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Origin and evolution of HIV-1 subtype A6
BACKGROUND: HIV outbreaks in the Former Soviet Union (FSU) countries were characterized by repeated transmission of the HIV variant AFSU, which is now classified as a distinct subtype A sub-subtype called A6. The current study used phylogenetic/phylodynamic and signature mutation analyses to determi...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8668117/ https://www.ncbi.nlm.nih.gov/pubmed/34898626 http://dx.doi.org/10.1371/journal.pone.0260604 |
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author | Abidi, Syed Hani Aibekova, Lazzat Davlidova, Salima Amangeldiyeva, Aidana Foley, Brian Ali, Syed |
author_facet | Abidi, Syed Hani Aibekova, Lazzat Davlidova, Salima Amangeldiyeva, Aidana Foley, Brian Ali, Syed |
author_sort | Abidi, Syed Hani |
collection | PubMed |
description | BACKGROUND: HIV outbreaks in the Former Soviet Union (FSU) countries were characterized by repeated transmission of the HIV variant AFSU, which is now classified as a distinct subtype A sub-subtype called A6. The current study used phylogenetic/phylodynamic and signature mutation analyses to determine likely evolutionary relationship between subtype A6 and other subtype A sub-subtypes. METHODS: For this study, an initial Maximum Likelihood phylogenetic analysis was performed using a total of 553 full-length, publicly available, reverse transcriptase sequences, from A1, A2, A3, A4, A5, and A6 sub-subtypes of subtype A. For phylogenetic clustering and signature mutation analysis, a total of 5961 and 3959 pol and env sequences, respectively, were used. RESULTS: Phylogenetic and signature mutation analysis showed that HIV-1 sub-subtype A6 likely originated from sub-subtype A1 of African origin. A6 and A1 pol and env genes shared several signature mutations that indicate genetic similarity between the two subtypes. For A6, tMRCA dated to 1975, 15 years later than that of A1. CONCLUSION: The current study provides insights into the evolution and diversification of A6 in the backdrop of FSU countries and indicates that A6 in FSU countries evolved from A1 of African origin and is getting bridged outside the FSU region. |
format | Online Article Text |
id | pubmed-8668117 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-86681172021-12-14 Origin and evolution of HIV-1 subtype A6 Abidi, Syed Hani Aibekova, Lazzat Davlidova, Salima Amangeldiyeva, Aidana Foley, Brian Ali, Syed PLoS One Research Article BACKGROUND: HIV outbreaks in the Former Soviet Union (FSU) countries were characterized by repeated transmission of the HIV variant AFSU, which is now classified as a distinct subtype A sub-subtype called A6. The current study used phylogenetic/phylodynamic and signature mutation analyses to determine likely evolutionary relationship between subtype A6 and other subtype A sub-subtypes. METHODS: For this study, an initial Maximum Likelihood phylogenetic analysis was performed using a total of 553 full-length, publicly available, reverse transcriptase sequences, from A1, A2, A3, A4, A5, and A6 sub-subtypes of subtype A. For phylogenetic clustering and signature mutation analysis, a total of 5961 and 3959 pol and env sequences, respectively, were used. RESULTS: Phylogenetic and signature mutation analysis showed that HIV-1 sub-subtype A6 likely originated from sub-subtype A1 of African origin. A6 and A1 pol and env genes shared several signature mutations that indicate genetic similarity between the two subtypes. For A6, tMRCA dated to 1975, 15 years later than that of A1. CONCLUSION: The current study provides insights into the evolution and diversification of A6 in the backdrop of FSU countries and indicates that A6 in FSU countries evolved from A1 of African origin and is getting bridged outside the FSU region. Public Library of Science 2021-12-13 /pmc/articles/PMC8668117/ /pubmed/34898626 http://dx.doi.org/10.1371/journal.pone.0260604 Text en https://creativecommons.org/publicdomain/zero/1.0/This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication. |
spellingShingle | Research Article Abidi, Syed Hani Aibekova, Lazzat Davlidova, Salima Amangeldiyeva, Aidana Foley, Brian Ali, Syed Origin and evolution of HIV-1 subtype A6 |
title | Origin and evolution of HIV-1 subtype A6 |
title_full | Origin and evolution of HIV-1 subtype A6 |
title_fullStr | Origin and evolution of HIV-1 subtype A6 |
title_full_unstemmed | Origin and evolution of HIV-1 subtype A6 |
title_short | Origin and evolution of HIV-1 subtype A6 |
title_sort | origin and evolution of hiv-1 subtype a6 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8668117/ https://www.ncbi.nlm.nih.gov/pubmed/34898626 http://dx.doi.org/10.1371/journal.pone.0260604 |
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