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

BACKGROUND: 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. METHODS AND FINDINGS: 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. CONCLUSIONS: 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.

The influence of between-farm distance and farm size on the spread of classical swine fever during the 1997-1998 epidemic in The Netherlands.

As the size of livestock farms in The Netherlands is on the increase for economic reasons, an important question is how disease introduction risks and risks of onward transmission scale with farm size (i.e. with the number of animals on the farm). Here we use the epidemic data of the 1997-1998 epidemic of Classical Swine Fever (CSF) Virus in The Netherlands to address this question for CSF risks. This dataset is one of the most powerful ones statistically as in this epidemic a total of 428 pig farms where infected, with the majority of farm sizes ranging between 27 and 1750 pigs, including piglets. We have extended the earlier models for the transmission risk as a function of between-farm distance, by adding two factors. These factors describe the effect of farm size on the susceptibility of a 'receiving' farm and on the infectivity of a 'sending' farm (or 'source' farm), respectively. Using the best-fitting model, we show that the size of a farm has a significant influence on both farm-level susceptibility and infectivity for CSF. Although larger farms are both more susceptible to CSF and, when infected, more infectious to other farms than smaller farms, the increase is less than linear. The higher the farm size, the smaller the effect of increments of farm size on the susceptibility and infectivity of a farm. Because of changes in the Dutch pig farming characteristics, a straightforward extrapolation of the observed farm size dependencies from 1997/1998 to present times would not be justified. However, based on our results one may expect that also for the current pig farming characteristics in The Netherlands, farm susceptibility and infectivity depend non-linearly on farm size, with some saturation effect for relatively large farm sizes.