title: A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland.
abstract: Phylogenetic clustering approaches can elucidate HIV transmission dynamics. Comparisons across countries are essential for evaluating public health policies. Here, we used a standardised approach to compare the UK HIV Drug Resistance Database and the Swiss HIV Cohort Study while maintaining data-protection requirements. Clusters were identified in subtype A1, B and C pol phylogenies. We generated degree distributions for each risk group and compared distributions between countries using Kolmogorov-Smirnov (KS) tests, Degree Distribution Quantification and Comparison (DDQC) and bootstrapping. We used logistic regression to predict cluster membership based on country, sampling date, risk group, ethnicity and sex. We analysed >8,000 Swiss and >30,000 UK subtype B sequences. At 4.5% genetic distance, the UK was more clustered and MSM and heterosexual degree distributions differed significantly by the KS test. The KS test is sensitive to variation in network scale, and jackknifing the UK MSM dataset to the size of the Swiss dataset removed the difference. Only heterosexuals varied based on the DDQC, due to UK male heterosexuals who clustered exclusively with MSM. Their removal eliminated this difference. In conclusion, the UK and Swiss HIV epidemics have similar underlying dynamics and observed differences in clustering are mainly due to different population sizes.
authors.affiliation: University of Edinburgh, Edinburgh, UK.
authors.forename: Manon L
authors.initials: ML
authors.lastname: Ragonnet-Cronin
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.|Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
authors.forename: Mohaned
authors.initials: M
authors.lastname: Shilaih
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.|Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
authors.forename: Huldrych F
authors.initials: HF
authors.lastname: Günthard
authors.affiliation: University of Edinburgh, Edinburgh, UK.
authors.forename: Emma B
authors.initials: EB
authors.lastname: Hodcroft
authors.affiliation: Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
authors.forename: Jürg
authors.initials: J
authors.lastname: Böni
authors.affiliation: MRC Clinical Trials Unit, London, UK.
authors.forename: Esther
authors.initials: E
authors.lastname: Fearnhill
authors.affiliation: MRC Clinical Trials Unit, London, UK.
authors.forename: David
authors.initials: D
authors.lastname: Dunn
authors.affiliation: Laboratory of Virology and AIDS Center, Geneva University Hospital, Geneva, Switzerland.
authors.forename: Sabine
authors.initials: S
authors.lastname: Yerly
authors.affiliation: Department Biomedicine-Petersplatz, University of Basel, Basel, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Klimkait
authors.affiliation: Division of Immunology and Allergy, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland.
authors.forename: Vincent
authors.initials: V
authors.lastname: Aubert
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
authors.forename: Wan-Lin
authors.initials: WL
authors.lastname: Yang
authors.affiliation: Public Health England, London, UK.
authors.forename: Alison E
authors.initials: AE
authors.lastname: Brown
authors.affiliation: University of Edinburgh, Edinburgh, UK.
authors.forename: Samantha J
authors.initials: SJ
authors.lastname: Lycett
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.|Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
authors.forename: Roger
authors.initials: R
authors.lastname: Kouyos
authors.affiliation: University of Edinburgh, Edinburgh, UK.
authors.forename: Andrew J Leigh
authors.initials: AJ
authors.lastname: Brown
mesh_terms: D016000:Cluster Analysis; D058872:Epidemics; D005260:Female; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D020010:Heterosexuality / Q000706:statistics & numerical data; D018451:Homosexuality, Male / Q000706:statistics & numerical data; D006801:Humans; D016015:Logistic Models; D008297:Male; D010802:Phylogeny; D012307:Risk Factors; D013557:Switzerland / Q000453:epidemiology; D006113:United Kingdom / Q000453:epidemiology; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000145:classification / Q000235:genetics
chemical_list: D054302:pol Gene Products, Human Immunodeficiency Virus