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HIV-1 molecular transmission clusters in nine European countries and Canada: association with demographic and clinical factors
BACKGROUND: Knowledge of HIV-1 molecular transmission clusters (MTCs) is important, especially in large-scale datasets, for designing prevention programmes and public health intervention strategies. We used a large-scale HIV-1 sequence dataset from nine European HIV cohorts and one Canadian, to iden...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323837/ https://www.ncbi.nlm.nih.gov/pubmed/30616632 http://dx.doi.org/10.1186/s12916-018-1241-1 |
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author | Paraskevis, Dimitrios Beloukas, Apostolos Stasinos, Kostantinos Pantazis, Nikos de Mendoza, Carmen Bannert, Norbert Meyer, Laurence Zangerle, Robert Gill, John Prins, Maria d’Arminio Montforte, Antonella Kran, Anne-Marte Bakken Porter, Kholoud Touloumi, Giota |
author_facet | Paraskevis, Dimitrios Beloukas, Apostolos Stasinos, Kostantinos Pantazis, Nikos de Mendoza, Carmen Bannert, Norbert Meyer, Laurence Zangerle, Robert Gill, John Prins, Maria d’Arminio Montforte, Antonella Kran, Anne-Marte Bakken Porter, Kholoud Touloumi, Giota |
author_sort | Paraskevis, Dimitrios |
collection | PubMed |
description | BACKGROUND: Knowledge of HIV-1 molecular transmission clusters (MTCs) is important, especially in large-scale datasets, for designing prevention programmes and public health intervention strategies. We used a large-scale HIV-1 sequence dataset from nine European HIV cohorts and one Canadian, to identify MTCs and investigate factors associated with the probability of belonging to MTCs. METHODS: To identify MTCs, we applied maximum likelihood inferences on partial pol sequences from 8955 HIV-positive individuals linked to demographic and clinical data. MTCs were defined using two different criteria: clusters with bootstrap support >75% (phylogenetic confidence criterion) and clusters consisting of sequences from a specific region at a proportion of >75% (geographic criterion) compared to the total number of sequences within the network. Multivariable logistic regression analysis was used to assess factors associated with MTC clustering. RESULTS: Although 3700 (41%) sequences belonged to MTCs, proportions differed substantially by country and subtype, ranging from 7% among UK subtype C sequences to 63% among German subtype B sequences. The probability of belonging to an MTC was independently less likely for women than men (OR = 0.66; P < 0.001), older individuals (OR = 0.79 per 10-year increase in age; P < 0.001) and people of non-white ethnicity (OR = 0.44; P < 0.001 and OR = 0.70; P = 0.002 for black and ‘other’ versus white, respectively). It was also more likely among men who have sex with men (MSM) than other risk groups (OR = 0.62; P < 0.001 and OR = 0.69; P = 0.002 for people who inject drugs, and sex between men and women, respectively), subtype B (ORs 0.36–0.70 for A, C, CRF01 and CRF02 versus B; all P < 0.05), having a well-estimated date of seroconversion (OR = 1.44; P < 0.001), a later calendar year of sampling (ORs 2.01–2.61 for all post-2002 periods versus pre-2002; all P < 0.01), and being naïve to antiretroviral therapy at sampling (OR = 1.19; P = 0.010). CONCLUSIONS: A high proportion (>40%) of individuals belonged to MTCs. Notably, the HIV epidemic dispersal appears to be driven by subtype B viruses spread within MSM networks. Expansion of regional epidemics seems mainly associated with recent MTCs, rather than the growth of older, established ones. This information is important for designing prevention and public health intervention strategies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12916-018-1241-1) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6323837 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-63238372019-01-11 HIV-1 molecular transmission clusters in nine European countries and Canada: association with demographic and clinical factors Paraskevis, Dimitrios Beloukas, Apostolos Stasinos, Kostantinos Pantazis, Nikos de Mendoza, Carmen Bannert, Norbert Meyer, Laurence Zangerle, Robert Gill, John Prins, Maria d’Arminio Montforte, Antonella