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Recombination analysis of near full-length HIV-1 sequences and the identification of a potential new Circulating Recombinant Form from Rakai, Uganda

The Phylogenetics and Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium has been vital in the generation and examination of near full-length HIV-1 sequences generated from sub-Saharan Africa. In this study, we examined a subset (n=275) of sequences from Rakai, Uganda collected... Full description

Journal Title: AIDS research and human retroviruses 2020, Vol.36 (ja), p.467-474
Main Author: Capoferri, Adam A
Other Authors: Lamers, Susanna , Grabowski, Mary , Rose, Rebecca R , Wawer, Maria , Serwadda, David , Gray, Ronald , Quinn, Thomas C , Kigozi, Godfrey , Kagaayi, Joseph , Laeyendecker, Oliver
Format: Electronic Article Electronic Article
Language: English
Subjects:
HIV
Quelle: Alma/SFX Local Collection
Publisher: United States: Mary Ann Liebert, Inc
ID: ISSN: 0889-2229
Link: https://www.ncbi.nlm.nih.gov/pubmed/31914792
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title: Recombination analysis of near full-length HIV-1 sequences and the identification of a potential new Circulating Recombinant Form from Rakai, Uganda
format: Article
creator:
  • Capoferri, Adam A
  • Lamers, Susanna
  • Grabowski, Mary
  • Rose, Rebecca R
  • Wawer, Maria
  • Serwadda, David
  • Gray, Ronald
  • Quinn, Thomas C
  • Kigozi, Godfrey
  • Kagaayi, Joseph
  • Laeyendecker, Oliver
subjects:
  • Adolescent
  • Adult
  • Breakpoints
  • circulating recombinant form
  • Cohort Studies
  • Consortia
  • Epidemics
  • Epidemiology
  • Evolution
  • Genetic diversity
  • Genome, Viral
  • HIV
  • HIV Infections - epidemiology
  • HIV Infections - virology
  • HIV-1
  • HIV-1 - classification
  • HIV-1 - genetics
  • HIV-1 - isolation & purification
  • HIV-1 diversity
  • HIV-1 recombination
  • Human immunodeficiency virus
  • Humans
  • Middle Aged
  • Phylogenetics
  • Phylogeny
  • Reassortant Viruses
  • Recombinants
  • Recombination
  • Rural Population
  • Sequence Analysis, DNA
  • subtype
  • Uganda - epidemiology
  • Vaccines
  • Viruses
  • Young Adult
ispartof: AIDS research and human retroviruses, 2020, Vol.36 (ja), p.467-474
description: The Phylogenetics and Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium has been vital in the generation and examination of near full-length HIV-1 sequences generated from sub-Saharan Africa. In this study, we examined a subset (n=275) of sequences from Rakai, Uganda collected between August 2011 and January 2015. Sequences were initially screened with COMET for subtyping and then evaluated using bootscanning and phylogenetic inference. Among 275 sequences, 38.6% were subtype D, 19.3% were subtype A, 2.9% were subtype C, and 39.3% were recombinant. The recombinants were structurally diverse in the number of breakpoints observed, the location of recombinant segments, and represented subtypes, with AD recombinants accounting for the majority of all recombinants (29.8%). Within the AD subpopulation, we identified a potential new circulating recombinant form in five individuals where the polymerase gene was subtype D and most of env was subtype A (D-A junctures at HXB2 6760 and 8709). While the breakpoints were identical for the viruses from these individuals, the viral fragments did not cluster together. These results suggest selection for a viral strain where properties of the subtype A and D portions of the virus confer a survival advantage. The continued study of recombinants will increase our breadth of knowledge for the genetic diversity and evolution of HIV-1 which can further contribute to our understanding towards a universal HIV-1 vaccine.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 0889-2229
fulltext: fulltext
issn:
  • 0889-2229
  • 1931-8405
url: Link


