ABSTRACT
Infectious diseases are an enormous public health burden and a growing threat to human health worldwide. Emerging or classic recurrent pathogens, or pathogens with resistant traits, challenge our ability to diagnose and control infectious diseases. Nanopore sequencing technology has the potential to enhance our ability to diagnose, interrogate, and track infectious diseases due to the unrestricted read length and system portability. This review focuses on the application of nanopore sequencing technology in the clinical diagnosis of infectious diseases and includes the following: (i) a brief introduction to nanopore sequencing technology and Oxford Nanopore Technologies (ONT) sequencing platforms; (ii) strategies for nanopore-based sequencing technologies; and (iii) applications of nanopore sequencing technology in monitoring emerging pathogenic microorganisms, molecular detection of clinically relevant drug-resistance genes, and characterization of disease-related microbial communities. Finally, we discuss the current challenges, potential opportunities, and future outlook for applying nanopore sequencing technology in the diagnosis of infectious diseases.
Subject(s)
Humans , Communicable Diseases/diagnosis , High-Throughput Nucleotide Sequencing , Microbiota/genetics , Nanopore Sequencing , Sequence Analysis, DNA , TechnologyABSTRACT
<p><b>BACKGROUND</b>To study the molecular mechanism of interferon alpha2b(IFNalpha2b) inhibiting the SARS virus replication. SARS-associated coronavirus (SARS virus) cDNA chip was developed and applied to detect the virus RNA transcription levels in the interferon-treated and untreated cell cultures, and the mechanism of anti-SARS virus activity of interferon alpha2b in cell culture system was explored.</p><p><b>METHODS</b>SARS virus cDNA chip was prepared by comparing the published SARS virus genome sequence, and the cDNA chip was used to study the interferon alpha2b function during SARS virus replication.</p><p><b>RESULTS</b>SARS virus cDNA chip was successfully prepared by using PCR method. The results showed that the cDNA chip could be used to detect the viral RNA transcription level. Interferon alpha2b could inhibit almost all the SARS virus gene transcription. An unknown gene at the position 28130-28426 bp, named as U gene, may play an important role during the viral replication.</p><p><b>CONCLUSION</b>A SARS virus whole genome cDNA chip was established. It could be used to study the virus molecular biology and antiviral drug screening. The results also showed that interferon alpha2b could inhibit almost the whole virus gene transcription by using the cDNA chip.</p>