7bec4f4f868095f3f603cf62110fcbf8 224198.pdf a99771dcfda7c36c4c1a45d306b88173c52ab6ea 224198.pdf fe4329140b0e1f279b3f3ab7e8f73d9bdd730658705386a0ddae95269ffdf762 224198.pdf Title: Reliable resolution of ambiguous hepatitis C virus genotype 1 results with the Abbott HCV Genotype Plus RUO assay Subject: Scientific Reports, doi:10.1038/s41598-019-40099-3 Keywords: Author: V. Saludes Creator: Springer Producer: iText® 5.3.5 ©2000-2012 1T3XT BVBA (AGPL-version) CreationDate: Wed Feb 20 07:29:06 2019 CET ModDate: Thu Feb 28 08:52:00 2019 CET Tagged: no UserProperties: no Suspects: no Form: AcroForm JavaScript: no Pages: 10 Encrypted: no Page size: 595.276 x 782.362 pts Page rot: 0 File size: 1460083 bytes Optimized: no PDF version: 1.4 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- IBEQWD+Corbel-Bold CID TrueType Identity-H yes yes yes 69 0 CEWBTA+Corbel-BoldItalic Type 1C WinAnsi yes yes yes 70 0 EuclidSymbol Type 1C Custom yes no yes 36 0 EuclidSymbol-Bold Type 1C Custom yes no yes 72 0 NIGOGB+Corbel-Bold2 Type 1C WinAnsi yes yes yes 38 0 MinionPro-Regular Type 1C Custom yes no yes 37 0 KDTBUC+Corbel2 Type 1C WinAnsi yes yes yes 41 0 TESJUH+Corbel CID TrueType Identity-H yes yes yes 42 0 MyriadPro-It Type 1C WinAnsi yes no yes 43 0 YXCPMX+TimesNewRomanPSMT Type 1C WinAnsi yes yes yes 352 0 KDTBUC+Corbel2 Type 1C WinAnsi yes yes yes 277 0 MinionPro-Bold Type 1C WinAnsi yes no yes 39 0 MinionPro-It Type 1C Custom yes no yes 40 0 XUNBTZ+STIXGeneral-Regular Type 1C Custom yes yes yes 71 0 MinionPro-BoldIt Type 1C WinAnsi yes no yes 103 0 STIXGeneral-Bold Type 1C Custom yes no yes 163 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2021-03-23 02:27:06 CET RepresentationInformation: 224198.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2021-03-22 18:28:40 CET Size: 1460083 Format: PDF Version: 1.4 Status: Well-Formed, but not valid SignatureMatches: PDF-hul ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd:Figure 1. Flowchart diagram of the study design and methods used. GT, genotype; ST, subtype; GT II, Abbott RealTime HCV Genotype II assay; GT Plus, Abbott HCV Genotype Plus RUO assay; LiPA, VERSANT HCV Genotype 2.0 assay; mGT, mixed genoty:44' cannot be found Offset: 1034670 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd: Table 1. Genotyping methods used and HCV genome target regions. GT II, Abbott RealTime HCV Genotype II assay (Abbott Molecular Inc.); GT Plus, HCV Genotype Plus RUO assay (Abbott Molecular Inc.); LiPA, VERSANT HCV Genotype:45' cannot be found Offset: 1034670 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd: Table 2. HCV genotype and subtype results according to the genotyping method used (n). GT II, Abbott RealTime HCV Genotype II assay; GT Plus, Abbott HCV Genotype Plus RUO assay; LiPA, VERSANT HCV Genotype 2.0 assay; :53' cannot be found Offset: 1034670 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd: Table 2. HCV genotype and subtype results according to the genotyping method used (n). GT II, Abbott RealTime HCV Genotype II assay; GT Plus, Abbott HCV Genotype Plus RUO assay; LiPA, VERSANT HCV Genotype 2.0 assay;:56' cannot be found Offset: 1034670 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd: Table 3. Sequencing results in samples with mixed HCV 1a⁜琀⬠㄀戀 猀甀戀琀礀瀀攀猀 愀猀 搀攀琀攀挀琀攀搀 戀礀 攀椀琀栀攀爀 琀栀攀 䜀吀 䤀䤀 愀渀搀⼀漀爀 琀栀攀 