An overview of technologies available to monitor behaviours of mosquitoes.

Mosquito-borne diseases such as malaria, dengue, Zika, and chikungunya cause significant morbidity and mortality globally, resulting in over 600,000 deaths from malaria and around 36,000 deaths from dengue each year, with millions of people infected annually, leading to substantial economic losses. The existing mosquito control measures, such as long-lasting insecticidal nets (LLINs) and indoor residual spraying (IRS), helped to reduce the infections. However, mosquito-borne diseases are still among the deadliest diseases, forcing us to improve the existing control methods and look for alternative methods simultaneously. Advanced monitoring techniques, including remote sensing, and geographic information systems (GIS) have significantly enhanced the efficiency and effectiveness of mosquito control measures. Mosquitoes' behavioural traits, such as locomotion, blood-feeding, and fertility are the key determinants of disease transmission and epidemiology. Technological advancements, such as high-resolution cameras, infrared imaging, and artificial intelligence (AI) driven object detection models, including groundbreaking convolutional neural networks, have provided efficient and precise options to monitor various mosquito behaviours, including locomotion, oviposition, fertility, and host-seeking. However, they are not commonly employed in mosquito-based research. This review highlights the novel and significant advancements in behaviour-monitoring tools, mostly from the last decade, due to cutting-edge video monitoring technology and artificial intelligence. These advancements can offer enhanced accuracy, efficiency, and the ability to quickly process large volumes of data, enabling detailed behavioural analysis over extended periods and large sample sizes, unlike traditional manual methods prone to human error and labour-intensive. The use of behaviour-assaying techniques can support or replace existing monitoring techniques and directly contribute to improving control measures by providing more accurate and real-time data on mosquito activity patterns and responses to interventions. This enhanced understanding can help establish the role of behavioural changes in improving epidemiological models, making them more precise and dynamic. As a result, mosquito management strategies can become more adaptive and responsive, leading to more effective and targeted interventions. Ultimately, this will reduce disease transmission and significantly improve public health outcomes.

Improving Hepatocellular Carcinoma Surveillance Outcomes in Patients with Cirrhosis after Hepatitis C Cure: A Modelling Study.

BACKGROUND & AIMS: Hepatocellular carcinoma (HCC) presents a significant global health challenge, particularly among individuals with liver cirrhosis, with hepatitis C (HCV) a major cause. In people with HCV-related cirrhosis, an increased risk of HCC remains after cure. HCC surveillance with six monthly ultrasounds has been shown to improve survival. However, adherence to biannual screening is currently suboptimal. This study aimed to evaluate the effect of increased HCC surveillance uptake and improved ultrasound sensitivity on mortality among people with HCV-related cirrhosis post HCV cure. METHODS: This study utilized mathematical modelling to assess HCC progression, surveillance, diagnosis, and treatment among individuals with cirrhosis who had successfully been treated for HCV. The deterministic compartmental model incorporated Barcelona Clinic Liver Cancer (BCLC) stages to simulate disease progression and diagnosis probabilities in 100 people with cirrhosis who had successfully been treated for hepatitis C over 10 years. Four interventions were modelled to assess their potential for improving life expectancy: realistic improvements to surveillance adherence, optimistic improvements to surveillance adherence, diagnosis sensitivity enhancements, and improved treatment efficacy Results: Realistic adherence improvements resulted in 9.8 (95% CI 7.9, 11.6) life years gained per cohort of 100 over a 10-year intervention period; 17.2 (13.9, 20.3) life years were achieved in optimistic adherence improvements. Diagnosis sensitivity improvements led to a 7.0 (3.6, 13.8) year gain in life years, and treatment improvements improved life years by 9.0 (7.5, 10.3) years. CONCLUSIONS: Regular HCC ultrasound surveillance remains crucial to reduce mortality among people with cured hepatitis C and cirrhosis. Our study highlights that even minor enhancements to adherence to ultrasound surveillance can significantly boost life expectancy across populations more effectively than strategies that increase surveillance sensitivity or treatment efficacy.

Factors associated with depression during pregnancy in women receiving high- and low-risk prenatal care: a predictive model.

