AUTHOR=Patiño Luz H. , Castañeda Sergio , Muñoz Marina , Ballesteros Nathalia , Ramirez Angie L. , Luna Nicolas , Guerrero-Araya Enzo , Pérez Julie , Correa-Cárdenas Camilo A. , Duque Maria Clara , Méndez Claudia , Oliveros Carolina , Shaban Maryia V. , Paniz-Mondolfi Alberto E. , Ramírez Juan David 

TITLE=Epidemiological Dynamics of SARS-CoV-2 Variants During Social Protests in Cali, Colombia

JOURNAL=Frontiers in Medicine

VOLUME=Volume 9 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2022.863911

DOI=10.3389/fmed.2022.863911

ISSN=2296-858X

ABSTRACT=Background:  The third wave of the global health crisis attributed to the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus reached Colombia in March 2021. Over the following six months, it was interpolated by manifestations of popular disapproval to the actual political regime—with multiple protests sprouting throughout the country. Large social gatherings seeded novel Coronavirus disease 2019 (COVID-19) variants in big cities and propagated their facile spread, leading to increased rates of hospitalizations and deaths. 
Methods:  In this paper, we evaluate the effective reproduction number (Rt) dynamics of SARS-CoV-2 in Cali, Colombia, between April 4 and July 31, 2021 based on the analysis of 228 genomes. 
Results:  Our results showed clear contrast in Rt values between the period of frequent protests (Rt > 1), and the preceding and following months (Rt < 1). Genomic analyses revealed 16 circulating SARS-CoV-2 strains during the initial period—including variants of concern (VOCs) (Alpha, Gamma, and Delta) and variants of interest (VOIs) (Lambda and Mu). Furthermore, we noticed the Mu variant dominating the COVID-19 distribution schema as the months progressed. We identified four principal clusters through phylogenomic analyses—each one of potentially independent introduction to the city. Two of these were associated with the Mu variant, one associated with the Gamma variant, and one with the Lambda variant. 
Conclusion:  Our results chronicle the impact of large group assemblies on the epidemiology of COVID-19 during this intersection of political turmoil and sanitary crisis in Cali, Colombia. We emphasize upon the effects of limited biosecurity strategies (which had characterized this time period), on the spread of highly virulent strains throughout Cali and greater Colombia.