{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T20:14:35Z","timestamp":1788293675851,"version":"build-2803163510"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T00:00:00Z","timestamp":1787011200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000276","name":"Department of Health and Social Care","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000276","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UK Health Security Agency"},{"DOI":"10.13039\/100015846","name":"Welsh Government","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100015846","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Northern Ireland Government"},{"DOI":"10.13039\/100012095","name":"Scottish Government","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012095","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007155","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007155","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000272","name":"National Institute of Health Research","doi-asserted-by":"publisher","award":["MC_PC_19027"],"award-info":[{"award-number":["MC_PC_19027"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Genome Research Limited"},{"name":"Wellcome Sanger Institute"},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["227438\/Z\/23\/Z"],"award-info":[{"award-number":["227438\/Z\/23\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["107652\/Z\/15\/Z"],"award-info":[{"award-number":["107652\/Z\/15\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["203141\/Z\/16\/Z"],"award-info":[{"award-number":["203141\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Oxford EPSRC Centre","award":["EP\/S02428X\/1"],"award-info":[{"award-number":["EP\/S02428X\/1"]}]},{"DOI":"10.13039\/501100000288","name":"Royal Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000288","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100013589","name":"Research England","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013589","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100018336","name":"Health Protection Research Unit","doi-asserted-by":"publisher","award":["NIHR207397"],"award-info":[{"award-number":["NIHR207397"]}],"id":[{"id":"10.13039\/100018336","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UK Health Security Agency"},{"DOI":"10.13039\/501100000769","name":"University of Oxford","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000769","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100013373","name":"Oxford NIHR Biomedical Research Centre","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013373","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007421","name":"Li Ka Shing Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007421","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100030827","name":"NHS","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100030827","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UKHSA"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Deep-sequencing data are increasingly used to study within-host viral diversity and to inform evolutionary inference. For SARS-CoV-2, analyses based on intra-host single-nucleotide variants (iSNVs) have been widely applied to quantify within-host diversity and infer transmission dynamics. However, these applications critically depend on the reliable identification of low-frequency variants, which remain vulnerable to systematic and technical artifacts. In this study, we show that recurrent artifactual iSNVs are common in large-scale SARS-CoV-2 sequencing data and can persist even under conservative minor allele frequency thresholds. Using data from the UK's Office for National Statistics COVID-19 Infection Survey, we demonstrate that such artifacts are predominantly sequencing center-specific rather than primer-specific. Each center exhibits a modest, distinct set of recurrent artifactual variants showing little overlap with sites routinely masked at the consensus level. To address this, we developed a systematic, dataset-aware framework that uses recurrence within sequencing datasets to identify small, noise-adapted sets of artifactual iSNVs to mask. Applying this framework reduces spurious sharing of low-frequency variants between samples and qualitatively alters downstream inferences, including estimates of within-host diversity and transmission bottleneck sizes. Although this study focused on SARS-CoV-2, it is likely that recurrent artifactual iSNVs will be problematic for other viruses as mass-sequencing becomes increasingly routine. Together, these findings highlight the importance of explicit, dataset-aware artifact control for robust inference from within-host variation, particularly as genomic studies increasingly seek to exploit sub-consensus diversity in rapidly evolving pathogens.