Introduction: Depression during pregnancy can put strain on pregnant women's interpersonal relationships, the formation of emotional bonds with the fetus, and the adaptation to the new routine and social role post-pregnancy. Some studies have associated socioeconomic factors, emotional factors, interpersonal relationships, perceived social support, gestational risk, and the occurrence of certain diseases during pregnancy with higher risk of depression. Objectives: This study aimed to investigate the prevalence of depression during pregnancy and associated factors in low- and high-risk prenatal patients at a Brazilian university hospital. Methods: This study presents a retrospective and prospective cross-sectional design. A total of 684 prenatal psychological analysis records from a Brazilian tertiary university service were retrospectively evaluated to assess depression through the PRIME-MD questionnaire between 2002-2017. Between 2017 and 2018, 76 patients treated at the same service were prospectively evaluated with the aforementioned instrument. Medical records were accessed to obtain labor and birth data. Multivariate analyses assessed the association between sociodemographic, gestational or obstetric, and health variables and the presence of depression during pregnancy. Results: A total of 760 pregnant women were included in the study, with a depression prevalence of 20.66% (n = 157). At the time of assessment, 48 (21.05%) women from the low-risk pregnancy group and 109 (20.49%) from the high-risk pregnancy group were depressed. The mean age was 30.01 ± 6.55 years in the group with depression and 29.81 ± 6.50 years in the group without depression. In the univariate analysis, there was an association of risk for depression with absence of paid work, absence of a partner, low family income and diagnosis of epilepsy, being a protective factor the presence of diabetes during pregnancy. However, in the multivariate analysis, a lower family income, not having a partner at the time of the assessment, and the prevalence of epilepsy were independently associated with an increased risk of depression during pregnancy. Conclusion: This study showed that 1 in 5 women had depression during pregnancy, with no association with obstetric risk, but those women living in unfavorable economic conditions, without a partner, and having epilepsy were at increased risk of depression.

JAGS model specification for spatiotemporal epidemiological modelling.

Bayesian inference in modelling infectious diseases using Bayesian inference using Gibbs Sampling (BUGS) is notable in the last two decades in parallel with the advancements in computing and model development. The ability of BUGS to easily implement the Markov chain Monte Carlo (MCMC) method brought Bayesian analysis to the mainstream of infectious disease modelling. However, with the existing software that runs MCMC to make Bayesian inferences, it is challenging, especially in terms of computational complexity, when infectious disease models become more complex with spatial and temporal components, in addition to the increasing number of parameters and large datasets. This study investigates two alternative subscripting strategies for creating models in Just Another Gibbs Sampler (JAGS) environment and their performance in terms of run times. Our results are useful for practitioners to ensure the efficiency and timely implementation of Bayesian spatiotemporal infectious disease modelling.

Modeling the effect of imported malaria on the elimination programme in KwaZulu-Natal province of South Africa.

Introduction: with imported malaria cases in a given population, the question arises as to what extent the local cases are a consequence of the imports or not. We perform a modeling analysis for a specific area, in a region aspiring for malaria-free status. Methods: data on malaria cases over ten years is subjected to a compartmental model which is assumed to be operating close to the equilibrium state. Two of the parameters of the model are fitted to the decadal data. The other parameters in the model are sourced from the literature. The model is utilized to simulate the malaria prevalence with or without imported cases. Results: in any given year the annual average of 460 imported cases, resulted in an end-of-year season malaria prevalence of 257 local active infectious cases, whereas without the imports the malaria prevalence at the end of the season would have been fewer than 10 active infectious cases. We calculate the numerical value of the basic reproduction number for the model, which reveals the extent to which the disease is being eliminated from the population or not. Conclusion: without the imported cases, over the ten seasons of malaria, 2008-2018, the KwaZulu-Natal province would have been malaria-free over at least the last 7 years of the decade indicated. This simple methodology works well even in situations where data is limited.

Evidence-based Decision Making: Infectious Disease Modeling Training for Policymakers in East Africa.

