Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein.
Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein.
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DOI：
10.1007/s00705-022-05385-y
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发表时间：
2022-04
影响因子：
2.7
通讯作者：
Raoult D
中科院分区：
文献类型：
--
作者：
Colson P;Delerce J;Burel E;Dahan J;Jouffret A;Fenollar F;Yahi N;Fantini J;La Scola B;Raoult D
SARS-CoV-2变异体已成为主要的病毒学、流行病学和临床问题，特别是关于疫苗诱导免疫逃逸的风险。在这里，我们描述了一个新的变种的出现，与索引的情况下，从喀麦隆旅行返回。对于生活在法国东南部同一地理区域的13名SARS-CoV-2阳性患者，用于筛查变体相关突变的qPCR检测显示非典型组合。在约8小时内，在GridION仪器上用Oxford Nanopore Technologies通过下一代测序获得基因组序列。分析发现46个核苷酸替换和37个缺失，导致30个氨基酸替换和12个缺失。14个氨基酸取代，包括N501 Y和E484 K，以及9个缺失位于刺突蛋白中。这种基因型模式导致了一个新的穿山甲谱系的建立，命名为B.1.640.2，它是旧的B.1.640谱系的系统发育姐妹群，现在已更名为B.1.640.1。该谱系的差异在于25个核苷酸取代和33个缺失。根据我们先前的定义，这些分离株中的突变组合及其系统发生位置表明，它们代表了一种新的变体，我们将其命名为“IHU”。这些数据进一步说明了SARS-CoV-2变异体的出现及其可能从国外传入特定地理区域的不可预测性。在线版本包含补充材料，可通过10.1007/s 00705 -022-05385-y获得。
SARS-CoV-2 variants have become a major virological, epidemiological, and clinical concern, particularly with regard to the risk of escape from vaccine-induced immunity. Here, we describe the emergence of a new variant, with the index case returning from travel in Cameroon. For 13 SARS-CoV-2-positive patients living in the same geographical area of southeastern France, a qPCR test for screening variant-associated mutations showed an atypical combination. The genome sequences were obtained by next-generation sequencing with Oxford Nanopore Technologies on GridION instruments within about 8 h. Analysis revealed 46 nucleotide substitutions and 37 deletions, resulting in 30 amino acid substitutions and 12 deletions. Fourteen of the amino acid substitutions, including N501Y and E484K, and nine deletions are located in the spike protein. This genotype pattern led to the establishment of a new Pangolin lineage, named B.1.640.2, that is a phylogenetic sister group to the old B.1.640 lineage, which has now been renamed B.1.640.1. The lineages differ by 25 nucleotide substitutions and 33 deletions. The combination of mutations in these isolates and their phylogenetic position indicate, based on our previous definition, that they represent a new variant, which we have named “IHU”. These data are a further example of the unpredictability of the emergence of SARS-CoV-2 variants, and of their possible introduction into a given geographical area from abroad. The online version contains supplementary material available at 10.1007/s00705-022-05385-y.
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DOI：
10.1007/s10096-020-04106-0
发表时间：
2021-03
期刊：
European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology
影响因子：
--
作者：
Wurtz N;Penant G;Jardot P;Duclos N;La Scola B
通讯作者：
La Scola B
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
DOI：
10.1016/j.jinf.2021.06.001
发表时间：
2021-08
期刊：
The Journal of infection
影响因子：
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作者：
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通讯作者：
Chahinian H
DOI：
10.3390/v13112177
发表时间：
2021-10-28
期刊：
Viruses
影响因子：
--
作者：
Jaafar R;Boschi C;Aherfi S;Bancod A;Le Bideau M;Edouard S;Colson P;Chahinian H;Raoult D;Yahi N;Fantini J;La Scola B
通讯作者：
La Scola B
DOI：
10.1016/s0262-4079(21)02091-1
发表时间：
2021-11-27
期刊：
New scientist (1971)
影响因子：
--
作者：
Le Page M
通讯作者：
Le Page M