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Genome-scale CRISPR-Cas9 knockout screens for enterovirus D68 and rhinovirus C15

ABSTRACT: Genome-scale CRISPR-Cas9 knockout screens for enterovirus D68 and rhinovirus C15

PROVIDER: PRJEB33400 | ENA |

REPOSITORIES: ENA

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Genome-scale CRISPR-Cas9 knockout screens for enterovirus D68 and rhinovirus C15

Project description:H1-HeLa cells were stably transduced with lentiCas9-Blast (Addgene, Plasmid #52962) and subsequently selected using blasticidin to generate constitutively expressing Cas9 H1-HeLa cells. A single Cas9-expressing H1-HeLa clone was then transduced with lentivirus without a selection marker to stably express CDHR3 C529Y (H1-HeLa+CDHR3). A single CDHR3-expressing H1-HeLa clone was then chosen based on RT-qPCR of CHDR3 expression and RV-C15 RNA levels for mutagenesis. 300 million of the H1-HeLa cells constitutively expressing CDHR3 and Cas9 were transduced with the lentiGuide-Puro from the GeCKO v2 library at a MOI of 0.3. Cells were selected using puromycin and heterogeneous H1-HeLa knockout cell populations were subsequently pooled together. The CRISPR genetic screens were started 10 days post transduction. >1000-fold coverage of mutagenized cells (libraries A and B) was infected with either RV-C15 (MOI=1 PFU/cell) or EV-D68 Missouri (MOI=1 PFU/cell). RV-C15 infection was repeated for an additional round at 6 days post-infection. As soon as appearance of visibly viable colonies was observed, populations of virus-resistant cells were pooled and harvested. Uninfected starting populations of mutagenized cells were used as the unselected reference. Total genomic DNA from both virus-resistant and uninfected cells was respectively extracted using QIAamp DNA Mini Kit (Qiagen). The inserted guide RNA sequences were retrieved from the genomic DNA by PCR amplification. The PCR products were then purified and subjected to NextSeq platform (Illumina) next-generation sequencing.

2019-07-10 | E-MTAB-8125 | biostudies-arrayexpress

Enterovirus D68

Project description:Enterovirus D68 Genome sequencing

| PRJNA266569 | ENA

Enterovirus D68

Project description:Enterovirus D68 Genome sequencing and assembly

| PRJNA274680 | ENA

Enterovirus D68

Project description:Enterovirus D68 sequence from clinical isolates (St. Louis, 2014)

| PRJNA263037 | ENA

Enterovirus D68

Project description:Complete Genome Sequences of Enterovirus D68 in the Philippines

| PRJDB11586 | ENA

Enterovirus D68 whole-genome analysis

Project description:Enterovirus D68 whole-genome analysis

| PRJEB32872 | ENA

Recent clinical isolates of enterovirus D68 have increased replication and induce enhanced epithelial immune response compared to the prototype Fermon strain.

Project description:In 2014, enterovirus D68 (EV-D68), previously associated primarily with mild respiratory illness, caused a large outbreak of severe respiratory illness and, in rare instances, paralysis. We compared viral binding and replication of eight recent EV-D68 clinical isolates and the prototype Fermon strain from 1962 in cultured HeLa cells and differentiated human primary bronchial epithelial cells (BEC) to understand the possible reasons for the change in virus pathogenicity. We found no significant differences in binding or replication in HeLa cell cultures between the recent clinical isolates. However, in HeLa cells, Fermon had significantly greater (1.5-2 log) binding and virus progeny yields but a similar level of replication (~2-log increase in viral RNA from 2h to 24h post infection) compared to recent isolates. In differentiated BECs, Fermon and the recent EV-D68 isolates had similar levels of binding; however, the recent isolates produced 1-2-log higher virus progeny yields than Fermon due to increased replication. We then utilized RNA-seq to define the transcriptional responses in BECs infected with four recent EV-D68 isolates, representing major phylogenetic clades, and Fermon strain. All the tested clinical isolates induced similar responses in BECs; however, numerous upregulated genes in antiviral and pro-inflammatory response pathways were identified when comparing the response to clinical isolates versus Fermon. These results indicate that the recent emergence in severe EV-D68 cases could be explained by increased replication efficiency and enhanced inflammatory response induced by newly emerged clinical isolates.

2023-07-06 | GSE233630 | GEO

Rhinoviruses and enterovirus-D68 replicate more robustly in respiratory tissues originating from asthmatic patients compared to non-asthmatic controls

Project description:Investigation of the mechanism leading to differential rhinovirus infection in airway epithelia from healty versus asthmatic patients

2023-02-13 | GSE222129 | GEO

Enterovirus D

Project description:Enterovirus-D68 genomic sequencing of 2014 US outbreak strains to understand its evolutionary dynamics and increased disease severity

| PRJNA270340 | ENA

Rhinovirus C

Project description:Human rhinovirus C

| PRJNA41899 | ENA