Background: Mathematical modeling of infectious diseases is an important decision-making tool for outbreak control. However, in Africa, limited expertise reduces the use and impact of these tools on policy. Therefore, there is a need to build capacity in Africa for the use of mathematical modeling to inform policy. Here we describe our experience implementing a mathematical modeling training program for public health professionals in East Africa. Methods: We used a deliverable-driven and learning-by-doing model to introduce trainees to the mathematical modeling of infectious diseases. The training comprised two two-week in-person sessions and a practicum where trainees received intensive mentorship. Trainees evaluated the content and structure of the course at the end of each week, and this feedback informed the strategy for subsequent weeks. Findings: Out of 875 applications from 38 countries, we selected ten trainees from three countries - Rwanda (6), Kenya (2), and Uganda (2) - with guidance from an advisory committee. Nine trainees were based at government institutions and one at an academic organization. Participants gained skills in developing models to answer questions of interest and critically appraising modeling studies. At the end of the training, trainees prepared policy briefs summarizing their modeling study findings. These were presented at a dissemination event to policymakers, researchers, and program managers. All trainees indicated they would recommend the course to colleagues and rated the quality of the training with a median score of 9/10. Conclusions: Mathematical modeling training programs for public health professionals in Africa can be an effective tool for research capacity building and policy support to mitigate infectious disease burden and forecast resources. Overall, the course was successful, owing to a combination of factors, including institutional support, trainees' commitment, intensive mentorship, a diverse trainee pool, and regular evaluations.

Modeling the health impact of increasing vaccine coverage and nonpharmaceutical interventions against coronavirus disease 2019 in Ghana.

Seroprevalence studies assessing community exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Ghana concluded that population-level immunity remained low as of February 2021. Thus, it is important to demonstrate how increasing vaccine coverage reduces the economic and public health impacts associated with SARS-CoV-2 transmission. To that end, this study used a Susceptible-Exposed-Presymptomatic-Symptomatic-Asymptomatic-Recovered-Dead-Vaccinated compartmental model to simulate coronavirus disease 2019 (COVID-19) transmission and the role of public health interventions in Ghana. The impact of increasing vaccination rates and decline in transmission rates due to nonpharmaceutical interventions (NPIs) on cumulative infections and deaths averted was explored under different scenarios. Latin hypercube sampling-partial rank correlation coefficient (LHS-PRCC) was used to investigate the uncertainty and sensitivity of the outcomes to the parameters. Simulation results suggest that increasing the vaccination rate to achieve 50% coverage was associated with almost 60,000 deaths and 25 million infections averted. In comparison, a 50% decrease in the transmission coefficient was associated with the prevention of about 150,000 deaths and 50 million infections. The LHS-PRCC results indicated that in the context of vaccination rate, cumulative infections and deaths averted were most sensitive to vaccination rate, waning immunity rates from vaccination, and waning immunity from natural infection. This study's findings illustrate the impact of increasing vaccination coverage and/or reducing the transmission rate by NPI adherence in the prevention of COVID-19 infections and deaths in Ghana.

Stochastic transmission in epidemiological models.

Recent empirical evidence suggests that the transmission coefficient in susceptible-exposed-infected-removed-like (SEIR-like) models evolves with time, presenting random patterns, and some stylized facts, such as mean-reversion and jumps. To address such observations we propose the use of jump-diffusion stochastic processes to parameterize the transmission coefficient in an SEIR-like model that accounts for death and time-dependent parameters. We provide a detailed theoretical analysis of the proposed model proving the existence and uniqueness of solutions as well as studying its asymptotic behavior. We also compare the proposed model with some variations possibly including jumps. The forecast performance of the considered models, using reported COVID-19 infections from New York City, is then tested in different scenarios. Despite the simplicity of the epidemiological model, by considering stochastic transmission, the forecasted scenarios were fairly accurate.

The effect of model structure and data availability on Usutu virus dynamics at three biological scales.

Understanding the epidemiology of emerging pathogens, such as Usutu virus (USUV) infections, requires systems investigation at each scale involved in the host-virus transmission cycle, from individual bird infections, to bird-to-vector transmissions, and to USUV incidence in bird and vector populations. For new pathogens field data are sparse, and predictions can be aided by the use of laboratory-type inoculation and transmission experiments combined with dynamical mathematical modelling. In this study, we investigated the dynamics of two strains of USUV by constructing mathematical models for the within-host scale, bird-to-vector transmission scale and vector-borne epidemiological scale. We used individual within-host infectious virus data and per cent mosquito infection data to predict USUV incidence in birds and mosquitoes. We addressed the dependence of predictions on model structure, data uncertainty and experimental design. We found that uncertainty in predictions at one scale change predicted results at another scale. We proposed in silico experiments that showed that sampling every 12 hours ensures practical identifiability of the within-host scale model. At the same time, we showed that practical identifiability of the transmission scale functions can only be improved under unrealistically high sampling regimes. Instead, we proposed optimal experimental designs and suggested the types of experiments that can ensure identifiability at the transmission scale and, hence, induce robustness in predictions at the epidemiological scale.

