SpatialWavePredict: a tutorial-based primer and toolbox for forecasting growth trajectories using the ensemble spatial wave sub-epidemic modeling framework.

BACKGROUND: Dynamical mathematical models defined by a system of differential equations are typically not easily accessible to non-experts. However, forecasts based on these types of models can help gain insights into the mechanisms driving the process and may outcompete simpler phenomenological growth models. Here we introduce a friendly toolbox, SpatialWavePredict, to characterize and forecast the spatial wave sub-epidemic model, which captures diverse wave dynamics by aggregating multiple asynchronous growth processes and has outperformed simpler phenomenological growth models in short-term forecasts of various infectious diseases outbreaks including SARS, Ebola, and the early waves of the COVID-19 pandemic in the US. RESULTS: This tutorial-based primer introduces and illustrates a user-friendly MATLAB toolbox for fitting and forecasting time-series trajectories using an ensemble spatial wave sub-epidemic model based on ordinary differential equations. Scientists, policymakers, and students can use the toolbox to conduct real-time short-term forecasts. The five-parameter epidemic wave model in the toolbox aggregates linked overlapping sub-epidemics and captures a rich spectrum of epidemic wave dynamics, including oscillatory wave behavior and plateaus. An ensemble strategy aims to improve forecasting performance by combining the resulting top-ranked models. The toolbox provides a tutorial for forecasting time-series trajectories, including the full uncertainty distribution derived through parametric bootstrapping, which is needed to construct prediction intervals and evaluate their accuracy. Functions are available to assess forecasting performance, estimation methods, error structures in the data, and forecasting horizons. The toolbox also includes functions to quantify forecasting performance using metrics that evaluate point and distributional forecasts, including the weighted interval score. CONCLUSIONS: We have developed the first comprehensive toolbox to characterize and forecast time-series data using an ensemble spatial wave sub-epidemic wave model. As an epidemic situation or contagion occurs, the tools presented in this tutorial can facilitate policymakers to guide the implementation of containment strategies and assess the impact of control interventions. We demonstrate the functionality of the toolbox with examples, including a tutorial video, and is illustrated using daily data on the COVID-19 pandemic in the USA.

SubEpiPredict: A tutorial-based primer and toolbox for fitting and forecasting growth trajectories using the ensemble n-sub-epidemic modeling framework.

An ensemble n-sub-epidemic modeling framework that integrates sub-epidemics to capture complex temporal dynamics has demonstrated powerful forecasting capability in previous works. This modeling framework can characterize complex epidemic patterns, including plateaus, epidemic resurgences, and epidemic waves characterized by multiple peaks of different sizes. In this tutorial paper, we introduce and illustrate SubEpiPredict, a user-friendly MATLAB toolbox for fitting and forecasting time series data using an ensemble n-sub-epidemic modeling framework. The toolbox can be used for model fitting, forecasting, and evaluation of model performance of the calibration and forecasting periods using metrics such as the weighted interval score (WIS). We also provide a detailed description of these methods including the concept of the n-sub-epidemic model, constructing ensemble forecasts from the top-ranking models, etc. For the illustration of the toolbox, we utilize publicly available daily COVID-19 death data at the national level for the United States. The MATLAB toolbox introduced in this paper can be very useful for a wider group of audiences, including policymakers, and can be easily utilized by those without extensive coding and modeling backgrounds.

GrowthPredict: A toolbox and tutorial-based primer for fitting and forecasting growth trajectories using phenomenological growth models.

