Virus variant quantification with Orthanq

Virus variant quantification with Orthanq | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Virus variant quantification with Orthanq Hamdiye Uzuner, Felix Wiegand, Sven Schrinner, David Lähnemann, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6673522/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background Existing tools for virus variant identification can pinpoint the most abundant virus variant in a sequencing sample. However, patients can be infected by more than one variant of the same virus species or strain, for example by multiple variants of SARS-CoV-2. This leads to the more complicated problem of virus variant quantification from samples with virus mixtures. Results We report on improvements of Orthanq, our generic tool for haplotype quantification, and show how it can be applied to perform uncertainty aware quantification of virus variants. We evaluate this ability on simulated and real SARS-CoV-2 and HIV-1 virus mixture datasets. Conclusions Orthanq is the first tool to accurately quantify multiple virus variants in co-infected SARS-CoV-2 samples. But it is not limited to SARS-CoV-2 and can be used for an uncertainty-aware quantification of virus variants in any virus mixture. haplotype quantification SARS-CoV-2 virus lineage quantification uncertainty-computation co-infection Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6673522","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":458596800,"identity":"f0a94d6b-f600-4027-9b99-3aed8f40b021","order_by":0,"name":"Hamdiye 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14:23:08","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6673522/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6673522/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":84699920,"identity":"140f7993-a42a-4fd0-9522-aba474a0d929","added_by":"auto","created_at":"2025-06-16 11:17:13","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":18127740,"visible":true,"origin":"","legend":"","description":"","filename":"Manuscriptshrink.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6673522/v1_covered_05aabd74-af2e-430d-9f03-4f99f4bff200.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Virus variant quantification with 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co-infection","lastPublishedDoi":"10.21203/rs.3.rs-6673522/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6673522/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eExisting tools for virus variant identification can pinpoint the most abundant virus variant in a sequencing sample. However, patients can be infected by more than one variant of the same virus species or strain, for example by multiple variants of SARS-CoV-2. This leads to the more complicated problem of virus variant quantification from samples with virus mixtures.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe report on improvements of Orthanq, our generic tool for haplotype quantification, and show how it can be applied to perform uncertainty aware quantification of virus variants. We evaluate this ability on simulated and real SARS-CoV-2 and HIV-1 virus mixture datasets.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eOrthanq is the first tool to accurately quantify multiple virus variants in co-infected SARS-CoV-2 samples. 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