High connectivity and human movement limits the impact of travel time on infectious disease transmission.

The speed of spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic highlights the importance of understanding how infections are transmitted in a highly connected world. Prior to vaccination, changes in human mobility patterns were used as non-pharmaceutical interventions to eliminate or suppress viral transmission. The rapid spread of respiratory viruses, various intervention approaches, and the global dissemination of SARS-CoV-2 underscore the necessity for epidemiological models that incorporate mobility to comprehend the spread of the virus. Here, we introduce a metapopulation susceptible-exposed-infectious-recovered model parametrized with human movement data from 340 cities in China. Our model replicates the early-case trajectory in the COVID-19 pandemic. We then use machine learning algorithms to determine which network properties best predict spread between cities and find travel time to be most important, followed by the human movement-weighted personalized PageRank. However, we show that travel time is most influential locally, after which the high connectivity between cities reduces the impact of travel time between individual cities on transmission speed. Additionally, we demonstrate that only significantly reduced movement substantially impacts infection spread times throughout the network.

Systems Biology Approaches to Understanding COVID-19 Spread in the Population.

In essence, the COVID-19 pandemic can be regarded as a systems biology problem, with the entire world as the system, and the human population as the element transitioning from one state to another with certain transition rates. While capturing all the relevant features of such a complex system is hardly possible, compartmental epidemiological models can be used as an appropriate simplification to model the system's dynamics and infer its important characteristics, such as basic and effective reproductive numbers of the virus. These measures can later be used as response variables in feature selection methods to uncover the main factors contributing to disease transmissibility. We here demonstrate that a combination of dynamic modeling and machine learning approaches can represent a powerful tool in understanding the spread, not only of COVID-19, but of any infectious disease of epidemiological proportions.

Tuberculosis incidence in Brazil: time series analysis between 2001 and 2021 and projection until 2030 / Incidência de tuberculose no Brasil: análise de série temporal entre 2001 e 2021 e projeção até 2030

ABSTRACT Objective: To assess the incidence of tuberculosis in Brazil between 2001 and 2022 and estimate the monthly incidence forecast until 2030. Methods: This is a time-series study based on monthly tuberculosis records from the Notifiable Diseases Information System and official projections of the Brazilian population. The monthly incidence of tuberculosis from 2001 to 2022 was evaluated using segmented linear regression to identify trend breaks. Seasonal autoregressive integrated moving average (Sarima) was used to predict the monthly incidence from 2023 to 2030, deadline for achieving the sustainable development goals (SDGs). Results: There was a decrease in incidence between January/2001 and December/2014 (4.60 to 3.19 cases-month/100,000 inhabitants; β=-0.005; p<0.001), followed by an increase between January/2015 and March /2020 (β=0.013; p<0.001). There was a sharp drop in cases in April/2020, with the onset of the pandemic, and acceleration of the increase in cases since then (β=0.025; p<0.001). A projection of 124,245 cases in 2030 was made, with an estimated incidence of 4.64 cases-month/100,000 inhabitants, levels similar to those in the 2000s. The Sarima model proved to be robust, with error of 4.1% when removing the pandemic period. Conclusion: The decreasing trend in tuberculosis cases was reversed from 2015 onwards, a period of economic crisis, and was also impacted by the pandemic when there was a reduction in records. The Sarima model can be a useful forecasting tool for epidemiological surveillance. Greater investments in prevention and control need to be made to reduce the occurrence of tuberculosis, in line with the SDGs.

