Hosaka Yoshie, Yan Yan, Naito Toshio, Oyama Rieko, Tsuchiya Koji, Yamamoto Norio, Nojiri Shuko, Hori Satoshi, Takahashi Kazuhiko, Tabe Yoko
Department of Clinical Laboratory Medicine, Juntendo University Faculty of Medicine, Tokyo, Japan.
Department of General Medicine, Juntendo University Faculty of Medicine, Tokyo, Japan.
Front Microbiol. 2023 Feb 9;14:944369. doi: 10.3389/fmicb.2023.944369. eCollection 2023.
Previous studies have shown that patients with immunosuppression tend to have longer-lasting SARS-CoV-2 infections and a number of mutations were observed during the infection period. However, these studies were, in general, conducted longitudinally. Mutation evolution among groups of patients with immunosuppression have not been well studied, especially among Asian populations.
Our study targeted a nosocomial cluster of SARS-CoV-2 infection in a Japanese medical center during Delta surge (AY.29 sublineage), involving ward nurses and inpatients. Whole-genome sequencing analyses were performed to examine mutation changes. Haplotype and minor variant analyses were furtherly performed to detect the mutations on the viral genomes in detail. In addition, sequences of the first wild-type strain hCoV-19/Wuhan/WIV04/2019 and AY.29 wild-type strain hCoV-19/Japan/TKYK15779/2021 were used as references to assess the phylogenetical development of this cluster.
A total of 6 nurses and 14 inpatients were identified as a nosocomial cluster from September 14 through 28, 2021. All were Delta variant (AY.29 sublineage) positive. 92.9% of infected patients (13 out of 14) were either cancer patients and/or receiving immunosuppressive or steroid treatments. Compared to AY.29 wild type, a total of 12 mutations were found in the 20 cases. Haplotype analysis found one index group of eight cases with F274F (N) mutation and 10 other haplotypes with one to three additional mutations. Furthermore, we found that cases with more than three minor variants were all cancer patients under immunosuppressive treatments. The phylogenetical tree analysis, including 20 nosocomial cluster-associated viral genomes, the first wild-type strain and the AY.29 wild-type strain as references, indicated the mutation development of the AY.29 virus in this cluster.
Our study of a nosocomial SARS-CoV-2 cluster highlights mutation acquisition during transmission. More importantly, it provided new evidence emphasizing the need to further improve infection control measures to prevent nosocomial infection among immunosuppressed patients.
先前的研究表明，免疫抑制患者往往会有持续时间更长的新冠病毒感染，并且在感染期间观察到了一些突变。然而，这些研究总体上是纵向进行的。免疫抑制患者群体中的突变演变尚未得到充分研究，尤其是在亚洲人群中。
我们的研究针对日本一家医疗中心在德尔塔毒株激增期间（AY.29亚谱系）出现的新冠病毒院内聚集性感染，涉及病房护士和住院患者。进行了全基因组测序分析以检查突变变化。进一步进行了单倍型和次要变异分析，以详细检测病毒基因组上的突变。此外，将首个野生型毒株hCoV-19/武汉/WIV04/2019和AY.29野生型毒株hCoV-19/日本/TKYK15779/2021的序列用作参考，以评估该聚集性感染的系统发育发展。
2021年9月14日至28日，共确定6名护士和14名住院患者为院内聚集性感染病例。所有病例均为德尔塔变异株（AY.29亚谱系）阳性。92.9%的感染患者（14例中的13例）为癌症患者和/或正在接受免疫抑制或类固醇治疗。与AY.29野生型相比，在这20例病例中总共发现了12个突变。单倍型分析发现一组8例的索引组有F274F（N）突变，另外10个单倍型有一到三个额外突变。此外，我们发现次要变异超过三个的病例均为接受免疫抑制治疗的癌症患者。系统发育树分析包括20个与院内聚集性感染相关的病毒基因组、首个野生型毒株和AY.29野生型毒株作为参考，显示了该聚集性感染中AY.29病毒的突变发展情况。
我们对新冠病毒院内聚集性感染的研究突出了传播过程中获得的突变。更重要的是，它提供了新的证据，强调需要进一步改进感染控制措施，以预防免疫抑制患者中的医院感染。
