Abstract
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.
Highlights
Viral pandemics that emerged over the last four decades were initiated across different geographic regions of the world and these includes the human immunodeficiency virus (HIV), severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses, influenza H1N1 virus, Ebola virus, Zika virus and most recently, the pandemic caused by SARSCoV-2 which was initiated in Wuhan, China (Zhu et al, 2020)
We were able to detect microbes that are rare and present in very low copy numbers. This technology is highly sensitive and has a relatively quick turnaround time to obtain results based in our pipeline, which can give results within 24 hours after samples are received at the laboratory. We have developed this technology as a potential resource that can be used as a sensitive diagnostic tool for early detection of highly infectious microorganisms in clinical samples, which includes all known respiratory viruses as well as SARS-CoV2
The SARS-CoV-2 probes, which include probes from conserved, unique and mutated regions, were able to successfuly detect the genomic RNA from the reference control sample (NR52285) from SARS-related Coronavirus-2, obtained from BEI resources (Figure 1) which was established by National Institute of Allergy and Infectious Diseases (NIAID)
Summary
Viral pandemics that emerged over the last four decades were initiated across different geographic regions of the world and these includes the human immunodeficiency virus (HIV), severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses, influenza H1N1 virus, Ebola virus, Zika virus and most recently, the pandemic caused by SARSCoV-2 which was initiated in Wuhan, China (Zhu et al, 2020). The serological antibody test is another widely used technique employed for determination of exposure to the virus through the detection of antibodies against the viral antigens, most prominently the Spike and Nucleocapsid proteins (Lim and Lee, 2020), does not indicate active infection. All these techniques come with some limitations
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