Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Structural and non-structural genes contribute to the genetic diversity of RNA viruses

ABSTRACT: With the advent of advanced sequencing technology, studies of RNA viruses have shown that genetic diversity contribute to both attenuation and virulence. The differences in genetic diversity of wild-type Asibi virus and 17D-204 vaccine provides an unique opportunity to investigate RNA population theory in the context of a well described live attenuated vaccine. Utilizing infectious clone-derived viruses containing some of the amino acid substitutions that differentiate yellow fever wild-type Asibi strain from 17D vaccine and recovered in a controlled experiment, establishes that the genetic diversity differences that exist between wild-type Asibi and 17D-204 vaccine viruses are not influenced by either different passage history or source of samples, but rather resulted from the attenuation of wild-type Asibi virus to yield the 17D vaccine sub-strains.

INSTRUMENT(S): Illumina HiSeq 1500

ORGANISM(S): Yellow fever virus

SUBMITTER: Steve Widen

PROVIDER: E-MTAB-6614 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Affect of antiviral ribavirin on YFV WT and vaccine strains.

Project description:Live-attenuated viral vaccines have been successfully used to combat infectious disease for decades but due to their empirical derivation, little is known about their mechanisms of attenuation. This lack of understanding makes the development of next generation live attenuated vaccines difficult. The success of the 17D vaccine and availability of the parent virus, Asibi, makes it an excellent model to understand the molecular basis of attenuation of a live attenuated vaccine and the effects of viral diversity on vaccine function. Due to the differences in genetic diversity between WT Asibi virus and its 17D vaccine derivative, we investigated the changes in genetic diversity of 17D and Asibi viruses following treatment with ribavirin.

2020-01-01 | E-MTAB-8504 | biostudies-arrayexpress

Profiling 11,639 genes in PBMCs from 2 donors: U133 A 2.0 Custom CDF Version 9

Project description:The immune responses generated by YF-17D by profiling 11,639 genes in PBMCs from 2 donors cultured with YF-17D vaccine were accessed after 3 and 12 hours. Keywords: time course, in vitro stimulaion PMBCs were isolated with citrate buffered cell preparation tubes (CPT) from 2 healthy donors who were not previously vaccinated with YF-17D. Total RNA was either isolated directly from the freshly collected cells or after cell culture. Cells were cultured for 3 and 12 hours in the presence or absence of YF-17D vaccine.

2010-05-15 | E-GEOD-13484 | biostudies-arrayexpress

Naïve-like Yellow-Fever specific CD8 T cells and reference CD8 T cell subsets in humans

Project description:Human Naïve-like CD8 T cells induced by the Yellow Fever Vaccine 17D were compared to the conventional subsets in total CD8 T cells Samples originate from peripheral blood mononuclear cells (PBMC) from 8 different donors vaccinated with the YF-17D vaccine 1'000 cells from various CD8 T cells subsets were purified by flow cytometry, from 8 vaccinees (donors d1 to d8); the subsets (cell types) include: A2/NS4b tetramer positive CCR7+ CD45RA+ CD8 T cells (A2_NS4b Naïve-like), Total Naive (CCR7+ CD45RA+), Total Tscm (CCR7+ CD45RA+ CD58+ CD95+), Total CM (CCR7+ CD45RA-) and Total Effectors (CCR7 negative).

2015-04-08 | E-GEOD-65804 | biostudies-arrayexpress

Naïve-like Yellow-Fever specific CD8 T cells and reference CD8 T cell subsets in humans

2015-04-08 | GSE65804 | GEO

Profiling 11,639 genes in PBMCs from 2 donors: U133 A 2.0 Custom CDF Version 9

2008-11-23 | GSE13484 | GEO

Gene expression profiling of PBMC from coinfected or non-coinfected mice at d0, d3, d7, and d21 post YFV-17D challenge

Project description:We tested the effects of co-infection on vaccine response to YFV-17D.

2016-03-22 | GSE79466 | GEO

Profiling 20,077 genes in 25 vaccine recipients: U133 Plus 2.0, Custom CDF Version 9

2008-11-23 | GSE13485 | GEO

Profiling 20,077 genes in 25 vaccine recipients: U133 Plus 2.0, Custom CDF Version 9

Project description:The immune responses generated by YF-17D by profiling 20,077 genes in 25 vaccine recipients were accessed at days 1, 3, 7, and 21 post-vaccination compared to pre-vaccination in PBMCs. The immune responses generated by YF-17D by profiling 20,077 genes in 25 vaccine recipients were accessed at days 1, 3, 7, and 21 post-vaccination compared to pre-vaccination in PBMCs. Keywords: time course This study is a combination of 2 separate YF-17D vaccination trials. Trial 1 has 15 subjects, and Trial 2 has 10 subjects. The two trials occurred 1 year apart and used different lots of the vaccine. Enrolled volunteers were healthy, aged 18 to 45, and signed a written informed consent form. Potential volunteers were excluded from participating in the study if they were pregnant, or if they had been vaccinated previously with YF-17D. Blood samples were taken pre-vaccinaion to serve as a reference point for each individual, and post-vaccination samples were taken a days 1, 3, 7, and 21 after YF-17D vaccination. All subjects received YF-17D. Blood samples for microarray analysis were collected either in blue and black topped citrate buffered cell preparation tubes (CPT). Following PMBC isolation from CPT, 2 x 106 cells were lysed in 1 ml of TRIzol and stored at -80?C (Cat# 15596-026; Invitrogen Life Technologies). After all time points were collected for a subject, the samples were thawed, and the RNA isolation proceeded according to the manufacturer’s protocol.

2008-11-22 | E-GEOD-13485 | biostudies-arrayexpress

Genetic analysis of a Zika Virus Envelope Glycosylation and Non-structural protein 4B P36 Double Mutant

Project description:Zika virus (ZIKV) is a mosquito-transmitted positive-sense RNA virus in the family Flaviviridae. Live attenuated vaccines have been successfully used to combat infection by flaviviruses, such as yellow fever and Japanese encephalitis viruses. A Zika virus harboring combined mutations in the envelope protein glycosylation site and in the nonstructural 4B protein amino acid 36 (ZE4B-36) was generated and assessed for stability, attenuation, and protection against infection. To determine the genetic stability of its RNA genome, ZE4B-36 was serially passaged in vitro in Vero cells. Virus harvested from passages (P)1 to P6 was subjected to next generation sequencing and downstream analysis to determine its nucleotide sequence variability. Specifically, single nucleotide variant analysis showed that the ZE4B-36 genome decreased its genetic diversity and resulted in a more stable nucleotide sequence. Thus, in addition to showing attenuation and protection, ZE4B-36 is a stable live attenuated virus that possesses characteristics important for a vaccine to combat Zika disease.

2021-12-31 | E-MTAB-9496 | biostudies-arrayexpress