inherent in predicting uncertain epidemic trajectories and lessons learned from one year of providing COVID-19 projections in Connecticut. [ABSTRACT FROM AUTHOR]

Although the availability of the measles vaccine, it is still epidemic in many countries globally, including Bangladesh. Eradication of measles needs to keep the basic reproduction number less than one (i. e. R 0 < 1) . This paper investigates a modified (SVEIR) measles compartmental model with double dose vaccination in Bangladesh to simulate the measles prevalence. We perform a dynamical analysis of the resulting system and find that the model contains two equilibrium points: a disease-free equilibrium and an endemic equilibrium. The disease will be died out if the basic reproduction number is less than one (i. e. R 0 < 1) , and if greater than one (i. e. R 0 > 1) epidemic occurs. While using the Routh-Hurwitz criteria, the equilibria are found to be locally asymptotically stable under the former condition on R 0 . The partial rank correlation coefficients (PRCCs), a global sensitivity analysis method is used to compute R 0 and measles prevalence I ∗ with respect to the estimated and fitted model parameters. We found that the transmission rate (β) had the most significant influence on measles prevalence. Numerical simulations were carried out to commissions our analytical outcomes. These findings show that how progression rate, transmission rate and double dose vaccination rate affect the dynamics of measles prevalence. The information that we generate from this study may help government and public health professionals in making strategies to deal with the omissions of a measles outbreak and thus control and prevent an epidemic in Bangladesh. [ABSTRACT FROM AUTHOR]

The coronavirus disease (COVID-19) outbreak has killed over a million people since its emergence in late 2019. However, there has been substantial variability in the policies and intensity of diagnostic efforts between countries. In this paper, we quantitatively evaluate the association between national contact tracing policies and case fatality rates of COVID-19 in 138 countries. Our regression analyses indicate that countries that implement comprehensive contact tracing have significantly lower case fatality rates. This association of contact tracing policy and case fatality rates is robust in our longitudinal regression models, even after controlling for the number of tests conducted and non-pharmaceutical control measures adopted by governments. Our results suggest that comprehensive contact tracing is instrumental not only to curtailing transmission but also to reducing case fatality rates. Contact tracing achieves the early detection and isolation of secondary cases which are particularly important given that the peak in infectiousness occurs during the presymptomatic phase. The early detection achieved by contact tracing accelerates the rate at which infected individuals receive medical care they need to maximize their chance of recovery. In addition, the combination of reduced transmission and more rapid recovery diminishes the burden on the healthcare system which in turn ensures that the resources remain available for individuals who do become infected. [ABSTRACT FROM AUTHOR]

The current outbreak of coronavirus disease 2019 (COVID-19) has become a global crisis due to its quick and wide spread over the world. A good understanding of the dynamic of the disease would greatly enhance the control and prevention of COVID19. However, to the best of our knowledge, the unique features of the outbreak have limited the applications of all existing dynamic models. In this paper, a novel stochastic model was proposed aiming to account for the unique transmission dynamics of COVID-19 and capture the effects of intervention measures implemented in Mainland China. We found that: (1) instead of aberration, there was a remarkable amount of asymptomatic virus carriers, (2) a virus carrier with symptoms was approximately twice more likely to pass the disease to others than that of an asymptomatic virus carrier, (3) the transmission rate reduced significantly since the implementation of control measures in Mainland China, and (4) it was expected that the epidemic outbreak would be contained by early March in the selected provinces and cities in China. [ABSTRACT FROM AUTHOR]

First identified in 2011, Schmallenberg virus (SBV) is principally transmitted by Culicoides midges and affects ruminants. Clinical presentation is typified by foetal abnormalities, but despite very high infection rates, relatively few animals present with clinical signs. In this paper we further develop a previously published stochastic mathematical model of SBV spread to investigate the optimal deployment of a vaccine for SBV in Scotland, a country that has experienced only sporadic and isolated cases of SBV.Weconsider the use of the vaccine under different temperatures and explore the effects of a vector preference for feeding on cattle. We demonstrate that vaccine impact is optimised by targeting it at the high risk areas in the south of Scotland, or vaccinating only cattle. At higher than average temperatures, and hence increased transmission potential, the relative impact of vaccination is considerably enhanced. Vaccine impact is also enhanced if vectors feed preferentially on cattle. These findings are of considerable importance when planning control strategies for SBV and also have important implications for management of other arboviruses such as Bluetongue virus. Environmental determinants and feeding preferences should be researched further to inform development of effective control strategies. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

Network-based modelling of infectious diseases apply compartmental models on a contact network, which makes the epidemic process crucially dependent on the network structure. For highly contagious diseases such as Ebola virus disease (EVD), interpersonal contact plays the most vital role in human-to-human transmission. Therefore, for accurate representation of EVD spreading, the contact network needs to resemble the reality. Prior research has mainly focused on static networks (only permanent contacts) or activity-driven networks (only temporal contacts) for Ebola spreading. A comprehensive network for EVD spreading should include both these network structures, as there are always some permanent contacts together with temporal contacts. Therefore, we propose a two-layer temporal network for Uganda, which is at risk of an Ebola outbreak from the neighboring Democratic Republic of Congo (DRC) epidemic. The network has a permanent layer representing permanent contacts among individuals within the family level, and a data-driven temporal network for human movements motivated by cattle trade, fish trade, or general communications. We propose a Gillespie algorithm with the susceptible-infected-recovered (SIR) compartmental model to simulate the evolution of EVD spreading as well as to evaluate the risk throughout our network. As an example, we applied our method to a network consisting of 23 districts along different movement routes in Uganda starting from bordering districts of the DRC to Kampala. Simulation results show that some regions are at higher risk of infection, suggesting some focal points for Ebola preparedness and providing direction to inform interventions in the field. Simulation results also show that decreasing physical contact as well as increasing preventive measures result in a reduction of chances to develop an outbreak. Overall, the main contribution of this paper lies in the novel method for risk assessment, which can be more precise with an increasing volume of accurate data for creating the network model. [ABSTRACT FROM AUTHOR]

Malaria remains a major global health burden, and new methods for low-cost, high-sensitivity, diagnosis are essential, particularly in remote areas with low-resource around the world. In this paper, a cost effective, optical cell-phone based transmission polarized light microscope system is presented for imaging the malaria pigment known as hemozoin. It can be difficult to determine the presence of the pigment from background and other artifacts, even for skilled microscopy technicians. The pigment is much easier to observe using polarized light microscopy. However, implementation of polarized light microscopy lacks widespread adoption because the existing commercial devices have complicated designs, require sophisticated maintenance, tend to be bulky, can be expensive, and would require re-training for existing microscopy technicians. To this end, a high fidelity and high optical resolution cell-phone based polarized light microscopy system is presented which is comparable to larger bench-top polarized microscopy systems but at much lower cost and complexity. The detection of malaria in fixed and stained blood smears is presented using both, a conventional polarized microscope and our cell-phone based system. The cell-phone based polarimetric microscopy design shows the potential to have both the resolution and specificity to detect malaria in a low-cost, easy-to-use, modular platform. [ABSTRACT FROM AUTHOR]