Decoupling between SARS-CoV-2 transmissibility and population mobility associated with increasing immunity from vaccination and infection in South America

Marcelo Fiori, Gonzalo Bello, Nicolás Wschebor, Federico Lecumberry, Andrés Ferragut, Ernesto Mordecki

This is the code used to produce the results and figures in the paper published in Scientific Reports: https://www.nature.com/articles/s41598-022-10896-4

Abstract of the paper: All South American countries from the Southern cone (Argentina, Brazil, Chile, Paraguay and Uruguay) experienced severe COVID-19 epidemic waves during early 2021 driven by the expansion of variants Gamma and Lambda, however, there was an improvement in different epidemic indicators since June 2021. To investigate the impact of national vaccination programs and natural infection on viral transmission in those South American countries, we analyzed the coupling between population mobility and the viral effective reproduction number 𝑅𝑡. Our analyses reveal that population mobility was highly correlated with viral 𝑅𝑡 from January to May 2021 in all countries analyzed; but a clear decoupling occurred since May–June 2021, when the rate of viral spread started to be lower than expected from the levels of social interactions. These findings support that populations from the South American Southern cone probably achieved the conditional herd immunity threshold to contain the spread of regional SARS-CoV-2 variants circulating at that time.