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Christian B Matranga Kristian G Andersen Sarah Winnicki Michele Busby Adrianne D Gladden Ryan Tewhey Matthew Stremlau Aaron Berlin Stephen K Gire Eleina England Lina M Moses Tarjei S Mikkelsen Ikponmwonsa Odia Philomena E Ehiane Onikepe Folarin Augustine Goba S Humarr Kahn Donald S Grant Anna Honko Lisa Hensley Christian Happi Robert F Garry Christine M Malboeuf Bruce W Birren Andreas Gnirke Joshua Z Levin Pardis C Sabeti 《Genome biology》2014,15(11)
We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targeted RNase H-based digestion to remove contaminating poly(rA) carrier and ribosomal RNA. This depletion step improves both the quality of data and quantity of informative reads in unbiased total RNA sequencing libraries. We have also developed a hybrid-selection protocol to further enrich the viral content of sequencing libraries. These protocols have enabled rapid deep sequencing of both Lassa and Ebola virus and are broadly applicable to other viral genomics studies.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0519-7) contains supplementary material, which is available to authorized users. 相似文献2.
Matthew H. Stremlau Kristian G. Andersen Onikepe A. Folarin Jessica N. Grove Ikponmwonsa Odia Philomena E. Ehiane Omowunmi Omoniwa Omigie Omoregie Pan-Pan Jiang Nathan L. Yozwiak Christian B. Matranga Xiao Yang Stephen K. Gire Sarah Winnicki Ridhi Tariyal Stephen F. Schaffner Peter O. Okokhere Sylvanus Okogbenin George O. Akpede Danny A. Asogun Dennis E. Agbonlahor Peter J. Walker Robert B. Tesh Joshua Z. Levin Robert F. Garry Pardis C. Sabeti Christian T. Happi 《PLoS neglected tropical diseases》2015,9(3)
Next-generation sequencing (NGS) has the potential to transform the discovery of viruses causing unexplained acute febrile illness (UAFI) because it does not depend on culturing the pathogen or a priori knowledge of the pathogen’s nucleic acid sequence. More generally, it has the potential to elucidate the complete human virome, including viruses that cause no overt symptoms of disease, but may have unrecognized immunological or developmental consequences. We have used NGS to identify RNA viruses in the blood of 195 patients with UAFI and compared them with those found in 328 apparently healthy (i.e., no overt signs of illness) control individuals, all from communities in southeastern Nigeria. Among UAFI patients, we identified the presence of nucleic acids from several well-characterized pathogenic viruses, such as HIV-1, hepatitis, and Lassa virus. In our cohort of healthy individuals, however, we detected the nucleic acids of two novel rhabdoviruses. These viruses, which we call Ekpoma virus-1 (EKV-1) and Ekpoma virus-2 (EKV-2), are highly divergent, with little identity to each other or other known viruses. The most closely related rhabdoviruses are members of the genus Tibrovirus and Bas-Congo virus (BASV), which was recently identified in an individual with symptoms resembling hemorrhagic fever. Furthermore, by conducting a serosurvey of our study cohort, we find evidence for remarkably high exposure rates to the identified rhabdoviruses. The recent discoveries of novel rhabdoviruses by multiple research groups suggest that human infection with rhabdoviruses might be common. While the prevalence and clinical significance of these viruses are currently unknown, these viruses could have previously unrecognized impacts on human health; further research to understand the immunological and developmental impact of these viruses should be explored. More generally, the identification of similar novel viruses in individuals with and without overt symptoms of disease highlights the need for a broader understanding of the human virome as efforts for viral detection and discovery advance. 相似文献
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