Cargando…

Characterization of New Recombinant Forms of HIV-1 From the Comunitat Valenciana (Spain) by Phylogenetic Incongruence

Recombination is one of the main processes shaping the evolution of HIV-1, with relevant consequences for its epidemiology. In fact, Circulating and Unique Recombinant Forms (CRFs and URFs) cause 23% of current infections. The routine analyses of antiretroviral resistance yield partial pol gene sequ...

Descripción completa

Detalles Bibliográficos
Autores principales: Beamud, Beatriz, Bracho, María Alma, González-Candelas, Fernando
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6540936/
https://www.ncbi.nlm.nih.gov/pubmed/31191463
http://dx.doi.org/10.3389/fmicb.2019.01006
_version_ 1783422707932594176
author Beamud, Beatriz
Bracho, María Alma
González-Candelas, Fernando
author_facet Beamud, Beatriz
Bracho, María Alma
González-Candelas, Fernando
author_sort Beamud, Beatriz
collection PubMed
description Recombination is one of the main processes shaping the evolution of HIV-1, with relevant consequences for its epidemiology. In fact, Circulating and Unique Recombinant Forms (CRFs and URFs) cause 23% of current infections. The routine analyses of antiretroviral resistance yield partial pol gene sequences that can be exploited for molecular epidemiology surveillance but also to study viral diversity and to detect potential recombinant samples. Among the pol sequences derived from a large sample dataset from the Comunitat Valenciana (Spain), we identified nine putative recombinant samples. We aimed at fully characterizing these samples and performing a detailed analysis of the corresponding recombination events. We obtained nearly full-genome sequences and used jpHMM and RDP4 to detect and characterize recombinant fragments. We assessed the confidence of these inferences by likelihood mapping and phylogenetic placement with topology congruence tests. Next, we performed a phylogenetic analysis of each putative recombinant fragment to determine its relationships to previously described recombinant forms. We found that two samples related to CRF44_BF whereas the rest corresponded to new URFs (two URF_AD, one URF_BG that can constitute a new CRF resulting from subtype B and CRF24_BG, and two URF_cpx composed of A, G, K, H, and J subtypes). These URFs have a complex recombination pattern that cannot be determined accurately. They seem to have arisen by successive recombination events among lineages, including other CRFs. Our results highlight the usefulness of routine surveillance analysis for the detection of new HIV-1 recombination forms and, at the same time, the need for full-genome sequencing and recombination detection guidelines to properly characterize this complex process.
format Online
Article
Text
id pubmed-6540936
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-65409362019-06-12 Characterization of New Recombinant Forms of HIV-1 From the Comunitat Valenciana (Spain) by Phylogenetic Incongruence Beamud, Beatriz Bracho, María Alma González-Candelas, Fernando Front Microbiol Microbiology Recombination is one of the main processes shaping the evolution of HIV-1, with relevant consequences for its epidemiology. In fact, Circulating and Unique Recombinant Forms (CRFs and URFs) cause 23% of current infections. The routine analyses of antiretroviral resistance yield partial pol gene sequences that can be exploited for molecular epidemiology surveillance but also to study viral diversity and to detect potential recombinant samples. Among the pol sequences derived from a large sample dataset from the Comunitat Valenciana (Spain), we identified nine putative recombinant samples. We aimed at fully characterizing these samples and performing a detailed analysis of the corresponding recombination events. We obtained nearly full-genome sequences and used jpHMM and RDP4 to detect and characterize recombinant fragments. We assessed the confidence of these inferences by likelihood mapping and phylogenetic placement with topology congruence tests. Next, we performed a phylogenetic analysis of each putative recombinant fragment to determine its relationships to previously described recombinant forms. We found that two samples related to CRF44_BF whereas the rest corresponded to new URFs (two URF_AD, one URF_BG that can constitute a new CRF resulting from subtype B and CRF24_BG, and two URF_cpx composed of A, G, K, H, and J subtypes). These URFs have a complex recombination pattern that cannot be determined accurately. They seem to have arisen by successive recombination events among lineages, including other CRFs. Our results highlight the usefulness of routine surveillance analysis for the detection of new HIV-1 recombination forms and, at the same time, the need for full-genome sequencing and recombination detection guidelines to properly characterize this complex process. Frontiers Media S.A. 2019-05-22 /pmc/articles/PMC6540936/ /pubmed/31191463 http://dx.doi.org/10.3389/fmicb.2019.01006 Text en Copyright © 2019 Beamud, Bracho and González-Candelas. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Beamud, Beatriz
Bracho, María Alma
González-Candelas, Fernando
Characterization of New Recombinant Forms of HIV-1 From the Comunitat Valenciana (Spain) by Phylogenetic Incongruence
title Characterization of New Recombinant Forms of HIV-1 From the Comunitat Valenciana (Spain) by Phylogenetic Incongruence
title_full Characterization of New Recombinant Forms of HIV-1 From the Comunitat Valenciana (Spain) by Phylogenetic Incongruence
title_fullStr Characterization of New Recombinant Forms of HIV-1 From the Comunitat Valenciana (Spain) by Phylogenetic Incongruence
title_full_unstemmed Characterization of New Recombinant Forms of HIV-1 From the Comunitat Valenciana (Spain) by Phylogenetic Incongruence
title_short Characterization of New Recombinant Forms of HIV-1 From the Comunitat Valenciana (Spain) by Phylogenetic Incongruence
title_sort characterization of new recombinant forms of hiv-1 from the comunitat valenciana (spain) by phylogenetic incongruence
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6540936/
https://www.ncbi.nlm.nih.gov/pubmed/31191463
http://dx.doi.org/10.3389/fmicb.2019.01006
work_keys_str_mv AT beamudbeatriz characterizationofnewrecombinantformsofhiv1fromthecomunitatvalencianaspainbyphylogeneticincongruence
AT brachomariaalma characterizationofnewrecombinantformsofhiv1fromthecomunitatvalencianaspainbyphylogeneticincongruence
AT gonzalezcandelasfernando characterizationofnewrecombinantformsofhiv1fromthecomunitatvalencianaspainbyphylogeneticincongruence