Simple dynamic modeling tools can help generate real-time short-term forecasts with quantified uncertainty of the trajectory of diverse growth processes unfolding in nature and society, including disease outbreaks. An easy-to-use and flexible toolbox for this purpose is lacking. This tutorial-based primer introduces and illustrates GrowthPredict, a user-friendly MATLAB toolbox for fitting and forecasting time-series trajectories using phenomenological dynamic growth models based on ordinary differential equations. This toolbox is accessible to a broad audience, including students training in mathematical biology, applied statistics, and infectious disease modeling, as well as researchers and policymakers who need to conduct short-term forecasts in real-time. The models included in the toolbox capture exponential and sub-exponential growth patterns that typically follow a rising pattern followed by a decline phase, a common feature of contagion processes. Models include the 1-parameter exponential growth model and the 2-parameter generalized-growth model, which have proven useful in characterizing and forecasting the ascending phase of epidemic outbreaks. It also includes the 2-parameter Gompertz model, the 3-parameter generalized logistic-growth model, and the 3-parameter Richards model, which have demonstrated competitive performance in forecasting single peak outbreaks. We provide detailed guidance on forecasting time-series trajectories and available software ( https://github.com/gchowell/forecasting_growthmodels ), including the full uncertainty distribution derived through parametric bootstrapping, which is needed to construct prediction intervals and evaluate their accuracy. Functions are available to assess forecasting performance across different models, estimation methods, error structures in the data, and forecasting horizons. The toolbox also includes functions to quantify forecasting performance using metrics that evaluate point and distributional forecasts, including the weighted interval score. This tutorial and toolbox can be broadly applied to characterizing and forecasting time-series data using simple phenomenological growth models. As a contagion process takes off, the tools presented in this tutorial can help create forecasts to guide policy regarding implementing control strategies and assess the impact of interventions. The toolbox functionality is demonstrated through various examples, including a tutorial video, and the examples use publicly available data on the monkeypox (mpox) epidemic in the USA.

Structural identifiability analysis of epidemic models based on differential equations: a tutorial-based primer.

The successful application of epidemic models hinges on our ability to estimate model parameters from limited observations reliably. An often-overlooked step before estimating model parameters consists of ensuring that the model parameters are structurally identifiable from the observed states of the system. In this tutorial-based primer, intended for a diverse audience, including students training in dynamic systems, we review and provide detailed guidance for conducting structural identifiability analysis of differential equation epidemic models based on a differential algebra approach using differential algebra for identifiability of systems (DAISY) and Mathematica (Wolfram Research). This approach aims to uncover any existing parameter correlations that preclude their estimation from the observed variables. We demonstrate this approach through examples, including tutorial videos of compartmental epidemic models previously employed to study transmission dynamics and control. We show that the lack of structural identifiability may be remedied by incorporating additional observations from different model states, assuming that the system's initial conditions are known, using prior information to fix some parameters involved in parameter correlations, or modifying the model based on existing parameter correlations. We also underscore how the results of structural identifiability analysis can help enrich compartmental diagrams of differential-equation models by indicating the observed state variables and the results of the structural identifiability analysis.

Associations between rurality and regional differences in sociodemographic factors and the 1918-20 influenza and 2020-21 COVID-19 pandemics in Missouri counties: An ecological study.

This study compares pandemic experiences of Missouri's 115 counties based on rurality and sociodemographic characteristics during the 1918-20 influenza and 2020-21 COVID-19 pandemics. The state's counties and overall population distribution have remained relatively stable over the last century, which enables identification of long-lasting pandemic attributes. Sociodemographic data available at the county level for both time periods were taken from U.S. census data and used to create clusters of similar counties. Counties were also grouped by rural status (RSU), including fully (100%) rural, semirural (1-49% living in urban areas), and urban (>50% of the population living in urban areas). Deaths from 1918 through 1920 were collated from the Missouri Digital Heritage database and COVID-19 cases and deaths were downloaded from the Missouri COVID-19 dashboard. Results from sociodemographic analyses indicate that, during both time periods, average farm value, proportion White, and literacy were the most important determinants of sociodemographic clusters. Furthermore, the Urban/Central and Southeastern regions experienced higher mortality during both pandemics than did the North and South. Analyses comparing county groups by rurality indicated that throughout the 1918-20 influenza pandemic, urban counties had the highest and rural had the lowest mortality rates. Early in the 2020-21 COVID-19 pandemic, urban counties saw the most extensive epidemic spread and highest mortality, but as the epidemic progressed, cumulative mortality became highest in semirural counties. Additional results highlight the greater effects both pandemics had on county groups with lower rates of education and a lower proportion of Whites in the population. This was especially true for the far southeastern counties of Missouri ("the Bootheel") during the COVID-19 pandemic. These results indicate that rural-urban and socioeconomic differences in health outcomes are long-standing problems that continue to be of significant importance, even though the overall quality of health care is substantially better in the 21st century.

