Project description:To search for host factors regulating Zika virus infection, we performed a genome-wide loss-of-function CRISPR/Cas9 screen in haploid human ESCs. The regulators were identified by the quantification of enrichment of their mutant clones within a pooled loss-of-function library upon Zika virus infection.
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.
Project description:RNA-seq count data at 3 timepoints was generated for Zika-exposed and Zika-naïve individuals in order to assess associated signatures
Project description:This study aims to study binding events between the Zika virus RNA genome and endogenous transcripts during infection of a human cell line. We develop a novel psolaren-based cross-linking technique to preserve interactions between mRNA and the Zika genome. Interacting RNA molecules are ligated together prior to reversal of the cross-links and selection for Zika-containing fragments. Reverse transcription and paired-end high-throughput sequencing then allow us to identify the interacting transcripts. We generated three batches of libraries, where all samples in each batch were generated from the same pool of RNA. Within each batch, we have the livefire sample, where the protocol was performed as described above; a reverse-control sample, where the protocol was performed by reversing the cross-links prior to ligation; and a no-cross-link control, where the protocol was performed without any cross-linking. The latter two samples represent negative controls where no genuine interactions should be observed.
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.
