SARS-CoV-2 Delta 和 Omicron 共感染和重组的证据。

Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination.

机构信息

Helix, San Mateo, CA 94401, USA.

Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA 98195, USA.

出版信息

Med. 2022 Dec 9;3(12):848-859.e4. doi: 10.1016/j.medj.2022.10.002. Epub 2022 Oct 20.

BACKGROUND

Between November 2021 and February 2022, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events.

METHODS

We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant.

FINDINGS

We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5' end of the viral genome was from the Delta genome and the 3' end from Omicron, including the majority of the spike protein gene, though the breakpoints were different.

CONCLUSIONS

Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared with the circulating Omicron lineages.

FUNDING

This research was supported by the NIH RADx initiative and by the Centers for Disease Control Contract 75D30121C12730 (Helix).

背景

2021 年 11 月至 2022 年 2 月期间，严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）Delta 和奥密克戎变异株在美国共同传播，允许发生共感染和可能的重组事件。

方法

在此期间，我们对 29719 个阳性样本进行了测序，并分析了支持 Delta 或奥密克戎变异株特有突变的读数的存在和比例。

结果

我们确定了 18 例共感染，其中 1 例显示出低 Delta-奥密克戎重组病毒群的证据。我们还发现了两例 Delta-奥密克戎重组病毒感染的独立病例，其中 100%的病毒 RNA 来自一个克隆重组。在这三个病例中，病毒基因组的 5'端来自 Delta 基因组，3'端来自奥密克戎，包括大多数刺突蛋白基因，但断点不同。