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Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database
The study of HIV-1 transmission networks inferred from viral genetic data can be used to clarify important factors about the dynamics of HIV-1 transmission, such as network growth rate and demographic composition. In Brazil, HIV transmission has been stable since the early 2000s and the study of tra...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9783618/ https://www.ncbi.nlm.nih.gov/pubmed/36560771 http://dx.doi.org/10.3390/v14122768 |
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author | Andrade, Paula Arantes, Ighor Tanuri, Amilcar Bello, Gonzalo Gräf, Tiago |
author_facet | Andrade, Paula Arantes, Ighor Tanuri, Amilcar Bello, Gonzalo Gräf, Tiago |
author_sort | Andrade, Paula |
collection | PubMed |
description | The study of HIV-1 transmission networks inferred from viral genetic data can be used to clarify important factors about the dynamics of HIV-1 transmission, such as network growth rate and demographic composition. In Brazil, HIV transmission has been stable since the early 2000s and the study of transmission clusters can provide valuable data to understand the drivers of virus spread. In this work, we analyzed a nation-wide database of approximately 53,000 HIV-1 nucleotide pol sequences sampled from genotyped patients from 2008–2017. Phylogenetic trees were reconstructed for the HIV-1 subtypes B, C and F1 in Brazil and transmission clusters were inferred by applying genetic distances thresholds of 1.5%, 3.0% and 4.5%, as well as high (>0.9) cluster statistical support. An odds ratio test revealed that young men (15–24 years) and individuals with more years of education presented higher odds to cluster. The assortativity coefficient revealed that individuals with similar demographic features tended to cluster together, with emphasis on features, such as place of residence and age. We also observed that assortativity weakens as the genetic distance threshold increases. Our results indicate that the phylogenetic clusters identified here are likely representative of the contact networks that shape HIV transmission, and this is a valuable tool even in sites with low sampling density, such as Brazil. |
format | Online Article Text |
id | pubmed-9783618 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-97836182022-12-24 Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database Andrade, Paula Arantes, Ighor Tanuri, Amilcar Bello, Gonzalo Gräf, Tiago Viruses Article The study of HIV-1 transmission networks inferred from viral genetic data can be used to clarify important factors about the dynamics of HIV-1 transmission, such as network growth rate and demographic composition. In Brazil, HIV transmission has been stable since the early 2000s and the study of transmission clusters can provide valuable data to understand the drivers of virus spread. In this work, we analyzed a nation-wide database of approximately 53,000 HIV-1 nucleotide pol sequences sampled from genotyped patients from 2008–2017. Phylogenetic trees were reconstructed for the HIV-1 subtypes B, C and F1 in Brazil and transmission clusters were inferred by applying genetic distances thresholds of 1.5%, 3.0% and 4.5%, as well as high (>0.9) cluster statistical support. An odds ratio test revealed that young men (15–24 years) and individuals with more years of education presented higher odds to cluster. The assortativity coefficient revealed that individuals with similar demographic features tended to cluster together, with emphasis on features, such as place of residence and age. We also observed that assortativity weakens as the genetic distance threshold increases. Our results indicate that the phylogenetic clusters identified here are likely representative of the contact networks that shape HIV transmission, and this is a valuable tool even in sites with low sampling density, such as Brazil. MDPI 2022-12-12 /pmc/articles/PMC9783618/ /pubmed/36560771 http://dx.doi.org/10.3390/v14122768 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Andrade, Paula Arantes, Ighor Tanuri, Amilcar Bello, Gonzalo Gräf, Tiago Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database |
title | Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database |
title_full | Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database |
title_fullStr | Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database |
title_full_unstemmed | Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database |
title_short | Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database |
title_sort | characterization of hiv-1 transmission clusters inferred from the brazilian nationwide genotyping service database |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9783618/ https://www.ncbi.nlm.nih.gov/pubmed/36560771 http://dx.doi.org/10.3390/v14122768 |
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