Detecting Viruses in Nasal and Fecal Samples Using High-Throughput Sequencing
Author Information
Author(s): Nakamura Shota, Yang Cheng-Song, Sakon Naomi, Ueda Mayo, Tougan Takahiro, Yamashita Akifumi, Goto Naohisa, Takahashi Kazuo, Yasunaga Teruo, Ikuta Kazuyoshi, Mizutani Tetsuya, Okamoto Yoshiko, Tagami Michihira, Morita Ryoji, Maeda Norihiro, Kawai Jun, Hayashizaki Yoshihide, Nagai Yoshiyuki, Horii Toshihiro, Iida Tetsuya, Nakaya Takaaki
Primary Institution: Research Institute for Microbial Diseases, Osaka University
Hypothesis
Can unbiased high-throughput sequencing effectively detect viral pathogens in clinical specimens?
Conclusion
The study demonstrates that high-throughput sequencing can directly detect viral pathogens in clinical samples, including influenza and norovirus.
Supporting Evidence
- High-throughput sequencing yielded an average of 24,738 reads per sample.
- Influenza A virus and norovirus were detected in all tested samples.
- More than 75% of the norovirus genome was covered in several fecal samples.
- Two novel human viruses were identified in the samples.
- The method showed higher sensitivity than conventional PCR for viral detection.
Takeaway
Researchers used a special sequencing method to find viruses in samples from sick people, helping to identify infections faster.
Methodology
The study used random RT-PCR to amplify RNA from clinical samples, followed by high-throughput sequencing to identify viral sequences.
Potential Biases
Potential bias in cDNA synthesis due to the quasi-random RT-PCR method used.
Limitations
The method may not be cost-effective for widespread diagnostic use and may require further refinement to reduce host-derived sequence contamination.
Participant Demographics
Samples were collected from children aged 3 to 7 years and other patients in various settings in Osaka, Japan.
Digital Object Identifier (DOI)
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