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

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

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Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis
Creator	Ratmann, Oliver Fraser, Christophe Bezemer, Daniela Gras, Luuk Reiss, Peter Rodrigues Faria, Nuno Dutilh, Bas De Wolf, Frank Duits, Ashley Hermanides, Hillegonda Van Den Hengel, Rob Van Sighem, Ard
Source	PMC
abstract	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.
has issue date	2015-11-03(xsd:dateTime)
bibo:doi	10.1371/journal.pmed.1001898
bibo:pmid	26529093
has license	cc-by
sha1sum (hex)	51a7b35db673f0d7cb14a80b607192e3f44cc7f5
schema:url	https://doi.org/10.1371/journal.pmed.1001898
resource representing a document's title	Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis
has PubMed Central identifier	PMC4631366
has PubMed identifier	26529093
schema:publication	PLoS Med
resource representing a document's body	covid:51a7b35db673f0d7cb14a80b607192e3f44cc7f5#body_text
is schema:about of	named entity 'MSM' named entity 'observational' covid:arg/51a7b35db673f0d7cb14a80b607192e3f44cc7f5 named entity 'extent' named entity 'strains' named entity 'introduced' named entity 'combination' named entity 'sex' named entity 'MSM' named entity 'epidemic' named entity 'HIV-1' named entity 'highest posterior density' named entity 'MSM' named entity 'heterosexually' named entity 'MSM' named entity 'Amsterdam' named entity 'sensitivity analysis' named entity 'HIV-1' named entity 'Netherlands' named entity 'gene' named entity 'rates of infection' named entity 'infection' named entity 'polymerase' named entity 'HIV' named entity 'probability' named entity 'time series' named entity 'reproduction number' named entity 'HIV-1' named entity 'Anonymized data' named entity 'reproduction number' named entity 'plasma' named entity 'HIV' named entity 'phylogenetic analysis' named entity 'scientific research' named entity 'index case' named entity '0.45' named entity 'MSM' named entity 'polymerase' named entity 'HIV epidemic' named entity 'MRCA' named entity 'bisexual' named entity 'interquartile range' named entity 'HIV-positive' named entity 'epidemic' named entity 'HIV-positive' named entity 'HIV-1' named entity 'MSM' named entity 'systematic bias' named entity 'MSM' named entity 'epidemic' named entity 'MSM' named entity 'HIV-1' named entity 'MSM' named entity 'infection' named entity 'amino acid' named entity 'combination antiretroviral therapy' named entity 'MSM' named entity 'Netherlands' named entity 'cART' named entity 'AIDS' named entity 'Netherlands' named entity 'multinomial distribution' named entity 'epidemic' named entity 'MSM' named entity 'Dutch' named entity 'reproduction number' named entity 'epidemic' named entity 'reproduction number' named entity 'cART' named entity 'HIV transmission'

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