{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T02:53:38Z","timestamp":1783133618856,"version":"3.54.6"},"reference-count":9,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2025,2,11]],"date-time":"2025-02-11T00:00:00Z","timestamp":1739232000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003130","name":"Fonds Wetenschappelijk Onderzoek","doi-asserted-by":"publisher","award":["18B2821N"],"award-info":[{"award-number":["18B2821N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>The ability to detect microbial reads from sequencing data has significantly advanced microbiome and infectious disease research. Recently, INVADEseq introduced a technique to extract microbial reads from single-cell RNA sequencing (scRNA-seq) data following 16S rRNA amplification. We hypothesized that this approach could be leveraged to detect viruses in eukaryotic cells without such amplification or prior knowledge, provided they produce viral mRNAs containing poly-A tails. To test this, we aimed to detect Hepatitis B Virus (HBV) reads from liver samples of patients with chronic HBV infection, both with and without HBsAg loss. We successfully detected HBV reads in the liver of viraemic patients, predominantly in hepatocytes and, to a lesser extent, in Kupffer cells. Functionally cured HBV patients with HBsAg loss had undetectable HBV mRNA in the liver. This study demonstrates the ability to extract and identify viral reads from scRNA-seq data without prior knowledge and without specific amplification. This approach can be used for screening scRNA-seq data for the presence of viral reads at single-cell resolution, potentially enhancing our understanding of the cellular distribution of viruses and virus-host interactions.<\/jats:p>","DOI":"10.1371\/journal.pone.0314060","type":"journal-article","created":{"date-parts":[[2025,2,11]],"date-time":"2025-02-11T18:30:37Z","timestamp":1739298637000},"page":"e0314060","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Detection of hepatitis B virus mRNA from single cell RNA sequencing data without prior knowledge"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3053-8835","authenticated-orcid":true,"given":"Nicolaas","family":"Van Renne","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Vanwolleghem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,2,11]]},"reference":[{"key":"pone.0314060.ref001","doi-asserted-by":"crossref","first-page":"209","DOI":"10.3322\/caac.21660","article-title":"Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries.","volume":"71","author":"H Sung","year":"2021","journal-title":"CA Cancer J Clin."},{"key":"pone.0314060.ref002","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1038\/s41586-022-05435-0","article-title":"Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer","volume":"611","author":"JL Galeano Ni\u00f1o","year":"2022","journal-title":"Nature"},{"key":"pone.0314060.ref003","doi-asserted-by":"crossref","first-page":"3355","DOI":"10.1038\/s41596-023-00888-7","article-title":"INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution.","volume":"18","author":"JL Galeano Ni\u00f1o","year":"2023","journal-title":"Nat Protoc."},{"key":"pone.0314060.ref004","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1038\/nbt.1868","article-title":"PathSeq: software to identify or discover microbes by deep sequencing of human tissue","volume":"29","author":"AD Kostic","year":"2011","journal-title":"Nat Biotechnol"},{"key":"pone.0314060.ref005","doi-asserted-by":"crossref","first-page":"4287","DOI":"10.1093\/bioinformatics\/bty501","article-title":"GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts","volume":"34","author":"MA Walker","year":"2018","journal-title":"Bioinformatics"},{"key":"pone.0314060.ref006","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.jhep.2024.02.017","article-title":"Single-cell landscape of functionally cured chronic hepatitis B patients reveals activation of innate and altered CD4-CTL-driven adaptive immunity","volume":"81","author":"BC Narmada","year":"2024","journal-title":"J Hepatol"},{"key":"pone.0314060.ref007","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Y Hao","year":"2021","journal-title":"Cell"},{"key":"pone.0314060.ref008","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony.","volume":"16","author":"I Korsunsky","year":"2019","journal-title":"Nat Methods"},{"key":"pone.0314060.ref009","doi-asserted-by":"crossref","first-page":"4383","DOI":"10.1038\/s41467-018-06318-7","article-title":"Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations","volume":"9","author":"SA MacParland","year":"2018","journal-title":"Nat Commun"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0314060","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,11]],"date-time":"2025-02-11T18:30:42Z","timestamp":1739298642000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0314060"}},"subtitle":[],"editor":[{"given":"Youkyung H.","family":"Choi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,2,11]]},"references-count":9,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2025,2,11]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0314060","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,11]]}}}