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Volumn 2, Issue 5, 2017, Pages

A multicenter study to evaluate the performance of high-throughput sequencing for virus detection

Author keywords

454 Roche; Adventitious viruses; High throughput sequencing; Illumina; Spiking study; Virus detection

Indexed keywords


EID: 85041534475     PISSN: None     EISSN: 23795042     Source Type: Journal    
DOI: 10.1128/mSphere.00307-17     Document Type: Article
Times cited : (27)

References (46)
  • 2
    • 78149344560 scopus 로고    scopus 로고
    • Testing considerations for novel cell substrates: a regulatory perspective
    • Khan AS. 2010. Testing considerations for novel cell substrates: a regulatory perspective. PDA J Pharm Sci Technol 64:426-431
    • (2010) PDA J Pharm Sci Technol , vol.64 , pp. 426-431
    • Khan, A.S.1
  • 3
    • 84855545153 scopus 로고    scopus 로고
    • Current testing methods and challenges for detection of adventitious viruses
    • Khan AS. 2011. Current testing methods and challenges for detection of adventitious viruses. PDA J Pharm Sci Technol 65:627-633. https://doi .org/10.5731/pdajpst.2011.00831
    • (2011) PDA J Pharm Sci Technol , vol.65 , pp. 627-633
    • Khan, A.S.1
  • 4
    • 84873643152 scopus 로고    scopus 로고
    • PDA/FDA Adventitious Agents and Novel Cell Substrates: Emerging Technologies and New Challenges, Nov 3 4 2011 Rockville, MD
    • Khan AS, Lubiniecki A, King KE. 2012. PDA/FDA Adventitious Agents and Novel Cell Substrates: Emerging Technologies and New Challenges, Nov. 3 4, 2011, Rockville, MD. PDA J Pharm Sci Technol 66:502-511. https:// doi.org/10.5731/pdajpst.2012.00895
    • (2012) PDA J Pharm Sci Technol , vol.66 , pp. 502-511
    • Khan, A.S.1    Lubiniecki, A.2    King, K.E.3
  • 5
    • 84915754759 scopus 로고    scopus 로고
    • Need for new technologies for detection of adventitious agents in vaccines and other biological products
    • Mallet L, Gisonni-Lex L. 2014. Need for new technologies for detection of adventitious agents in vaccines and other biological products. PDA J Pharm Sci Technol 68:556-562. https://doi.org/10.5731/pdajpst.2014 .01012
    • (2014) PDA J Pharm Sci Technol , vol.68 , pp. 556-562
    • Mallet, L.1    Gisonni-Lex, L.2
  • 6
    • 78149352540 scopus 로고    scopus 로고
    • Regulatory considerations for raw materials used in biological products
    • Khan AS. 2010. Regulatory considerations for raw materials used in biological products. PDA J Pharm Sci Technol 64:451-457
    • (2010) PDA J Pharm Sci Technol , vol.64 , pp. 451-457
    • Khan, A.S.1
  • 7
    • 0345424863 scopus 로고    scopus 로고
    • Characterization and qualification of cell substrates and other biological materials used in the production of viral vaccines for infectious disease indications. Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD
    • US Food and Drug Administration. 2010. Guidance for industry. Characterization and qualification of cell substrates and other biological materials used in the production of viral vaccines for infectious disease indications. Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD. http://www.fda.gov/downloads/ BiologicsBloodVaccines/GuidanceComplianceRegulatoryInformation /Guidances/Vaccines/UCM202439.pdf
    • (2010) Guidance for industry
  • 8
    • 77952692589 scopus 로고    scopus 로고
    • Viral nucleic acids in live-attenuated vaccines: detection of minority variants and an adventitious virus
    • Victoria JG, Wang C, Jones MS, Jaing C, McLoughlin K, Gardner S, Delwart EL. 2010. Viral nucleic acids in live-attenuated vaccines: detection of minority variants and an adventitious virus. J Virol 84:6033-6040. https://doi.org/10.1128/JVI.02690-09
    • (2010) J Virol , vol.84 , pp. 6033-6040
    • Victoria, J.G.1    Wang, C.2    Jones, M.S.3    Jaing, C.4    McLoughlin, K.5    Gardner, S.6    Delwart, E.L.7
  • 9
    • 84899650653 scopus 로고    scopus 로고
    • Identification of a novel rhabdovirus in Spodoptera frugiperda cell lines
    • Ma H, Galvin TA, Glasner DR, Shaheduzzaman S, Khan AS. 2014. Identification of a novel rhabdovirus in Spodoptera frugiperda cell lines. J Virol 88:6576-6585. https://doi.org/10.1128/JVI.00780-14
