Seckar Tyler, Lin Xiang, Bose Dipayan, Wei Zhi, Rohrbaugh Joseph, Collman Ronald G, Robertson Erle S
Department of Otorhinolaryngology-Head and Neck Surgery, and Microbiology, The Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, United States.
Front Microbiol. 2021 Mar 9;12:637202. doi: 10.3389/fmicb.2021.637202. eCollection 2021.
The novel coronavirus outbreak started in December 2019 and rapidly spread around the globe, leading to a global pandemic. Here we reported the association of microbial agents identified in oropharyngeal and nasopharyngeal samples from patients with SARS-CoV-2 infection, using a Pan-microarray based technology referred to as PathoChIP. To validate the efficiency of PathoChIP, reference viral genomes obtained from BEI resource and 25 SARS-CoV-2 positive clinical samples were tested. This technology successfully detected femtogram levels of SARS-CoV-2 viral RNA, which demonstrated greater sensitivity and specificity than conventional diagnostic techniques. Simultaneously, a broad range of other microorganisms, including other viruses, bacteria, fungi and parasites can be detected in those samples. We identified 7 viral, 12 bacterial and 6 fungal agents common across all clinical samples suggesting an associated microbial signature in individuals who are infected with SARS-CoV-2. This technology is robust and has a flexible detection methodology that can be employed to detect the presence of all human respiratory pathogens in different sample preparations with precision. It will be important for differentiating the causative agents of respiratory illnesses, including SARS-CoV-2.
新型冠状病毒疫情始于2019年12月，并迅速在全球蔓延，引发了全球大流行。在此，我们报告了使用一种基于全微阵列的技术（称为PathoChIP），对严重急性呼吸综合征冠状病毒2（SARS-CoV-2）感染患者的口咽和鼻咽样本中鉴定出的微生物因子之间的关联。为了验证PathoChIP的效率，对从BEI资源获得的参考病毒基因组和25份SARS-CoV-2阳性临床样本进行了检测。该技术成功检测到了飞克水平的SARS-CoV-2病毒RNA，其灵敏度和特异性均高于传统诊断技术。同时，在这些样本中还可以检测到广泛的其他微生物，包括其他病毒、细菌、真菌和寄生虫。我们在所有临床样本中鉴定出了7种病毒、12种细菌和6种真菌因子，这表明感染SARS-CoV-2的个体存在相关的微生物特征。该技术强大且具有灵活的检测方法，可用于精确检测不同样本制剂中所有人类呼吸道病原体的存在。这对于区分包括SARS-CoV-2在内的呼吸道疾病的病原体非常重要。