䜀吀⃾＀倀氀甀現＀ 愀猀猀愀礀⻾￾￾￾＀⃾￾￾＀䜀吀 䤀䤀Ⰰ 䄀戀戀漀琀琀 刀攀愀氀吀槾＀洀旾＀ 䠀䌀嘀 䜀攀渀漀琀礀瀀攀 䤀䤀 愀猀猀愀礀 䄀戀戀漀琀琀 䴀漀氀攀挀甀氀愀爀 䤀渀挀⸀㬀 䜀吀⃾＀倀氀甀現＀Ⰰ 䠀䌀嘀 㨀㔀㜩⽂潲摥牛〠〠そ⽓畢瑹灥⽌楮欯䉓㰼⽗‰⽔祰支䉯牤敲⽓⽓㸾⽒散瑛㔴㔮〹㈠㈸㘮㜶㌠㔴㤮㐴㈠㈷㐮㘲㉝⽈⽎⽁值㰯丠㤸‰⁒㸾㸾੥湤潢樊㤳‰扪਼㰯䘠㐯呹灥⽁湮潴⽄敳琨SpringerNature_SciRep_40099.indd: Table 4. Sequencing results in samples with mixed genotypes detected by the GT II assay. GT II, Abbott RealTime HCV Genotype II assay (Abbott Molecular Inc.); GT Plus, HCV Genotype Plus RUO assay (Abbott Molecu:58' cannot be found Offset: 1034670 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd: Table 4. Sequencing results in samples with mixed genotypes detected by the GT II assay. GT II, Abbott RealTime HCV Genotype II assay (Abbott Molecular Inc.); GT Plus, HCV Genotype Plus RUO assay (Abbott Molecu:58' cannot be found Offset: 1034670 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd: Table 4. Sequencing results in samples with mixed genotypes detected by the GT II assay. GT II, Abbott RealTime HCV Genotype II assay (Abbott Molecular Inc.); GT Plus, HCV Genotype Plus RUO assay (Abbott Molec:60' cannot be found Offset: 1034670 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd: Table 4. Sequencing results in samples with mixed genotypes detected by the GT II assay. GT II, Abbott RealTime HCV Genotype II assay (Abbott Molecular Inc.); GT Plus, HCV Genotype Plus RUO assay (Abbott Mole:61' cannot be found Offset: 1034670 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd: 11. Mokhtari, C. et al. Characterization of Samples Identified as Hepatitis C Virus Genotype 1 without Subtype by Abbott RealTime HCV Genotype II Assay Using the New Abbott HCV Genotype Plus RUO Test. J. Clin. Microbiol. 54, 296–299 (20:65' cannot be found Offset: 1034670 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd: 21. Herman, S. A. et al. Cobas(R) HCV Gt for Use on the Cobas(R) 4800 System: A Highly Accurate HCV Genotyping Test. J. Hepatol. 64, S612 (2016). :68' cannot be found Offset: 1034670 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd: 14. González, V. et al. Accuracy of a commercially available assay for HCV genotyping and subtyping in the clinical practice. J. Clin. Virol. 58, 249–253 (2013). :71' cannot be found Offset: 1034670 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd: 13. Mallory, M. A., Lucic, D. X., Sears, M. T., Cloherty, G. A. & Hillyard, D. R. Evaluation of the Abbott realtime HCV genotype II RUO (GT II) assay with reference to 5’UTR, core and NS5B sequencing. J. Clin. Virol. 60, 22–26 (2014). :75' cannot be found Offset: 1034670 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd: 33. He, C. et al. Utility of the Abbott RealTime HCV Genotype Plus RUO assay used in combination with the Abbott RealTime HCV Genotype II assay. J. Clin. Virol. 99–100, 97–100 (2018). :78' cannot be found Offset: 1034670 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd: 34. Mallory, M. A. et al. Evaluation of the Abbott RealTime HCV genotype II plus RUO (PLUS) assay with reference to core and NS5B sequencing. J. Clin. Virol. 90, 26–31 (2017). :83' cannot be found Offset: 1034670 ID: PDF-HUL-122 ErrorMessage: edu.harvard.hul.ois.jhove.module.pdf.PdfInvalidException: Invalid indirect destination - referenced object 'SpringerNature_SciRep_40099.indd: 37. Cunningham, E. B., Applegate, T. L., Lloyd, A. R., Dore, G. J. & Grebely, J. Mixed HCV infection and reinfection in people who inject drugs–impact on therapy. Nat. Rev. Gastroenterol. Hepatol. 