    • (2014) J Virol , vol.88 , pp. 6576-6585
    • Ma, H.1    Galvin, T.A.2    Glasner, D.R.3    Shaheduzzaman, S.4    Khan, A.S.5
  • 11
    • 85015914002 scopus 로고    scopus 로고
    • Advanced Virus Detection Technologies Interest Group (AVDTIG): efforts for high throughput sequencing (HTS) for virus detection
    • Khan AS, Vacante DA, Cassart JP, Ng SH, Lambert C, Charlebois RL, King KE. 2016. Advanced Virus Detection Technologies Interest Group (AVDTIG): efforts for high throughput sequencing (HTS) for virus detection. PDA J Pharm Sci Technol 70:591-595. https://doi.org/10.5731/ pdajpst.2016.007161
    • (2016) PDA J Pharm Sci Technol , vol.70 , pp. 591-595
    • Khan, A.S.1    Vacante, D.A.2    Cassart, J.P.3    Ng, S.H.4    Lambert, C.5    Charlebois, R.L.6    King, K.E.7
  • 12
    • 84908211470 scopus 로고    scopus 로고
    • Adventitious agents in viral vaccines: lessons learned from 4 case studies
    • Petricciani J, Sheets R, Griffiths E, Knezevic I. 2014. Adventitious agents in viral vaccines: lessons learned from 4 case studies. Biologicals 42: 223-236. https://doi.org/10.1016/j.biologicals.2014.07.003
    • (2014) Biologicals , vol.42 , pp. 223-236
    • Petricciani, J.1    Sheets, R.2    Griffiths, E.3    Knezevic, I.4
  • 13
    • 70349328625 scopus 로고    scopus 로고
    • European Medicines Agency, London, United Kingdom
    • The International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH). 1999. Q5A(R1): viral safety evaluation of biotechnology products derived from cell lines of human or animal origin. European Medicines Agency, London, United Kingdom. http://www.ich.org/fileadmin/Public_Web_Site/ICH_Products/Guidelines /Quality/Q5A_R1/Step4/Q5A_R1__Guideline.pdf
    • (1999) Q5A(R1): viral safety evaluation of biotechnology products derived from cell lines of human or animal origin
  • 14
    • 18544400550 scopus 로고
    • The integration of HPV-18 into HeLa cells has involved duplication of part of the viral genome as well as human DNA flanking sequences
    • Picken RN, Yang HL. 1987. The integration of HPV-18 into HeLa cells has involved duplication of part of the viral genome as well as human DNA flanking sequences. Nucleic Acids Res 15:10068. https://doi.org/10.1093/ nar/15.23.10068
    • (1987) Nucleic Acids Res , vol.15
    • Picken, R.N.1    Yang, H.L.2
  • 15
    • 84926429701 scopus 로고    scopus 로고
    • Identification of HPV integration and gene mutation in HeLa cell line by integrated analysis of RNA-Seq and MS/MS data
    • Sun H, Chen C, Lian B, Zhang M, Wang X, Zhang B, Li Y, Yang P, Xie L. 2015. Identification of HPV integration and gene mutation in HeLa cell line by integrated analysis of RNA-Seq and MS/MS data. J Proteome Res 14:1678-1686. https://doi.org/10.1021/pr500944c
    • (2015) J Proteome Res , vol.14 , pp. 1678-1686
    • Sun, H.1    Chen, C.2    Lian, B.3    Zhang, M.4    Wang, X.5    Zhang, B.6    Li, Y.7    Yang, P.8    Xie, L.9
  • 17
    • 84904730587 scopus 로고    scopus 로고
    • Comparison of RNA-Seq by poly(A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling
    • Zhao W, He X, Hoadley KA, Parker JS, Hayes DN, Perou CM. 2014. Comparison of RNA-Seq by poly(A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling. BMC Genomics 15:419. https://doi.org/10.1186/1471-2164-15-419
    • (2014) BMC Genomics , vol.15 , pp. 419
    • Zhao, W.1    He, X.2    Hoadley, K.A.3    Parker, J.S.4    Hayes, D.N.5    Perou, C.M.6
  • 19
    • 84899633209 scopus 로고    scopus 로고
    • Evaluation of the broad-range PCR-electrospray ionization mass spectrometry (PCR/ESI-MS) system and virus microarrays for virus detection
    • Taliaferro LP, Galvin TA, Ma H, Shaheduzzaman S, Williams DK, Glasner DR, Khan AS. 2014. Evaluation of the broad-range PCR-electrospray ionization mass spectrometry (PCR/ESI-MS) system and virus microarrays for virus detection. Viruses 6:1876-1896. https://doi.org/10.3390/ v6051876
    • (2014) Viruses , vol.6 , pp. 1876-1896
    • Taliaferro, L.P.1    Galvin, T.A.2    Ma, H.3    Shaheduzzaman, S.4    Williams, D.K.5    Glasner, D.R.6    Khan, A.S.7
