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Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods

In 2018, the World Health Organization identified the Zika virus (ZIKV) as a pathogen that should be prioritized for public health research due to its epidemic potential. In this study, whole-genome sequencing (WGS) of travel-acquired ZIKV infections was used to examine the limitations of phylogenet...

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Autores principales: Kamelian, Kimia, Montoya, Vincent, Olmstead, Andrea, Dong, Winnie, Harrigan, Richard, Morshed, Muhammad, Joy, Jeffrey B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6848190/
https://www.ncbi.nlm.nih.gov/pubmed/31712570
http://dx.doi.org/10.1038/s41598-019-52613-8
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author Kamelian, Kimia
Montoya, Vincent
Olmstead, Andrea
Dong, Winnie
Harrigan, Richard
Morshed, Muhammad
Joy, Jeffrey B.
author_facet Kamelian, Kimia
Montoya, Vincent
Olmstead, Andrea
Dong, Winnie
Harrigan, Richard
Morshed, Muhammad
Joy, Jeffrey B.
author_sort Kamelian, Kimia
collection PubMed
description In 2018, the World Health Organization identified the Zika virus (ZIKV) as a pathogen that should be prioritized for public health research due to its epidemic potential. In this study, whole-genome sequencing (WGS) of travel-acquired ZIKV infections was used to examine the limitations of phylogenetic analysis. WGS and phylogenetic analysis were performed to investigate geographic clustering of samples from five Canadians with travel-acquired ZIKV infections and to assess the limitations of phylogenetic analysis of ZIKV sequences using a phylogenetic cluster approach. Genomic variability of ZIKV samples was assessed and for context, compared with hepatitis C virus (HCV) samples. Phylogenetic analysis confirmed the suspected region of ZIKV infection for one of five samples and one sample failed to cluster with sequences from its suspected country of infection. Travel-acquired ZIKV samples depicted low genomic variability relative to HCV samples. A floating patristic distance threshold classified all pre-2000 ZIKV sequences into separate clusters, while only Cambodian, Peruvian, Malaysian, and South Korean sequences were similarly classifiable. While phylogenetic analysis of ZIKV data can identify the broad geographical region of ZIKV infection, ZIKV’s low genomic variability is likely to limit precise interpretations of phylogenetic analysis of the origins of travel-related cases.
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spelling pubmed-68481902019-11-19 Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods Kamelian, Kimia Montoya, Vincent Olmstead, Andrea Dong, Winnie Harrigan, Richard Morshed, Muhammad Joy, Jeffrey B. Sci Rep Article In 2018, the World Health Organization identified the Zika virus (ZIKV) as a pathogen that should be prioritized for public health research due to its epidemic potential. In this study, whole-genome sequencing (WGS) of travel-acquired ZIKV infections was used to examine the limitations of phylogenetic analysis. WGS and phylogenetic analysis were performed to investigate geographic clustering of samples from five Canadians with travel-acquired ZIKV infections and to assess the limitations of phylogenetic analysis of ZIKV sequences using a phylogenetic cluster approach. Genomic variability of ZIKV samples was assessed and for context, compared with hepatitis C virus (HCV) samples. Phylogenetic analysis confirmed the suspected region of ZIKV infection for one of five samples and one sample failed to cluster with sequences from its suspected country of infection. Travel-acquired ZIKV samples depicted low genomic variability relative to HCV samples. A floating patristic distance threshold classified all pre-2000 ZIKV sequences into separate clusters, while only Cambodian, Peruvian, Malaysian, and South Korean sequences were similarly classifiable. While phylogenetic analysis of ZIKV data can identify the broad geographical region of ZIKV infection, ZIKV’s low genomic variability is likely to limit precise interpretations of phylogenetic analysis of the origins of travel-related cases. Nature Publishing Group UK 2019-11-11 /pmc/articles/PMC6848190/ /pubmed/31712570 http://dx.doi.org/10.1038/s41598-019-52613-8 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Kamelian, Kimia
Montoya, Vincent
Olmstead, Andrea
Dong, Winnie
Harrigan, Richard
Morshed, Muhammad
Joy, Jeffrey B.
Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods
title Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods
title_full Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods
title_fullStr Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods
title_full_unstemmed Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods
title_short Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods
title_sort phylogenetic surveillance of travel-related zika virus infections through whole-genome sequencing methods
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6848190/
https://www.ncbi.nlm.nih.gov/pubmed/31712570
http://dx.doi.org/10.1038/s41598-019-52613-8
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