<\/jats:p>","DOI":"10.1093\/molbev\/msag209","type":"journal-article","created":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T11:16:50Z","timestamp":1786965410000},"source":"Crossref","is-referenced-by-count":0,"title":["Identification and masking of artifactual and misleading within-host variants in deep-sequencing SARS-CoV-2 data"],"prefix":"10.1093","volume":"43","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2459-8583","authenticated-orcid":false,"given":"Klara Marie","family":"Anker","sequence":"first","affiliation":[{"name":"Pandemic Sciences Institute, University of Oxford , Oxford ,","place":["UK"]},{"name":"Big Data Institute, Nuffield Department of Medicine, University of Oxford , Oxford ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5777-8049","authenticated-orcid":false,"given":"Rosario","family":"Evans Pena","sequence":"additional","affiliation":[{"name":"Pandemic Sciences Institute, University of Oxford , Oxford ,","place":["UK"]},{"name":"Department of Biology, University of Oxford , Oxford ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7077-6793","authenticated-orcid":false,"given":"Steven A","family":"Kemp","sequence":"additional","affiliation":[{"name":"Pandemic Sciences Institute, University of Oxford , Oxford ,","place":["UK"]},{"name":"Big Data Institute, Nuffield Department of Medicine, University of Oxford , Oxford ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-2466-9932","authenticated-orcid":false,"given":"Joseph","family":"Clarke","sequence":"additional","affiliation":[{"name":"Big Data Institute, Nuffield Department of Medicine, University of Oxford , Oxford ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2807-1914","authenticated-orcid":false,"given":"Lele","family":"Zhao","sequence":"additional","affiliation":[{"name":"Pandemic Sciences Institute, University of Oxford , Oxford ,","place":["UK"]},{"name":"Big Data Institute, Nuffield Department of Medicine, University of Oxford , Oxford ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2187-0550","authenticated-orcid":false,"given":"David","family":"Bonsall","sequence":"additional","affiliation":[{"name":"Pandemic Sciences Institute, University of Oxford , Oxford ,","place":["UK"]},{"name":"Big Data Institute, Nuffield Department of Medicine, University of Oxford , Oxford ,","place":["UK"]},{"name":"Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford , Oxford ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9998-6783","authenticated-orcid":false,"given":"Nicholas","family":"Grayson","sequence":"additional","affiliation":[{"name":"Pandemic Sciences Institute, University of Oxford , Oxford ,","place":["UK"]},{"name":"Big Data Institute, Nuffield Department of Medicine, University of Oxford , Oxford ,","place":["UK"]},{"name":"Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford , Oxford ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6847-1525","authenticated-orcid":false,"given":"Matthew","family":"Bashton","sequence":"additional","affiliation":[{"name":"Hub for Biotechnology in the Built Environment, Northumbria University , Newcastle-Upon-Tyne ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0412-8509","authenticated-orcid":false,"given":"Ann Sarah","family":"Walker","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, University of Oxford , Oxford ,","place":["UK"]},{"name":"The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford , Oxford ,","place":["UK"]},{"name":"The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford , Oxford ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2765-9828","authenticated-orcid":false,"given":"Tanya","family":"Golubchik","sequence":"additional","affiliation":[{"name":"Big Data Institute, Nuffield Department of Medicine, University of Oxford , Oxford ,","place":["UK"]},{"name":"The Sydney Infectious Diseases Institute (Sydney ID), School of Medical Sciences, University of Sydney , Sydney ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2671-3864","authenticated-orcid":false,"given":"Matthew","family":"Hall","sequence":"additional","affiliation":[{"name":"Pandemic Sciences Institute, University of Oxford , Oxford ,","place":["UK"]},{"name":"Big Data Institute, Nuffield Department of Medicine, University of Oxford , Oxford ,","place":["UK"]},{"name":"Department of Clinical Research, London School of Hygiene & Tropical Medicine , London ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7089-7680","authenticated-orcid":false,"given":"Katrina","family":"Lythgoe","sequence":"additional","affiliation":[{"name":"Pandemic Sciences Institute, University of Oxford , Oxford ,","place":["UK"]},{"name":"Big Data Institute, Nuffield Department of Medicine, University of Oxford , Oxford ,","place":["UK"]},{"name":"Department of Biology, University of Oxford , Oxford ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,8,18]]},"reference":[{"key":"2026090115261996200_msag209-B1","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1186\/s13073-021-00839-5","article-title":"Coronahit: high-throughput sequencing of SARS-CoV-2 genomes","volume":"13","author":"Baker","year":"2021","journal-title":"Genome Med."