Genotypic Resistance Tests Sequences Reveal the Role of Marginalized Populations in HIV-1 Transmission in Switzerland.
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.
Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.|Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
Mohaned
M
Shilaih
Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.|Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
Alex
A
Marzel
Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.
Wan Lin
WL
Yang
Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.|Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
Alexandra U
AU
Scherrer
Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
Jörg
J
Schüpbach
Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
Jürg
J
Böni
Laboratory of Virology, Geneva University Hospital, Geneva, Switzerland.
Sabine
S
Yerly
Department of Biomedicine-Petersplatz, University of Basel, Basel, Switzerland.
Hans H
HH
Hirsch
Division of Immunology and Allergy, University Hospital Lausanne, Lausanne, Switzerland.
Vincent
V
Aubert
Division of Immunology, University Hospital Lausanne, Lausanne, Switzerland.
Matthias
M
Cavassini
Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.
Thomas
T
Klimkait
Division of Infectious Diseases, Cantonal Hospital St. Gallen, St. Gallen, Switzerland.
Pietro L
PL
Vernazza
Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland.
Enos
E
Bernasconi
Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland.
Hansjakob
H
Furrer
Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.|Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
Huldrych F
HF
Günthard
Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.|Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
Roger
R
Kouyos
D000328:Adult; D019380:Anti-HIV Agents / Q000627:therapeutic use; D015331:Cohort Studies; D024882:Drug Resistance, Viral / Q000235:genetics*; D005260:Female; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy / Q000453:epidemiology* / Q000635:transmission / Q000821:virology; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D020010:Heterosexuality; D018451:Homosexuality, Male; D006801:Humans; D008297:Male; D008875:Middle Aged; D058889:Molecular Typing; D015999:Multivariate Analysis; D010802:Phylogeny; D015819:Substance Abuse, Intravenous / Q000188:drug therapy / Q000453:epidemiology* / Q000821:virology; D013557:Switzerland / Q000453:epidemiology
D019380:Anti-HIV Agents