Genome Biology | Abstract | Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples

Genome Biology | Abstract | Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples

Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses in clinical and biological samples

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, Ikponmwosa Odia, Philomena E Ehiane, Onikepe Folarin,Augustine Goba, S.Humarr Khan, Donald S Grant, Anna Honko, Lisa Hensley, Christian Happi, Robert F Garry, Christine M Malboeuf, Bruce W Birren, Andreas Gnirke, Joshua Z Levin and Pardis C Sabeti

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Genome Biology 2014, 15:519  doi:10.1186/s13059-014-0519-7

Published: 18 November 2014

Abstract (provisional)

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.

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