RESUMO Objetivo: Avaliar a incidência de tuberculose no Brasil entre 2001 e 2022 e estimar a previsão de incidência mensal até 2030. Métodos: Trata-se de estudo de série temporal que partiu de registros mensais de tuberculose do Sistema de Informação de Agravos de Notificação e projeções oficiais da população brasileira. Avaliou-se a incidência mensal de tuberculose entre 2001 e 2022 por meio de regressão linear segmentada para identificar quebras de tendências. Utilizou-se o modelo autorregressivo integrado de médias móveis sazonais (Sarima) para prever a incidência mensal de 2023 a 2030, prazo para alcançar os objetivos de desenvolvimento sustentável (ODS). Resultados: Observou-se diminuição da incidência entre janeiro/2001 e dezembro/2014 (de 4,60 para 3,19 casos-mês/100 mil habitantes; β=-0,005; p<0,001), seguida de aumento entre janeiro/2015 e março/2020 (β=0,013; p<0,001). Houve queda abrupta de casos em abril/2020, com início da pandemia e aceleração do aumento de casos desde então (β=0,025; p<0,001). Projetaram-se 124.245 casos de tuberculose em 2030, com incidência estimada em 4,64 casos-mês/100 mil habitantes, patamares da década de 2000. O modelo Sarima mostrou-se robusto, com erro de 4,1% ao remover o período pandêmico. Conclusão: A tendência decrescente nos casos de tuberculose foi revertida a partir de 2015, período de crises econômicas, e foi também impactada pela pandemia quando houve redução nos registros. O modelo Sarima pode ser uma ferramenta de previsão útil para a vigilância epidemiológica. Maiores investimentos na prevenção e controle precisam ser aportados para reduzir a ocorrência de tuberculose, em linha com os ODS.

Modeling the impact of COVID-19 nonpharmaceutical interventions on respiratory syncytial virus transmission in South Africa.

Background: The South African government employed various nonpharmaceutical interventions (NPIs) to reduce the spread of SARS-CoV-2. Surveillance data from South Africa indicates reduced circulation of respiratory syncytial virus (RSV) throughout the 2020-2021 seasons. Here, we use a mechanistic transmission model to project the rebound of RSV in the two subsequent seasons. Methods: We fit an age-structured epidemiological model to hospitalization data from national RSV surveillance in South Africa, allowing for time-varying reduction in RSV transmission during periods of COVID-19 circulation. We apply the model to project the rebound of RSV in the 2022 and 2023 seasons. Results: We projected an early and intense outbreak of RSV in April 2022, with an age shift to older infants (6-23 months old) experiencing a larger portion of severe disease burden than typical. In March 2022, government alerts were issued to prepare the hospital system for this potentially intense outbreak. We then assess the 2022 predictions and project the 2023 season. Model predictions for 2023 indicate that RSV activity has not fully returned to normal, with a projected early and moderately intense wave. We estimate that NPIs reduced RSV transmission between 15% and 50% during periods of COVID-19 circulation. Conclusions: A wide range of NPIs impacted the dynamics of the RSV outbreaks throughout 2020-2023 in regard to timing, magnitude, and age structure, with important implications in a low- and middle-income countries (LMICs) setting where RSV interventions remain limited. More efforts should focus on adapting RSV models to LMIC data to project the impact of upcoming medical interventions for this disease.

Construction and validation of a predictive model of pneumonia for ICU patients with traumatic brain injury (TBI).

The incidence of pneumonia in ICU patients with TBI is very high, seriously affecting the prognosis. This study aims to construct a predictive model for pneumonia in ICU patients with TBI and provide help for the prevention of TBI-related pneumonia.Clinical data of ICU patients with TBI were collected from the Medical Information Mart for Intensive Care (MIMIC)-IV database and hospital data. Variables were screened by lasso and multivariate logistic regression to construct a predictive nomogram model, verified in internal validation cohort and external validation cohort by receiver operator characteristic (ROC) curve, calibration curve and decision curve analysis (DCA).A total of 1850 ICU patients with TBI were enrolled in the study from the MIMIC-IV database, including 1298 in the training cohort and 552 in internal validation cohort. The external validation cohort included 240 ICU patients with TBI from hospital data. Nine variables were selected from the training cohort by lasso regression and multivariate logistic regression, and a pneumonia prediction nomogram was constructed. This nomogram has a high discrimination in training, internal validation and external validation cohorts (AUC = 0.857, 0.877, 0.836). The calibration curve and DCA showed that this nomogram had a high calibration and better clinical decision-making efficiency.The nomogram showed excellent discrimination and clinical utility to predict pneumonia, and could identify pneumonia high-risk patients early, thus providing personalised treatment strategies for ICU patients with TBI.

