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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...

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Autores principales: Andrade, Paula, Arantes, Ighor, Tanuri, Amilcar, Bello, Gonzalo, Gräf, Tiago
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
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.
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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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