A MATLAB toolbox to fit and forecast growth trajectories using phenomenological growth models: Application to epidemic outbreaks.

Background: Simple dynamic modeling tools can be useful for generating real-time short-term forecasts with quantified uncertainty of the trajectory of diverse growth processes unfolding in nature and society, including disease outbreaks. An easy-to-use and flexible toolbox for this purpose is lacking. Results: In this tutorial-based primer, we introduce and illustrate a user-friendly MATLAB toolbox for fitting and forecasting time-series trajectories using phenomenological dynamic growth models based on ordinary differential equations. This toolbox is accessible to various audiences, including students training in time-series forecasting, dynamic growth modeling, parameter estimation, parameter uncertainty and identifiability, model comparison, performance metrics, and forecast evaluation, as well as researchers and policymakers who need to conduct short-term forecasts in real-time. The models included in the toolbox capture exponential and sub-exponential growth patterns that typically follow a rising pattern followed by a decline phase, a common feature of contagion processes. Models include the 2-parameter generalized-growth model, which has proved useful to characterize and forecast the ascending phase of epidemic outbreaks, and the Gompertz model as well as the 3-parameter generalized logistic-growth model and the Richards model, which have demonstrated competitive performance in forecasting single peak outbreaks.The toolbox provides a tutorial for forecasting time-series trajectories that include the full uncertainty distribution, derived through parametric bootstrapping, which is needed to construct prediction intervals and evaluate their accuracy. Functions are available to assess forecasting performance across different models, estimation methods, error structures in the data, and forecasting horizons. The toolbox also includes functions to quantify forecasting performance using metrics that evaluate point and distributional forecasts, including the weighted interval score. Conclusions: We have developed the first comprehensive toolbox to characterize and forecast time-series data using simple phenomenological growth models. As a contagion process takes off, the tools presented in this tutorial can facilitate policymaking to guide the implementation of control strategies and assess the impact of interventions. The toolbox functionality is demonstrated through various examples, including a tutorial video, and is illustrated using weekly data on the monkeypox epidemic in the USA.

Age-specific mortality and the role of living remotely: The 1918-20 influenza pandemic in Kautokeino and Karasjok, Norway.

The 1918-20 pandemic influenza killed 50-100 million people worldwide, but mortality varied by ethnicity and geography. In Norway, areas dominated by Sámi experienced 3-5 times higher mortality than the country's average. We here use data from burial registers and censuses to calculate all-cause excess mortality by age and wave in two remote Sámi areas of Norway 1918-20. We hypothesise that geographic isolation, less prior exposure to seasonal influenza, and thus less immunity led to higher Indigenous mortality and a different age distribution of mortality (higher mortality for all) than was typical for this pandemic in non-isolated majority populations (higher young adult mortality & sparing of the elderly). Our results show that in the fall of 1918 (Karasjok), winter of 1919 (Kautokeino), and winter of 1920 (Karasjok), young adults had the highest excess mortality, followed by also high excess mortality among the elderly and children. Children did not exhibit excess mortality in the second wave in Karasjok in 1920. It was not the young adults alone who produced the excess mortality in Kautokeino and Karasjok. We conclude that geographic isolation caused higher mortality among the elderly in the first and second waves, and among children in the first wave.

Real-time forecasting the trajectory of monkeypox outbreaks at the national and global levels, July-October 2022.

