Epidemiological Dynamics of SARS-CoV-2 Variants During Social Protests in Cali, Colombia
BackgroundThe 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 mult...
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-03-01
|
| Series: | Frontiers in Medicine |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmed.2022.863911/full |
| _version_ | 1830211067781840896 |
|---|---|
| author | Luz H. Patiño Sergio Castañeda Marina Muñoz Marina Muñoz Nathalia Ballesteros Angie L. Ramirez Nicolas Luna Enzo Guerrero-Araya Enzo Guerrero-Araya Julie Pérez Camilo A. Correa-Cárdenas Maria Clara Duque Claudia Méndez Carolina Oliveros Maryia V. Shaban Alberto E. Paniz-Mondolfi Juan David Ramírez Juan David Ramírez |
| author_facet | Luz H. Patiño Sergio Castañeda Marina Muñoz Marina Muñoz Nathalia Ballesteros Angie L. Ramirez Nicolas Luna Enzo Guerrero-Araya Enzo Guerrero-Araya Julie Pérez Camilo A. Correa-Cárdenas Maria Clara Duque Claudia Méndez Carolina Oliveros Maryia V. Shaban Alberto E. Paniz-Mondolfi Juan David Ramírez Juan David Ramírez |
| author_sort | Luz H. Patiño |
| collection | DOAJ |
| description | BackgroundThe 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 (COVID-19) variants in big cities and propagated their facile spread, leading to increased rates of hospitalizations and deaths.MethodsIn 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.ResultsOur 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.ConclusionOur 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. |
| first_indexed | 2024-12-18T05:38:03Z |
| format | Article |
| id | doaj.art-d9c1c9ae3ee8421995d38d917cb0a972 |
| institution | Directory Open Access Journal |
| issn | 2296-858X |
| language | English |
| last_indexed | 2024-12-18T05:38:03Z |
| publishDate | 2022-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Medicine |
| spelling | doaj.art-d9c1c9ae3ee8421995d38d917cb0a9722022-12-21T21:19:15ZengFrontiers Media S.A.Frontiers in Medicine2296-858X2022-03-01910.3389/fmed.2022.863911863911Epidemiological Dynamics of SARS-CoV-2 Variants During Social Protests in Cali, ColombiaLuz H. Patiño0Sergio Castañeda1Marina Muñoz2Marina Muñoz3Nathalia Ballesteros4Angie L. Ramirez5Nicolas Luna6Enzo Guerrero-Araya7Enzo Guerrero-Araya8Julie Pérez9Camilo A. Correa-Cárdenas10Maria Clara Duque11Claudia Méndez12Carolina Oliveros13Maryia V. Shaban14Alberto E. Paniz-Mondolfi15Juan David Ramírez16Juan David Ramírez17Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaAgencia Nacional de Investigación y Desarrollo (ANID)—Millennium Science Initiative Program—Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, ChileCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaAgencia Nacional de Investigación y Desarrollo (ANID)—Millennium Science Initiative Program—Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, ChileMicrobiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, ChileGrupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, ColombiaGrupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, ColombiaGrupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, ColombiaGrupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, ColombiaGrupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, ColombiaIncubadora Venezolana de la Ciencia (IVC), Centro de Investigaciones Biomédicas IDB, Barquisimeto, VenezuelaMolecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United StatesCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaMolecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United StatesBackgroundThe 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 (COVID-19) variants in big cities and propagated their facile spread, leading to increased rates of hospitalizations and deaths.MethodsIn 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.ResultsOur 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.ConclusionOur 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.https://www.frontiersin.org/articles/10.3389/fmed.2022.863911/fullSARS-CoV-2COVID-19effective reproduction numberlineagesCali |
| spellingShingle | Luz H. Patiño Sergio Castañeda Marina Muñoz Marina Muñoz Nathalia Ballesteros Angie L. Ramirez Nicolas Luna Enzo Guerrero-Araya Enzo Guerrero-Araya Julie Pérez Camilo A. Correa-Cárdenas Maria Clara Duque Claudia Méndez Carolina Oliveros Maryia V. Shaban Alberto E. Paniz-Mondolfi Juan David Ramírez Juan David Ramírez Epidemiological Dynamics of SARS-CoV-2 Variants During Social Protests in Cali, Colombia Frontiers in Medicine SARS-CoV-2 COVID-19 effective reproduction number lineages Cali |
| title | Epidemiological Dynamics of SARS-CoV-2 Variants During Social Protests in Cali, Colombia |
| title_full | Epidemiological Dynamics of SARS-CoV-2 Variants During Social Protests in Cali, Colombia |
| title_fullStr | Epidemiological Dynamics of SARS-CoV-2 Variants During Social Protests in Cali, Colombia |
| title_full_unstemmed | Epidemiological Dynamics of SARS-CoV-2 Variants During Social Protests in Cali, Colombia |
| title_short | Epidemiological Dynamics of SARS-CoV-2 Variants During Social Protests in Cali, Colombia |
| title_sort | epidemiological dynamics of sars cov 2 variants during social protests in cali colombia |
| topic | SARS-CoV-2 COVID-19 effective reproduction number lineages Cali |
| url | https://www.frontiersin.org/articles/10.3389/fmed.2022.863911/full |
| work_keys_str_mv | AT luzhpatino epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT sergiocastaneda epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT marinamunoz epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT marinamunoz epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT nathaliaballesteros epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT angielramirez epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT nicolasluna epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT enzoguerreroaraya epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT enzoguerreroaraya epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT julieperez epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT camiloacorreacardenas epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT mariaclaraduque epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT claudiamendez epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT carolinaoliveros epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT maryiavshaban epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT albertoepanizmondolfi epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT juandavidramirez epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia AT juandavidramirez epidemiologicaldynamicsofsarscov2variantsduringsocialprotestsincalicolombia |