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

Frontiers in Medicine

article

Luz H. Patiño¹  Sergio Castañeda¹  Marina Muñoz¹  Nathalia Ballesteros¹  Angie L. Ramirez¹  Nicolas Luna¹  Enzo Guerrero-Araya²  Julie Pérez⁴  Camilo A. Correa-Cárdenas⁴  Maria Clara Duque⁴  Claudia Méndez⁴  Carolina Oliveros⁴  Maryia V. Shaban⁵  Alberto E. Paniz-Mondolfi⁶  Juan David Ramírez¹ 

[1] Centro de Investigaciones en Microbiología y Biotecnología-UR ,(CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario;Agencia Nacional de Investigación y Desarrollo ,(ANID)—Millennium Science Initiative Program—Millennium Nucleus in the Biology of the Intestinal Microbiota;Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello;Grupo de Investigación en Enfermedades Tropicales del Ejército ,(GINETEJ), Laboratorio de Referencia e Investigación;Incubadora Venezolana de la Ciencia;Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai

关键词: SARS-CoV-2;    COVID-19;    effective reproduction number;    lineages;    Cali;   

DOI  :  10.3389/fmed.2022.863911

学科分类：社会科学、人文和艺术（综合）

来源: Frontiers

【 摘 要 】

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 6 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 (COVID19) variants in big cities and propagated their facile spread, leading to increased rates of hospitalizations and deaths. Methods: In this article, we evaluate the effective reproduction number (Rt) dynamics of SARS-CoV-2 in Cali, Colombia, between 4 April 2021 and 31 July 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 lineages 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.

【 授权许可】

CC BY