Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York.
Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York.
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DOI：
10.1038/s41467-021-25168-4
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发表时间：
2021-08-09
影响因子：
16.6
通讯作者：
Bjorkman PJ
中科院分区：
文献类型：
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作者：
West AP Jr;Wertheim JO;Wang JC;Vasylyeva TI;Havens JL;Chowdhury MA;Gonzalez E;Fang CE;Di Lonardo SS;Hughes S;Rakeman JL;Lee HH;Barnes CO;Gnanapragasam PNP;Yang Z;Gaebler C;Caskey M;Nussenzweig MC;Keeffe JR;Bjorkman PJ
大规模的SARS-CoV-2基因组测序对于跟踪SARS-CoV-2大流行期间的病毒演变至关重要。我们开发了软件工具，变体数据库(VDB)，用于快速检查不断变化的尖峰突变情况。利用VDB，我们在纽约地区检测到一种新的SARS-CoV-2谱系，它与之前报道的变异株具有相同的突变。这个谱系中最常见的一组尖峰突变(现在被指定为B.1.526)是L5F、T95I、D253G、E484K或S477N、D614G和A701V。这一谱系于2020年11月下旬首次测序。系统动力学推断证实了B.1.526世系的快速生长。与B.1.1.7等其他变种一起，B.1.526的兴起似乎延长了2021年初纽约市第二波新冠肺炎案件的持续时间。伪病毒中和实验表明，B.1.526尖峰突变对恢复期和接种者血浆的中和滴度产生不利影响，支持这一谱系的公共卫生相关性。韦斯特和他的同事开发了变异数据库软件工具，用于检查SARS-CoV-2基因组中变化的尖峰突变。作者用它来检测纽约新出现的SARS-CoV-2谱系，并报告B.1.526谱系在该市的迅速传播。
Wide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. We develop the software tool, Variant Database (VDB), for quickly examining the changing landscape of spike mutations. Using VDB, we detect an emerging lineage of SARS-CoV-2 in the New York region that shares mutations with previously reported variants. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. This lineage was first sequenced in late November 2020. Phylodynamic inference confirmed the rapid growth of the B.1.526 lineage. In concert with other variants, like B.1.1.7, the rise of B.1.526 appears to have extended the duration of the second wave of COVID-19 cases in NYC in early 2021. Pseudovirus neutralization experiments demonstrated that B.1.526 spike mutations adversely affect the neutralization titer of convalescent and vaccinee plasma, supporting the public health relevance of this lineage. West and colleagues develop the Variant Database software tool for examination of changing Spike mutations in SARS-CoV-2 genomes. The authors use this to detect emerging lineages of SARS-CoV-2 in New York and report the rapid spread of the B.1.526 lineage in the city.