Detection of Microbial Agents in Oropharyngeal and Nasopharyngeal Samples of SARS-CoV-2 Patients

Tyler Seckar, Xiang Lin, Dipayan Bose, Zhi Wei, Joseph Rohrbaugh, Ronald G. Collman, Erle S. Robertson

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Article number637202
JournalFrontiers in Microbiology
StatePublished - Mar 9 2021

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Microbiology (medical)


  • COVID-19
  • PathoChIP
  • SARS-COV-2
  • microbes
  • probes
  • respiratory agents


Dive into the research topics of 'Detection of Microbial Agents in Oropharyngeal and Nasopharyngeal Samples of SARS-CoV-2 Patients'. Together they form a unique fingerprint.

Cite this