},{"key":"2026090115261996200_msag209-B2","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1038\/s41467-023-36001-5","article-title":"Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants","volume":"14","author":"Bendall","year":"2023","journal-title":"Nat Commun."},{"key":"2026090115261996200_msag209-B3","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1013134","article-title":"In depth sequencing of a serially sampled household cohort reveals the within-host dynamics of Omicron SARS-CoV-2 and rare selection of novel spike variants","volume":"21","author":"Bendall","year":"2025","journal-title":"PLoS Pathog."},{"key":"2026090115261996200_msag209-B4","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veaf047","article-title":"Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients","volume":"11","author":"Ben Zvi","year":"2025","journal-title":"Virus Evol."},{"key":"2026090115261996200_msag209-B5","doi-asserted-by":"publisher","first-page":"1058","DOI":"10.3390\/pathogens11091058","article-title":"SARS-CoV-2 variants identification: overview of molecular existing methods","volume":"11","author":"Berno","year":"2022","journal-title":"Pathogens"},{"key":"2026090115261996200_msag209-B6","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2026090115261996200_msag209-B7","doi-asserted-by":"publisher","first-page":"1062","DOI":"10.12688\/f1000research.7111.1","article-title":"ve-SEQ: robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens","volume":"4","author":"Bonsall","year":"2015","journal-title":"F1000Res"},{"key":"2026090115261996200_msag209-B8","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00382-20","article-title":"A comprehensive genomics solution for HIV surveillance and clinical monitoring in low-income settings","volume":"58","author":"Bonsall","year":"2020","journal-title":"J Clin Microbiol"},{"key":"2026090115261996200_msag209-B9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1009849","article-title":"Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks","volume":"17","author":"Braun","year":"2021","journal-title":"PLoS Pathog."},{"key":"2026090115261996200_msag209-B10","doi-asserted-by":"publisher","first-page":"1735","DOI":"10.1093\/bioinformatics\/btab856","article-title":"CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants","volume":"38","author":"Chen","year":"2022","journal-title":"Bioinformatics"},{"key":"2026090115261996200_msag209-B11","doi-asserted-by":"publisher","first-page":"616","DOI":"10.1093\/bib\/bbaa297","article-title":"Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities","volume":"22","author":"Chiara","year":"2020","journal-title":"Brief Bioinform."},{"key":"2026090115261996200_msag209-B12","doi-asserted-by":"publisher","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","article-title":"Upsetr: an R package for the visualization of intersecting sets and their properties","volume":"33","author":"Conway","year":"2017","journal-title":"Bioinformatics"},{"key":"2026090115261996200_msag209-B13","doi-asserted-by":"publisher","DOI":"10.1128\/Spectrum.01803-21","article-title":"Analysis of the ARTIC version 3 and version 4 SARS-CoV-2 primers and their impact on the detection of the G142D amino acid substitution in the spike protein","volume":"9","author":"Davis James","year":"2021","journal-title":"Microbiol Spectr."},{"key":"2026090115261996200_msag209-B14","author":"De Maio"},{"key":"2026090115261996200_msag209-B15","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf077","article-title":"Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time","volume":"53","author":"Dong","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"2026090115261996200_msag209-B16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0334009","article-title":"SARS-CoV-2 sequencing artifacts associated with targeted PCR enrichment and read mapping","volume":"20","author":"Ellegaard","year":"2025","journal-title":"PLoS One"},{"key":"2026090115261996200_msag209-B17","doi-asserted-by":"publisher","author":"Goh","year":"2019","DOI":"10.1101\/716902"},{"key":"2026090115261996200_msag209-B18","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/s13059-018-1618-7","article-title":"An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar","volume":"20","author":"Grubaugh","year":"2019","journal-title":"Genome Biol"},{"key":"2026090115261996200_msag209-B19","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1186\/1471-2164-13-666","article-title":"The effect of strand bias in Illumina short-read sequencing