Chapter title |
Targeted Sequencing of Respiratory Viruses in Clinical Specimens for Pathogen Identification and Genome-Wide Analysis
|
---|---|
Chapter number | 10 |
Book title |
The Human Virome
|
Published in |
Methods in molecular biology, August 2018
|
DOI | 10.1007/978-1-4939-8682-8_10 |
Pubmed ID | |
Book ISBNs |
978-1-4939-8681-1, 978-1-4939-8682-8
|
Authors |
Yu Yang, Shannon D. Walls, Stephen M. Gross, Gary P. Schroth, Richard G. Jarman, Jun Hang, Yang, Yu, Walls, Shannon D., Gross, Stephen M., Schroth, Gary P., Jarman, Richard G., Hang, Jun |
Abstract |
A large number of viruses can individually and concurrently cause various respiratory illnesses. Metagenomic sequencing using next-generation sequencing (NGS) technology is capable of identifying a variety of pathogens. Here, we describe a method using a large panel of oligo probes to enrich sequence targets of 34 respiratory DNA and RNA viruses that reduces non-viral reads in NGS data and achieves high performance of sequencing-based pathogen identification. The approach can be applied to total nucleic acids purified from respiratory swabs stored in viral transport medium. Illumina TruSeq RNA Access Library procedure is used in targeted sequencing of respiratory viruses. The samples are subjected to RNA fragmentation, random reverse transcription, random PCR amplification, and ligation with barcoded library adaptors. The libraries are pooled and subjected to two rounds of enrichments by using a large panel of oligos designed to capture whole genomes of 34 respiratory viruses. The enriched libraries are amplified and sequenced using Illumina MiSeq sequencing system and reagents. This method can achieve viral detection sensitivity comparable with molecular assay and obtain partial to complete genome sequences for each virus to allow accurate genotyping and variant analysis. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United States | 2 | 29% |
Unknown | 5 | 71% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 7 | 100% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Unknown | 37 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 7 | 19% |
Student > Bachelor | 5 | 14% |
Professor > Associate Professor | 3 | 8% |
Student > Master | 3 | 8% |
Student > Doctoral Student | 2 | 5% |
Other | 6 | 16% |
Unknown | 11 | 30% |
Readers by discipline | Count | As % |
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Biochemistry, Genetics and Molecular Biology | 9 | 24% |
Medicine and Dentistry | 3 | 8% |
Immunology and Microbiology | 3 | 8% |
Agricultural and Biological Sciences | 2 | 5% |
Veterinary Science and Veterinary Medicine | 2 | 5% |
Other | 4 | 11% |
Unknown | 14 | 38% |