BACKGROUND: Beginning May 7, 2022, multiple nations reported an unprecedented surge in monkeypox cases. Unlike past outbreaks, differences in affected populations, transmission mode, and clinical characteristics have been noted. With the existing uncertainties of the outbreak, real-time short-term forecasting can guide and evaluate the effectiveness of public health measures. METHODS: We obtained publicly available data on confirmed weekly cases of monkeypox at the global level and for seven countries (with the highest burden of disease at the time this study was initiated) from the Our World in Data (OWID) GitHub repository and CDC website. We generated short-term forecasts of new cases of monkeypox across the study areas using an ensemble n-sub-epidemic modeling framework based on weekly cases using 10-week calibration periods. We report and assess the weekly forecasts with quantified uncertainty from the top-ranked, second-ranked, and ensemble sub-epidemic models. Overall, we conducted 324 weekly sequential 4-week ahead forecasts across the models from the week of July 28th, 2022, to the week of October 13th, 2022. RESULTS: The last 10 of 12 forecasting periods (starting the week of August 11th, 2022) show either a plateauing or declining trend of monkeypox cases for all models and areas of study. According to our latest 4-week ahead forecast from the top-ranked model, a total of 6232 (95% PI 487.8, 12,468.0) cases could be added globally from the week of 10/20/2022 to the week of 11/10/2022. At the country level, the top-ranked model predicts that the USA will report the highest cumulative number of new cases for the 4-week forecasts (median based on OWID data: 1806 (95% PI 0.0, 5544.5)). The top-ranked and weighted ensemble models outperformed all other models in short-term forecasts. CONCLUSIONS: Our top-ranked model consistently predicted a decreasing trend in monkeypox cases on the global and country-specific scale during the last ten sequential forecasting periods. Our findings reflect the potential impact of increased immunity, and behavioral modification among high-risk populations.

An ensemble n-sub-epidemic modeling framework for short-term forecasting epidemic trajectories: Application to the COVID-19 pandemic in the USA.

We analyze an ensemble of n-sub-epidemic modeling for forecasting the trajectory of epidemics and pandemics. These ensemble modeling approaches, and models that integrate sub-epidemics to capture complex temporal dynamics, have demonstrated powerful forecasting capability. This modeling framework can characterize complex epidemic patterns, including plateaus, epidemic resurgences, and epidemic waves characterized by multiple peaks of different sizes. We systematically assess their calibration and short-term forecasting performance in short-term forecasts for the COVID-19 pandemic in the USA from late April 2020 to late February 2022. We compare their performance with two commonly used statistical ARIMA models. The best fit sub-epidemic model and three ensemble models constructed using the top-ranking sub-epidemic models consistently outperformed the ARIMA models in terms of the weighted interval score (WIS) and the coverage of the 95% prediction interval across the 10-, 20-, and 30-day short-term forecasts. In our 30-day forecasts, the average WIS ranged from 377.6 to 421.3 for the sub-epidemic models, whereas it ranged from 439.29 to 767.05 for the ARIMA models. Across 98 short-term forecasts, the ensemble model incorporating the top four ranking sub-epidemic models (Ensemble(4)) outperformed the (log) ARIMA model 66.3% of the time, and the ARIMA model, 69.4% of the time in 30-day ahead forecasts in terms of the WIS. Ensemble(4) consistently yielded the best performance in terms of the metrics that account for the uncertainty of the predictions. This framework can be readily applied to investigate the spread of epidemics and pandemics beyond COVID-19, as well as other dynamic growth processes found in nature and society that would benefit from short-term predictions.

An ensemble n -sub-epidemic modeling framework for short-term forecasting epidemic trajectories: Application to the COVID-19 pandemic in the USA.

