Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.
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DOI：
10.1038/s41467-022-31247-x
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发表时间：
2022-06-25
影响因子：
16.6
通讯作者：
中科院分区：
文献类型：
--
作者：
重组是许多病原体产生多样性并获得新功能的进化过程。虽然重组在冠状病毒复制过程中很常见，但只有当遗传不同的病毒同时感染同一宿主时，重组检测才可行。在这里，我们发现了 SARS-CoV-2 双重感染的一个实例，即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该变体的经典 S 基因目标失败行为时，这种双重感染首次被注意到。对四个独立提取物的全基因组测序表明，Alpha 变体等位基因约占基因组的 75%，而 Epsilon 变体等位基因约占样本的 20%。进一步的研究揭示了跨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。这些发现支持重组重塑 SARS-CoV-2 遗传多样性的潜力。在这里，作者描述了一个带有 Alpha 和 Epsilon 变体的 SARS-CoV-2 重复感染病例，其中通过全基因组测序分析，他们鉴定了刺突、核衣壳和 ORF 8 编码区的重组单倍型，表明重组可能在 SARS-CoV-2 遗传多样性中发挥作用。
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. Here, the authors characterize a case of SARS-CoV-2 superinfection with Alpha and Epsilon variants, in which, via full genome sequencing analyses, they identify recombinant haplotypes in the spike, nucleocapsid, and ORF 8 coding regions, suggesting recombination could play a role in SARS-CoV-2 genetic diversity.
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