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Exploring the Evolutionary History and Phylodynamics of Human Immunodeficiency Virus Type 1 Outbreak From Unnao, India Using Phylogenetic Approach

Certain rural and semiurban settings in the Unnao district, Uttar Pradesh, India observed an unprecedented increase in the detection of HIV cases during July 2017. Subsequent investigations through health camps and a follow-up case-control study attributed the outbreak to the unsafe injection exposu...

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Autores principales: Patil, Ajit, Patil, Sandip, Rao, Amrita, Gadhe, Sharda, Kurle, Swarali, Panda, Samiran
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9158528/
https://www.ncbi.nlm.nih.gov/pubmed/35663884
http://dx.doi.org/10.3389/fmicb.2022.848250
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author Patil, Ajit
Patil, Sandip
Rao, Amrita
Gadhe, Sharda
Kurle, Swarali
Panda, Samiran
author_facet Patil, Ajit
Patil, Sandip
Rao, Amrita
Gadhe, Sharda
Kurle, Swarali
Panda, Samiran
author_sort Patil, Ajit
collection PubMed
description Certain rural and semiurban settings in the Unnao district, Uttar Pradesh, India observed an unprecedented increase in the detection of HIV cases during July 2017. Subsequent investigations through health camps and a follow-up case-control study attributed the outbreak to the unsafe injection exposures during treatment. In this study, we have undertaken a secondary analysis to understand the phylogenetic aspects of the outbreak-associated HIV-1 sequences along with the origin and phylodynamics of these sequences. The initial phylogenetic analysis indicated separate monophyletic grouping and there was no mixing of outbreak-associated sequences with sequences from other parts of India. Transmission network analysis using distance-based and non-distance-based methods revealed the existence of transmission clusters within the monophyletic Unnao clade. The median time to the most recent common ancestor (tMRCA) for sequences from Unnao using the pol gene region was observed to be 2011.87 [95% highest posterior density (HPD): 2010.09–2013.53], while the estimates using envelope (env) gene region sequences traced the tMRCA to 2010.33 (95% HPD: 2007.76–2012.99). Phylodynamics estimates demonstrated that the pace of this local epidemic has slowed down in recent times before the time of sampling, but was certainly on an upward track since its inception till 2014.
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spelling pubmed-91585282022-06-02 Exploring the Evolutionary History and Phylodynamics of Human Immunodeficiency Virus Type 1 Outbreak From Unnao, India Using Phylogenetic Approach Patil, Ajit Patil, Sandip Rao, Amrita Gadhe, Sharda Kurle, Swarali Panda, Samiran Front Microbiol Microbiology Certain rural and semiurban settings in the Unnao district, Uttar Pradesh, India observed an unprecedented increase in the detection of HIV cases during July 2017. Subsequent investigations through health camps and a follow-up case-control study attributed the outbreak to the unsafe injection exposures during treatment. In this study, we have undertaken a secondary analysis to understand the phylogenetic aspects of the outbreak-associated HIV-1 sequences along with the origin and phylodynamics of these sequences. The initial phylogenetic analysis indicated separate monophyletic grouping and there was no mixing of outbreak-associated sequences with sequences from other parts of India. Transmission network analysis using distance-based and non-distance-based methods revealed the existence of transmission clusters within the monophyletic Unnao clade. The median time to the most recent common ancestor (tMRCA) for sequences from Unnao using the pol gene region was observed to be 2011.87 [95% highest posterior density (HPD): 2010.09–2013.53], while the estimates using envelope (env) gene region sequences traced the tMRCA to 2010.33 (95% HPD: 2007.76–2012.99). Phylodynamics estimates demonstrated that the pace of this local epidemic has slowed down in recent times before the time of sampling, but was certainly on an upward track since its inception till 2014. Frontiers Media S.A. 2022-05-18 /pmc/articles/PMC9158528/ /pubmed/35663884 http://dx.doi.org/10.3389/fmicb.2022.848250 Text en Copyright © 2022 Patil, Patil, Rao, Gadhe, Kurle and Panda. https://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
Patil, Ajit
Patil, Sandip
Rao, Amrita
Gadhe, Sharda
Kurle, Swarali
Panda, Samiran
Exploring the Evolutionary History and Phylodynamics of Human Immunodeficiency Virus Type 1 Outbreak From Unnao, India Using Phylogenetic Approach
title Exploring the Evolutionary History and Phylodynamics of Human Immunodeficiency Virus Type 1 Outbreak From Unnao, India Using Phylogenetic Approach
title_full Exploring the Evolutionary History and Phylodynamics of Human Immunodeficiency Virus Type 1 Outbreak From Unnao, India Using Phylogenetic Approach
title_fullStr Exploring the Evolutionary History and Phylodynamics of Human Immunodeficiency Virus Type 1 Outbreak From Unnao, India Using Phylogenetic Approach
title_full_unstemmed Exploring the Evolutionary History and Phylodynamics of Human Immunodeficiency Virus Type 1 Outbreak From Unnao, India Using Phylogenetic Approach
title_short Exploring the Evolutionary History and Phylodynamics of Human Immunodeficiency Virus Type 1 Outbreak From Unnao, India Using Phylogenetic Approach
title_sort exploring the evolutionary history and phylodynamics of human immunodeficiency virus type 1 outbreak from unnao, india using phylogenetic approach
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9158528/
https://www.ncbi.nlm.nih.gov/pubmed/35663884
http://dx.doi.org/10.3389/fmicb.2022.848250
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