Identification of Various Recombinants in a Patient Coinfected With the Different SARS-CoV-2 Variants

IF 4.3 4区 医学 Q1 INFECTIOUS DISEASES Influenza and Other Respiratory Viruses Pub Date : 2024-06-18 DOI:10.1111/irv.13340
Yusuke Sayama, Akie Sakagami, Michiko Okamoto, Masahiro Sakamoto, Hikari Koizumi, Yoko Kimura, Clyde Dapat, Mayuko Saito, Yuko Suzuki, Mie Sasaki, Naoko Sugawara, Hitoshi Oshitani
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Abstract

Background

Viral recombination that occurs by exchanging genetic materials between two viral genomes coinfecting the same host cells is associated with the emergence of new viruses with different virulence. Herein, we detected a patient coinfected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants and identified various recombinants in the SARS-CoV-2 full-length spike gene using long-read and Sanger sequencing.

Methods

Samples from five patients in Japan with household transmission of coronavirus disease 2019 (COVID-19) were analyzed using molecular assays for detection and identification of SARS-CoV-2. Whole-genome sequencing was conducted using multiplex PCR with short-read sequencing.

Results

Among the five SARS-CoV-2-positive patients, the mutation-specific assay identified the Delta variant in three, the Omicron variant in one, and an undetermined in one. The undermined patient was identified as Delta using whole-genome sequencing, but samples showed a mixed population of Delta and Omicron variants. This patient was analyzed for viral quasispecies by long-read and Sanger sequencing using a full-length spike gene amplicon. In addition to the Delta and Omicron sequences, the viral quasispecies analysis identified nine different genetic recombinant sequences with various breakpoints between Delta and Omicron sequences. The nine detected recombinant sequences in the spike gene showed over 99% identity with viruses that were detected during the Delta and Omicron cocirculation period from the United States and Europe.

Conclusions

This study demonstrates that patients coinfected with different SARS-CoV-2 variants can generate various viral recombinants and that various recombinant viruses may be produced during the cocirculation of different variants.

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在一名合并感染不同 SARS-CoV-2 变体的患者体内鉴定各种重组体
背景:病毒重组是通过共同感染同一宿主细胞的两个病毒基因组之间交换遗传物质而发生的,它与具有不同毒力的新病毒的出现有关。在本文中,我们检测了一名同时感染严重急性呼吸系统综合征冠状病毒 2(SARS-CoV-2)Delta 和 Omicron 变体的患者,并使用长读取和 Sanger 测序方法确定了 SARS-CoV-2 全长尖峰基因中的各种重组子:方法:使用分子检测方法分析了日本 5 名冠状病毒病 2019(COVID-19)家庭传播患者的样本,以检测和鉴定 SARS-CoV-2。利用多重 PCR 和短线程测序技术进行了全基因组测序:结果:在 5 名 SARS-CoV-2 阳性患者中,变异特异性检测确定了 3 名患者的 Delta 变异,1 名患者的 Omicron 变异,1 名患者的变异未确定。通过全基因组测序,确定了一名病情不稳定的患者为德尔塔变异体,但样本显示德尔塔变异体和奥米克隆变异体混合存在。该患者使用全长尖峰基因扩增片段,通过长线程和桑格测序分析了病毒类群。除 Delta 和 Omicron 序列外,病毒类群分析还发现了九种不同的基因重组序列,其断点介于 Delta 和 Omicron 序列之间。在尖峰基因中检测到的 9 个重组序列与美国和欧洲在 Delta 和 Omicron 共循环期间检测到的病毒的同一性超过 99%:这项研究表明,合并感染不同 SARS-CoV-2 变体的患者可产生各种病毒重组体,而且在不同变体的共循环期间也可能产生各种重组病毒。
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来源期刊
CiteScore
7.20
自引率
4.50%
发文量
120
审稿时长
6-12 weeks
期刊介绍: Influenza and Other Respiratory Viruses is the official journal of the International Society of Influenza and Other Respiratory Virus Diseases - an independent scientific professional society - dedicated to promoting the prevention, detection, treatment, and control of influenza and other respiratory virus diseases. Influenza and Other Respiratory Viruses is an Open Access journal. Copyright on any research article published by Influenza and Other Respiratory Viruses is retained by the author(s). Authors grant Wiley a license to publish the article and identify itself as the original publisher. Authors also grant any third party the right to use the article freely as long as its integrity is maintained and its original authors, citation details and publisher are identified.
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