title: Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome.
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.
authors.affiliation: Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. ldc1988@163.com.|Genomics Center of Academy of Military Medical Sciences, 27 Taiping Road, Beijing, 100850, People's Republic of China. ldc1988@163.com.
authors.forename: Dingchen
authors.initials: D
authors.lastname: Li
authors.affiliation: Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. 787237936@qq.com.|Genomics Center of Academy of Military Medical Sciences, 27 Taiping Road, Beijing, 100850, People's Republic of China. 787237936@qq.com.
authors.forename: Zongwei
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. zhouzhe@bmi.ac.cn.|Genomics Center of Academy of Military Medical Sciences, 27 Taiping Road, Beijing, 100850, People's Republic of China. zhouzhe@bmi.ac.cn.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. lizhen0131@163.com.|Genomics Center of Academy of Military Medical Sciences, 27 Taiping Road, Beijing, 100850, People's Republic of China. lizhen0131@163.com.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. xinyan19880117@163.com.|Genomics Center of Academy of Military Medical Sciences, 27 Taiping Road, Beijing, 100850, People's Republic of China. xinyan19880117@163.com.
authors.forename: Xinyan
authors.initials: X
authors.lastname: Qu
authors.affiliation: Department of Research Service, Zhiyuan Inspection Medical Institute, 8 Huazangsi Lane, Hangzhou, 310009, People's Republic of China. 550742305@qq.com.
authors.forename: Peisong
authors.initials: P
authors.lastname: Xu
authors.affiliation: 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.
authors.forename: Pingkun
authors.initials: P
authors.lastname: Zhou
authors.affiliation: Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. boxiaoc@163.com.|Genomics Center of Academy of Military Medical Sciences, 27 Taiping Road, Beijing, 100850, People's Republic of China. boxiaoc@163.com.
authors.forename: Xiaochen
authors.initials: X
authors.lastname: Bo
authors.affiliation: Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850, People's Republic of China. ni.ming@163.com.|Genomics Center of Academy of Military Medical Sciences, 27 Taiping Road, Beijing, 100850, People's Republic of China. ni.ming@163.com.
authors.forename: Ming
authors.initials: M
authors.lastname: Ni
mesh_terms: D016679:Genome, Viral / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics*