SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay
SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay
Abstract COVID-19 is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and declared by the World Health Organization as a global public health emergency. Among the severe outbreaks across South America, Uruguay has become known for curtailing SARS-CoV-2 exceptionally well. To understand the SARS-CoV-2 introductions, local transmissions, and associations with genomic and clinical parameters in Uruguay, we sequenced the viral genomes of 44 outpatients and inpatients in a private healthcare system in its capital, Montevideo, from March to May 2020. We performed a phylogeographic analysis using sequences from our cohort and other studies that indicate a minimum of 23 independent introductions into Uruguay, resulting in five major transmission clusters. Our data suggest that most introductions resulting in chains of transmission originate from other South American countries, with the earliest seeding of the virus in late February 2020, weeks before the borders were closed to all non-citizens and a partial lockdown implemented. Genetic analyses suggest a dominance of S and G clades (G, GH, GR) that make up >90% of the viral strains in our study. In our cohort, lethal outcome of SARS-CoV-2 infection significantly correlated with arterial hypertension, kidney failure, and ICU admission (FDR < 0.01), but not with any mutation in a structural or non-structural protein, such as the spike D614G mutation. Our study contributes genetic, phylodynamic, and clinical correlation data about the exceptionally well-curbed SARS-CoV-2 outbreak in Uruguay, which furthers the understanding of disease patterns and regional aspects of the pandemic in Latin America.
Dellicour Simon、Elizondo Victoria、Smidt Sabine、Maurano Matthew、Perez Victoria、Mazza Natalia、Perez Veronica、Estevez Veronica、Manrique Gonzalo、Nin Matilde、Marier Christian、Ifran Silvana、Zubillaga Maria Noel、Perez Leticia、Beloso Carolina、Duerr Ralf、Mabvakure Batsirai、Harkins Gordon W.、Fernandez Mariana、Balleste Raquel、Boschi Susana、Zappile Paul、Ross Fabiana、Heguy Adriana、Santini Andrea
Spatial Epidemiology Lab. (SpELL), Universit¨| Libre de Bruxelles||Department of Microbiology, Immunology and Transplantation, Rega InstituteLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en SaludSouth African Medical Research Council Capacity Development Unit, South African National Bioinformatics Institute, University of the Western CapeDepartment of Pathology, NYU Grossman School of MedicineLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en Salud||Departamento de Desarrollo Biotecnol¨?gico, Instituto de Higiene, Facultad de MedicinaLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en SaludLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en SaludLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en SaludLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en SaludLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en SaludGenome Technology Center, Office for Science and Research, NYU Langone HealthLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en SaludLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en SaludLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en SaludLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en Salud||Departamento de Biodiversidad y Gen¨|tica. Instituto de Investigaciones Biol¨?gicas Clemente EstableDepartment of Pathology, NYU Grossman School of MedicineDepartment of Medicine, Johns Hopkins School of MedicineSouth African Medical Research Council Capacity Development Unit, South African National Bioinformatics Institute, University of the Western CapeLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en SaludLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en SaludLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en SaludGenome Technology Center, Office for Science and Research, NYU Langone HealthLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en SaludGenome Technology Center, Office for Science and Research, NYU Langone Health||Department of Pathology, NYU Grossman School of MedicineLaboratorio de Biolog¨aa Molecular, Asociaci¨?n Espa?ola Primera en Salud
医药卫生理论医学研究方法临床医学
SARS-CoV-2COVID-19 outbreakUruguaySouth Americafull genome amplicon sequencingspike D614G genetic mutationphylogeographic BEAST analysisclinical correlations
Dellicour Simon,Elizondo Victoria,Smidt Sabine,Maurano Matthew,Perez Victoria,Mazza Natalia,Perez Veronica,Estevez Veronica,Manrique Gonzalo,Nin Matilde,Marier Christian,Ifran Silvana,Zubillaga Maria Noel,Perez Leticia,Beloso Carolina,Duerr Ralf,Mabvakure Batsirai,Harkins Gordon W.,Fernandez Mariana,Balleste Raquel,Boschi Susana,Zappile Paul,Ross Fabiana,Heguy Adriana,Santini Andrea.SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay[EB/OL].(2025-03-28)[2025-08-02].https://www.medrxiv.org/content/10.1101/2020.10.08.20208546.点此复制
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