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Biol Direct. 2016 Jan 12;11(1):3. doi: 10.1186/s13062-016-0105-x.

Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome.

Li D1,2, Li Z3,4, Zhou Z5,6, Li Z7,8, Qu X9,10, Xu P11, Zhou P12, Bo X13,14, Ni M15,16.

Author information

1
Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. ldc1988@163.com.
2
Genomics Center of Academy of Military Medical Sciences, 27 Taiping Road, Beijing, 100850, People's Republic of China. ldc1988@163.com.
3
Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. 787237936@qq.com.
4
Genomics Center of Academy of Military Medical Sciences, 27 Taiping Road, Beijing, 100850, People's Republic of China. 787237936@qq.com.
5
Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. zhouzhe@bmi.ac.cn.
6
Genomics Center of Academy of Military Medical Sciences, 27 Taiping Road, Beijing, 100850, People's Republic of China. zhouzhe@bmi.ac.cn.
7
Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. lizhen0131@163.com.
8
Genomics Center of Academy of Military Medical Sciences, 27 Taiping Road, Beijing, 100850, People's Republic of China. lizhen0131@163.com.
9
Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. xinyan19880117@163.com.
10
Genomics Center of Academy of Military Medical Sciences, 27 Taiping Road, Beijing, 100850, People's Republic of China. xinyan19880117@163.com.
11
Department of Research Service, Zhiyuan Inspection Medical Institute, 8 Huazangsi Lane, Hangzhou, 310009, People's Republic of China. 550742305@qq.com.
12
Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. zhoupk@bmi.ac.cn.
13
Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. boxiaoc@163.com.
14
Genomics Center of Academy of Military Medical Sciences, 27 Taiping Road, Beijing, 100850, People's Republic of China. boxiaoc@163.com.
15
Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. ni.ming@163.com.
16
Genomics Center of Academy of Military Medical Sciences, 27 Taiping Road, Beijing, 100850, People's Republic of China. ni.ming@163.com.

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.

PMID:
26754142
PMCID:
PMC4710016
DOI:
10.1186/s13062-016-0105-x
[Indexed for MEDLINE]
Free PMC Article

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