Abstract
Current efforts to understand the epidemiology, transmission dynamics and emergence of novel SARS-CoV-2 variants worldwide has enabled the scientific community to generate critical information aimed at implementing disease surveillance and control measures, as well as to reduce the social, economic and health impact of the pandemic. Herein, we applied an epidemic model coupled with genomic analysis to assess the SARS-CoV-2 transmission dynamics in Colombia. This epidemic model allowed to identify the geographical distribution, Rt dynamics and predict the course of the pandemic considering current implementation of countermeasures. The analysis of the incidence rate per 100,000 inhabitants carried out across different regions of Colombia allowed visualizing the changes in the geographic distribution of cases. The cumulative incidence during the timeframe March 2020 to March 2021 revealed that Bogotá (8063.0), Quindío (5482.71), Amazonas (5055.68), Antioquia (4922.35) and Tolima (4724.41) were the departments with the highest incidence rate. The highest median Rt during the first period evaluated was 2.13 and 1.09 in the second period; with this model, we identified improving opportunities in health decision making related to controlling the pandemic, diagnostic testing capacity, case registration and reporting, among others. Genomic analysis revealed 52 circulating SARS-CoV-2 lineages in Colombia detected from 774 genomes sequenced throughout the first year of the pandemic. The genomes grouped into four main clusters and exhibited 19 polymorphisms. Our results provide essential information on the spread of the pandemic countrywide despite implementation of early containment measures. In addition, we aim to provide deeper phylogenetic insights to better understand the evolution of SARS-CoV-2 in light of the latent emergence of novel variants and how these may potentially influence transmissibility and infectivity.
Highlights
Coronavirus disease 2019 (COVID-19), caused by Severe Acute Respiratory SyndromeCoronavirus 2 (SARS-CoV-2), represents a global challenge, with over 185 million infections and close to 4 million deaths reported worldwide [1]
We provide an assessment of the epidemiology of SARS-CoV-2 in Colombia, following the report of the first COVID-19 case detected in early March 2020 and its progression throughout the pandemic based on publicly available data
Results obtained from analyzing all SARS-CoV-2 genome assemblies revealed an exponential growth in the number of circulating lineages across the country; this since the last large-scale genomic study performed in Colombia [15]
Summary
Coronavirus disease 2019 (COVID-19), caused by Severe Acute Respiratory SyndromeCoronavirus 2 (SARS-CoV-2), represents a global challenge, with over 185 million infections and close to 4 million deaths reported worldwide [1]. COVID-19 is considered a global disease, the virus has spread in a heterogeneous fashion across different countries, with certain regions throughout the globe being affected. Such is the case for South America, with over 33,885,519 cases and 1,033,800 deaths reported as of 11 July 2021 [1]. Multiple emerging variants circulating globally have raised concerns about increased transmissibility, infectivity and ability to evade vaccine immunity [4] Amongst these is the Gamma variant (P.1 lineage), originating and linked to multiple outbreaks across
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