Serving the Society Since 1986
Advanced Search
Volume 33 Issue 6
December 2018
    Citation: Ming Ni, Chen Chen, Di Liu. An Assessment of Amplicon-Sequencing Based Method for Viral Intrahost Analysis .VIROLOGICA SINICA, 2018, 33(6) : 557-560.  http://dx.doi.org/10.1007/s12250-018-0052-z
    shu

    An Assessment of Amplicon-Sequencing Based Method for Viral Intrahost Analysis

    • 1.

      Beijing Institute of Radiation Medicine, Beijing 100850, China

    • 2.

      Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China

    • 3.

      Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China

    • Corresponding author: Di Liu, liud@wh.iov.cn, ORCID: http://orcid.org/0000-0003-3693-2726
    • Received Date: 07 May 2018
      Accepted Date: 13 September 2018
      Published Date: 05 November 2018
      Available online: 01 December 2018
    • 加载中
    • 10.1007s12250-018-0052-z.pdf

      1. Chen C, Jiang D, Ni M, Li J, Chen Z, Liu J, Ye H, Wong G, Li W, Zhang Y et al (2018) Phylogenomic analysis unravels evolution of yellow fever virus within hosts. PLoS Negl Trop D 12:e0006738
          doi: 10.1371/journal.pntd.0006738

      2. Debbink K, McCrone JT, Petrie JG, Truscon R, Johnson E, Mantlo EK, Monto AS, Lauring AS (2017) Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses. PLoS Pathog 13:e1006194
          doi: 10.1371/journal.ppat.1006194

      3. Domingo E, Sheldon J, Perales C (2012) Viral quasispecies evolution. Microbiol Mol Biol Rev 76:159-216
          doi: 10.1128/MMBR.05023-11

      4. Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G et al (2014) Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345:1369
          doi: 10.1126/science.1259657

      5. Holmes EC, Dudas G, Rambaut Andersen KG (2016) The evolution of Ebola virus: insights from the 2013-2016 epidemic. Nature 538:193-200
          doi: 10.1038/nature19790

      6. Lakdawala SS, Jayaraman A, Halpin RA, Lamirande EW, Shih AR, Stockwell TB, Lin X, Simenauer A, Hanson CT, Vogel L et al (2015) The soft palate is an important site of adaptation for transmissible influenza viruses. Nature 526:122-125
          doi: 10.1038/nature15379

      7. Matranga CB, Andersen KG, Winnicki S, Busby M, Gladden AD, Tewhey R, Stremlau M, Berlin A, Gire SK, England E et al (2014) Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples. Genome Biol 15:519
          doi: 10.1186/s13059-014-0519-7

      8. Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A et al (2017) Zika virus evolution and spread in the Americas. Nature 546:411-415
          doi: 10.1038/nature22402

      9. Ni M, Chen C, Qian J, Xiao HX, Shi WF, Luo Y, Wang HY, Li Z, Wu J, Xu PS et al (2016) Intra-host dynamics of Ebola virus during 2014. Nat Microbiol 1:16151
          doi: 10.1038/nmicrobiol.2016.151

      10. Park DJ, Dudas G, Wohl S, Goba A, Whitmer SL, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR et al (2015) Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone. Cell 161:1516-1526
          doi: 10.1016/j.cell.2015.06.007

      11. Poon LL, Song T, Rosenfeld R, Lin X, Rogers MB, Zhou B, Sebra R, Halpin RA, Guan Y, Twaddle A et al (2016) Quantifying influenza virus diversity and transmission in humans. Nat Genet 48:195-200
          doi: 10.1038/ng.3479

      12. Yang X, Charlebois P, Macalalad A, Henn MR, Zody MC (2013) V-Phaser 2: variant inference for viral populations. BMC Genom 14:674
          doi: 10.1186/1471-2164-14-674

      13. Joshi NA and Fass JN (2011) Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software]. Available at https://github.com/najoshi/sickle. Accessed June 5th 2016.

      14. Langmead B and Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357-359.
          doi: 10.1038/nmeth.1923

      15. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.

      16. Nikolenko SI, Korobeynikov AI, and Alekseyev MA (2013) BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics, 14: Suppl 1, S7.
          doi: 10.1186/1471-2164-14-S1-S7

      17. Schirmer M, Ijaz UZ, D'Amore R, Hall N, Sloan WT, Quince C (2015) Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res 43:e37
          doi: 10.1093/nar/gku1341

    • 加载中

    Figures(1) / Tables(3)

    PDF

    Article Metrics

    Article views(4556) PDF downloads(19) Cited by()

    Related
    Proportional views

      An Assessment of Amplicon-Sequencing Based Method for Viral Intrahost Analysis

        Corresponding author: Di Liu, liud@wh.iov.cn
      • 1. Beijing Institute of Radiation Medicine, Beijing 100850, China
      • 2. Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
      • 3. Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
      • Received Date: 07 May 2018
      • Accepted Date: 13 September 2018
      • Published Date: 05 November 2018

      Abstract: 

        HTML