Genotypic Resistance Tests Sequences Reveal the Role of Marginalized Populations in HIV-1 Transmission in Switzerland

• Published in: Scientific reports 2016-06, Vol.6 (1), p.27580-27580, Article 27580
• Main Authors: Shilaih, Mohaned, Marzel, Alex, Yang, Wan Lin, Scherrer, Alexandra U., Schüpbach, Jörg, Böni, Jürg, Yerly, Sabine, Hirsch, Hans H., Aubert, Vincent, Cavassini, Matthias, Klimkait, Thomas, Vernazza, Pietro L., Bernasconi, Enos, Furrer, Hansjakob, Günthard, Huldrych F., Kouyos, Roger
• Format: Article
• Language: English
• Subjects: 692/308/174; 692/699/255/1901; Adult; Anti-HIV Agents - therapeutic use; Cohort analysis; Cohort Studies; Demographics; Drug Resistance, Viral - genetics; Epidemics; Epidemiology; Female; Genotype; Heterosexuality; HIV Infections - drug therapy; HIV Infections - epidemiology; HIV Infections - transmission; HIV Infections - virology; HIV-1 - classification; HIV-1 - genetics; HIV-1 - isolation & purification; Homosexuality, Male; Hospitals; Humanities and Social Sciences; Humans; Immunology; Infectious diseases; Laboratories; Male; Middle Aged; Molecular Typing; multidisciplinary; Multivariate Analysis; Patients; Phylogenetics; Phylogeny; Science; Science (multidisciplinary); Substance Abuse, Intravenous - drug therapy; Substance Abuse, Intravenous - epidemiology; Substance Abuse, Intravenous - virology; Switzerland - epidemiology; Virology
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep27580

Targeting hard-to-reach/marginalized populations is essential for preventing HIV-transmission. A unique opportunity to identify such populations in Switzerland is provided by a database of all genotypic-resistance-tests from Switzerland, including both sequences from the Swiss HIV Cohort Study (SHCS) and non-cohort sequences. A phylogenetic tree was built using 11,127 SHCS and 2,875 Swiss non-SHCS sequences. Demographics were imputed for non-SHCS patients using a phylogenetic proximity approach. Factors associated with non-cohort outbreaks were determined using logistic regression. Non-B subtype (univariable odds-ratio (OR): 1.9; 95% confidence interval (CI): 1.8–2.1), female gender (OR: 1.6; 95% CI: 1.4–1.7), black ethnicity (OR: 1.9; 95% CI: 1.7–2.1) and heterosexual transmission group (OR:1.8; 95% CI: 1.6–2.0), were all associated with underrepresentation in the SHCS. We found 344 purely non-SHCS transmission clusters, however, these outbreaks were small (median 2, maximum 7 patients) with a strong overlap with the SHCS’. 65% of non-SHCS sequences were part of clusters composed of >= 50% SHCS sequences. Our data suggests that marginalized-populations are underrepresented in the SHCS. However, the limited size of outbreaks among non-SHCS patients in-care implies that no major HIV outbreak in Switzerland was missed by the SHCS surveillance. This study demonstrates the potential of sequence data to assess and extend the scope of infectious-disease surveillance.