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Volume 22, Number 8—August 2016
Dispatch

Use of Unamplified RNA/cDNA–Hybrid Nanopore Sequencing for Rapid Detection and Characterization of RNA Viruses

Andy Kilianski, Pierce A. Roth, Alvin T. Liem, Jessica M. Hill, Kristen L. Willis, Rebecca D. Rossmaier, Andrew V. Marinich, Michele N. Maughan, Mark A. Karavis, Jens H. Kuhn, Anna N. Honko, and C. Nicole RosenzweigComments to Author 
Author affiliations: US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA (A. Kilianski, P.A. Roth, A.T. Liem, J.M. Hill, K.L. Willis, R.D. Rossmaier, A.V. Marinich, M.N. Maughan, M.A. Karavis, C.N. Rosenzweig); Defense Threat Reduction Agency, Fort Belvoir, Virginia, USA (K.L. Willis); National Institutes of Health, Fort Detrick, Frederick, Maryland, USA (J.H. Kuhn, A.N. Honko)

Main Article

Table

Alignment statistics for detection of VEEV TC-83 and EBOV/Mak-C05 using unamplified RNA/cDNA-hybrid nanopore sequencing*

Virus samples and time points, min
 Top hits (GenBank accession no.)
 LAST score
 Total bases mapped, %
 Coverage, %
 Average base depth
 Per read accuracy, %
VEEV TC-83 (GenBank accession no. L01443)
Viral genomes (RefSeq databases†)
15 VEEV TC-83 (L01443) 138,321 5.54 76.14 50.94x 59–80
VEEV WT (NC_001449.1) 789 0.05 18.59 1.76x 60–78
60 VEEV TC-83 (L01443) 419,153 17.17 78.54 153.16x 57–80
VEEV WT (NC_001449.1) 1,182 0.08 32.12 1.82x 58–78
Alphavirus genomes
15 VEEV TC-83 (L01443) 31,320 1.13 48.92 16.21x 67–69
VEEV E541/73 (AF093102.1 6,463 0.27 95.07 5.26x 62–73
VEEV 71–180 (AF069903.1) 5,865 0.22 30.18 5.08x 65–73
60
VEEV TC-83 (L01443) 96,348 3.55 48.92 50.84x 62–74
VEEV E541/73 (AF093102.1) 21,411 0.89 99.91 16.36x 61–73
VEEV 71–180 (AF069903.1)
 16,429
 0.64
 51.04
 8.78x
 65–73
EBOV/Mak-C05 (GenBank accession no. KX000400)
Viral genomes (RefSeq databases)
15 EBOV/Mak-137 (KX000400) 529 0.11 9.29 1.00x 68
Bovine herpesvirus (NC_024303.1) 73 0.02 0.18 1.00x 67
60 EBOV/Mak-137 (KX000400) 2,371 0.53 22.23 2.09x 66–71
Bovine herpesvirus (NC_024303.1) 239 0.04 0.27 1.58x 67–74

*VEEV, Venezuelan equine encephalitis virus; EBOV, Ebolavirus; LAST (Computational Biology Research Consortium, Tokyo, Japan), multiple sequence alignment program.
†RefSeq, NCBI Reference Sequence Database (http://www.ncbi.nlm.nih.gov/RefSeq/).

Main Article

Page created: July 15, 2016
Page updated: July 15, 2016
Page reviewed: July 15, 2016
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
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