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

Abstract

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 R _t<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.

Author summary

As the COVID-19 pandemic continues to spread across Colombia, studies highlighting the intensity of the pandemic have become imperative for appropriate resource allocation and informing public health policies. In this study we utilize mathematical models to infer the transmission dynamics of SARS-CoV-2 at the regional and national level as well as short-term forecasting of the COVID-19 epidemic trajectory. Moreover, we examine the geographic heterogeneity of the COVID-19 case incidence in Colombia along with the analysis of mobility and social media trends in relation to the observed COVID-19 case incidence in the country. The estimates of reproduction numbers at the national and regional level show a decline in disease transmission as of October 31, 2021. Moreover, the 30-day ahead short-term forecasts for the most recent time-period (October 2-October 31, 2021) generated using the mathematical models needs to be interpreted with caution as the single peak models point towards a sustained decline in case incidence contrary to the sub-epidemic wave model. Nevertheless, the spatial analysis in Colombia shows distinct variations in incidence rate patterns across different departments which can be grouped into four distinct clusters. Moreover, the social media and mobility trends also explain the occurrence of case resurgences over time.