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Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City
Nature Communications ( IF 16.6 ) Pub Date : 2022-06-25 , DOI: 10.1038/s41467-022-31247-x
Joel O Wertheim 1 , Jade C Wang 2 , Mindy Leelawong 2 , Darren P Martin 3 , Jennifer L Havens 4 , Moinuddin A Chowdhury 2 , Jonathan E Pekar 4 , Helly Amin 2 , Anthony Arroyo 2 , Gordon A Awandare 5 , Hoi Yan Chow 2 , Edimarlyn Gonzalez 2 , Elizabeth Luoma 6 , Collins M Morang'a 5 , Anton Nekrutenko 7 , Stephen D Shank 8 , Stefan Silver 2 , Peter K Quashie 5 , Jennifer L Rakeman 2 , Victoria Ruiz 2 , Lucia V Torian 2 , Tetyana I Vasylyeva 1 , Sergei L Kosakovsky Pond 8 , Scott Hughes 2
Affiliation  

Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, detection of recombination is only feasible when genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was infected with two distinct viral variants: Alpha (B.1.1.7) and Epsilon (B.1.429). This superinfection was first noted when an Alpha genome sequence failed to exhibit the classic S gene target failure behavior used to track this variant. Full genome sequencing from four independent extracts reveals that Alpha variant alleles comprise around 75% of the genomes, whereas the Epsilon variant alleles comprise around 20% of the sample. Further investigation reveals the presence of numerous recombinant haplotypes spanning the genome, specifically in the spike, nucleocapsid, and ORF 8 coding regions. These findings support the potential for recombination to reshape SARS-CoV-2 genetic diversity.



中文翻译:

在纽约市用 Alpha 和 Epsilon 变体重复感染期间检测 SARS-CoV-2 宿主内重组

重组是许多病原体产生多样性并获得新功能的进化过程。尽管在冠状病毒复制过程中很常见,但只有当基因不同的病毒同时感染同一宿主时,重组检测才可行。在这里,我们确定了一个 SARS-CoV-2 重叠感染的实例,其中一个人感染了两种不同的病毒变体:Alpha (B.1.1.7) 和 Epsilon (B.1.429)。当 Alpha 基因组序列未能表现出用于追踪此变体的经典 S 基因目标失败行为时,首次注意到这种重复感染。来自四个独立提取物的全基因组测序表明,Alpha 变异等位基因约占基因组的 75%,而 Epsilon 变异等位基因约占样本的 20%。进一步的调查揭示了跨越基因组的大量重组单倍型的存在,特别是在刺突、核衣壳和 ORF 8 编码区域。这些发现支持重组重塑 SARS-CoV-2 遗传多样性的潜力。

更新日期:2022-06-27
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