  • 20
    • 80055060612 scopus 로고    scopus 로고
    • Evaluation of the human host range of bovine and porcine viruses that may contaminate bovine serum and porcine trypsin used in the manufacture of biological products
    • Marcus-Sekura C, Richardson JC, Harston RK, Sane N, Sheets RL. 2011. Evaluation of the human host range of bovine and porcine viruses that may contaminate bovine serum and porcine trypsin used in the manufacture of biological products. Biologicals 39:359-369. https://doi.org/ 10.1016/j.biologicals.2011.08.003
    • (2011) Biologicals , vol.39 , pp. 359-369
    • Marcus-Sekura, C.1    Richardson, J.C.2    Harston, R.K.3    Sane, N.4    Sheets, R.L.5
  • 21
    • 84862883106 scopus 로고    scopus 로고
    • Animal virus discovery: improving animal health, understanding zoonoses, and opportunities for vaccine development
    • Delwart E. 2012. Animal virus discovery: improving animal health, understanding zoonoses, and opportunities for vaccine development. Curr Opin Virol 2:344-352. https://doi.org/10.1016/j.coviro.2012.02.012
    • (2012) Curr Opin Virol , vol.2 , pp. 344-352
    • Delwart, E.1
  • 22
    • 85007529828 scopus 로고    scopus 로고
    • The virome: a missing component of biological interaction networks in health and disease
    • Handley SA. 2016. The virome: a missing component of biological interaction networks in health and disease. Genome Med 8:32. https:// doi.org/10.1186/s13073-016-0287-y
    • (2016) Genome Med , vol.8 , pp. 32
    • Handley, S.A.1
  • 23
    • 85028165246 scopus 로고    scopus 로고
    • Ten years of next-generation sequencing technology
    • van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. 2014. Ten years of next-generation sequencing technology. Trends Genet 30:418-426. https://doi.org/10.1016/j.tig.2014.07.001
    • (2014) Trends Genet , vol.30 , pp. 418-426
    • van Dijk, E.L.1    Auger, H.2    Jaszczyszyn, Y.3    Thermes, C.4
  • 24
    • 84957436423 scopus 로고    scopus 로고
    • The sequence of sequencers: the history of sequencing DNA
    • Heather JM, Chain B. 2016. The sequence of sequencers: the history of sequencing DNA. Genomics 107:1-8. https://doi.org/10.1016/j.ygeno .2015.11.003
    • (2016) Genomics , vol.107 , pp. 1-8
    • Heather, J.M.1    Chain, B.2
  • 26
    • 84960968448 scopus 로고    scopus 로고
    • Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing
    • Mee ET, Preston MD, Minor PD, Schepelmann S, CS533 Study Participants. 2016. Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing. Vaccine 34:2035-2043. https://doi.org/10.1016/j.vaccine .2015.12.020
    • (2016) Vaccine , vol.34 , pp. 2035-2043
    • Mee, E.T.1    Preston, M.D.2    Minor, P.D.3    Schepelmann, S.4
  • 28
    • 78751470706 scopus 로고    scopus 로고
    • Selection of a cutoff value for real-time polymerase chain reaction results to fit a diagnostic purpose: analytical and epidemiologic approaches
    • Caraguel CGB, Stryhn H, Gagné N, Dohoo IR, Hammell KL. 2011. Selection of a cutoff value for real-time polymerase chain reaction results to fit a diagnostic purpose: analytical and epidemiologic approaches. J Vet Diagn Invest 23:2-15. https://doi.org/10.1177/104063871102300102
    • (2011) J Vet Diagn Invest , vol.23 , pp. 2-15
    • Caraguel, C.G.B.1    Stryhn, H.2    Gagné, N.3    Dohoo, I.R.4    Hammell, K.L.5
  • 29
    • 25144439528 scopus 로고    scopus 로고
    • A kinetic model of quantitative real-time polymerase chain reaction
    • Mehra S, Hu WS. 2005. A kinetic model of quantitative real-time polymerase chain reaction. Biotechnol Bioeng 91:848-860. https://doi.org/ 10.1002/bit.20555
    • (2005) Biotechnol Bioeng , vol.91 , pp. 848-860
    • Mehra, S.1    Hu, W.S.2
  • 30
    • 83355170695 scopus 로고    scopus 로고
    • Quantification bias caused by plasmid DNA conformation in quantitative real-time PCR assay
    • Lin CH, Chen YC, Pan TM. 2011. Quantification bias caused by plasmid DNA conformation in quantitative real-time PCR assay. PLoS One 6:e29101. https://doi.org/10.1371/journal.pone.0029101
    • (2011) PLoS One , vol.6
