Moreira Filipe Romero Rebello, D'arc Mirela, Mariani Diana, Herlinger Alice Laschuk, Schiffler Francine Bittencourt, Rossi Átila Duque, Leitão Isabela de Carvalho, Miranda Thamiris Dos Santos, Cosentino Matheus Augusto Calvano, Tôrres Marcelo Calado de Paula, da Costa Raíssa Mirella Dos Santos Cunha, Gonçalves Cássia Cristina Alves, Faffe Débora Souza, Galliez Rafael Mello, Junior Orlando da Costa Ferreira, Aguiar Renato Santana, Dos Santos André Felipe Andrade, Voloch Carolina Moreira, Castiñeiras Terezinha Marta Pereira Pinto, Tanuri Amilcar
Departamento de Genética, Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 121, Cidade Universitária, Rio de Janeiro 21941-902, Brazil.
Departamento de Genética, Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Centro de Ciências da Saúde, Bloco A, lab 120, Cidade Universitária, Rio de Janeiro 21941-902, Brazil.
Virus Evol. 2021 Oct 1;7(2):veab087. doi: 10.1093/ve/veab087. eCollection 2021.
The emergence and widespread circulation of severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) or interest impose an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates that this variant has circulated locally since the first weeks of 2021 and only 7 weeks were necessary for it to achieve a frequency above 70 per cent, consistent with rates of growth observed in Manaus and other states. Moreover, a Bayesian phylogeographic reconstruction indicates that VOC Gamma spread throughout Brazil between December 2020 and January 2021 and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) cycle threshold (Ct) values provides further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95 per cent confidence interval = ± 0.7). This analysis corroborates the previously proposed mechanistic basis for this variant-enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions.
严重急性呼吸综合征冠状病毒2变异株（VOCs）或关注变异株的出现和广泛传播对全球公共卫生构成了更大威胁。在整个疫情期间受影响最严重的国家之一巴西，随着2020年末VOC伽马变异株在玛瑙斯的出现和传播，记录到了涉及变异株共同传播和更替事件的复杂动态。在此背景下，我们基于2020年12月至2021年5月在巴西第二大城市里约热内卢收集的样本进行了一项基因组流行病学调查。通过对这一时期所有流行病学周的244个新基因组进行测序，我们得以记录VOC伽马变异株在该市的引入和快速传播，推动了当地第三波疫情的上升。分子钟分析表明，该变异株自2021年第一周起就在当地传播，仅用了7周时间其频率就达到了70%以上，这与在玛瑙斯和其他州观察到的增长速度一致。此外，贝叶斯系统发育地理重建表明，VOC伽马变异株在2020年12月至2021年1月期间在巴西各地传播，并且它是通过至少13起来自该国几乎所有地区的事件引入里约热内卢的。逆转录定量聚合酶链反应（RT-qPCR）循环阈值（Ct）值的比较分析提供了进一步证据，表明VOC伽马变异株会诱导更高的病毒载量（N1靶点；Ct平均降低：2.7，95%置信区间=±0.7）。该分析证实了先前提出的该变异株增强传播性和独特流行病学行为的机制基础。我们的结果记录了VOC伽马变异株的演变，并对先前在玛瑙斯研究过的情况进行了独立评估，因此有助于更好地理解目前在巴西其他地区正在调查的流行病学动态。
