Data-driven methods for present and future pandemics: Monitoring, modelling and managing

Changes to Public Health Surveillance Methods Due to the COVID-19 Pandemic: Scoping Review

BACKGROUND

Public health surveillance plays a vital role in informing public health decision-making. The onset of the COVID-19 pandemic in early 2020 caused a widespread shift in public health priorities. Global efforts focused on COVID-19 monitoring and contact tracing. Existing public health programs were interrupted due to physical distancing measures and reallocation of resources. The onset of the COVID-19 pandemic intersected with advancements in technologies that have the potential to support public health surveillance efforts.

OBJECTIVE

This scoping review aims to explore emergent public health surveillance methods during the early COVID-19 pandemic to characterize the impact of the pandemic on surveillance methods.

METHODS

A scoping search was conducted in multiple databases and by scanning key government and public health organization websites from March 2020 to January 2022. Published papers and gray literature that described the application of new or revised approaches to public health surveillance were included. Papers that discussed the implications of novel public health surveillance approaches from ethical, legal, security, and equity perspectives were also included. The surveillance subject, method, location, and setting were extracted from each paper to identify trends in surveillance practices. Two public health epidemiologists were invited to provide their perspectives as peer reviewers.

RESULTS

Of the 14,238 unique papers, a total of 241 papers describing novel surveillance methods and changes to surveillance methods are included. Eighty papers were review papers and 161 were single studies. Overall, the literature heavily featured papers detailing surveillance of COVID-19 transmission (n=187). Surveillance of other infectious diseases was also described, including other pathogens (n=12). Other public health topics included vaccines (n=9), mental health (n=11), substance use (n=4), healthy nutrition (n=1), maternal and child health (n=3), antimicrobial resistance (n=2), and misinformation (n=6). The literature was dominated by applications of digital surveillance, for example, by using big data through mobility tracking and infodemiology (n=163). Wastewater surveillance was also heavily represented (n=48). Other papers described adaptations to programs or methods that existed prior to the COVID-19 pandemic (n=9). The scoping search also found 109 papers that discuss the ethical, legal, security, and equity implications of emerging surveillance methods. The peer reviewer public health epidemiologists noted that additional changes likely exist, beyond what has been reported and available for evidence syntheses.

CONCLUSIONS

The COVID-19 pandemic accelerated advancements in surveillance and the adoption of new technologies, especially for digital and wastewater surveillance methods. Given the investments in these systems, further applications for public health surveillance are likely. The literature for surveillance methods was dominated by surveillance of infectious diseases, particularly COVID-19. A substantial amount of literature on the ethical, legal, security, and equity implications of these emerging surveillance methods also points to a need for cautious consideration of potential harm.

Utilising routine clinical laboratory data to support quality improvement in health care: Application of a national acute kidney injury alert system as a proof of concept

BACKGROUND

Acute kidney injury (AKI) is a global health issue known to cause avoidable harm and death. Improvement in its prevention and management is therefore considered an important goal for the health-care sector. The work here aimed to develop a tool which could be used to robustly and reliably measure, monitor, and compare the effectiveness of health-care interventions related to AKI across the Welsh NHS, a mechanism which did not exist previously.

METHODS

Using serum creatinine (SCr) as a biomarker for AKI and a validated national data-set collected from the all Wales Laboratory Information Management System, work involved applying Donabedian's framework to develop indicators with which to measure outcomes related to AKI, and exploring the potential of statistical process control (SPC) techniques for analysing data on these indicators.

RESULTS

Rate of AKI incidence and 30-day AKI-associated mortality are proposed as valid, feasible indicators with which to measure the effectiveness of health-care interventions related to AKI. The control chart, funnel plot, and Pareto chart are proposed as appropriate, robust SPC techniques to analyse and visualise variation in AKI-related outcomes.

CONCLUSIONS

This work demonstrates that routinely collected large SCr data offer a significant opportunity to monitor and therefore inform improvement in patient outcomes related to AKI. Moreover, while this work concerns utilisation of SCr data for improvement in AKI strategies, it is a proof of concept which could be replicated for other routinely collected clinical laboratory data, to improve the prevention and/or management of the conditions to which they relate.

Fitting Early Phases of the COVID-19 Outbreak: A Comparison of the Performances of Used Models

The COVID-19 outbreak involved a spread of prediction efforts, especially in the early pandemic phase. A better understanding of the epidemiological implications of the different models seems crucial for tailoring prevention policies. This study aims to explore the concordance and discrepancies in outbreak prediction produced by models implemented and used in the first wave of the epidemic. To evaluate the performance of the model, an analysis was carried out on Italian pandemic data from February 24, 2020. The epidemic models were fitted to data collected at 20, 30, 40, 50, 60, 70, 80, 90, and 98 days (the entire time series). At each time step, we made predictions until May 31, 2020. The Mean Absolute Error (MAE) and the Mean Absolute Percentage Error (MAPE) were calculated. The GAM model is the most suitable parameterization for predicting the number of new cases; exponential or Poisson models help predict the cumulative number of cases. When the goal is to predict the epidemic peak, GAM, ARIMA, or Bayesian models are preferable. However, the prediction of the pandemic peak could be made carefully during the early stages of the epidemic because the forecast is affected by high uncertainty and may very likely produce the wrong results.

