Abstract
Although viruses infect various organs and are associated with diseases, there may be many unidentified pathogenic viruses. The recent development of next-generation sequencing technologies has facilitated the establishment of an environmental viral metagenomic approach targeting the intracellular viral genome. However, an efficient method for the detection of a viral genome derived from an RNA virus in animal or human samples has not been established. Here, we established a method for the efficient detection of RNA viruses in human clinical samples. We then tested the efficiency of the method compared to other conventional methods by using tissue samples collected from 57 recipients of living donor liver transplantations performed between June 2017 and February 2019 at Kyushu University Hospital. The viral read ratio in human clinical samples was higher by the new method than by the other conventional methods. In addition, the new method correctly identified viral RNA from liver tissues infected with hepatitis C virus. This new technique will be an effective tool for intracellular RNA virus surveillance in human clinical samples and may be useful for the detection of new RNA viruses associated with diseases.
Highlights
Viruses are intracellular parasites; they can replicate only within cells
Comparison between Modified double-stranded RNA (dsRNA)-Seq and Other Conventional Methods. We examined whether this modified dsRNA-seq method was more efficient at detecting virus reads than other conventional methods
For every 100,000 reads, the total RNA-seq method detected 22 reads (0.02%) and 10 reads (0.01%), the FLDS method detected 91 reads (0.09%) and 68 reads (0.07%), and the modified dsRNA-seq method detected 411 reads (0.41%) and 388 reads (0.39%) of viral genome in the two samples, respectively (Figure 2A, Table 2)
Summary
Viruses are intracellular parasites; they can replicate only within cells. They were first identified from plants at the end of nineteenth century [1]. It is too difficult to detect exclusively RNA virus genomes efficiently, because the genome size of RNA viruses is small and the volume of the viral genome is very low compared to that of the host genome. To resolve this problem, a method targeting intracellular double-stranded RNA (dsRNA) has been established [7,8,9]. A method for detecting only dsRNA would be more efficient to detect RNA virus genomes To this end, an environmental viral metagenomic approach targeting intracellular dsRNA has been established in plants and fungi [12,13]. We investigated whether novel RNA viruses associated with diseases could be identified from liver tissue samples of LDLT recipients using a modified dsRNA sequencing method
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