    • Lin, C.H.1    Chen, Y.C.2    Pan, T.M.3
  • 31
    • 77949667195 scopus 로고    scopus 로고
    • Serious overestimation in quantitative PCR by circular (supercoiled) plasmid standard: microalgal pcna as the model gene
    • Hou Y, Zhang H, Miranda L, Lin S. 2010. Serious overestimation in quantitative PCR by circular (supercoiled) plasmid standard: microalgal pcna as the model gene. PLoS One 5:e9545. https://doi.org/10.1371/ journal.pone.0009545
    • (2010) PLoS One , vol.5
    • Hou, Y.1    Zhang, H.2    Miranda, L.3    Lin, S.4
  • 36
    • 84896727346 scopus 로고    scopus 로고
    • Quantitative characterization of defective virus emergence by deep sequencing
    • Timm C, Akpinar F, Yin J. 2014. Quantitative characterization of defective virus emergence by deep sequencing. J Virol 88:2623-2632. https://doi .org/10.1128/JVI.02675-13
    • (2014) J Virol , vol.88 , pp. 2623-2632
    • Timm, C.1    Akpinar, F.2    Yin, J.3
  • 37
    • 84932638917 scopus 로고    scopus 로고
    • Evaluation of unbiased next-generation sequencing of RNA (RNA-seq) as a diagnostic method in influenza virus-positive respiratory samples
    • Fischer N, Indenbirken D, Meyer T, Lütgehetmann M, Lellek H, Spohn M, Aepfelbacher M, Alawi M, Grundhoff A. 2015. Evaluation of unbiased next-generation sequencing of RNA (RNA-seq) as a diagnostic method in influenza virus-positive respiratory samples. J Clin Microbiol 53: 2238-2250. https://doi.org/10.1128/JCM.02495-14
    • (2015) J Clin Microbiol , vol.53 , pp. 2238-2250
    • Fischer, N.1    Indenbirken, D.2    Meyer, T.3    Lütgehetmann, M.4    Lellek, H.5    Spohn, M.6    Aepfelbacher, M.7    Alawi, M.8    Grundhoff, A.9
  • 40
    • 84887431948 scopus 로고    scopus 로고
    • Investigation of a regulatory agency enquiry into potential porcine circovirus type 1 contamination of the human rotavirus vaccine, Rotarix: approach and outcome
    • Dubin G, Toussaint JF, Cassart JP, Howe B, Boyce D, Friedland L, Abu-Elyazeed R, Poncelet S, Han HH, Debrus S. 2013. Investigation of a regulatory agency enquiry into potential porcine circovirus type 1 contamination of the human rotavirus vaccine, Rotarix: approach and outcome. Hum Vaccin Immunother 9:2398-2408. https://doi.org/10.4161/ hv.25973
    • (2013) Hum Vaccin Immunother , vol.9 , pp. 2398-2408
    • Dubin, G.1    Toussaint, J.F.2    Cassart, J.P.3    Howe, B.4    Boyce, D.5    Friedland, L.6    Abu-Elyazeed, R.7    Poncelet, S.8    Han, H.H.9    Debrus, S.10
  • 41
    • 84915760928 scopus 로고    scopus 로고
    • Cataloguing the taxonomic origins of sequences from a heterogeneous sample using phylogenomics: applications in adventitious agent detection
    • Charlebois RL, Ng SH, Gisonni-Lex L, Mallet L. 2014. Cataloguing the taxonomic origins of sequences from a heterogeneous sample using phylogenomics: applications in adventitious agent detection. PDA J Pharm Sci Technol 68:602-618. https://doi.org/10.5731/pdajpst.2014 .01023
    • (2014) PDA J Pharm Sci Technol , vol.68 , pp. 602-618
    • Charlebois, R.L.1    Ng, S.H.2    Gisonni-Lex, L.3    Mallet, L.4
  • 42
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: a flexible trimmer for Illumina sequence data
    • Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114-2120. https://doi.org/10 .1093/bioinformatics/btu170
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 43
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589-595. https://doi.org/ 10.1093/bioinformatics/btp698
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 44
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: the European Molecular Biology Open Software Suite
    • Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16:276-277. https://doi.org/ 10.1016/S0168-9525(00)02024-2
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 45
    • 55249099393 scopus 로고    scopus 로고
    • Steps used by the BLAST algorithm
    • Mount DW. 2007. Steps used by the BLAST algorithm. CSH Protoc 2007:pdb.ip41. https://doi.org/10.1101/pdb.ip41
    • (2007) CSH Protoc , vol.2007
    • Mount, D.W.1


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