We analyze an ensemble of n -sub-epidemic modeling for forecasting the trajectory of epidemics and pandemics. These ensemble modeling approaches, and models that integrate sub-epidemics to capture complex temporal dynamics, have demonstrated powerful forecasting capability. This modeling framework can characterize complex epidemic patterns, including plateaus, epidemic resurgences, and epidemic waves characterized by multiple peaks of different sizes. We systematically assess their calibration and short-term forecasting performance in short-term forecasts for the COVID-19 pandemic in the USA from late April 2020 to late February 2022. We compare their performance with two commonly used statistical ARIMA models. The best fit sub-epidemic model and three ensemble models constructed using the top-ranking sub-epidemic models consistently outperformed the ARIMA models in terms of the weighted interval score (WIS) and the coverage of the 95% prediction interval across the 10-, 20-, and 30-day short-term forecasts. In the 30-day forecasts, the average WIS ranged from 377.6 to 421.3 for the sub-epidemic models, whereas it ranged from 439.29 to 767.05 for the ARIMA models. Across 98 short-term forecasts, the ensemble model incorporating the top four ranking sub-epidemic models (Ensemble(4)) outperformed the (log) ARIMA model 66.3% of the time, and the ARIMA model 69.4% of the time in 30-day ahead forecasts in terms of the WIS. Ensemble(4) consistently yielded the best performance in terms of the metrics that account for the uncertainty of the predictions. This framework could be readily applied to investigate the spread of epidemics and pandemics beyond COVID-19, as well as other dynamic growth processes found in nature and society that would benefit from short-term predictions. Summary: The COVID-19 pandemic has highlighted the urgent need to develop reliable tools to forecast the trajectory of epidemics and pandemics in near real-time. We describe and apply an ensemble n -sub-epidemic modeling framework for forecasting the trajectory of epidemics and pandemics. We systematically assess its calibration and short-term forecasting performance in weekly 10-30 days ahead forecasts for the COVID-19 pandemic in the USA from late April 2020 to late February 2022 and compare its performance with two different statistical ARIMA models. This framework demonstrated reliable forecasting performance and substantially outcompeted the ARIMA models. The forecasting performance was consistently best for the ensemble sub-epidemic models incorporating a higher number of top-ranking sub-epidemic models. The ensemble model incorporating the top four ranking sub-epidemic models consistently yielded the best performance, particularly in terms of the coverage rate of the 95% prediction interval and the weighted interval score. This framework can be applied to forecast other growth processes found in nature and society including the spread of information through social media.

Investigating COVID-19 transmission and mortality differences between indigenous and non-indigenous populations in Mexico.

OBJECTIVES: Indigenous populations have been disproportionately affected during pandemics. We investigated COVID-19 mortality estimates among indigenous and non-indigenous populations at national and sub-national levels in Mexico. METHODS: We obtained data from the Ministry of Health, Mexico, on 2,173,036 laboratory-confirmed RT-PCR positive COVID-19 cases and 238,803 deaths. We estimated mortality per 1000 person-weeks, mortality rate ratio (RR) among indigenous vs. non-indigenous groups, and hazard ratio (HR) for COVID-19 deaths across four waves of the pandemic, from February 2020 to March 2022. We also assessed differences in the reproduction number (Rt). RESULTS: The mortality rate among indigenous populations of Mexico was 68% higher than that of non-indigenous groups. Out of 32 federal entities, 23 exhibited higher mortality rates among indigenous groups (P < 0.05 in 13 entities). The fourth wave showed the highest RR (2.40). The crude HR was 1.67 (95% CI: 1.62, 1.72), which decreased to 1.08 (95% CI: 1.04, 1.11) after controlling for other covariates. During the intense fourth wave, the Rt among the two groups was comparable. CONCLUSION: Indigenous status is a significant risk factor for COVID-19 mortality in Mexico. Our findings may reflect disparities in non-pharmaceutical (e.g., handwashing and using facemasks), and COVID-19 vaccination interventions among indigenous and non-indigenous populations in Mexico.

Effects of Climatic Factors on Diarrheal Diseases among Children below 5 Years of Age at National and Subnational Levels in Nepal: An Ecological Study.

