Leveraging Deep Learning to Improve COVID-19 Forecasting Using Wastewater Viral Load

Mehrdad Fazli, Heman Shakeri

Abstract: The outburst of COVID-19 in late 2019 was the start of a health crisis that shook the world and took millions of lives in the ensuing years. Many governments and health officials failed to arrest the rapid circulation of infection in their communities. The long incubation period and the large proportion of asymptomatic cases made COVID-19 particularly elusive to track. However, wastewater surveillance soon became a promising data source in addition to conventional indicators such as confirmed daily cases, hospitalizations, and deaths. Despite the consensus on the effectiveness of wastewater viral load, there is a lack of methodological approaches that leverage viral load to improve COVID-19 forecasting. This paper proposes a deep learning framework to automatically discover the relationship between daily cases and viral load data. We trained a Deep Temporal Convolutional Network (DeepTCN) and a Temporal Fusion Transformer (TFT) model to obtain a global forecasting model. We supplement the daily confirmed cases with viral loads and other socio-economic factors as covariates to the models. Our results suggest that TFT outperforms DeepTCN and learns a better association between viral load and daily cases. We demonstrate that equipping the models with the viral load improves forecasting accuracy and reduces uncertainty. Moreover, viral load is shown to be the second most predictive input, following the containment and health index. Our results reveal the feasibility of training a location-agnostic deep-learning model to capture the dynamics of infection diffusion when wastewater viral load data is available.