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Updated: Sep 18, 2025

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples
Published on: June 30, 2023
Behavioral Dynamics, Genomic Insights, and Social Drivers of SARS-CoV-2 Waves and Variants in Cali, Colombia
Diana López-Alvarez1,2, Nelson Rivera-Franco1,3, Erica Aristizabal1
1Grupo VIREM-Virus Emergentes y Enfermedad, Departamento de Microbiología, Escuela de Ciencias Básicas, Facultad de Salud, Universidad del Valle, Cali 760043, Colombia.
Abstract:
In Cali, Colombia, 405,689 COVID-19 cases were reported until March 2023, with 2463 complete genome sequences available for analysis. SARS-CoV-2 genomic data from Cali were analyzed to determine the prevalence of variants as well as the mutation frequencies. This study identified Nextstrain clades, Pango lineages, and specific mutations in key viral proteins. A total of 23 Nextstrain clades and 118 Pango lineages were detected, including variants of interest (Lambda, Mu) and variants of concern (Alpha, Gamma, Delta, Omicron). Analysis identified 2424 missense mutations, with notable frequencies in NSP3 (465), S (367), NSP2 (205), N (180), ORF3a (144), NSP12b (113), and NSP13 (108). The study also observed a high prevalence of simultaneous transmission of multiple variants. The COVID-19 epidemic waves in Cali were shaped more by social and economic dynamics than by the emergence of specific SARS-CoV-2 variants. These findings highlight the importance of context-specific public health interventions to mitigate future outbreaks effectively.
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