{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T01:50:45Z","timestamp":1774317045072,"version":"3.50.1"},"reference-count":40,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T00:00:00Z","timestamp":1748563200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institutes of Health (NIH)","award":["R01NS110122"],"award-info":[{"award-number":["R01NS110122"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/v17060800","type":"journal-article","created":{"date-parts":[[2025,6,2]],"date-time":"2025-06-02T12:27:09Z","timestamp":1748867229000},"page":"800","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Behavioral Dynamics, Genomic Insights, and Social Drivers of SARS-CoV-2 Waves and Variants in Cali, Colombia (2020\u20132023)"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7734-8481","authenticated-orcid":false,"given":"Diana","family":"L\u00f3pez-Alvarez","sequence":"first","affiliation":[{"name":"Grupo VIREM\u2014Virus Emergentes y Enfermedad, Departamento de Microbiolog\u00eda, Escuela de Ciencias B\u00e1sicas, Facultad de Salud, Universidad del Valle, Cali 760043, Colombia"},{"name":"Departamento de Ciencias Biol\u00f3gicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Palmira 763533, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4733-5452","authenticated-orcid":false,"given":"Nelson","family":"Rivera-Franco","sequence":"additional","affiliation":[{"name":"Grupo VIREM\u2014Virus Emergentes y Enfermedad, Departamento de Microbiolog\u00eda, Escuela de Ciencias B\u00e1sicas, Facultad de Salud, Universidad del Valle, Cali 760043, Colombia"},{"name":"Laboratorio de T\u00e9cnicas y An\u00e1lisis \u00d3micos\u2014TAOLab\/CiBioFi, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Calle 13 No 100-00, Cali 760015, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erica","family":"Aristizabal","sequence":"additional","affiliation":[{"name":"Grupo VIREM\u2014Virus Emergentes y Enfermedad, Departamento de Microbiolog\u00eda, Escuela de Ciencias B\u00e1sicas, Facultad de Salud, Universidad del Valle, Cali 760043, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melissa","family":"Solarte","sequence":"additional","affiliation":[{"name":"Grupo VIREM\u2014Virus Emergentes y Enfermedad, Departamento de Microbiolog\u00eda, Escuela de Ciencias B\u00e1sicas, Facultad de Salud, Universidad del Valle, Cali 760043, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9006-6721","authenticated-orcid":false,"given":"Andr\u00e9s","family":"Castillo","sequence":"additional","affiliation":[{"name":"Laboratorio de T\u00e9cnicas y An\u00e1lisis \u00d3micos\u2014TAOLab\/CiBioFi, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Calle 13 No 100-00, Cali 760015, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4128-5335","authenticated-orcid":false,"given":"Carlos A.","family":"Pardo","sequence":"additional","affiliation":[{"name":"Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA"},{"name":"Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5371-7449","authenticated-orcid":false,"given":"Beatriz","family":"Parra","sequence":"additional","affiliation":[{"name":"Grupo VIREM\u2014Virus Emergentes y Enfermedad, Departamento de Microbiolog\u00eda, Escuela de Ciencias B\u00e1sicas, Facultad de Salud, Universidad del Valle, Cali 760043, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,5,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e12","DOI":"10.1016\/S2468-2667(20)30263-2","article-title":"Effect of internationally imported cases on internal spread of COVID-19: A mathematical modelling study","volume":"6","author":"Russell","year":"2021","journal-title":"Lancet Public Health"},{"key":"ref_2","first-page":"100072","article-title":"Complex correlates of Colombia\u2019s COVID-19 surge","volume":"3","author":"Shultz","year":"2021","journal-title":"Lancet Reg. 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