Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods
| العنوان: | Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods |
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| المؤلفون: | Jiming Chen, Guangyu Hou, Qingye Zhuang, Yuan Qiu, Tong Wang, Kaicheng Wang, Run Wu |
| المصدر: | Virus Research |
| بيانات النشر: | Elsevier BV, 2017. |
| سنة النشر: | 2017 |
| مصطلحات موضوعية: | Library, 0301 basic medicine, Cancer Research, animal structures, animal diseases, viruses, AIV, avian influenza virus, IBV, infectious bronchitis virus, PBS, phosphate buffered solution, Computational biology, Biology, Article, DNA sequencing, law.invention, Duck, Feces, 03 medical and health sciences, PCR, polymerase chain reaction, law, SISPA, sequence independent single primer amplification, Next generation sequencing, Virology, Animals, RNA Viruses, Human virome, Polymerase chain reaction, DNA Primers, RT, reverse transcription, Reverse Transcriptase Polymerase Chain Reaction, Virome, virus diseases, High-Throughput Nucleotide Sequencing, RNA, PGM, Personal Genome Machine, Amplicon, Reverse transcriptase, Virus, NGS, next-generation sequencing, Detection, Ducks, 030104 developmental biology, Infectious Diseases, Mink, NDV, Newcastle disease virus, Metagenome, Metagenomics, Primer (molecular biology), Personal genomics |
| الوصف: | Highlights • RNA-Seq libraries were constructed using three methods. • RNA virome in ducks was detected. • RNA virome in mink was detected. • Various viruses in ducks or minks were possibly first identified. Virome (viral megagenomics) detection using next generation sequencing has been widely applied in virology, but its methods remain complicated and need optimization. In this study, we detected the viromes of RNA viruses of one mock sample, one pooled duck feces sample and one pooled mink feces sample on the Personal Genome Machine platform using the sequencing libraries prepared by three methods. The sequencing primers were added through random hybridization and ligation to fragmented viral RNA using a RNA-Seq kit in method 1, through random reverse transcription (RT) and polymerase chain reaction (PCR) in method 2 which was developed in our laboratory, and through hybridization and ligation to fragmented amplicons of random RT-PCR using a single primer in method 3. Although the results of these three samples (nine libraries) all showed that more classified viral families and genera were identified using methods 2 and 3 than using method 1, and more classified viral families and genera were identified using method 2 than using method 3, most of the differences were of no statistical significance. Moreover, 11 mammalian viral genera in minks were possibly identified for the first time through this study. |
| تدمد: | 0168-1702 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fe87a8f4c39030125577e5cac17dcac0Test https://doi.org/10.1016/j.virusres.2017.05.003Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....fe87a8f4c39030125577e5cac17dcac0 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 01681702 |
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