Introduction: The incidence of diarrhea, a leading cause of morbidity and mortality in low-income countries such as Nepal, is temperature-sensitive, suggesting it could be associated with climate change. With climate change fueled increases in the mean and variability of temperature and precipitation, the incidence of water and food-borne diseases are increasing, particularly in sub-Saharan Africa and South Asia. This national-level ecological study was undertaken to provide evidence linking weather and climate with diarrhea incidence in Nepal. Method: We analyzed monthly diarrheal disease count and meteorological data from all districts, spanning 15 eco-development regions of Nepal. Meteorological data and monthly data on diarrheal disease were sourced, respectively, from the Department of Hydrology and Meteorology and Health Management Information System (HMIS) of the Government of Nepal for the period from 2002 to 2014. Time-series log-linear regression models assessed the relationship between maximum temperature, minimum temperature, rainfall, relative humidity, and diarrhea burden. Predictors with p-values < 0.25 were retained in the fitted models. Results: Overall, diarrheal disease incidence in Nepal significantly increased with 1 °C increase in mean temperature (4.4%; 95% CI: 3.95, 4.85) and 1 cm increase in rainfall (0.28%; 95% CI: 0.15, 0.41). Seasonal variation of diarrheal incidence was prominent at the national level (11.63% rise in diarrheal cases in summer (95% CI: 4.17, 19.61) and 14.5% decrease in spring (95% CI: −18.81, −10.02) compared to winter season). Moreover, the effects of temperature and rainfall were highest in the mountain region compared to other ecological regions of Nepal. Conclusion: Our study provides empirical evidence linking weather factors and diarrheal disease burden in Nepal. This evidence suggests that additional climate change could increase diarrheal disease incidence across the nation. Mountainous regions are more sensitive to climate variability and consequently the burden of diarrheal diseases. These findings can be utilized to allocate necessary resources and envision a weather-based early warning system for the prevention and control of diarrheal diseases in Nepal.

A Nationwide Prevalence of Common Mental Disorders and Suicidality in Nepal: Evidence from National Mental Health Survey, 2019-2020.

BACKGROUND: Mental disorders account for a large portion of burden of disease. In Nepal, the prevalence of mental disorders has been rising steadily, but national and province level prevalence is not available. This study aims to assess the prevalence of common mental disorders and suicidality in Nepal. METHODS: We conducted nationwide descriptive cross-sectional community-based prevalence study of mental disorders and suicidality among adults (aged 18 years and above) and adolescents (aged 13 to 17 years) in Nepal. We included a total of 9200 adults and 5888 adolescents from seven provinces of Nepal by using a multistage Probability Proportionate to Size sampling technique. Mental disorders and suicidality were assessed using translated and adapted Nepalese version of Mini International Neuropsychiatric Interview (MINI) for disorders, English version 7.0.2 for Diagnostic and Statistical Manual of Mental disorders,5th Edition (DSM-5). Data were entered in CSPro v7.2. Weighted estimates for different mental disorders were calculated. RESULTS: The overall weighted lifetime prevalence of any mental disorder among adults and adolescents was estimated at 10% and 5.2%, respectively. Suicidality was present among 7.2% of the adult and 4.1% of the adolescent participants. Among adult participants, the current prevalence of suicidal thoughts and lifetime suicidal attempts were found to be 6.5% and 1.1%, respectively. CONCLUSIONS: This survey indicated that mental health problems are major public health concerns in Nepal that should not be overlooked. Hence, a multisectoral approach is needed to address the burden of mental health problems among adults and adolescents in Nepal.

An investigation of spatial-temporal patterns and predictions of the coronavirus 2019 pandemic in Colombia, 2020-2021.

Colombia announced the first case of severe acute respiratory syndrome coronavirus 2 on March 6, 2020. Since then, the country has reported a total of 5,002,387 cases and 127,258 deaths as of October 31, 2021. The aggressive transmission dynamics of SARS-CoV-2 motivate an investigation of COVID-19 at the national and regional levels in Colombia. We utilize the case incidence and mortality data to estimate the transmission potential and generate short-term forecasts of the COVID-19 pandemic to inform the public health policies using previously validated mathematical models. The analysis is augmented by the examination of geographic heterogeneity of COVID-19 at the departmental level along with the investigation of mobility and social media trends. Overall, the national and regional reproduction numbers show sustained disease transmission during the early phase of the pandemic, exhibiting sub-exponential growth dynamics. Whereas the most recent estimates of reproduction number indicate disease containment, with Rt<1.0 as of October 31, 2021. On the forecasting front, the sub-epidemic model performs best at capturing the 30-day ahead COVID-19 trajectory compared to the Richards and generalized logistic growth model. Nevertheless, the spatial variability in the incidence rate patterns across different departments can be grouped into four distinct clusters. As the case incidence surged in July 2020, an increase in mobility patterns was also observed. On the contrary, a spike in the number of tweets indicating the stay-at-home orders was observed in November 2020 when the case incidence had already plateaued, indicating the pandemic fatigue in the country.

