Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis

The HIV-1 subtype B epidemic amongst men who have sex with men (MSM) is resurgent in many countries despite the widespread use of effective combination antiretroviral therapy (cART). In this combined mathematical and phylogenetic study of observational data, we aimed to find out the extent to which the resurgent epidemic is the result of newly introduced strains or of growth of already circulating strains.

As of November 2011, the ATHENA observational HIV cohort of all patients in care in the Netherlands since 1996 included HIV-1 subtype B polymerase sequences from 5,852 patients. Patients who were diagnosed between 1981 and 1995 were included in the cohort if they were still alive in 1996. The ten most similar sequences to each ATHENA sequence were selected from the Los Alamos HIV Sequence Database, and a phylogenetic tree was created of a total of 8,320 sequences. Large transmission clusters that included ≥10 ATHENA sequences were selected, with a local support value ≥ 0.9 and median pairwise patristic distance below the fifth percentile of distances in the whole tree. Time-varying reproduction numbers of the large MSM-majority clusters were estimated through mathematical modeling. We identified 106 large transmission clusters, including 3,061 (52%) ATHENA and 652 Los Alamos sequences. Half of the HIV sequences from MSM registered in the cohort in the Netherlands (2,128 of 4,288) were included in 91 large MSM-majority clusters. Strikingly, at least 54 (59%) of these 91 MSM-majority clusters were already circulating before 1996, when cART was introduced, and have persisted to the present. 

Overall, 1,226 (35%) of the 3,460 diagnoses among MSM since 1996 were found in these 54 long-standing clusters. The reproduction numbers of all large MSM-majority clusters were around the epidemic threshold value of one over the whole study period. A tendency towards higher numbers was visible in recent years, especially in the more recently introduced clusters. The mean age of MSM at diagnosis increased by 0.45 years/year within clusters, but new clusters appeared with lower mean age. 

Major strengths of this study are the high proportion of HIV-positive MSM with a sequence in this study and the combined application of phylogenetic and modeling approaches. Main limitations are the assumption that the sampled population is representative of the overall HIV-positive population and the assumption that the diagnosis interval distribution is similar between clusters.

The resurgent HIV epidemic amongst MSM in the Netherlands is driven by several large, persistent, self-sustaining, and, in many cases, growing sub-epidemics shifting towards new generations of MSM. Many of the sub-epidemics have been present since the early epidemic, to which new sub-epidemics are being added.

Below:  Proportional contribution of new HIV-1 diagnoses amongst all MSM in the ATHENA cohort by decade of birth

Below:  Diagnosis and growth of transmission clusters over time.

Cluster types within the phylogenetic tree are defined as follows. Singletons (in blue) are clusters of size 1, or cases whose sequence solely clustered with sequences from the Los Alamos HIV Sequence Database. Small clusters (in green) comprise sequences from 2–9 ATHENA patients. Large clusters comprise sequences from ten or more patients in the ATHENA cohort. Amongst those, non-MSM-dominant clusters (in brown) contain a majority of sequences from non-MSM patients, whilst MSM-majority clusters contain a majority of sequences from MSM patients. Among large MSM-majority clusters, pre-1996 clusters (in dark orange) are defined as those in which the first diagnosed patient in the cluster was diagnosed before 1996, and post-1996 clusters are defined as those in which all patients in the cluster were diagnosed in or after 1996. Large MSM-majority post-1996 clusters are stratified as “time of MRCA pre-1996” (in light orange) when the estimated time of the MRCA is before 1996, and “time of MRCA post-1996” (in purple) when the estimated time of the MRCA is in or after 1996. (A) Number of MSM registered in the ATHENA cohort in the Netherlands with a sequence in this study by year of diagnosis and by cluster type. (B) Number of clusters of each type by year of first diagnosed case in each cluster.

Full article at: http://goo.gl/b6NYFQ

By:

Daniela Bezemer, Ard van Sighem, Luuk Gras, Rob van den Hengel, Peter Reiss

HIV Monitoring Foundation, Amsterdam, the Netherlands

Anne Cori, Oliver Ratmann, Frank de Wolf, Christophe Fraser

Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom

Hillegonda S. Hermanides, Ashley J. Duits

Red Cross Blood Bank Foundation, Willemstad, Curaçao

Bas E. Dutilh

Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands

Bas E. Dutilh

Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil

Bas E. Dutilh

Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands

Nuno Rodrigues Faria

Department of Zoology, University of Oxford, Oxford, United Kingdom

Peter Reiss

Department of Global Health, Academic Medical Center, Amsterdam, the Netherlands

Peter Reiss

Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands

  

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