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...
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doaj-205fafaf8ca0476d84d62e9e5ef5076b2020-12-08T03:58:52ZengNature Publishing GroupScientific Reports2045-23222018-10-018111110.1038/s41598-018-34147-7Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strainsSusmita Shrivastava0Vinita Puri1Kari A. Dilley2Erica Ngouajio3Jessica Shifflett4Lauren M. Oldfield5Nadia B. Fedorova6Lihui Hu7Torrey Williams8Alan Durbin9Paolo Amedeo10Sujatha Rashid11Reed S. Shabman12Brett E. Pickett13J. Craig Venter InstituteJ. Craig Venter InstituteJ. Craig Venter InstituteJ. Craig Venter InstituteBEI Resources, ATCCJ. Craig Venter InstituteJ. Craig Venter InstituteJ. Craig Venter InstituteJ. Craig Venter InstituteJ. Craig Venter InstituteJ. Craig Venter InstituteBEI Resources, ATCCJ. Craig Venter InstituteJ. Craig Venter InstituteAbstract 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.https://doi.org/10.1038/s41598-018-34147-7Zika Virus (ZIKV)ZIKV StrainsRapid Amplification Of cDNA Ends (RACE)J. Craig Venter Institute (JCVI)ZIKV Infection |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
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 |
spellingShingle |
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 Scientific Reports Zika Virus (ZIKV) ZIKV Strains Rapid Amplification Of cDNA Ends (RACE) J. Craig Venter Institute (JCVI) ZIKV Infection |
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 Publishing Group |
series |
Scientific Reports |
issn |
2045-2322 |
publishDate |
2018-10-01 |
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. |
topic |
Zika Virus (ZIKV) ZIKV Strains Rapid Amplification Of cDNA Ends (RACE) J. Craig Venter Institute (JCVI) ZIKV Infection |
url |
https://doi.org/10.1038/s41598-018-34147-7 |
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