Geospatial Variability in Excess Death Rates during the COVID-19 Pandemic in Mexico: Examining Socio Demographic, Climate and Population Health Characteristics.

OBJECTIVES: This study examined how socio-demographic, climate and population health characteristics shaped the geospatial variability in excess mortality patterns during the COVID-19 pandemic in Mexico. METHODS: We used Serfling regression models to estimate all-cause excess mortality rates for all 32 Mexican states. The association between socio-demographic, climate, health indicators and excess mortality rates were determined using multiple linear regression analyses. Functional data analysis characterized clusters of states with distinct excess mortality growth rate curves. RESULTS: The overall all-cause excess deaths rate during the COVID-19 pandemic in Mexico until April 10, 2021 was estimated at 39.66 per 10 000 population. The lowest excess death rates were observed in southeastern states including Chiapas (12.72) and Oaxaca (13.42), whereas Mexico City had the highest rate (106.17), followed by Tlaxcala (51.99). We found a positive association of excess mortality rates with aging index, marginalization index, and average household size (P < 0.001) in the final adjusted model (Model R2=77%). We identified four distinct clusters with qualitatively similar excess mortality curves. CONCLUSION: Central states exhibited the highest excess mortality rates, whereas the distribution of aging index, marginalization index, and average household size explained the variability in excess mortality rates across Mexico.

Barriers and facilitators to the implementation of a national multisectoral action plan for the prevention and control of noncommunicable diseases in Nepal: perspectives of stakeholders.

BACKGROUND: Nepal adopted the Multisectoral Action Plan for the Prevention and Control of Non-Communicable Diseases (MSAP) in 2014. Implementation of the plan has been challenging, with limited participation from non-health sectors. OBJECTIVES: The overall aim of the study was to gain the perspectives of key stakeholders involved in the Nepal MSAP on the barriers and facilitators to its implementation, through the participation of relevant sectors in the plan. METHODS: We held face-to-face semi-structured interviews with 12 stakeholders working in sectors involved in the MSAP. These sectors included the Office of the Prime Minister and Council of Ministries; Ministry of Health and Population (MOHP); Ministry of Education, Science and Technology; Ministry of Forest and Environment; academia; and professional organizations. Thematic analysis of transcripts was used to identify themes on awareness of NCDs, awareness of the MSAP, and barriers and facilitators to participation in the MSAP. RESULTS: Participants recognised NCDs as a growing and major burden in Nepal. However, a number of participants were not familiar with the MSAP, identifying a lack of leadership and poor dissemination. Political and systemic transformation, since the adoption of the MSAP, was seen as a key barrier to implementation. International commitments to develop multisectoral action made by the Government of Nepal were identified as drivers. The recent establishment of a separate section for NCDs and Mental Health within the Department of Health Services of MOHP and the promotion of a Health in All Policies (HiAP) approach in recent national documents, were both considered to support implementation. CONCLUSIONS: The establishment of permanent multisectoral or multistakeholder mechanisms has been challenging despite strong political calls for their development. Moving beyond 2020, multisectoral action plans should engage with stakeholders from federal, provincial and local governments in order to develop costed action plans with specific roles and responsibilities for each sector.

Harnessing testing strategies and public health measures to avert COVID-19 outbreaks during ocean cruises.

