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Inter- and intra-lineage genetic diversity of wild-type Zika viruses reveals both common and distinctive nucleotide variants and clusters of genomic diversity

ABSTRACT: Inter- and intra-lineage genetic diversity of wild-type Zika viruses reveals both common and distinctive nucleotide variants and clusters of genomic diversity

PROVIDER: PRJEB31678 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3218780_1.fastq.gz	Fastqsanger.gz
	ERR3218780_2.fastq.gz	Fastqsanger.gz
	ERR3218781_1.fastq.gz	Fastqsanger.gz
	ERR3218781_2.fastq.gz	Fastqsanger.gz
	ERR3218782_1.fastq.gz	Fastqsanger.gz

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Inter- and intra-lineage genetic diversity of wild-type Zika viruses reveals both common and distinctive nucleotide variants and clusters of genomic diversity

Project description:ZIKV strains belong to three phylogenetic lineages: East African, West African, and Asian/American. RNA virus genomes exist as populations of genetically-related sequences whose heterogeneity may impact viral fitness, evolution, and virulence. The genetic diversity of representative ZIKVs (N=7) from each lineage was examined using next generation sequencing (NGS) paired with downstream Shannon entropy calculation and single nucleotide variant (SNV) analysis. This comprehensive analysis of ZIKV genetic diversity provides insight into the genetic diversity of ZKIV and repository of SNV positions across lineages.

2019-07-30 | E-MTAB-7771 | biostudies-arrayexpress

Inter and intra-lineage genetic diversity of Zika virus differs for American isolates

Project description:Zika virus (ZIKV) is a mosquito-transmitted positive-sense RNA virus in the family Flaviviridae. ZIKV infections are associated with neurodevelopmental deficiencies termed Congenital Zika Syndrome. ZIKV strains are grouped into three phylogenetic lineages: East African, West African, and Asian, which contains the American lineage. RNA virus genomes exist as genetically-related sequences. The heterogeneity of these viral populations is implicated in viral fitness, and genome diversity is correlated to virulence. This study examines genetic diversity of representative ZIKV strains from all lineages utilizing next generation sequencing (NGS). Inter-lineage diversity results indicate that ZIKV lineages differ broadly from each other; however, intra-lineage comparisons of American ZIKV strains isolated from human serum or placenta show differences in diversity when compared to ZIKVs from Asia and West Africa. This study describes the first comprehensive NGS analysis of all ZIKV lineages and posits that sub-consensus-level diversity may provide a framework for understanding ZIKV fitness during infection.

2018-12-31 | E-MTAB-5945 | biostudies-arrayexpress

Inter- and intra-lineage genetic diversity of wild-type Zika viruses reveals both common and distinctive nucleotide variants and clusters of genomic diversity.

Project description:Zika virus (ZIKV) strains belong to the East African, West African, and Asian/American phylogenetic lineages. RNA viruses, like ZIKV, exist as populations of genetically-related sequences whose heterogeneity may impact viral fitness, evolution, and virulence. Genetic diversity of representative ZIKVs from each lineage was examined using next generation sequencing (NGS) paired with downstream entropy and single nucleotide variant (SNV) analysis. Comparisons showed that inter-lineage diversity was statistically supported, while intra-lineage diversity. Intra-lineage diversity was significant for East but not West Africa strains. Furthermore, intra-lineage diversity for the Asian/American lineage was not supported for human serum isolates; however, a placenta isolate differed significantly. Relative in the pre-membrane/membrane (prM/M) gene of several ZIKV strains. Additionally, the East African lineage contained a greater number of synonymous SNVs, while a greater number of non-synonymous SNVs were identified for American strains. Further, inter-lineage SNVs were dispersed throughout the genome, whereas intra-lineage non-synonymous SNVs for Asian/American strains clustered within prM/M and NS1 gene. This comprehensive analysis of ZIKV genetic diversity provides a repository of SNV positions across lineages. We posit that increased non-synonymous SNV populations and increased relative genetic diversity of the prM/M and NS1 proteins provides more evidence for their role in ZIKV virulence and fitness.

| S-EPMC6711133 | biostudies-literature

Inter and intra-lineage genetic diversity of Zika virus differs for American isolates

Project description:Inter and intra-lineage genetic diversity of Zika virus differs for American isolates

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Genome organization of dengue and Zika viruses

Project description:Dengue and Zika are closely related members of the Flaviviridae family of positive, single-stranded RNA viruses and are of global clinical importance. These viruses utilize an 11kb RNA genome for translation and replication, and much remains to be learnt about how the entire genome folds to enable virus function. Here, we performed high throughput RNA secondary structure and pair-wise interaction mapping on four dengue serotypes and four Zika strains within their virus particles. We identified structures that are associated with translation pausing, and are evolutionary conserved by integrating synonymous mutation rates into our analysis. Genome-wide interaction mapping revealed alternative structures, as well as extensive long-range RNA interactions – including the known circularization signals– within the virus particles. Many of these long-range interactions are conserved across the viruses and/or clustered into “hubs” that are shown to be functionally important. This comprehensive structural resource of dengue and Zika viruses reveals that viral genome organization is much more complex than previously appreciated and deepens our understanding of the molecular basis for viral pathogenesis.

2019-02-28 | GSE106483 | GEO

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Project description:Zika virus (ZIKV) is a mosquito-transmitted positive-sense RNA virus in the family Flaviviridae. Candidate live-attenuated vaccine (LAV) viruses with engineered deletions in the 3’UTR provide immunity and protection in animal models of ZIKV infection, and phenotypic studies show that LAVs retain protective abilities following in vitro passage. The present study investigates the genetic diversity of wild-type (WT) parent ZIKV and its candidate LAVs using next generation sequencing analysis of five sequential in vitro passages. ZIKV RNA from was transfected into Vero cells, incubated for nine days, harvested, and clarified by centrifugation to generate passage 0 (P0) ZIKV infectious clones. Subsequently, P0 ZIKVs were blind-passaged into fresh cultures to generate P1, then serially through P5. P1-P5 stocks were harvested from cell media at 4-5 days post-infection. ZIKV RNA from 3’UTR deletion mutants were transfected into Vero cells, incubated for nine days, harvested, and clarified by centrifugation to generate passage 0 (P0) ZIKV infectious clones. Subsequently, P0 ZIKVs were blind-passaged into fresh cultures to generate P1, then serially through P5. P1-P5 stocks were harvested from cell media at 4-5 days post-infection. Genetic diversity of the viruses were assessed by evaluating both the variability (or uncertainty) at each nucleotide position was determined using Shannon entropy calculations and identified single nucleotide variants (SNVs). The results showed both the parental WT and LAV derivatives increase in genetic diversity with evidence of adaptation following passage.

2020-04-13 | E-MTAB-8905 | 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

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Genome organization of dengue and Zika viruses

Project description:Genome organization of dengue and Zika viruses

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Project description:To better understand the critical drivers of Zika virus pathogenicity, we used microarray analysis to evaluate the host responses triggered by Zika virus infection in MRC-5 cells.

2021-03-23 | E-MTAB-10292 | biostudies-arrayexpress

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