{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T12:41:28Z","timestamp":1773924088480,"version":"3.50.1"},"reference-count":52,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2019,11,26]],"date-time":"2019-11-26T00:00:00Z","timestamp":1574726400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006282","name":"Koning Boudewijnstichting","doi-asserted-by":"publisher","award":["2013-J1820640-201099"],"award-info":[{"award-number":["2013-J1820640-201099"]}],"id":[{"id":"10.13039\/501100006282","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>HIV-1 pol sequences obtained through baseline drug resistance testing of patients newly diagnosed between 2013 and 2017 were analyzed for genetic similarity. For 927 patients the information on genetic similarity was combined with demographic data and with information on the recency of infection. Overall, 48.3% of the patients were genetically linked with 11.4% belonging to a pair and 36.9% involved in a cluster of \u22653 members. The percentage of early diagnosed (\u22644 months after infection) was 28.6%. Patients of Belgian origin were more frequently involved in transmission clusters (49.7% compared to 15.3%) and diagnosed earlier (37.4% compared to 12.2%) than patients of Sub-Saharan African origin. Of the infections reported to be locally acquired, 69.5% were linked (14.1% paired and 55.4% in a cluster). Equal parts of early and late diagnosed individuals (59.9% and 52.4%, respectively) were involved in clusters. The identification of a genetically linked individual for the majority of locally infected patients suggests a high rate of diagnosis in this population. Diagnosis however is often delayed for &gt;4 months after infection increasing the opportunities for onward transmission. Prevention of local infection should focus on earlier diagnosis and protection of the still uninfected members of sexual networks with human immunodeficiency virus (HIV)-infected members.<\/jats:p>","DOI":"10.3390\/v11121096","type":"journal-article","created":{"date-parts":[[2019,11,26]],"date-time":"2019-11-26T10:57:27Z","timestamp":1574765847000},"page":"1096","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Exploring HIV-1 Transmission Dynamics by Combining Phylogenetic Analysis and Infection Timing"],"prefix":"10.3390","volume":"11","author":[{"given":"Chris","family":"Verhofstede","sequence":"first","affiliation":[{"name":"Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Virginie","family":"Mortier","sequence":"additional","affiliation":[{"name":"Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kenny","family":"Dauwe","sequence":"additional","affiliation":[{"name":"Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7245-527X","authenticated-orcid":false,"given":"Steven","family":"Callens","sequence":"additional","affiliation":[{"name":"Aids Reference Center, Department of Internal Medicine, Ghent University Hospital, 9000 Ghent, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessika","family":"Deblonde","sequence":"additional","affiliation":[{"name":"Epidemiology of Infectious Diseases Unit, Scientific Institute of Public Health Sciensano, 1050 Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"G\u00e9raldine","family":"Dessilly","sequence":"additional","affiliation":[{"name":"Aids Reference Laboratory, Medical Microbiology Unit, Universit\u00e9 Catholique de Louvain, 1200 Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marie-Luce","family":"Delforge","sequence":"additional","affiliation":[{"name":"Aids Reference Laboratory, Universit\u00e9 Libre de Bruxelles, 1050 Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katrien","family":"Fransen","sequence":"additional","affiliation":[{"name":"HIV\/STD Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andr\u00e9","family":"Sasse","sequence":"additional","affiliation":[{"name":"Epidemiology of Infectious Diseases Unit, Scientific Institute of Public Health Sciensano, 1050 Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karolien","family":"Stoffels","sequence":"additional","affiliation":[{"name":"Aids Reference Laboratory, Centre Hospitalier Universitaire St. Pierre, 1000 Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dominique","family":"Van Beckhoven","sequence":"additional","affiliation":[{"name":"Epidemiology of Infectious Diseases Unit, Scientific Institute of Public Health Sciensano, 1050 Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fien","family":"Vanroye","sequence":"additional","affiliation":[{"name":"HIV\/STD Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dolores","family":"Vaira","sequence":"additional","affiliation":[{"name":"Aids Reference Laboratory, Centre Hospitalier Universitaire de Li\u00e8ge, 4000 Li\u00e8ge, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ellen","family":"Vancutsem","sequence":"additional","affiliation":[{"name":"Aids Reference Laboratory, Vrije Universiteit Brussel VUB, 1090 Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kristel","family":"Van Laethem","sequence":"additional","affiliation":[{"name":"Aids Reference Laboratory, University Hospital Leuven, 3000 Leuven, Belgium"},{"name":"Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2019,11,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Van Beckhoven, D., Florence, E., Ruelle, J., Deblonde, J., Verhofstede, C., Callens, S., Vancutsem, E., Lacor, P., Demeester, R., and Goffard, J.C. 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