a730f1f20cbdfffab13eabd8e740a36f pmc_9867078.pdf 2347f9ba6dd66fc183b445d4ad8e0387c38aa732 pmc_9867078.pdf 6b1ba8d52d8452ee4398da1ad28bea7dceca3492377fa62545f0cd85a28e952f pmc_9867078.pdf Title: Quantifying In-Host Quasispecies Evolution Subject: What takes decades, centuries or millennia to happen with a natural ecosystem, it takes only days, weeks or months with a replicating viral quasispecies in a host, especially when under treatment. Some methods to quantify the evolution of a quasispecies are introduced and discussed, along with simple simulated examples to help in the interpretation and understanding of the results. The proposed methods treat the molecules in a quasispecies as individuals of competing species in an ecosystem, where the haplotypes are the competing species, and the ecosystem is the quasispecies in a host, and the evolution of the system is quantified by monitoring changes in their haplotype frequencies. The correlation between the proposed indices is also discussed, and the R code used to generate the simulations, the data and the plots is provided. The virtues of the proposed indices are finally shown on a clinical case. Keywords: quasispecies evolution; distributions similarity; quasispecies fitness partition; viral treatment; mutagenesis Author: Josep Gregori, Marta Ibañez-Lligoña, and Josep Quer Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Mon Jan 9 13:36:38 2023 CET ModDate: Mon Jan 9 16:14:07 2023 CET Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 16 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 600746 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- JZDXOF+URWPalladioL-Bold Type 1 Custom yes yes no 10 0 SWBTIM+URWPalladioL-Roma Type 1 Custom yes yes no 15 0 GRRHJN+URWPalladioL-Ital Type 1 Custom yes yes no 19 0 IRWHZX+TimesNewRomanPSMT Type 1C WinAnsi yes yes no 37 0 CKUPDE+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 40 0 NZTUFL+URWPalladioL-BoldItal Type 1 Custom yes yes no 62 0 JMHQPT+CMSY10 Type 1 Builtin yes yes no 76 0 GIGFZE+CMR10 Type 1 Builtin yes yes no 94 0 SYFPBV+CMMI10 Type 1 Builtin yes yes no 127 0 GQYBUE+PazoMath Type 1 Builtin yes yes no 131 0 IZBVMP+CMEX10 Type 1 Builtin yes yes no 138 0 PKBMQF+SFTT1000 Type 1 Custom yes yes no 145 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2023-03-17 02:39:32 CET RepresentationInformation: pmc_9867078.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2023-01-26 02:11:23 CET Size: 600746 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 271 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@12f41634 Item: Title: Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@13c27452 Children: Item: Title: Simulated Pairs of Quasispecies Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Children: Item: Title: Correlations Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Item: Title: Illustration of Selected Pairs Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Item: Title: Simulated Treatment Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Item: Title: A Clinical Case Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Item: Title: Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Item: Title: Materials and Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77ec78b9 Children: Item: Title: Data Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1a3869f4 Children: Item: Title: Simulation of Paired Quasispecies Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@a38d7a3 Item: Title: Simulation of a Viral Treatment Follow-Up Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77f99a05 Item: Title: A Clinical HEV Case Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@63440df3 Item: Title: Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3aeaafa6 Children: Item: Title: Similarity between Distributions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@76a3e297 Item: Title: Genetic Distance between Quasispecies Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4d3167f4 Item: Title: Quasispecies Fitness Partition (QFP) Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@ed9d034 Item: Title: Software and Statistics Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6121c9d6 Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@87f383f Info: Title: Quantifying In-Host Quasispecies Evolution Author: Josep Gregori, Marta Ibañez-Lligoña, and Josep Quer Subject: What takes decades, centuries or millennia to happen with a natural ecosystem, it takes only days, weeks or months with a replicating viral quasispecies in a host, especially when under treatment. Some methods to quantify the evolution of a quasispecies are introduced and discussed, along with simple simulated examples to help in the interpretation and understanding of the results. The proposed methods treat the molecules in a quasispecies as individuals of competing species in an ecosystem, where the haplotypes are the competing species, and the ecosystem is the quasispecies in a host, and the evolution of the system is quantified by monitoring changes in their haplotype frequencies. The correlation between the proposed indices is also discussed, and the R code used to generate the simulations, the data and the plots is provided. The virtues of the proposed indices are finally shown on a clinical case. 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