Title |
Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome
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Published in |
Biology Direct, January 2016
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DOI | 10.1186/s13062-016-0105-x |
Pubmed ID | |
Authors |
Dingchen Li, Zongwei Li, Zhe Zhou, Zhen Li, Xinyan Qu, Peisong Xu, Pingkun Zhou, Xiaochen Bo, Ming Ni |
Abstract |
Next-generation sequencing (NGS) enables the recovery of pathogen genomes from clinical samples without the need for culturing. Depletion of host/microbiota components (e.g., ribosomal RNA and poly-A RNA) and whole DNA/cDNA amplification are routine methods to improve recovery results. Using mixtures of human and influenza A virus (H1N1) RNA as a model, we found that background depletion and whole transcriptome amplification introduced biased distributions of read coverage over the H1N1 genome, thereby hampering genome assembly. Influenza serotyping was also affected by pretreatments. We propose that direct sequencing of noncultured samples without pretreatment is a favorable option for pathogen genome recovery applications. This article was reviewed by Sebastian Maurer-Stroh. |
X Demographics
Geographical breakdown
Country | Count | As % |
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Unknown | 5 | 100% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 5 | 100% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Malaysia | 1 | 2% |
United States | 1 | 2% |
Germany | 1 | 2% |
Unknown | 59 | 95% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 18 | 29% |
Student > Ph. D. Student | 17 | 27% |
Student > Master | 6 | 10% |
Student > Postgraduate | 4 | 6% |
Student > Doctoral Student | 3 | 5% |
Other | 8 | 13% |
Unknown | 6 | 10% |
Readers by discipline | Count | As % |
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Biochemistry, Genetics and Molecular Biology | 15 | 24% |
Agricultural and Biological Sciences | 12 | 19% |
Immunology and Microbiology | 9 | 15% |
Veterinary Science and Veterinary Medicine | 5 | 8% |
Medicine and Dentistry | 3 | 5% |
Other | 8 | 13% |
Unknown | 10 | 16% |