data","volume":"13","author":"Guo","year":"2012","journal-title":"BMC Genomics"},{"key":"2026090115261996200_msag209-B20","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veac052","article-title":"Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat","volume":"8","author":"Hannon","year":"2022","journal-title":"Virus Evol"},{"key":"2026090115261996200_msag209-B21","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1038\/s41592-025-02947-1","article-title":"Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny","volume":"23","author":"Hunt","journal-title":"Nat. Methods"},{"key":"2026090115261996200_msag209-B22","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1146\/annurev-virology-010320-061642","article-title":"Within-host viral diversity: a window into viral evolution","volume":"7","author":"Lauring","year":"2020","journal-title":"Annu Rev Virol."},{"key":"2026090115261996200_msag209-B23","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1038\/s41467-022-28089-y","article-title":"Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant","volume":"13","author":"Li","year":"2022","journal-title":"Nat Commun."},{"key":"2026090115261996200_msag209-B24","doi-asserted-by":"publisher","DOI":"10.1126\/science.abg0821","article-title":"SARS-CoV-2 within-host diversity and transmission","volume":"372","author":"Lythgoe","year":"2021","journal-title":"Science"},{"key":"2026090115261996200_msag209-B25","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2023.1284","article-title":"Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey","volume":"290","author":"Lythgoe","year":"2023","journal-title":"Proc R Soc Lond B Biol Sci."},{"key":"2026090115261996200_msag209-B26","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.abh1803","article-title":"Comment on \u201cGenomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2\u201d","volume":"13","author":"Martin","year":"2021","journal-title":"Sci Transl Med."},{"key":"2026090115261996200_msag209-B27","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.35962","article-title":"Stochastic processes constrain the within and between host evolution of influenza virus","volume":"7","author":"McCrone","year":"2018","journal-title":"eLife"},{"key":"2026090115261996200_msag209-B28","doi-asserted-by":"publisher","first-page":"6884","DOI":"10.1128\/JVI.00667-16","article-title":"Measurements of intrahost viral diversity are extremely sensitive to systematic errors in variant calling","volume":"90","author":"McCrone","year":"2016","journal-title":"J Virol."},{"key":"2026090115261996200_msag209-B29","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1186\/1471-2105-12-451","article-title":"Identification and correction of systematic error in high-throughput sequence data","volume":"12","author":"Meacham","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2026090115261996200_msag209-B30","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqae145","article-title":"Refining SARS-CoV-2 intra-host variation by leveraging large-scale sequencing data","volume":"6","author":"Mostefai","year":"2024","journal-title":"NAR Genom Bioinform."},{"key":"2026090115261996200_msag209-B31","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1186\/s13059-021-02395-y","article-title":"CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance","volume":"22","author":"Nicholls","year":"2021","journal-title":"Genome Biol."},{"key":"2026090115261996200_msag209-B32","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veab064","article-title":"Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool","volume":"7","author":"O\u2019Toole","year":"2021","journal-title":"Virus Evol."},{"key":"2026090115261996200_msag209-B33","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1038\/ng.3479","article-title":"Quantifying influenza virus diversity and transmission in humans","volume":"48","author":"Poon","year":"2016","journal-title":"Nat Genet."},{"key":"2026090115261996200_msag209-B34","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.abe2555","article-title":"Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2","volume":"12","author":"Popa","year":"2020","journal-title":"Sci Transl Med"},{"key":"2026090115261996200_msag209-B35","doi-asserted-by":"publisher","first-page":"e30","DOI":"10.1016\/S2468-2667(20)30282-6","article-title":"Community prevalence of SARS-CoV-2 in England from April to November, 2020: results from the ONS Coronavirus Infection Survey","volume":"6","author":"Pouwels","year":"2021","journal-title":"Lancet Public Health."