EggCountAI: a convolutional neural network-based software for counting of Aedes aegypti mosquito eggs.

BACKGROUND: Mosquito-borne diseases exert a huge impact on both animal and human populations, posing substantial health risks. The behavioural and fitness traits of mosquitoes, such as locomotion and fecundity, are crucial factors that influence the spread of diseases. In existing egg-counting tools, each image requires separate processing with adjustments to various parameters such as intensity threshold and egg area size. Furthermore, accuracy decreases significantly when dealing with clustered or overlapping eggs. To overcome these issues, we have developed EggCountAI, a Mask Region-based Convolutional Neural Network (RCNN)-based free automatic egg-counting tool for Aedes aegypti mosquitoes. METHODS: The study design involves developing EggCountAI for counting mosquito eggs and comparing its performance with two commonly employed tools-ICount and MECVision-using 10 microscopic and 10 macroscopic images of eggs laid by females on a paper strip. The results were validated through manual egg counting on the strips using ImageJ software. Two different models were trained on macroscopic and microscopic images to enhance egg detection accuracy, achieving mean average precision, mean average recall, and F1-scores of 0.92, 0.90, and 0.91 for the microscopic model, and 0.91, 0.90, and 0.90 for the macroscopic model, respectively. EggCountAI automatically counts eggs in a folder containing egg strip images, offering adaptable filtration for handling impurities of varying sizes. RESULTS: The results obtained from EggCountAI highlight its remarkable performance, achieving overall accuracy of 98.88% for micro images and 96.06% for macro images. EggCountAI significantly outperformed ICount and MECVision, with ICount achieving 81.71% accuracy for micro images and 82.22% for macro images, while MECVision achieved 68.01% accuracy for micro images and 51.71% for macro images. EggCountAI also excelled in other statistical parameters, with mean absolute error of 1.90 eggs for micro, 74.30 eggs for macro, and a strong correlation and R-squared value (0.99) for both micro and macro. The superior performance of EggCountAI was most evident when handling overlapping or clustered eggs. CONCLUSION: Accurate detection and counting of mosquito eggs enables the identification of preferred egg-laying sites and facilitates optimal placement of oviposition traps, enhancing targeted vector control efforts and disease transmission prevention. In future research, the tool holds the potential to extend its application to monitor mosquito feeding preferences.

Public health impact of 2-, 4-, and 9-valent HPV vaccination in females on cervical and noncervical diseases in men and women under different coverage scenarios in China: A simulation study.

The high prevalence of human papillomavirus (HPV) infection in China suggests there would be a substantial positive health impact of widespread vaccination against HPV. We adapted a previously described dynamic transmission model of the natural history of HPV infection and related diseases to the Chinese setting to estimate the public health impact in China of 2-valent (with and without cross-protection), 4-valent, and 9-valent HPV vaccination strategies. The model predicted the incidence and mortality associated with HPV-related diseases, including cervical and noncervical cancers, genital warts, and recurrent respiratory papillomatosis (RRP), based on the various vaccination coverage rate (VCR) scenarios, over a 100-year time horizon. The public health impact of the 4 vaccination strategies was estimated in terms of cases and deaths averted compared to a scenario with no vaccination. Under the assumption of various primary and catch-up VCR scenarios, all 4 vaccination strategies reduced the incidence of cervical cancer in females and noncervical cancers in both sexes, and the 4-valent and 9-valent vaccines reduced the incidence of genital warts and RRP in both sexes. The 9-valent vaccination strategy was superior on all outcomes. The number of cervical cancer cases averted over 100 years ranged from ~ 1 million to ~ 5 million while the number of cervical cancer deaths averted was ~ 345,000 to ~ 1.9 million cases, depending on the VCR scenario. The VCR for primary vaccination was the major driver of cases averted.

Host-pathogen interactions under pressure: A review and meta-analysis of stress-mediated effects on disease dynamics.

