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

Tariq, Amna; Banda, Juan M.; Skums, Pavel; Dahal, Sushma; Castillo-Garsow, Carlos; Espinoza, Baltazar; Brizuela, Noel G.; Saenz, Roberto A.; Kirpich, Alexander; Luo, Ruiyan; Srivastava, Anuj; Gutierrez, Humberto; Chan, Nestor Garcia; Bento, Ana I.; Jimenez-Corona, Maria-Eugenia; Chowell, Gerardo

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 R(t) ~1.1–1.3 from the genomic and case incidence data. Moreover, the mean estimate of R(t) 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.