Use of unamplified RNA/cDNA-hybrid nanopore sequencing for rapid detection and characterization of RNA viruses

Emerging Infectious Diseases

Volumn 22, Issue 8, 2016, Pages 1448-1451

  Kilianski, Andy ^a   Roth, Pierce A ^a   Liem, Alvin T ^a   Hill, Jessica M ^a   Willis, Kristen L ^a,b   Rossmaier, Rebecca D ^a   Marinich, Andrew V ^a   Maughan, Michele N ^a   Karavis, Mark A ^a   Kuhn, Jens H ^c   Honko, Anna N ^c   Rosenzweig, C Nicole ^a  

^a EDGEWOOD CHEMICAL BIOLOGICAL CENTER   (United States)

^b DEFENSE THREAT REDUCTION AGENCY   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BIOSURVEILLANCE; CLINICAL DECISION MAKING; EBOLAVIRUS; ENCEPHALITIS; GENE AMPLIFICATION; HUMAN; METAGENOMICS; NANOPORE; POLYMERASE CHAIN REACTION; RNA VIRUS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; VIRUS CHARACTERIZATION; GENETICS; ISOLATION AND PURIFICATION; NUCLEIC ACID AMPLIFICATION; PROCEDURES; TIME FACTOR; VENEZUELAN EQUINE ENCEPHALITIS VIRUS;

COMPLEMENTARY DNA; RNA;

DNA, COMPLEMENTARY; EBOLAVIRUS; ENCEPHALITIS VIRUS, VENEZUELAN EQUINE; NANOPORES; NUCLEIC ACID AMPLIFICATION TECHNIQUES; RNA; RNA VIRUSES; TIME FACTORS;

EID: 84978759414     PISSN: 10806040     EISSN: 10806059     Source Type: Journal    
DOI: 10.3201/eid2208.160270     Document Type: Article

References (15)

1. Kilianski A, Haas JL, Corriveau EJ, Liem AT, Willis KL, Kadavy DR, et al. Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer. Gigascience. 2015;4:12.http://dx.doi.org/10.1186/ s13742-015-0051-z
2. Hoenen T, Groseth A, Rosenke K, Fischer RJ, Hoenen A, Judson SD, et al. Nanopore sequencing as a rapidly deployable Ebola outbreak tool. Emerg Infect Dis. 2016;22:331-4; Epub ahead of print.
3. Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016;530:228-32.http://dx.doi.org/10.1038/ nature16996
4. Wang J, Moore NE, Deng Y-M, Eccles DA, Hall RJ. MinION nanopore sequencing of an influenza genome. Front Microbiol. 2015;6:766. http://dx.doi.org/10.3389/fmicb.2015.00766
5. Greninger AL, Naccache SN, Federman S, Yu G, Mbala P, Bres V, et al. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med. 2015;7:99.http://dx.doi.org/10.1186/s13073-015-0220-9
6. Quick J, Ashton P, Calus S, Chatt C, Gossain S, Hawker J, et al. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 2015;16:114.http://dx.doi.org/10.1186/s13059-015-0677-2
7. Ashton PM, Nair S, Dallman T, Rubino S, Rabsch W, Mwaigwisya S, et al. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol. 2014;33:296-300; Epub ahead of print. http://dx.doi.org/10.1038/nbt.3103
8. Kilianski A, Carcel P, Yao S, Roth P, Schulte J, Donarum GB, et al. Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform. BMC Bioinformatics. 2015;16:416.http://dx.doi.org/10.1186/s12859-015-0840-5
9. Mate SE, Kugelman JR, Nyenswah TG, Ladner JT, Wiley MR, Cordier-Lassalle T, et al. Molecular evidence of sexual transmission of Ebola virus. N Engl J Med. 2015;373:2448-54.http://dx.doi.org/26465384
10. Park DJ, Dudas G, Wohl S, Goba A, Whitmer SLM, Andersen KG, et al. Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone. Cell. 2015;161:1516-26.http://dx.doi.org/10.1016/j.cell.2015.06.007
11. Kugelman JR, Sanchez-Lockhart M, Andersen KG, Gire S, Park DJ, Sealfon R, et al. Evaluation of the potential impact of Ebola virus genomic drift on the efficacy of sequence-based candidate therapeutics. MBiol. 2015;6.http://dx.doi.org/10.1128/ mBio.02227-14
12. Gire SK, Goba A, Andersen KG, Sealfon RSG, Park DJ, Kanneh L, et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science. 2014;345:1369-72.http://dx.doi.org/10.1126/science.1259657
13. Carroll MW, Matthews DA, Hiscox JA, Elmore MJ, Pollakis G, Rambaut A, et al. Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa. Nature. 2015;524:97-101.http://dx.doi.org/10.1038/nature14594
14. Ip CLC, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, et al. MinION analysis and reference consortium: phase 1 data release and analysis. F1000Research. 2015;4:1075.http://dx.doi.org/10.12688/f1000research.7201.1 PMID: 26834992
15. Faria N, Azevedo R do S da S, Kraemer MUG, Souza R, Cunha MS, Hill SC, et al. Zika virus in the Americas: early epidemiological and genetic findings. Science. 2016;352:345-9.http://dx.doi.org/10.1126/science.aaf5036