Human activities have increased the intensity and frequency of natural stressors and created novel stressors, altering host-pathogen interactions and changing the risk of emerging infectious diseases. Despite the ubiquity of such anthropogenic impacts, predicting the directionality of outcomes has proven challenging. Here, we conduct a review and meta-analysis to determine the primary mechanisms through which stressors affect host-pathogen interactions and to evaluate the impacts stress has on host fitness (survival and fecundity) and pathogen infectivity (prevalence and intensity). We assessed 891 effect sizes from 71 host species (representing seven taxonomic groups) and 78 parasite taxa from 98 studies. We found that infected and uninfected hosts had similar sensitivity to stressors and that responses varied according to stressor type. Specifically, limited resources compromised host fecundity and decreased pathogen intensity, while abiotic environmental stressors (e.g., temperature and salinity) decreased host survivorship and increased pathogen intensity, and pollution increased mortality but decreased pathogen prevalence. We then used our meta-analysis results to develop susceptible-infected theoretical models to illustrate scenarios where infection rates are expected to increase or decrease in response to resource limitations or environmental stress gradients. Our results carry implications for conservation and disease emergence and reveal areas for future work.

Forecasting the effects of vaccination on the COVID-19 pandemic in Malaysia using SEIRV compartmental models.

OBJECTIVES: This study aimed to develop susceptible-exposed-infectious-recovered-vaccinated (SEIRV) models to examine the effects of vaccination on coronavirus disease 2019 (COVID-19) case trends in Malaysia during Phase 3 of the National COVID-19 Immunization Program amidst the Delta outbreak. METHODS: SEIRV models were developed and validated using COVID-19 case and vaccination data from the Ministry of Health, Malaysia, from June 21, 2021 to July 21, 2021 to generate forecasts of COVID-19 cases from July 22, 2021 to December 31, 2021. Three scenarios were examined to measure the effects of vaccination on COVID-19 case trends. Scenarios 1 and 2 represented the trends taking into account the earliest and latest possible times of achieving full vaccination for 80% of the adult population by October 31, 2021 and December 31, 2021, respectively. Scenario 3 described a scenario without vaccination for comparison. RESULTS: In scenario 1, forecasted cases peaked on August 28, 2021, which was close to the peak of observed cases on August 26, 2021. The observed peak was 20.27% higher than in scenario 1 and 10.37% lower than in scenario 2. The cumulative observed cases from July 22, 2021 to December 31, 2021 were 13.29% higher than in scenario 1 and 55.19% lower than in scenario 2. The daily COVID-19 case trends closely mirrored the forecast of COVID-19 cases in scenario 1 (best-case scenario). CONCLUSIONS: Our study demonstrated that COVID-19 vaccination reduced COVID-19 case trends during the Delta outbreak. The compartmental models developed assisted in the management and control of the COVID-19 pandemic in Malaysia.

[Quantitative evaluation of a SEIR model for forecasting COVID-19 cases]. / Evaluación cuantitativa de un modelo SEIR para predecir casos de COVID-19.

INTRODUCTION: Epidemiological models have been widely used during the COVID-19 pandemic, although performance evaluation has been limited. The objective of this work was to thoroughly evaluate a SEIR model used for the short-term (1 to 3 weeks) prediction of cases, quantifying its actual past performance, and its potential performance by optimizing the model parameters. METHODS: Daily case forecasts were obtained for the first wave of cases (July 31, 2020 to March 11, 2021) in the district of General Pueyrredón (Argentina), quantifying the model performance in terms of uncertainty, inaccuracy and imprecision. The evaluation was carried out with the original parameters of the model (used in the forecasts that were published), and also varying different parameters in order to identify optimal values. RESULTS: The analysis of the model performance showed that alternative values of some parameters, and the correction of the input values using a "moving average" filter to eliminate the weekly variations in the case reports, would have yielded better results. The model with the optimized parameters was able to reduce the uncertainty from almost 40% to less than 15%, with similar values of inaccuracy, and with slightly greater imprecision. DISCUSSION: Simple epidemiological models, without large requirements for their implementation, can be very useful for making quick decisions in small cities or cities with limited resources, as long as the importance of their evaluation is taken into account and their scope and limitations are considered.

