{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,27]],"date-time":"2025-02-27T05:31:09Z","timestamp":1740634269522,"version":"3.38.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: G \u2192 A hypermutation is an innate antiviral defense mechanism, mediated by host enzymes, which leads to the mutational impairment of viruses. Sensitive and specific identification of host-mediated G \u2192 A hypermutation is a novel sequence analysis challenge, particularly for viral deep sequencing studies. For example, two of the most common hepatitis B virus (HBV) reverse transcriptase (RT) drug-resistance mutations, A181T and M204I, arise from G \u2192 A changes and are routinely detected as low-abundance variants in nearly all HBV deep sequencing samples.<\/jats:p><jats:p>Results: We developed a classification model using measures of G \u2192 A excess and predicted indicators of lethal mutation and applied this model to 325 920 unique deep sequencing reads from plasma virus samples from 45 drug treatment-na\u00efve HBV-infected individuals. The 2.9% of sequence reads that were classified as hypermutated by our model included most of the reads with A181T and\/or M204I, indicating the usefulness of this model for distinguishing viral adaptive changes from host-mediated viral editing.<\/jats:p><jats:p>Availability: Source code and sequence data are available at http:\/\/hivdb.stanford.edu\/pages\/resources.html.<\/jats:p><jats:p>Contact: \u00a0ereuman@stanfordalumni.org<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq570","type":"journal-article","created":{"date-parts":[[2010,10,19]],"date-time":"2010-10-19T04:15:50Z","timestamp":1287461750000},"page":"2929-2932","source":"Crossref","is-referenced-by-count":13,"title":["A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads"],"prefix":"10.1093","volume":"26","author":[{"given":"Elizabeth C.","family":"Reuman","sequence":"first","affiliation":[{"name":"1 Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, 2Gilead Sciences, Foster City, CA 94404 and 3Department of Statistics, Stanford University, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Severine","family":"Margeridon-Thermet","sequence":"additional","affiliation":[{"name":"1 Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, 2Gilead Sciences, Foster City, CA 94404 and 3Department of Statistics, Stanford University, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Harrison B.","family":"Caudill","sequence":"additional","affiliation":[{"name":"1 Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, 2Gilead Sciences, Foster City, CA 94404 and 3Department of Statistics, Stanford University, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tommy","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, 2Gilead Sciences, Foster City, CA 94404 and 3Department of Statistics, Stanford University, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katyna","family":"Borroto-Esoda","sequence":"additional","affiliation":[{"name":"1 Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, 2Gilead Sciences, Foster City, CA 94404 and 3Department of Statistics, Stanford University, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Evguenia S.","family":"Svarovskaia","sequence":"additional","affiliation":[{"name":"1 Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, 2Gilead Sciences, Foster City, CA 94404 and 3Department of Statistics, Stanford University, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Susan P.","family":"Holmes","sequence":"additional","affiliation":[{"name":"1 Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, 2Gilead Sciences, Foster City, CA 94404 and 3Department of Statistics, Stanford University, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert W.","family":"Shafer","sequence":"additional","affiliation":[{"name":"1 Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, 2Gilead Sciences, Foster City, CA 94404 and 3Department of Statistics, Stanford University, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,10,11]]},"reference":[{"key":"2023012507514029800_B1","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1128\/JVI.80.3.1067-1076.2006","article-title":"Role and mechanism of action of the APOBEC3 family of antiretroviral resistance factors","volume":"80","author":"Cullen","year":"2006","journal-title":"J. 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