Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

尽管此前感染水平较高，但巴西马瑙斯的严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 感染病例于 2020 年底再次出现。对 2020 年 11 月至 2021 年 1 月在马瑙斯采样的病毒进行基因组测序，揭示了一种令人关注的新型 SARS-CoV-2 变种的出现和传播。谱系 P.1 获得了 17 个突变，其中包括与人类 ACE2（血管紧张素转换酶 2）受体结合增加相关的刺突蛋白中的三个突变（K417T、E484K 和 N501Y）。分子钟分析显示，P.1 的出现发生在 2020 年 11 月中旬左右，在此之前是一段更快的分子进化时期。使用整合基因组和死亡率数据的二类动态模型，我们估计 P.1 的传染性可能高出 1.7 至 2.4 倍，并且先前（非 P.1）感染提供了 54％ 至 79％ 的保护P.1 感染，它可以对抗非 P.1 谱系。加强对受关注变异的全球基因组监测对于加速大流行应对至关重要，这些变异可能表现出传播性和/或免疫逃避的增加。