COVID-19 multiwaves as multiphase percolation: a general N-sigmoidal equation to model the spread

Abstract

The aim of the current study is to investigate the spread of the COVID-19 pandemic as a multiphase percolation process. Mathematical equations have been developed to describe the time dependence of the number of cumulative infected individuals, I t , and the velocity of the pandemic, V p t , as well as to calculate epidemiological characteristics. The study focuses on the use of sigmoidal growth models to investigate multiwave COVID-19. Hill, logistic dose response and sigmoid Boltzmann models fitted successfully a pandemic wave. The sigmoid Boltzmann model and the dose response model were found to be effective in fitting the cumulative number of COVID-19 cases over time 2 waves spread (N = 2). However, for multiwave spread (N > 2), the dose response model was found to be more suitable due to its ability to overcome convergence issues. The spread of N successive waves has also been described as multiphase percolation with a period of pandemic relaxation between two successive waves.

Graphical abstract

Airline flight delays using artificial intelligence in COVID-19 with perspective analytics

This study envisages assessing the effects of the COVID-19 on the on-time performance of US-airlines industry in the disrupted situations. The deep learning techniques used are neural network regression, decision forest regression, boosted decision tree regression and multi class logistic regression. The best technique is identified. In the perspective data analytics, it is suggested what the airlines should do for the on-time performance in the disrupted situation. The performances of all the methods are satisfactory. The coefficient of determination for the neural network regression is 0.86 and for decision forest regression is 0.85, respectively. The coefficient of determination for the boosted decision tree is 0.870984. Thus boosted decision tree regression is better. Multi class logistic regression gives an overall accuracy and precision of 98.4%. Recalling/remembering performance is 99%. Thus multi class logistic regression is the best model for prediction of flight delays in the COVID-19. The confusion matrix for the multi class logistic regression shows that 87.2% flights actually not delayed are predicted not delayed. The flights actually not delayed but wrongly predicted delayed are12.7%. The strength of relation with departure delay, carrier delay, late aircraft delay, weather delay and NAS delay, are 94%, 53%, 35%, 21%, and 14%, respectively. There is a weak negative relation (almost unrelated) with the air time and arrival delay. Security delay and arrival delay are also almost unrelated with strength of 1% relationship. Based on these diagnostic analytics, it is recommended as perspective to take due care reducing departure delay, carrier delay, Late aircraft delay, weather delay and Nas delay, respectively, considerably with effect of 94%, 53%, 35%, 21%, and 14% in disrupted situations. The proposed models have MAE of 2% for Neural Network Regression, Decision Forest Regression, Boosted Decision Tree Regression, respectively, and, RMSE approximately, 11%, 12%, 11%, respectively.

Climate Change Influences the Spread of African Swine Fever Virus

Climate change is an inevitable and urgent issue in the current world. African swine fever virus (ASFV) is a re-emerging viral animal disease. This study investigates the quantitative association between climate change and the potential spread of ASFV to a global extent. ASFV in wild boar outbreak locations recorded from 1 January 2019 to 29 July 2022 were sampled and investigated using the ecological distribution tool, the Maxent model, with WorldClim bioclimatic data as the predictor variables. The future impacts of climate change on ASFV distribution based on the model were scoped with Representative Concentration Pathways (RCP 2.6, 4.5, 6.0, and 8.5) scenarios of Coupled Model Intercomparison Project 5 (CMIP5) bioclimatic data for 2050 and 2070. The results show that precipitation of the driest month (Bio14) was the highest contributor, and annual mean temperature (Bio1) was obtained as the highest permutation importance variable on the spread of ASFV. Based on the analyzed scenarios, we found that the future climate is favourable for ASFV disease; only quantitative ratios are different and directly associated with climate change. The current study could be a reference material for wildlife health management, climate change issues, and World Health Organization sustainability goal 13: climate action.

Epidemiological model based periodic intervention policies for COVID-19 mitigation in the United Kingdom

As the UK, together with numerous countries in the world, moves towards a new phase of the COVID-19 pandemic, there is a need to be able to predict trends in sufficient time to limit the pressure faced by the National Health Service (NHS) and maintain low hospitalisation levels. In this study, we explore the use of an epidemiological compartmental model to devise a periodic adaptive suppression/intervention policy to alleviate the pressure on the NHS. The proposed model facilitates the understanding of the progression of the specific stages of COVID-19 in communities in the UK including: the susceptible population, the infected population, the hospitalised population, the recovered population, the deceased population, and the vaccinated population. We identify the parameters of the model by relying on past data within the period from 1 October 2020 to 1 June 2021. We use the total number of hospitalised patients and the fraction of those infected who are being admitted to hospital to develop adaptive policies: these modulate the recommended level of social restriction measures and realisable vaccination target adjustments. The analysis over the period 1 October 2020 to 1 June 2021 demonstrates our periodic adaptive policies have the potential to reduce the hospitalisation by 58% on average per month. In a further prospective analysis over the period August 2021 to May 2022, we analyse several future scenarios, characterised by the relaxation of restrictions, the vaccination ineffectiveness and the gradual decay of the vaccination-induced immunity within the population. In addition, we simulate the surge of plausible variants characterised by an higher transmission rate. In such scenarios, we show that our periodic intervention is effective and able to maintain the hospitalisation rate to a manageable level.