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Genome Biol DOI:10.1186/PREACCEPT-1698056557139770

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

Publication TypeJournal Article
Year of Publication2014
AuthorsMatranga, CB, Andersen, KG, Winnicki, S, Busby, M, Gladden, AD, Tewhey, R, Stremlau, M, Berlin, A, Gire, SK, England, E, Moses, LM, Mikkelsen, TS, Odia, I, Ehiane, PE, Folarin, O, Goba, A, S Kahn, H, Grant, DS, Honko, A, Hensley, L, Happi, C, Garry, RF, Malboeuf, CM, Birren, BW, Gnirke, A, Levin, JZ, Sabeti, PC
JournalGenome Biol
Volume15
Issue11
Pages519
Date Published2014
ISSN1474-760X
KeywordsEbolavirus, Hemorrhagic Fever, Ebola, High-Throughput Nucleotide Sequencing, Humans, Lassa Fever, Lassa virus, RNA, Viral
Abstract

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.

URLhttp://genomebiology.com/content/15/11/519
DOI10.1186/PREACCEPT-1698056557139770
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/25403361?dopt=Abstract

Alternate JournalGenome Biol.
PubMed ID25403361
PubMed Central IDPMC4262991
Grant ListU19 AI115589 / AI / NIAID NIH HHS / United States
HHSN272200900018C / AI / NIAID NIH HHS / United States
DP2OD06514 / OD / NIH HHS / United States
U01 HG007480 / HG / NHGRI NIH HHS / United States
HHSN272200900049C / AI / NIAID NIH HHS / United States
R01 AI104621 / AI / NIAID NIH HHS / United States
DP2 OD006514 / OD / NIH HHS / United States
U19 AI110818 / AI / NIAID NIH HHS / United States