Infectious Diseases

Pandemic SEIR and SEIRV modelling software and infrastructure for the Corona SARS-COV-2 COVID-19 disease with data from Johns-Hopkins-University CSSE, Robert Koch-Institute and vaccination data from Our World In Data.

Communicable diseases including COVID-19 pose a major threat to public health worldwide.

To curb the spread of communicable diseases effectively, timely surveillance and prediction of the risk of pandemics are essential.

The aim of this study is to analyze free and publicly available data to construct useful travel data records for network statistics other than common descriptive statistics.

This study describes analytical findings of time-series plots and spatial-temporal maps to illustrate or visualize pandemic connectedness.

We observed similar patterns in the time-series plots of worldwide daily flights from January to early-March of 2019 and 2020. A sharp reduction in the number of daily flights recorded in mid-March 2020 was likely related to large-scale air travel restrictions owing to the COVID-19 pandemic. The levels of connectedness between places are strong indicators of the risk of a pandemic.

Since the initial reports of COVID-19 cases worldwide, a high network density and reciprocity in early-March 2020 served as early signals of the COVID-19 pandemic and were associated with the rapid increase in COVID-19 cases in mid-March 2020.

The spatial-temporal map of connectedness in Europe on March 13, 2020, shows the highest level of connectedness among European countries, which reflected severe outbreaks of COVID-19 in late March and early April of 2020.

The analysis can facilitate early recognition of the risk of a current communicable disease pandemic and newly emerging communicable diseases in the future.

read the study at https://publichealth.jmir.org/2021/3/e27317

National governments worldwide have implemented non-pharmaceutical interventions to control the COVID-19 pandemic and mitigate its effects.

Objective: The aim of this study was to investigate the prediction of future daily national confirmed COVID-19 infection growth—the percentage change in total cumulative cases—across 14 days for 114 countries using non-pharmaceutical intervention metrics and cultural dimension metrics, which are indicative of specific national socio-cultural norms.

Methods: We combined the Oxford COVID-19 Government Response Tracker data set, Hofstede cultural dimensions, and daily reported COVID-19 infection case numbers to train and evaluate five non–time series machine learning models in predicting confirmed infection growth.

We used three validation methods—in-distribution, out-of-distribution, and country-based cross-validation—for the evaluation, each of which was applicable to a different use case of the models.

Results: Our results demonstrate high R2 values between the labels and predictions for the in-distribution method (0.959) and moderate R2 values for the out-of-distribution and country-based cross-validation methods (0.513 and 0.574, respectively) using random forest and adaptive boosting (AdaBoost) regression.

Although these models may be used to predict confirmed infection growth, the differing accuracies obtained from the three tasks suggest a strong influence of the use case.

Conclusions:  This study adds to the rapidly growing body of work related to predicting COVID-19 infection rates by introducing an approach that incorporates routinely available data on NPIs and cultural dimensions. Importantly, this study emphasizes the utility of NPIs and cultural dimensions for predicting country-level growth of confirmed infections of COVID-19, which to date have been limited in existing forecasting models. Our findings offer a new direction for the broader inclusion of these types of measures, which are also relevant for other infectious diseases, using non–time series machine learning models. Our experiments also provide insight into validation methods for different applications of the models.

read the entire study at https://www.jmir.org/2021/4/e26628