Kran, Anne-Marte Bakken Porter, Kholoud Touloumi, Giota BMC Med Research Article BACKGROUND: Knowledge of HIV-1 molecular transmission clusters (MTCs) is important, especially in large-scale datasets, for designing prevention programmes and public health intervention strategies. We used a large-scale HIV-1 sequence dataset from nine European HIV cohorts and one Canadian, to identify MTCs and investigate factors associated with the probability of belonging to MTCs. METHODS: To identify MTCs, we applied maximum likelihood inferences on partial pol sequences from 8955 HIV-positive individuals linked to demographic and clinical data. MTCs were defined using two different criteria: clusters with bootstrap support >75% (phylogenetic confidence criterion) and clusters consisting of sequences from a specific region at a proportion of >75% (geographic criterion) compared to the total number of sequences within the network. Multivariable logistic regression analysis was used to assess factors associated with MTC clustering. RESULTS: Although 3700 (41%) sequences belonged to MTCs, proportions differed substantially by country and subtype, ranging from 7% among UK subtype C sequences to 63% among German subtype B sequences. The probability of belonging to an MTC was independently less likely for women than men (OR = 0.66; P < 0.001), older individuals (OR = 0.79 per 10-year increase in age; P < 0.001) and people of non-white ethnicity (OR = 0.44; P < 0.001 and OR = 0.70; P = 0.002 for black and ‘other’ versus white, respectively). It was also more likely among men who have sex with men (MSM) than other risk groups (OR = 0.62; P < 0.001 and OR = 0.69; P = 0.002 for people who inject drugs, and sex between men and women, respectively), subtype B (ORs 0.36–0.70 for A, C, CRF01 and CRF02 versus B; all P < 0.05), having a well-estimated date of seroconversion (OR = 1.44; P < 0.001), a later calendar year of sampling (ORs 2.01–2.61 for all post-2002 periods versus pre-2002; all P < 0.01), and being naïve to antiretroviral therapy at sampling (OR = 1.19; P = 0.010). CONCLUSIONS: A high proportion (>40%) of individuals belonged to MTCs. Notably, the HIV epidemic dispersal appears to be driven by subtype B viruses spread within MSM networks. Expansion of regional epidemics seems mainly associated with recent MTCs, rather than the growth of older, established ones. This information is important for designing prevention and public health intervention strategies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12916-018-1241-1) contains supplementary material, which is available to authorized users. BioMed Central 2019-01-08 /pmc/articles/PMC6323837/ /pubmed/30616632 http://dx.doi.org/10.1186/s12916-018-1241-1 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Paraskevis, Dimitrios Beloukas, Apostolos Stasinos, Kostantinos Pantazis, Nikos de Mendoza, Carmen Bannert, Norbert Meyer, Laurence Zangerle, Robert Gill, John Prins, Maria d’Arminio Montforte, Antonella Kran, Anne-Marte Bakken Porter, Kholoud Touloumi, Giota HIV-1 molecular transmission clusters in nine European countries and Canada: association with demographic and clinical factors |
title | HIV-1 molecular transmission clusters in nine European countries and Canada: association with demographic and clinical factors |
title_full | HIV-1 molecular transmission clusters in nine European countries and Canada: association with demographic and clinical factors |
title_fullStr | HIV-1 molecular transmission clusters in nine European countries and Canada: association with demographic and clinical factors |
title_full_unstemmed | HIV-1 molecular transmission clusters in nine European countries and Canada: association with demographic and clinical factors |
title_short | HIV-1 molecular transmission clusters in nine European countries and Canada: association with demographic and clinical factors |
title_sort | hiv-1 molecular transmission clusters in nine european countries and canada: association with demographic and clinical factors |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323837/ https://www.ncbi.nlm.nih.gov/pubmed/30616632 http://dx.doi.org/10.1186/s12916-018-1241-1 |
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