Delta 变异株在巴西不同地区的出现和传播

Emergence and Spread of the SARS-CoV-2 Variant of Concern Delta across Different Brazilian Regions.

机构信息

Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil.

Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil.

出版信息

Microbiol Spectr. 2022 Oct 26;10(5):e0264121. doi: 10.1128/spectrum.02641-21. Epub 2022 Aug 24.

Abstract

The SARS-CoV-2 variant of concern (VOC) Delta was first detected in India in October 2020. The first imported cases of the Delta variant in Brazil were identified in April 2021 in the southern region, followed by more cases in different regions during the following months. By early September 2021, Delta was already the dominant variant in the southeastern (87%), southern (73%), and northeastern (52%) Brazilian regions. This study aimed to understand the spatiotemporal dissemination dynamics of Delta in Brazil. To this end, we employed a combination of maximum likelihood (ML) and Bayesian methods to reconstruct the evolutionary relationship of 2,264 VOC Delta complete genomes (482 from this study) recovered across 21 of the 27 Brazilian federal units. Our phylogeographic analyses identified three major transmission clusters of Delta in Brazil. The clade BR-I (= 1,560) arose in Rio de Janeiro in late April 2021 and was the major cluster behind the dissemination of the VOC Delta in the southeastern, northeastern, northern, and central-western regions. The AY.101 lineage (= 207) that arose in the Paraná state in late April 2021 and aggregated the largest fraction of sampled genomes from the southern region. Lastly, the AY.46.3 lineage emerged in Brazil in the São Paulo state in early June 2021 and remained mostly restricted to this state. In the rapid turnover of viral variants characteristic of the SARS-CoV-2 pandemic, Brazilian regions seem to occupy different stages of an increasing prevalence of the VOC Delta in their epidemic profiles. This process demands continuous genomic and epidemiological surveillance toward identifying and mitigating new introductions, limiting their dissemination, and preventing the establishment of more significant outbreaks in a population already heavily affected by the COVID-19 pandemic. Amid the SARS-CoV-2 continuously changing epidemic profile, this study details the space-time dynamics of the emergence of the Delta lineage across Brazilian territories, pointing out its multiple introductions in the country and its most prevalent sublineages. Some of these sublineages have their emergence, alongside their genomic composition and geographic distribution, detailed here for the first time. A special focus is given to the emergence process of Delta outside the country's south and southeast regions, the most populated and subjects of most published SARS-CoV-2 studies in Brazil. In summary, the study allows a better comprehension of the evolution process of a SARS-CoV-2 lineage that would be associated with a significant recrudescence of the pandemic in Brazil.

摘要

关注的 SARS-CoV-2 变体(VOC)Delta 于 2020 年 10 月在印度首次被发现。巴西首例输入性 Delta 变体病例于 2021 年 4 月在南部地区被发现,随后在接下来的几个月里,不同地区出现了更多的病例。到 2021 年 9 月初,Delta 已成为巴西东南部(87%)、南部(73%)和东北部(52%)地区的主要变体。本研究旨在了解巴西境内 Delta 的时空传播动态。为此,我们采用最大似然(ML)和贝叶斯方法相结合,对从巴西 27 个联邦单位中的 21 个单位中恢复的 2,264 个 VOC Delta 完整基因组(本研究中的 482 个)进行了进化关系重建。我们的系统地理学分析确定了巴西 Delta 的三个主要传播群。BR-I 分支(= 1,560)于 2021 年 4 月下旬在里约热内卢出现,是东南部、东北部、北部和中西部地区传播 VOC Delta 的主要集群。AY.101 谱系(= 207)于 2021 年 4 月下旬在巴拉那州出现,聚集了来自南部地区的最大部分采样基因组。最后,AY.46.3 谱系于 2021 年 6 月初在巴西圣保罗州出现,主要局限于该州。在 SARS-CoV-2 大流行中病毒变体快速更替的情况下,巴西各地区似乎在其流行特征中处于 Delta VOC 流行率不断增加的不同阶段。这一过程需要不断进行基因组和流行病学监测,以识别和减轻新的传入,限制其传播,并防止在已经深受 COVID-19 大流行影响的人群中发生更严重的疫情爆发。在 SARS-CoV-2 不断变化的流行特征中,本研究详细描述了 Delta 谱系在巴西各地的出现时空动态,指出了其在该国的多次传入及其最流行的亚谱系。其中一些亚谱系的出现及其基因组组成和地理分布在此首次详细描述。特别关注的是 Delta 在该国南部和东南部以外地区的出现过程,该地区是巴西人口最多、发表的 SARS-CoV-2 研究最多的地区。总之,该研究有助于更好地理解与巴西大流行显著复发相关的 SARS-CoV-2 谱系的进化过程。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7803/9604183/ffd9d4ffc2b6/spectrum.02641-21-f001.jpg

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