},{"key":"2026090115261996200_msag209-B36","doi-asserted-by":"publisher","author":"Quick","DOI":"10.17504\/protocols.io.bp2l6n26rgqe\/v3"},{"key":"2026090115261996200_msag209-B37","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.01046-23","article-title":"Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data","volume":"14","author":"Roder","year":"2023","journal-title":"mBio"},{"key":"2026090115261996200_msag209-B38","doi-asserted-by":"publisher","first-page":"6397","DOI":"10.1038\/s41467-023-42211-8","article-title":"Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data","volume":"14","author":"Senghore","year":"2023","journal-title":"Nat Commun."},{"key":"2026090115261996200_msag209-B39","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.00171-17","article-title":"Transmission bottleneck size estimation from pathogen deep-sequencing data, with an application to human influenza A virus","volume":"91","author":"Sobel Leonard","year":"2017","journal-title":"J Virol."},{"key":"2026090115261996200_msag209-B40","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqab019","article-title":"Sequencing error profiles of Illumina sequencing instruments","volume":"3","author":"Stoler","year":"2021","journal-title":"NAR Genom Bioinform."},{"key":"2026090115261996200_msag209-B41","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.66857","article-title":"Patterns of within-host genetic diversity in SARS-CoV-2","volume":"10","author":"Tonkin-Hill","year":"2021","journal-title":"eLife"},{"key":"2026090115261996200_msag209-B42","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1009175","article-title":"Stability of SARS-CoV-2 phylogenies","volume":"16","author":"Turakhia","year":"2020","journal-title":"PLoS Genet."},{"key":"2026090115261996200_msag209-B43","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000991","article-title":"Analysis of the ARTIC V4 and V4.1 SARS-CoV-2 primers and their impact on the detection of Omicron BA.1 and BA.2 lineage-defining mutations","volume":"9","author":"Ulhuq","year":"2023","journal-title":"Microb Genom."},{"key":"2026090115261996200_msag209-B44","doi-asserted-by":"publisher","first-page":"11.10.1","DOI":"10.1002\/0471250953.bi1110s43","article-title":"From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline","volume":"43","author":"Van der Auwera","year":"2013","journal-title":"Curr Protoc Bioinformatics."},{"key":"2026090115261996200_msag209-B45","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofad001","article-title":"Challenges in harnessing shared within-host severe acute respiratory syndrome coronavirus 2 variation for transmission inference","volume":"10","author":"Walter","year":"2023","journal-title":"Open Forum Infect Dis."},{"key":"2026090115261996200_msag209-B46","doi-asserted-by":"publisher","first-page":"11189","DOI":"10.1093\/nar\/gks918","article-title":"Lofreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets","volume":"40","author":"Wilm","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2026090115261996200_msag209-B47","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"2026090115261996200_msag209-B48","doi-asserted-by":"publisher","first-page":"1209","DOI":"10.1093\/aje\/kwx182","article-title":"Shared genomic variants: identification of transmission routes using pathogen deep-sequence data","volume":"186","author":"Worby","year":"2017","journal-title":"Am J Epidemiol."},{"key":"2026090115261996200_msag209-B49","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/vey007","article-title":"Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver","volume":"4","author":"Wymant","year":"2018","journal-title":"Virus Evol"},{"key":"2026090115261996200_msag209-B50","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/vey041","article-title":"Measurements of intrahost viral diversity require an unbiased diversity metric","volume":"5","author":"Zhao","year":"2019","journal-title":"Virus Evol."},{"key":"2026090115261996200_msag209-B51","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","article-title":"A pneumonia outbreak associated with a new coronavirus of probable bat origin","volume":"579","author":"Zhou","year":"2020","journal-title":"Nature"}],"container-title":["Molecular Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/mbe\/advance-article-pdf\/doi\/10.1093\/molbev\/msag209\/70683529\/msag209.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/43\/9\/msag209\/70683529\/msag209.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/43\/9\/msag209\/70683529\/msag209.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T19:26:30Z","timestamp":1788290790000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/mbe\/article\/doi\/10.1093\/molbev\/msag209\/8763642"}},"subtitle":[],"editor":[{"given":"Weiwei","family":"Zhai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,18]]},"references-count":51,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/molbev\/msag209","relation":{},"ISSN":["0737-4038","1537-1719"],"issn-type":[{"value":"0737-4038","type":"print"},{"value":"1537-1719","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,8,18]]},"article-number":"msag209"}}