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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| Format: | Article |
| Language: | English |
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MDPI AG
2022-12-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/14/12/2768 |
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| author | Paula Andrade Ighor Arantes Amilcar Tanuri Gonzalo Bello Tiago Gräf |
| author_facet | Paula Andrade Ighor Arantes Amilcar Tanuri Gonzalo Bello Tiago Gräf |
| author_sort | Paula Andrade |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T15:44:38Z |
| format | Article |
| id | doaj.art-45e537bdf37044e4b693b92e739e6d4a |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T15:44:38Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-45e537bdf37044e4b693b92e739e6d4a2023-11-24T18:39:18ZengMDPI AGViruses1999-49152022-12-011412276810.3390/v14122768Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service DatabasePaula Andrade0Ighor Arantes1Amilcar Tanuri2Gonzalo Bello3Tiago Gräf4Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, BrazilLaboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, BrazilLaboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, BrazilLaboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, BrazilLaboratório de Virologia Molecular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba 81350-010, BrazilThe 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.https://www.mdpi.com/1999-4915/14/12/2768HIV-1transmission dynamicsphylogenetic clustersBrazil |
| spellingShingle | Paula Andrade Ighor Arantes Amilcar Tanuri Gonzalo Bello Tiago Gräf Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database Viruses HIV-1 transmission dynamics phylogenetic clusters Brazil |
| 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 | HIV-1 transmission dynamics phylogenetic clusters Brazil |
| url | https://www.mdpi.com/1999-4915/14/12/2768 |
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