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A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland

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-pro...

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Autores principales: Ragonnet-Cronin, Manon L., Shilaih, Mohaned, Günthard, Huldrych F., Hodcroft, Emma B., Böni, Jürg, Fearnhill, Esther, Dunn, David, Yerly, Sabine, Klimkait, Thomas, Aubert, Vincent, Yang, Wan-Lin, Brown, Alison E., Lycett, Samantha J., Kouyos, Roger, Brown, Andrew J. Leigh
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5027562/
https://www.ncbi.nlm.nih.gov/pubmed/27642070
http://dx.doi.org/10.1038/srep32251
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author Ragonnet-Cronin, Manon L.
Shilaih, Mohaned
Günthard, Huldrych F.
Hodcroft, Emma B.
Böni, Jürg
Fearnhill, Esther
Dunn, David
Yerly, Sabine
Klimkait, Thomas
Aubert, Vincent
Yang, Wan-Lin
Brown, Alison E.
Lycett, Samantha J.
Kouyos, Roger
Brown, Andrew J. Leigh
author_facet Ragonnet-Cronin, Manon L.
Shilaih, Mohaned
Günthard, Huldrych F.
Hodcroft, Emma B.
Böni, Jürg
Fearnhill, Esther
Dunn, David
Yerly, Sabine
Klimkait, Thomas
Aubert, Vincent
Yang, Wan-Lin
Brown, Alison E.
Lycett, Samantha J.
Kouyos, Roger
Brown, Andrew J. Leigh
author_sort Ragonnet-Cronin, Manon L.
collection PubMed
description 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.
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spelling pubmed-50275622016-09-22 A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland Ragonnet-Cronin, Manon L. Shilaih, Mohaned Günthard, Huldrych F. Hodcroft, Emma B. Böni, Jürg Fearnhill, Esther Dunn, David Yerly, Sabine Klimkait, Thomas Aubert, Vincent Yang, Wan-Lin Brown, Alison E. Lycett, Samantha J. Kouyos, Roger Brown, Andrew J. Leigh Sci Rep Article 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. Nature Publishing Group 2016-09-19 /pmc/articles/PMC5027562/ /pubmed/27642070 http://dx.doi.org/10.1038/srep32251 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Ragonnet-Cronin, Manon L.
Shilaih, Mohaned
Günthard, Huldrych F.
Hodcroft, Emma B.
Böni, Jürg
Fearnhill, Esther
Dunn, David
Yerly, Sabine
Klimkait, Thomas
Aubert, Vincent
Yang, Wan-Lin
Brown, Alison E.
Lycett, Samantha J.
Kouyos, Roger
Brown, Andrew J. Leigh
A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland
title A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland
title_full A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland
title_fullStr A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland
title_full_unstemmed A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland
title_short A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland
title_sort direct comparison of two densely sampled hiv epidemics: the uk and switzerland
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5027562/
https://www.ncbi.nlm.nih.gov/pubmed/27642070
http://dx.doi.org/10.1038/srep32251
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