Evolution and Epidemic Spread of SARS-CoV-2 in Colombia: A Year into the Pandemic.
Evolution and Epidemic Spread of SARS-CoV-2 in Colombia: A Year into the Pandemic.
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DOI：
10.3390/vaccines9080837
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发表时间：
2021-07-30
期刊：
影响因子：
7.8
通讯作者：
Ramírez JD
中科院分区：
文献类型：
--
作者：
Castañeda S;Patiño LH;Muñoz M;Ballesteros N;Guerrero-Araya E;Paredes-Sabja D;Flórez C;Gomez S;Ramírez-Santana C;Salguero G;Gallo JE;Paniz-Mondolfi AE;Ramírez JD
目前为了解流行病学、传播动力学和世界范围内新的SARS-CoV-2变种的出现所作的努力，使科学界能够提供关键信息，以实施疾病监测和控制措施，并减少这一大流行病的社会、经济和健康影响。在此，我们应用流行病模型与基因组分析相结合，以评估SARS-CoV-2在哥伦比亚的传播动态。该流行病模型允许识别地理分布、Rt动态，并在考虑当前对策实施的情况下预测大流行的进程。对哥伦比亚不同地区每100 000名居民的发病率进行的分析使人们能够看到病例地理分布的变化。2020年3月至2021年3月期间的累积发病率显示，博戈塔（8063.0）、金迪奥（5482.71）、亚马孙（5055.68）、安蒂奥基亚（4922.35）和托利马（4724.41）是发病率最高的省份。第一个评估期的最高中位Rt为2.13，第二个评估期为1.09;通过该模型，我们确定了与控制大流行、诊断检测能力、病例登记和报告等相关的卫生决策的改进机会。基因组分析显示，在哥伦比亚流行的第一年，从774个基因组测序中检测到52个流行的SARS-CoV-2谱系。基因组分为四个主要的集群，并表现出19个多态性。我们的研究结果提供了重要信息，说明尽管实施了早期遏制措施，但大流行病在全国范围内的传播情况。此外，我们的目标是提供更深入的系统发育见解，以更好地了解SARS-CoV-2的进化，因为新变体的潜在出现以及这些变体如何可能影响传播性和感染性。
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.
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