{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T05:20:44Z","timestamp":1773465644004,"version":"3.50.1"},"reference-count":41,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2020,10,31]],"date-time":"2020-10-31T00:00:00Z","timestamp":1604102400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["BSSGI0_155851"],"award-info":[{"award-number":["BSSGI0_155851"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["179571"],"award-info":[{"award-number":["179571"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["148522"],"award-info":[{"award-number":["148522"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["324730_179567"],"award-info":[{"award-number":["324730_179567"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["324730_146143"],"award-info":[{"award-number":["324730_146143"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>HIV-1 genetic diversity can be used to infer time since infection (TSI) and infection recency. We adapted this approach for HCV and identified genomic regions with informative diversity. We included 72 HCV\/HIV-1 coinfected participants of the Swiss HIV Cohort Study, for whom reliable estimates of infection date and viral sequences were available. Average pairwise diversity (APD) was calculated over each codon position for the entire open reading frame of HCV. Utilizing cross validation, we evaluated the correlation of APD with TSI, and its ability to infer TSI via a linear model. We additionally studied the ability of diversity to classify infections as recent (infected for &lt;1 year) or chronic, using receiver-operator-characteristic area under the curve (ROC-AUC) in 50 patients whose infection could be unambiguously classified as either recent or chronic. Measuring HCV diversity over third or all codon positions gave similar performances, and notable improvement over first or second codon positions. APD calculated over the entire genome enabled classification of infection recency (ROC-AUC = 0.76). Additionally, APD correlated with TSI (R2 = 0.33) and could predict TSI (mean absolute error = 1.67 years). Restricting the region over which APD was calculated to E2-NS2 further improved accuracy (ROC-AUC = 0.85, R2 = 0.54, mean absolute error = 1.38 years). Genetic diversity in HCV correlates with TSI and is a proxy for infection recency and TSI, even several years post-infection.<\/jats:p>","DOI":"10.3390\/v12111241","type":"journal-article","created":{"date-parts":[[2020,10,31]],"date-time":"2020-10-31T21:39:56Z","timestamp":1604180396000},"page":"1241","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["HCV Genetic Diversity Can Be Used to Infer Infection Recency and Time since Infection"],"prefix":"10.3390","volume":"12","author":[{"given":"Louisa A.","family":"Carlisle","sequence":"first","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, CH-8091 Zurich, Switzerland"},{"name":"Institute of Medical Virology, University of Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Teja","family":"Turk","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, CH-8091 Zurich, Switzerland"},{"name":"Institute of Medical Virology, University of Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4862-1503","authenticated-orcid":false,"given":"Karin J.","family":"Metzner","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, CH-8091 Zurich, Switzerland"},{"name":"Institute of Medical Virology, University of Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Herbert A.","family":"Mbunkah","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, CH-8091 Zurich, Switzerland"},{"name":"Institute of Medical Virology, University of Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cyril","family":"Shah","sequence":"additional","affiliation":[{"name":"Institute of Medical Virology, University of Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7925-4852","authenticated-orcid":false,"given":"J\u00fcrg","family":"B\u00f6ni","sequence":"additional","affiliation":[{"name":"Institute of Medical Virology, University of Zurich, CH-8057 Zurich, Switzerland"},{"name":"Swiss National Reference Center for Retroviruses, University of Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0384-0000","authenticated-orcid":false,"given":"Michael","family":"Huber","sequence":"additional","affiliation":[{"name":"Institute of Medical Virology, University of Zurich, CH-8057 Zurich, Switzerland"},{"name":"Swiss National Reference Center for Retroviruses, University of Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dominique L.","family":"Braun","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, CH-8091 Zurich, Switzerland"},{"name":"Institute of Medical Virology, University of Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jan","family":"Fehr","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, CH-8091 Zurich, Switzerland"},{"name":"Department of Public Health, Epidemiology Biostatistics and Prevention Institute, University of Zurich, CH-8001 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luisa","family":"Salazar-Vizcaya","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Bern University Hospital, University of Bern, CH-3010 Bern, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5297-6062","authenticated-orcid":false,"given":"Andri","family":"Rauch","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Bern University Hospital, University of Bern, CH-3010 Bern, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabine","family":"Yerly","sequence":"additional","affiliation":[{"name":"Laboratory of Virology, Division of Infectious Diseases, Geneva University Hospital, University of Geneva, CH-1205 Geneva, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aude","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Laboratory of Virology, Division of Infectious Diseases, Geneva University Hospital, University of Geneva, CH-1205 Geneva, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthias","family":"Cavassini","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Lausanne University Hospital, CH-1011 Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcel","family":"Stoeckle","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, CH-4031 Basel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pietro","family":"Vernazza","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Cantonal Hospital St Gallen, CH-9007 St. Gallen, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9724-8373","authenticated-orcid":false,"given":"Enos","family":"Bernasconi","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Regional Hospital Lugano, CH-6900 Lugano, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1142-6723","authenticated-orcid":false,"given":"Huldrych F.","family":"G\u00fcnthard","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, CH-8091 Zurich, Switzerland"},{"name":"Institute of Medical Virology, University of Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roger D.","family":"Kouyos","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, CH-8091 Zurich, Switzerland"},{"name":"Institute of Medical Virology, University of Zurich, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,10,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1111\/jvh.12249","article-title":"Strategies to manage hepatitis C virus (HCV) disease burden","volume":"21","author":"Wedemeyer","year":"2014","journal-title":"J. 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