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titleRecombination analysis of near full-length HIV-1 sequences and the identification of a potential new Circulating Recombinant Form from Rakai, Uganda
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creatorCapoferri, Adam A ; Lamers, Susanna ; Grabowski, Mary ; Rose, Rebecca R ; Wawer, Maria ; Serwadda, David ; Gray, Ronald ; Quinn, Thomas C ; Kigozi, Godfrey ; Kagaayi, Joseph ; Laeyendecker, Oliver
creatorcontribCapoferri, Adam A ; Lamers, Susanna ; Grabowski, Mary ; Rose, Rebecca R ; Wawer, Maria ; Serwadda, David ; Gray, Ronald ; Quinn, Thomas C ; Kigozi, Godfrey ; Kagaayi, Joseph ; Laeyendecker, Oliver ; Rakai Health Sciences Program and the PANGEA Consortium ; for the Rakai Health Sciences Program and the PANGEA Consortium
descriptionThe Phylogenetics and Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium has been vital in the generation and examination of near full-length HIV-1 sequences generated from sub-Saharan Africa. In this study, we examined a subset (n=275) of sequences from Rakai, Uganda collected between August 2011 and January 2015. Sequences were initially screened with COMET for subtyping and then evaluated using bootscanning and phylogenetic inference. Among 275 sequences, 38.6% were subtype D, 19.3% were subtype A, 2.9% were subtype C, and 39.3% were recombinant. The recombinants were structurally diverse in the number of breakpoints observed, the location of recombinant segments, and represented subtypes, with AD recombinants accounting for the majority of all recombinants (29.8%). Within the AD subpopulation, we identified a potential new circulating recombinant form in five individuals where the polymerase gene was subtype D and most of env was subtype A (D-A junctures at HXB2 6760 and 8709). While the breakpoints were identical for the viruses from these individuals, the viral fragments did not cluster together. These results suggest selection for a viral strain where properties of the subtype A and D portions of the virus confer a survival advantage. The continued study of recombinants will increase our breadth of knowledge for the genetic diversity and evolution of HIV-1 which can further contribute to our understanding towards a universal HIV-1 vaccine.
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subjectAdolescent ; Adult ; Breakpoints ; circulating recombinant form ; Cohort Studies ; Consortia ; Epidemics ; Epidemiology ; Evolution ; Genetic diversity ; Genome, Viral ; HIV ; HIV Infections - epidemiology ; HIV Infections - virology ; HIV-1 ; HIV-1 - classification ; HIV-1 - genetics ; HIV-1 - isolation & purification ; HIV-1 diversity ; HIV-1 recombination ; Human immunodeficiency virus ; Humans ; Middle Aged ; Phylogenetics ; Phylogeny ; Reassortant Viruses ; Recombinants ; Recombination ; Rural Population ; Sequence Analysis, DNA ; subtype ; Uganda - epidemiology ; Vaccines ; Viruses ; Young Adult
ispartofAIDS research and human retroviruses, 2020, Vol.36 (ja), p.467-474
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descriptionThe Phylogenetics and Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium has been vital in the generation and examination of near full-length HIV-1 sequences generated from sub-Saharan Africa. In this study, we examined a subset (n=275) of sequences from Rakai, Uganda collected between August 2011 and January 2015. Sequences were initially screened with COMET for subtyping and then evaluated using bootscanning and phylogenetic inference. Among 275 sequences, 38.6% were subtype D, 19.3% were subtype A, 2.9% were subtype C, and 39.3% were recombinant. The recombinants were structurally diverse in the number of breakpoints observed, the location of recombinant segments, and represented subtypes, with AD recombinants accounting for the majority of all recombinants (29.8%). Within the AD subpopulation, we identified a potential new circulating recombinant form in five individuals where the polymerase gene was subtype D and most of env was subtype A (D-A junctures at HXB2 6760 and 8709). While the breakpoints were identical for the viruses from these individuals, the viral fragments did not cluster together. These results suggest selection for a viral strain where properties of the subtype A and D portions of the virus confer a survival advantage. The continued study of recombinants will increase our breadth of knowledge for the genetic diversity and evolution of HIV-1 which can further contribute to our understanding towards a universal HIV-1 vaccine.
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atitleRecombination analysis of near full-length HIV-1 sequences and the identification of a potential new Circulating Recombinant Form from Rakai, Uganda
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abstractThe Phylogenetics and Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium has been vital in the generation and examination of near full-length HIV-1 sequences generated from sub-Saharan Africa. In this study, we examined a subset (n=275) of sequences from Rakai, Uganda collected between August 2011 and January 2015. Sequences were initially screened with COMET for subtyping and then evaluated using bootscanning and phylogenetic inference. Among 275 sequences, 38.6% were subtype D, 19.3% were subtype A, 2.9% were subtype C, and 39.3% were recombinant. The recombinants were structurally diverse in the number of breakpoints observed, the location of recombinant segments, and represented subtypes, with AD recombinants accounting for the majority of all recombinants (29.8%). Within the AD subpopulation, we identified a potential new circulating recombinant form in five individuals where the polymerase gene was subtype D and most of env was subtype A (D-A junctures at HXB2 6760 and 8709). While the breakpoints were identical for the viruses from these individuals, the viral fragments did not cluster together. These results suggest selection for a viral strain where properties of the subtype A and D portions of the virus confer a survival advantage. The continued study of recombinants will increase our breadth of knowledge for the genetic diversity and evolution of HIV-1 which can further contribute to our understanding towards a universal HIV-1 vaccine.
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pmid31914792
doi10.1089/AID.2019.0150
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