PDF(Pubmed)
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.
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.
摘要：
背景：通过在共同感染相同宿主细胞的两个病毒基因组之间交换遗传物质而发生的病毒重组与具有不同毒力的新病毒的出现有关。在这里，我们检测到1例合并感染了严重急性呼吸综合征冠状病毒2(SARS-CoV-2)Delta和Omicron变异体的患者,并使用长读和Sanger测序在SARS-CoV-2全长尖峰基因中鉴定了各种重组体.
方法：使用分子测定法分析了日本5名2019年家庭传播冠状病毒病（COVID-19）患者的样本，以检测和鉴定SARS-CoV-2。使用具有短读取测序的多重PCR进行全基因组测序。
结果：在5名SARS-CoV-2阳性患者中，突变特异性试验鉴定了三个Delta变异体，Omicron变体之一，和一个不确定的。使用全基因组测序将受损患者鉴定为Delta，但样本显示Delta和Omicron变异的混合群体。通过使用全长刺突基因扩增子的长读和Sanger测序来分析该患者的病毒准种。除了Delta和Omicron序列，病毒准种分析确定了9种不同的遗传重组序列，在Delta和Omicron序列之间具有不同的断点。在刺突基因中检测到的9个重组序列与来自美国和欧洲的Delta和Omicron共循环期间检测到的病毒显示出超过99％的同一性。
结论：这项研究表明，合并感染不同SARS-CoV-2变体的患者可以产生各种病毒重组体，并且在不同变体的共同循环过程中可以产生各种重组病毒。
方法：使用分子测定法分析了日本5名2019年家庭传播冠状病毒病（COVID-19）患者的样本，以检测和鉴定SARS-CoV-2。使用具有短读取测序的多重PCR进行全基因组测序。
结果：在5名SARS-CoV-2阳性患者中，突变特异性试验鉴定了三个Delta变异体，Omicron变体之一，和一个不确定的。使用全基因组测序将受损患者鉴定为Delta，但样本显示Delta和Omicron变异的混合群体。通过使用全长刺突基因扩增子的长读和Sanger测序来分析该患者的病毒准种。除了Delta和Omicron序列，病毒准种分析确定了9种不同的遗传重组序列，在Delta和Omicron序列之间具有不同的断点。在刺突基因中检测到的9个重组序列与来自美国和欧洲的Delta和Omicron共循环期间检测到的病毒显示出超过99％的同一性。
结论：这项研究表明，合并感染不同SARS-CoV-2变体的患者可以产生各种病毒重组体，并且在不同变体的共同循环过程中可以产生各种重组病毒。
