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

Genome Biol
Authors
Keywords
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.

Year of Publication
2014
Journal
Genome Biol
Volume
15
Issue
11
Pages
519
Date Published
2014
ISSN
1474-760X
URL
DOI
10.1186/PREACCEPT-1698056557139770
PubMed ID
25403361
PubMed Central ID
PMC4262991
Links
Grant list
U19 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