ABSTRACT
OBJECTIVES: The analysis of transmission dynamics is crucial to determine whether mitigation or suppression measures reduce the spread of coronavirus disease 2019 (COVID-19). This study sought to estimate the basic (R0 ) and time-varying (Rt ) reproduction number of COVID-19 and contrast the public health measures for ten South American countries. METHODS: Data was obtained from the European Centre for Disease Prevention and Control. Country-specific R0 values during the first two weeks of the outbreak and Rt values after 90 days were estimated. RESULTS: Countries used a combination of isolation, physical distancing, quarantine, and community-wide containment measures to staunch the spread of COVID-19 at different points in time. R0 ranged from 1.52 (95% confidence interval: 1.13-1.99) in Venezuela to 3.83 (3.04-4.75) in Chile, whereas Rt after 90 days ranged from 0.71 (95% credible interval: 0.39-1.05) in Uruguay to 1.20 (1.19-1.20) in Brazil. Different R0 and Rt values may be related to the testing capacity of each country. CONCLUSION: R0 in the early phase of the outbreak varied across the South American countries. The public health measures adopted in the initial period of the pandemic appear to have reduced Rt over time in each country, albeit to different levels.
OBJETIVOS: Estimar el número de reproducción básico (R0 ) y el número de reproducción efectivo (Rt ) de la COVID-19 y contrastarlos con las medidas de salud pública implementadas en diez países de América del Sur. MÉTODOS: Los datos se obtuvieron del Centro Europeo para la Prevención y el Control de las Enfermedades. Se estimó el R0 de cada país durante las dos primeras semanas del brote y el Rt después de 90 días. RESULTADOS: Los países utilizaron una combinación de aislamiento, distanciamiento físico, cuarentena y medidas de contención en toda la comunidad para detener la propagación de la COVID-19 en diferentes momentos. El R0 osciló entre 1,52 (IC95%: 1,13-1,99) en Venezuela y 3,83 (IC95%: 3,04-4,75) en Chile, mientras que el Rt después de 90 días varió entre 0,71 (intervalo de credibilidad 95%: 0,39-1,05) en Uruguay y 1,20 (intervalo de credibilidad 95%: 1,19-1,20) en Brasil. Los diferentes valores de R0 y Rt pueden estar relacionados con la capacidad de llevar a cabo pruebas de detección viral de cada país. CONCLUSIÓN: Los valores del R0 en la fase inicial del brote variaron entre los países sudamericanos. Las medidas de salud pública adoptadas en el período inicial de la pandemia parecen haber reducido el Rt con el tiempo en cada país, aunque en niveles diferentes.
ABSTRACT
During a pandemic, science needs data to generate helpful evidence, and researchers assume this responsibility despite the risk of potential bias. This is the response to the comment made by Pedro Romero, who argued that our manuscript did not use reassembling and mapping strategies for corroborating mutations, and lacked bootstrap support in the phylogenetic analysis.
Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Pandemics , Phylogeny , South America/epidemiologyABSTRACT
After more than 4 months of the COVID-19 pandemics with genomic information of SARS-CoV-2 around the globe, there are more than 1000 complete genomes of this virus. We used 691 genomes from the GISAID database. Several studies have been reporting mutations and hotspots according to viral evolution. Our work intends to show and compare positions that have variants in 30 complete viral genomes from South American countries. We classified strains according to point alterations and portray the source where strains came into this region. Most viruses entered South America from Europe, followed by Oceania. Only Chilean isolates demonstrated a relationship with Asian isolates. Some changes in South American genomes are near to specific domains related to viral replication or the S protein. Our work contributes to the global understanding of which sort of strains are spreading throughout South America, and the differences among them according to the first isolates introduced to this region.