To ensure the safe operation of schools, workplaces, nursing homes, and other businesses during COVID-19 pandemic there is an urgent need to develop cost-effective public health strategies. Here we focus on the cruise industry which was hit early by the COVID-19 pandemic, with more than 40 cruise ships reporting COVID-19 infections. We apply mathematical modeling to assess the impact of testing strategies together with social distancing protocols on the spread of the novel coronavirus during ocean cruises using an individual-level stochastic model of the transmission dynamics of COVID-19. We model the contact network, the potential importation of cases arising during shore excursions, the temporal course of infectivity at the individual level, the effects of social distancing strategies, different testing scenarios characterized by the test's sensitivity profile, and testing frequency. Our findings indicate that PCR testing at embarkation and daily testing of all individuals aboard, together with increased social distancing and other public health measures, should allow for rapid detection and isolation of COVID-19 infections and dramatically reducing the probability of onboard COVID-19 community spread. In contrast, relying only on PCR testing at embarkation would not be sufficient to avert outbreaks, even when implementing substantial levels of social distancing measures.

Basic emergency obstetric and newborn care service availability and readiness in Nepal: Analysis of the 2015 Nepal Health Facility Survey.

BACKGROUND: Achieving maternal and newborn related Sustainable Development Goals targets is challenging for Nepal, mainly due to poor quality of maternity services. In this context, we aim to assess the Basic Emergency Obstetric and Newborn Care (BEmONC) service availability and readiness in health facilities in Nepal by analyzing data from Nepal Health Facility Survey (NHFS), 2015. METHODS: We utilized cross-sectional data from the nationally representative NHFS, 2015. Service availability was measured by seven signal functions of BEmONC, and service readiness by the availability and functioning of supportive items categorized into three domains: staff and guidelines, diagnostic equipment, and basic medicine and commodities. We used the World Health Organization's service availability and readiness indicators to estimate the readiness scores. We performed a multiple linear regression to identify important factors in the readiness of the health facilities to provide BEmONC services. RESULTS: The BEmONC service readiness score was significantly higher in public hospitals compared with private hospitals and peripheral public health facilities. Significant factors associated with service readiness score were the facility type (14.69 points higher in public hospitals, P<0.001), number of service delivery staff (2.49 points increase per each additional delivery staff, P<0.001), the service hours (4.89 points higher in facilities offering 24-hour services, P = 0.01) and status of periodic review of maternal and newborn deaths (4.88 points higher in facilities that conducted periodic review, P = 0.043). CONCLUSIONS: These findings suggest that BEmONC services in Nepal could be improved by increasing the number of service delivery staff, expanding service hours to 24-hours a day, and conducting periodic review of maternal and newborn deaths at health facilities, mainly in the peripheral public health facilities. The private hospitals need to be encouraged for BEmONC service readiness.

Transmission dynamics and forecasts of the COVID-19 pandemic in Mexico, March-December 2020.

Mexico has experienced one of the highest COVID-19 mortality rates in the world. A delayed implementation of social distancing interventions in late March 2020 and a phased reopening of the country in June 2020 has facilitated sustained disease transmission in the region. In this study we systematically generate and compare 30-day ahead forecasts using previously validated growth models based on mortality trends from the Institute for Health Metrics and Evaluation for Mexico and Mexico City in near real-time. Moreover, we estimate reproduction numbers for SARS-CoV-2 based on the methods that rely on genomic data as well as case incidence data. Subsequently, functional data analysis techniques are utilized to analyze the shapes of COVID-19 growth rate curves at the state level to characterize the spatiotemporal transmission patterns of SARS-CoV-2. The early estimates of the reproduction number for Mexico were estimated between Rt ~1.1-1.3 from the genomic and case incidence data. Moreover, the mean estimate of Rt has fluctuated around ~1.0 from late July till end of September 2020. The spatial analysis characterizes the state-level dynamics of COVID-19 into four groups with distinct epidemic trajectories based on epidemic growth rates. Our results show that the sequential mortality forecasts from the GLM and Richards model predict a downward trend in the number of deaths for all thirteen forecast periods for Mexico and Mexico City. However, the sub-epidemic and IHME models perform better predicting a more realistic stable trajectory of COVID-19 mortality trends for the last three forecast periods (09/21-10/21, 09/28-10/27, 09/28-10/27) for Mexico and Mexico City. Our findings indicate that phenomenological models are useful tools for short-term epidemic forecasting albeit forecasts need to be interpreted with caution given the dynamic implementation and lifting of social distancing measures.