Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants.

<strong>These are the supplementary files and scripts used in the the manuscript "Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants"</strong> <br> <strong>Abstract </strong> During the first semester of 2021, all of Brazil has suffered an intense wave of COVID-19 associated with the Gamma variant. In July, the first cases of Delta variant were detected in the state of Rio de Janeiro. In this work, we have employed phylodynamic methods to analyze more than 1,600 genomic sequences of Delta variant collected until September in Rio de Janeiro to reconstruct how this variant has surpassed Gamma and dispersed throughout the state. After the introduction of Delta, it has initially spread mostly in the homonymous city of Rio de Janeiro, the most populous of the state. In a second stage, dispersal occurred to mid- and long-range cities, which acted as new close-range hubs for spread. We observed that the substitution of Gamma by Delta was possibly caused by its higher viral load, a proxy for transmissibility. This variant turnover prompted a new surge in cases, but with lower lethality than was observed during the peak caused by Gamma. We reason that high vaccination rates in the state of Rio de Janeiro were possibly what prevented a higher number of deaths.

本数据集为论文《巴西里约热内卢州新型冠状病毒（SARS-CoV-2）传播的系统发育动力学分析：揭示大都市如何成为新型变异株传播枢纽》所配套的补充文件与脚本。
摘要：2021年上半年，巴西全境遭遇了与Gamma变异株相关的新冠肺炎（COVID-19）高强度流行浪潮。同年7月，里约热内卢州首次检出Delta变异株感染病例。本研究采用系统发育动力学方法，对截至2021年9月在里约热内卢州采集的1600余条Delta变异株基因组序列展开分析，以重构该变异株取代Gamma并在全州范围内传播的过程。Delta变异株传入后，最初主要在该州人口最多的同名城市——里约热内卢市扩散。第二阶段，传播扩散至中远程城市，这些城市随后成为新一轮近距离传播的枢纽。研究发现，Delta取代Gamma的原因可能在于其更高的病毒载量——这一指标可作为传播能力的替代指标。此次变异株替换引发了新一轮病例激增，但致死率低于Gamma变异株引发的疫情峰值期。我们推测，里约热内卢州较高的疫苗接种率可能是避免更多死亡病例出现的关键因素。