Tsuchiya Koji, Yamamoto Norio, Hosaka Yoshie, Wakita Mitsuru, Hiki Makoto, Matsushita Yasushi, Mori Hirotake, Hori Satoshi, Misawa Shigeki, Miida Takashi, Nojiri Shuko, Takahashi Kazuhisa, Naito Toshio, Tabe Yoko
Department of Clinical Laboratory, Juntendo University Hospital, Bunkyo, Tokyo, Japan.
Department of General Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan.
Front Microbiol. 2022 Jul 27;13:912061. doi: 10.3389/fmicb.2022.912061. eCollection 2022.
Many variants of SARS-CoV-2 have emerged around the world. It is therefore important to understand its global viral evolution and the corresponding mutations associated with transmissibility and severity. In this study, we analyzed 112 whole genome sequences of SARS-CoV-2 collected from patients at Juntendo University Hospital in Tokyo and the genome data from entire Japan deposited in Global Initiative on Sharing Avian Influenza Data (GISAID) to examine the relationship of amino acid changes with the transmissibility and the severity of each strain/lineage. We identified 12 lineages, including B.1.1.284, B.1.1.214, R.1, AY.29, and AY.29.1, which were prevalent specifically in Japan. B.1.1.284 was most frequently detected in the second wave, but B.1.1.214 became the predominant lineage in the third wave, indicating that B.1.1.214 has a higher transmissibility than B.1.1.284. The most prevalent lineage during the fourth and fifth wave was B.1.1.7 and AY.29, respectively. In regard to the severity of identified lineages, B.1.1.214 was significantly lower than the reference lineage, B.1.1.284. Analysis of the genome sequence and other traits of each lineage/strain revealed the mutations in S, N, and NSPs that increase the transmissibility and/or severity. These mutations include S: M153T, N: P151L, NSP3: S543P, NSP5: P108S, and NSP12: A423V in B.1.1.284; S: W152L and E484K in R.1; S: H69del, V70del, and N501Y in the Alpha strain; S: L452R, T478K, and P681R in the Delta strain. Furthermore, it is suggested that the transmissibility of B.1.1.214 could be enhanced by the mutations N: M234I, NSP14: P43L, and NSP16: R287I. To address the issue of the virus evolution, it is necessary to continuously monitor the genomes of SARS-CoV-2 and analyze the effects of mutations for developing vaccines and antiviral drugs effective against SARS-CoV-2 variants.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的许多变种已在全球出现。因此，了解其全球病毒进化以及与传播性和严重性相关的相应突变非常重要。在本研究中，我们分析了从东京顺天堂大学医院患者中收集的112个SARS-CoV-2全基因组序列，以及存于全球共享禽流感数据倡议组织（GISAID）中的日本全国基因组数据，以研究氨基酸变化与各毒株/谱系的传播性和严重性之间的关系。我们鉴定出12个谱系，包括B.1.1.284、B.1.1.214、R.1、AY.29和AY.29.1，这些谱系在日本尤为流行。B.1.1.284在第二波疫情中检测频率最高，但B.1.1.214在第三波疫情中成为主要谱系，这表明B.1.1.214的传播性高于B.1.1.284。第四波和第五波疫情中最流行的谱系分别是B.1.1.7和AY.29。关于已鉴定谱系的严重性，B.1.1.214显著低于参考谱系B.1.1.284。对每个谱系/毒株的基因组序列和其他特征进行分析后，发现了S、N和非结构蛋白（NSP）中增加传播性和/或严重性的突变。这些突变包括B.1.1.284中的S：M153T、N：P151L、NSP3：S543P、NSP5：P108S和NSP12：A423V；R.1中的S：W152L和E484K；阿尔法毒株中的S：H69缺失、V70缺失和N501Y；德尔塔毒株中的S：L452R、T478K和P681R。此外，有人提出，N：M234I、NSP14：P43L和NSP16：R287I这些突变可能会增强B.1.1.214的传播性。为了解决病毒进化问题，有必要持续监测SARS-CoV-2的基因组，并分析突变的影响，以便研发出对SARS-CoV-2变种有效的疫苗和抗病毒药物。