Introducción: Los modelos epidemiológicos han sido ampliamente utilizados durante la pandemia de COVID-19, aunque la evaluación de su desempeño ha sido limitada. El objetivo del presente trabajo fue evaluar de forma retrospectiva un modelo SEIR para la predicción de casos a corto plazo (1 a 3 semanas), cuantificando su desempeño real y potencial, mediante la optimización de los parámetros del modelo. Métodos: Se realizaron proyecciones para cada día de la primera ola de casos (31 de julio de 2020 al 11 de marzo de 2021) en el municipio de General Pueyrredón (Argentina), cuantificando el desempeño del modelo en términos de incertidumbre, inexactitud e imprecisión. La evaluación se realizó con los parámetros originales del modelo (utilizados en proyecciones que fueron oportunamente publicadas), y luego variando distintos parámetros a fin de identificar valores óptimos. Resultados: El análisis del desempeño del modelo mostró que valores alternativos de algunos parámetros, y la corrección de los valores de entrada utilizando un filtro de "media móvil" para eliminar las variaciones semanales en los reportes de casos, habrían otorgado mejores resultados. El modelo con los parámetros optimizados logró disminuir desde casi 40% a menos de 15% la incertidumbre, con valores similares de inexactitud, y con una imprecisión levemente mayor. Discusión: Modelos epidemiológicos sencillos, sin grandes requerimientos para su implementación, pueden ser de utilidad para la toma de decisiones rápidas en localidades pequeñas o con recursos limitados, siempre y cuando se tenga en cuenta la importancia de su evaluación y la consideración de sus alcances y limitaciones.

Evaluación cuantitativa de un modelo SEIR para predecir casos de COVID-19 / Quantitative evaluation of a SEIR model for forecasting COVID-19 cases

Resumen Introducción : Los modelos epidemiológicos han sido ampliamente utilizados durante la pandemia de COVID-19, aunque la evaluación de su desempeño ha sido limitada. El objetivo del presente trabajo fue evaluar de forma retrospectiva un modelo SEIR para la predicción de casos a corto plazo (1 a 3 semanas), cuantificando su desempeño real y potencial, me diante la optimización de los parámetros del modelo. Métodos : Se realizaron proyecciones para cada día de la primera ola de casos (31 de julio de 2020 al 11 de marzo de 2021) en el municipio de General Pueyrredón (Argentina), cuantificando el desempeño del modelo en términos de incertidumbre, inexactitud e imprecisión. La evaluación se realizó con los parámetros originales del modelo (utilizados en proyecciones que fueron oportunamente publicadas), y luego variando distintos parámetros a fin de identificar valores óptimos. Resultados : El análisis del desempeño del modelo mostró que valores alternativos de algunos parámetros, y la corrección de los valores de entrada utilizando un filtro de "media móvil" para eliminar las variaciones semanales en los reportes de casos, habrían otorgado mejores resultados. El modelo con los parámetros opti mizados logró disminuir desde casi 40% a menos de 15% la incertidumbre, con valores similares de inexactitud, y con una imprecisión levemente mayor. Discusión : Modelos epidemiológicos sencillos, sin grandes requerimientos para su implementación, pue den ser de utilidad para la toma de decisiones rápi das en localidades pequeñas o con recursos limitados, siempre y cuando se tenga en cuenta la importancia de su evaluación y la consideración de sus alcances y limitaciones.

Abstract Introduction : Epidemiological models have been widely used during the COVID-19 pandemic, although performance evaluation has been limited. The objec tive of this work was to thoroughly evaluate a SEIR model used for the short-term (1 to 3 weeks) predic tion of cases, quantifying its actual past performance, and its potential performance by optimizing the model parameters. Methods : Daily case forecasts were obtained for the first wave of cases (July 31, 2020 to March 11, 2021) in the district of General Pueyrredón (Argentina), quantifying the model performance in terms of uncertainty, inac curacy and imprecision. The evaluation was carried out with the original parameters of the model (used in the forecasts that were published), and also varying different parameters in order to identify optimal values. Results : The analysis of the model performance showed that alternative values of some parameters, and the correction of the input values using a "mov ing average" filter to eliminate the weekly variations in the case reports, would have yielded better results. The model with the optimized parameters was able to reduce the uncertainty from almost 40% to less than 15%, with similar values of inaccuracy, and with slightly greater imprecision. Discussion : Simple epidemiological models, without large requirements for their implementation, can be very useful for making quick decisions in small cities or cities with limited resources, as long as the importance of their evaluation is taken into account and their scope and limitations are considered.