Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains

Abstract The recent emergence of Zika virus (ZIKV) has been concentrated in the Caribbean, Southeastern United States, and South- and Central America; resulting in travel-based cases being reported around the globe. As multi-disciplinary collaborations are combatting the ZIKV outbreak, the need to v...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Susmita Shrivastava, Vinita Puri, Kari A. Dilley, Erica Ngouajio, Jessica Shifflett, Lauren M. Oldfield, Nadia B. Fedorova, Lihui Hu, Torrey Williams, Alan Durbin, Paolo Amedeo, Sujatha Rashid, Reed S. Shabman, Brett E. Pickett
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Zika Virus (ZIKV) ZIKV Strains Rapid Amplification Of cDNA Ends (RACE) J. Craig Venter Institute (JCVI) ZIKV Infection Medicine R Science Q
Acceso en línea:	https://doaj.org/article/205fafaf8ca0476d84d62e9e5ef5076b
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:205fafaf8ca0476d84d62e9e5ef5076b
record_format	dspace
spelling	oai:doaj.org-article:205fafaf8ca0476d84d62e9e5ef5076b2021-12-02T15:08:24ZWhole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains10.1038/s41598-018-34147-72045-2322https://doaj.org/article/205fafaf8ca0476d84d62e9e5ef5076b2018-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-34147-7https://doaj.org/toc/2045-2322Abstract The recent emergence of Zika virus (ZIKV) has been concentrated in the Caribbean, Southeastern United States, and South- and Central America; resulting in travel-based cases being reported around the globe. As multi-disciplinary collaborations are combatting the ZIKV outbreak, the need to validate the sequence of existing strains has become apparent. Here, we report high-quality sequence data for multiple ZIKV strains made publicly available through the National Institutes of Health- (NIH) funded biorepository, BEI Resources (www.beiresources.org). Next-generation sequencing, 3′ rapid amplification of cDNA ends (RACE), and viral genome annotation pipelines generated GenBank sequence records for 16 BEI Resources strains. Minor variants, consensus mutations, and consensus insertions/deletions were identified within the viral stocks using next-generation sequencing (NGS) and consensus changes were confirmed with Sanger sequencing. Bioinformatics analyses of the sequencing results confirm that the virus stocks available to the scientific research community through BEI Resources adequately represent the viral population diversity of ZIKV.Susmita ShrivastavaVinita PuriKari A. DilleyErica NgouajioJessica ShifflettLauren M. OldfieldNadia B. FedorovaLihui HuTorrey WilliamsAlan DurbinPaolo AmedeoSujatha RashidReed S. ShabmanBrett E. PickettNature PortfolioarticleZika Virus (ZIKV)ZIKV StrainsRapid Amplification Of cDNA Ends (RACE)J. Craig Venter Institute (JCVI)ZIKV InfectionMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-11 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Zika Virus (ZIKV) ZIKV Strains Rapid Amplification Of cDNA Ends (RACE) J. Craig Venter Institute (JCVI) ZIKV Infection Medicine R Science Q
spellingShingle	Zika Virus (ZIKV) ZIKV Strains Rapid Amplification Of cDNA Ends (RACE) J. Craig Venter Institute (JCVI) ZIKV Infection Medicine R Science Q Susmita Shrivastava Vinita Puri Kari A. Dilley Erica Ngouajio Jessica Shifflett Lauren M. Oldfield Nadia B. Fedorova Lihui Hu Torrey Williams Alan Durbin Paolo Amedeo Sujatha Rashid Reed S. Shabman Brett E. Pickett Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains
description	Abstract The recent emergence of Zika virus (ZIKV) has been concentrated in the Caribbean, Southeastern United States, and South- and Central America; resulting in travel-based cases being reported around the globe. As multi-disciplinary collaborations are combatting the ZIKV outbreak, the need to validate the sequence of existing strains has become apparent. Here, we report high-quality sequence data for multiple ZIKV strains made publicly available through the National Institutes of Health- (NIH) funded biorepository, BEI Resources (www.beiresources.org). Next-generation sequencing, 3′ rapid amplification of cDNA ends (RACE), and viral genome annotation pipelines generated GenBank sequence records for 16 BEI Resources strains. Minor variants, consensus mutations, and consensus insertions/deletions were identified within the viral stocks using next-generation sequencing (NGS) and consensus changes were confirmed with Sanger sequencing. Bioinformatics analyses of the sequencing results confirm that the virus stocks available to the scientific research community through BEI Resources adequately represent the viral population diversity of ZIKV.
format	article
author	Susmita Shrivastava Vinita Puri Kari A. Dilley Erica Ngouajio Jessica Shifflett Lauren M. Oldfield Nadia B. Fedorova Lihui Hu Torrey Williams Alan Durbin Paolo Amedeo Sujatha Rashid Reed S. Shabman Brett E. Pickett
author_facet	Susmita Shrivastava Vinita Puri Kari A. Dilley Erica Ngouajio Jessica Shifflett Lauren M. Oldfield Nadia B. Fedorova Lihui Hu Torrey Williams Alan Durbin Paolo Amedeo Sujatha Rashid Reed S. Shabman Brett E. Pickett
author_sort	Susmita Shrivastava
title	Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains
title_short	Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains
title_full	Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains
title_fullStr	Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains
title_full_unstemmed	Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains
title_sort	whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of zika virus strains
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/205fafaf8ca0476d84d62e9e5ef5076b
work_keys_str_mv	AT susmitashrivastava wholegenomesequencingvariantanalysisphylogeneticsanddeepsequencingofzikavirusstrains AT vinitapuri wholegenomesequencingvariantanalysisphylogeneticsanddeepsequencingofzikavirusstrains AT kariadilley wholegenomesequencingvariantanalysisphylogeneticsanddeepsequencingofzikavirusstrains AT ericangouajio wholegenomesequencingvariantanalysisphylogeneticsanddeepsequencingofzikavirusstrains AT jessicashifflett wholegenomesequencingvariantanalysisphylogeneticsanddeepsequencingofzikavirusstrains AT laurenmoldfield wholegenomesequencingvariantanalysisphylogeneticsanddeepsequencingofzikavirusstrains AT nadiabfedorova wholegenomesequencingvariantanalysisphylogeneticsanddeepsequencingofzikavirusstrains AT lihuihu wholegenomesequencingvariantanalysisphylogeneticsanddeepsequencingofzikavirusstrains AT torreywilliams wholegenomesequencingvariantanalysisphylogeneticsanddeepsequencingofzikavirusstrains AT alandurbin wholegenomesequencingvariantanalysisphylogeneticsanddeepsequencingofzikavirusstrains AT paoloamedeo wholegenomesequencingvariantanalysisphylogeneticsanddeepsequencingofzikavirusstrains AT sujatharashid wholegenomesequencingvariantanalysisphylogeneticsanddeepsequencingofzikavirusstrains AT reedsshabman wholegenomesequencingvariantanalysisphylogeneticsanddeepsequencingofzikavirusstrains AT brettepickett wholegenomesequencingvariantanalysisphylogeneticsanddeepsequencingofzikavirusstrains
_version_	1718388110039973888

Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains

Ejemplares similares