Virus Variation Resource – improved response to emergent viral outbreaks

Hatcher, Eneida L.; Zhdanov, Sergey; Bào, Yīmíng; Blinkova, Olga; Nawrocki, Eric P.; Ostapchuck, Yuri; Schäffer, Alejandro A.; Brister, J. Rodney

doi:10.1093/nar/gkw1065

Cited by 373 publications

(322 citation statements)

References 34 publications

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“…We identified all unique sequences of natural and laboratory WNV strains by using the Virus Variation Resource ( 25 ). Virus sequences meeting the following criteria were included in this study: 1) the nucleotide sequence spanned the complete open reading frame, 2) the sequence was derived from natural isolates and not laboratory strains, 3) the sequence was unique (i.e., all sequences differed by > 1 nt), and 4) the sequence contained no degenerate nucleotides.…”

Section: Methodsmentioning

confidence: 99%

Terrestrial Bird Migration and West Nile Virus Circulation, United States

Swetnam¹,

Widen²,

Wood³

et al. 2018

Emerg. Infect. Dis.

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Host migration and emerging pathogens are strongly associated, especially with regard to zoonotic diseases. West Nile virus (WNV), a mosquitoborne pathogen capable of causing severe, sometimes fatal, neuroinvasive disease in humans, is maintained in highly mobile avian hosts. Using phylogeographic approaches, we investigated the relationship between WNV circulation in the United States and the flight paths of terrestrial birds. We demonstrated southward migration of WNV in the eastern flyway and northward migration in the central flyway, which is consistent with the looped flight paths of many terrestrial birds. We also identified 3 optimal locations for targeted WNV surveillance campaigns in the United States—Illinois, New York, and Texas. These results illustrate the value of multidisciplinary approaches to surveillance of infectious diseases, especially zoonotic diseases.

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Section: Methodsmentioning

confidence: 99%

Terrestrial Bird Migration and West Nile Virus Circulation, United States

Swetnam¹,

Widen²,

Wood³

et al. 2018

Emerg. Infect. Dis.

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“…For bacterial genomes, these limitations were addressed by the release of NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) [21], which is now available for download as a standalone package (https://github.com/ncbi/pgap/releases). For influenza virus, the limitations were addressed first by FLAN [2] and then by the influenza virus submission tools provided by GenBank [3]. Tools for checking submissions of non-influenza viruses have lagged but VADR begins to close the gap.…”

Section: Discussionmentioning

confidence: 99%

“…The influenza virus sequence submission tool (https://www.ncbi.nlm.nih.gov/ genome/viruses/variation/help/flu-help-center/submitflu-sequences/) is implemented specifically for influenza with many hard-coded features. It has proven [3] (https:// www.ncbi.nlm.nih.gov/genome/viruses/variation) includes specialized components that attempt to normalize annotation of previously submitted sequences for rotaviruses, dengue virus, West Nile virus, ebolaviruses, Zika virus, and MERS coronavirus. The resulting standardized annotation supports virus-specific searches using gene and protein names.…”

Section: Introductionmentioning

confidence: 99%

VADR: validation and annotation of virus sequence submissions to GenBank

Schäffer

Hatcher

Yankie

et al. 2019

Preprint

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Background: GenBank contains over 3 million viral sequences. The National Center for Biotechnology Information (NCBI) previously made available a tool for validating and annotating influenza virus sequences that is used to check submissions to GenBank. Before this project, there was no analogous tool in use for non-influenza viral sequence submissions. Results: We developed a system called VADR (Viral Annotation DefineR) that validates and annotates viral sequences in GenBank submissions. The annotation system is based on analysis of the input nucleotide sequence using models built from curated RefSeqs. Hidden Markov models are used to classify sequences by determining the RefSeq they are most similar to, and feature annotation from the RefSeq is mapped based on a nucleotide alignment of the full sequence to a covariance model. Predicted proteins encoded by the sequence are validated with nucleotide-to-protein alignments using BLAST. The system identifies 43 types of "alerts" that (unlike the previous BLAST-based system) provide deterministic and rigorous feedback to researchers who submit sequences with unexpected characteristics. VADR has been integrated into GenBank's submission processing pipeline allowing for viral submissions passing all tests to be accepted and annotated automatically, without the need for any human (GenBank indexer) intervention. Unlike the previous submission-checking system, VADR is freely available (https://github.com/nawrockie/vadr) for local installation and use. VADR has been used for Norovirus submissions since May 2018 and for Dengue virus submissions since January 2019. Other viruses with high numbers of submissions will be added incrementally. Conclusion: VADR improves the speed with which non-flu virus submissions to GenBank can be checked and improves the content and quality of the GenBank annotations. The availability and portability of the software allows researchers to run the GenBank checks prior to submitting their viral sequences, and thereby gain confidence that their submissions will be accepted immediately without the need to correspond with GenBank staff. Reciprocally, the adoption of VADR frees GenBank staff to spend more time on services other than checking routine viral sequence submissions.

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“…Primary amino acid sequences of the complete genome for full polyprotein of Zika Virus were collected using Virus Variation tool (https://www.ncbi.nlm.nih.gov/ genome/viruses/variation) of NCBI (Hatcher et al, 2017). Only full-length sequences have been selected and fully identical sequences were excluded.…”

Section: Retrieval Of Protein Sequencesmentioning

confidence: 99%

Recognition of A Highly Conserved DSRCPTQ Epitope in Envelope Protein of Zika Virus Through in silico Approaches

Rahman

Hossain

Tamanna

et al. 2020

Preprint

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The recurrent and recent outbreak of Zika Virus (ZIKV) has turned into global concern as yet there is no appropriate preventive measure been found. Situation getting worse as this virus also associates with several birth defects in neonatal such as primary microcephaly as well as many other neurological disorders. ZIKV adopts a wide host range which has hastened its expansion more recklessly. Hence, now there is an acute demand for developing a preventive vaccine against ZIKV. Immunoinformatic techniques have been employed in this study to pick out a highly conserved versatile antigenic B-cell linear epitope for all strains of ZIKV. Capsid protein (C), Membrane Glycoprotein Precursor (PrM), envelope protein (E) and RNA-dependent RNA Polymerase (NS5) have investigated by the implementation of sequence analysis and different epitope prediction methods. Some potential linear peptides have been recognized and tested for hydrophilicity and conservancy. Peptide with best antigenic properties was selected as ultimate final epitope and further structural exploration revealed its compatible position in protein 3D structure. Being fully conserved in all strains of ZIKV and its position in Envelope protein suggested epitope DSRCPTQ can be a quantum leap in the advancement of ZIKV prevention. However, extensive in vitro plus in vivo experimentations are needed to be clarified about the real potency of the selected epitope.

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Virus Variation Resource – improved response to emergent viral outbreaks

Cited by 373 publications

References 34 publications

Terrestrial Bird Migration and West Nile Virus Circulation, United States

Terrestrial Bird Migration and West Nile Virus Circulation, United States

VADR: validation and annotation of virus sequence submissions to GenBank

Recognition of A Highly Conserved DSRCPTQ Epitope in Envelope Protein of Zika Virus Through in silico Approaches

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