12, 218–230 (2015). :104' cannot be found Offset: 1034670 MIMEtype: application/pdf PDFMetadata: Objects: 441 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: false CenterWindow: false DisplayDocTitle: false NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseOutlines Language: EN Outlines: Item: Title: Reliable resolution of ambiguous hepatitis C virus genotype 1 results with the Abbott HCV Genotype Plus RUO assay Children: Item: Title: Material and Methods Children: Item: Title: Study design. Item: Title: Clinical specimens. Item: Title: Genotyping by Abbott GT II and GT Plus assays. Item: Title: Genotyping by NS5B and core sequencing and phylogenetic analysis. Item: Title: Genotyping with the VERSANT HCV Genotype 2.0 Assay (LiPA). Item: Title: Assessment of mixed infections by NGS. Item: Title: Results Children: Item: Title: Ability of the GT Plus assay for subtyping genotype 1 samples with no subtype assigned by the GT II assay. Item: Title: Concordance at the subtype level of the GT Plus assay with the reference method or LiPA in genotype 1 samples with no subty ... Item: Title: Concordance at the subtype level between the GT Plus assay and the GT II assay in genotype 1a and 1b samples. Item: Title: Assessment of mixed infections. Item: Title: Discussion Item: Title: Acknowledgements Item: Title: Figure 1 Flowchart diagram of the study design and methods used. Item: Title: Figure 2 Maximum likelihood phylogenetic subtree of the genotype 1 core region (which includes the region targeted by the GT Plus assay) for samples belonging to Group 1 with a “not detected” result by the GT Plus assay. Item: Title: Table 1 Genotyping methods used and HCV genome target regions. Item: Title: Table 2 HCV genotype and subtype results according to the genotyping method used (n). Item: Title: Table 3 Sequencing results in samples with mixed HCV 1a + 1b subtypes as detected by either the GT II and/or the GT Plus assay. Item: Title: Table 4 Sequencing results in samples with mixed genotypes detected by the GT II assay. Info: Title: Reliable resolution of ambiguous hepatitis C virus genotype 1 results with the Abbott HCV Genotype Plus RUO assay Author: V. 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1 results with the Abbott HCV Genotype Plus RUO assay V. Saludes A. Antuori B. Reinhardt I. Viciana E. Clavijo L. Schreiber M. Tenenbaum F. Rodriguez-Frias J. Quer L. Matas E. Martramp#x000F3; 10.1038/s41598-019-40099-3 http://dx.doi.org/10.1038/s41598-019-40099-3 journal Scientific Reports © 2019, The Author(s) 2045-2322 10.1038/s41598-019-40099-3 Springer 2019-02-28T08:52:00+01:00 2019-02-20T11:59:06+05:30 2019-02-28T08:52:00+01:00 True iText® 5.3.5 ©2000-2012 1T3XT BVBA (AGPL-version) VoR uuid:4c45e900-c32c-4b5a-9a53-97c2244ea339 uuid:9b0b927e-b4ab-47b1-a947-9a43e5b20b21 default 1 converted uuid:1fb77e28-507f-4123-8e73-9d129a8700ca converted to PDF/A-2b pdfToolbox 2019-02-20T11:59:49+05:30 2 B http://ns.adobe.com/xap/1.0/mm/ xmpMM XMP Media Management Schema internal UUID based identifier for specific incarnation of a document InstanceID URI internal The common identifier for all versions and renditions of a document. 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