Embekkat Kaviyil Jyothi, Raja Kavita, Gaitonde Rakhal, Easwaran Sreekumar, Kala V Kumari, Korol Ponnambath Dinoop
Microbiology, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum, IND.
Public Health, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum, IND.
Cureus. 2023 Sep 5;15(9):e44755. doi: 10.7759/cureus.44755. eCollection 2023 Sep.
Small clusters of infection due to SARS-CoV-2 in a non-COVID-19 healthcare facility can disrupt services. Here, we investigated a cluster of SARS-CoV-2 cases by targeted Sanger sequencing and clinical epidemiological methods in a non-COVID-19 super-specialty hospital. Epidemiological data were collected in a blinded manner using a proforma to find the risk factors associated with infection. Targeted Sanger sequencing of the spike protein receptor binding domain (RBD) coding region was performed on all the available real-time reverse transcription polymerase chain reaction (RT-PCR)-positive samples that included a patient, his mother, and 11 healthcare workers (HCWs) to determine any genomic variations in the samples from the cluster. All positive cases were due to the Delta variant. However, it detected a unique mutation, N501I, in the RBD region of the SARS-CoV-2 strains. The viral genome extracted from the mother's sample lacked the mutation, thus excluding her from the cluster and pointing out that the outbreak was nosocomial, leading to a focus on infection control measures. Though whole genome sequencing is more universally accepted, in this study, targeted sanger sequencing provided a rapid and cost-effective solution to correctly delineate between the actual cases that form the cluster and other community cases in a pandemic situation.
在非新冠肺炎医疗设施中，由严重急性呼吸综合征冠状病毒2（SARS-CoV-2）引起的小规模感染群可能会扰乱服务。在此，我们通过靶向桑格测序和临床流行病学方法，对一家非新冠肺炎超级专科医院中的一组SARS-CoV-2病例进行了调查。使用一份表格以盲法收集流行病学数据，以找出与感染相关的风险因素。对所有可用的实时逆转录聚合酶链反应（RT-PCR）阳性样本进行了刺突蛋白受体结合域（RBD）编码区的靶向桑格测序，这些样本包括一名患者、其母亲以及11名医护人员（HCW），以确定该感染群样本中的任何基因组变异。所有阳性病例均由德尔塔变异株引起。然而，在SARS-CoV-2毒株的RBD区域检测到了一个独特的突变，即N501I。从母亲样本中提取的病毒基因组没有该突变，因此将她排除在感染群之外，并指出此次疫情是医院感染，这导致了对感染控制措施的关注。尽管全基因组测序更被广泛接受，但在本研究中，靶向桑格测序提供了一种快速且经济高效的解决方案，能够在大流行情况下正确区分构成感染群的实际病例和其他社区病例。
