One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages.
One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages.
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DOI：
10.1016/j.meegid.2021.104869
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发表时间：
2021-08
期刊：
影响因子：
--
通讯作者：
Sironi M
中科院分区：
文献类型：
--
作者：
González-Candelas F;Shaw MA;Phan T;Kulkarni-Kale U;Paraskevis D;Luciani F;Kimura H;Sironi M
2019冠状病毒病大流行于2020年3月11日正式宣布。从一开始，全世界的基因组测序工作就几乎实时地跟踪了病毒的传播。截至2021年3月，GISAID已上传超过830，000个SARS-CoV-2基因组，这些丰富的数据使研究人员能够在第一个大流行年研究SARS-CoV-2的演变。与此同时，命名系统，往往与彼此之间的一致性差，已开发出指定新兴的病毒谱系。尽管人们普遍担心该病毒可能会发生突变，变得更具毒性或传播性，但在持续的人际传播的前8个月内，SARS-CoV-2的遗传多样性仍然相对较低。然而，在2020年底/2021年初，一些令人担忧的事件开始引起人们对病毒进化轨迹可能发生变化的担忧。具体而言，与广泛传播相关的三种新病毒变异已被描述为关注变异（VOC）。这些变体首先在英国（B.1.1.7）、南非（B.1.351）和巴西（P.1）报告。它们被指定为挥发性有机化合物是由当地病例的增加和这些谱系所携带的大量氨基酸取代决定的。后一个特征让人想起从长期感染的免疫功能低下患者中分离的病毒序列，表明可能存在因果关系。在这里，我们审查的事件，导致这些谱系的识别，以及新出现的数据，其可能的影响，病毒表型，再感染风险，疫苗的效率和流行潜力。到目前为止，大多数现有证据都是临时性的，但仍然是揭示VOCs潜在威胁的起点。我们还强调，必须加强基因组监测，特别是在疫苗接种运动之后。
The COVID-19 pandemic was officially declared on March 11th, 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by worldwide genome sequencing efforts. As of March 2021, more than 830,000 SARS-CoV-2 genomes have been uploaded in GISAID and this wealth of data allowed researchers to study the evolution of SARS-CoV-2 during this first pandemic year. In parallel, nomenclatures systems, often with poor consistency among each other, have been developed to designate emerging viral lineages. Despite general fears that the virus might mutate to become more virulent or transmissible, SARS-CoV-2 genetic diversity has remained relatively low during the first ~ 8 months of sustained human-to-human transmission. At the end of 2020/beginning of 2021, though, some alarming events started to raise concerns of possible changes in the evolutionary trajectory of the virus. Specifically, three new viral variants associated with extensive transmission have been described as variants of concern (VOC). These variants were first reported in the UK (B.1.1.7), South Africa (B.1.351) and Brazil (P.1). Their designation as VOCs was determined by an increase of local cases and by the high number of amino acid substitutions harboured by these lineages. This latter feature is reminiscent of viral sequences isolated from immunocompromised patients with long-term infection, suggesting a possible causal link. Here we review the events that led to the identification of these lineages, as well as emerging data concerning their possible implications for viral phenotypes, reinfection risk, vaccine efficiency and epidemic potential. Most of the available evidence is, to date, provisional, but still represents a starting point to uncover the potential threat posed by the VOCs. We also stress that genomic surveillance must be strengthened, especially in the wake of the vaccination campaigns.
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