Journal: PLOS ONE

Article Title: Evaluation of the Kaira COVID-19/Flu/RSV Detection Kit for detection of SARS-CoV-2, influenza A/B, and respiratory syncytial virus: A comparative study with the PowerChek SARS-CoV-2, influenza A&B, RSV Multiplex Real-time PCR Kit

doi: 10.1371/journal.pone.0278530

Figure Lengend Snippet: Analytical specificity evaluation results of the Kaira assay.

Article Snippet: Human coronavirus 229E , ATCC (VR-740D) , Negative.

Techniques: Virus

Journal: Journal of Clinical Virology

Article Title: A RT-PCR assay for the detection of coronaviruses from four genera

doi: 10.1016/j.jcv.2020.104391

Figure Lengend Snippet: The pan-CoV assay was evaluated against a panel of known coronaviruses and other unrelated human respiratory virus pathogens.

Article Snippet: Human coronavirus OC43 , β CoV , Lab strain , Betacoronavirus 1; ATCC.

Techniques: Virus, Plasmid Preparation, Derivative Assay

Journal: NPJ Genomic Medicine

Article Title: Myeloablation-associated deletion of ORF4 in a human coronavirus 229E infection

doi: 10.1038/s41525-017-0033-4

Figure Lengend Snippet: Detection of a 548-nucleotide deletion in a HCoV 229E strain associated with myeloablation. a Depiction of the case history surrounding myeloablation and coronavirus infection. A woman in her 40s with AML was found to be infected with a HCoV 229E just before her HCT. Due to the patient’s advanced disease, the decision was made to continue with the transplant. Four successive HCoV-positive nasal swab specimens were available from the patient; two from before treatment with myeloablative cyclophosphamide and total body irradiation and two from after. All days are reported relative to HCT. b Coverage plots of mNGS reads mapped to the reference genome for HCoV 229E (NC_002645) of three samples from the patient revealed the generation of a 548-nucleotide deletion in the ORF4a/4b gene. In addition to deleting 83% of the coding region from ORF4a/4b, the deletion resulted in a frame shift that resulted in a premature stop codon 10 amino acids before the reference genome stop codon. Primer binding sites are denoted in blue for confirmatory junction RT-PCR. c Confirmatory junction RT-PCR of the four available HCoV-positive nasal swabs revealed the absence of the deletion before myeloablation and the presence of the deletion in specimens taken after myeloablation. NTC , no template control

Article Snippet: No CPE was visualized for any of the patient’s four clinical samples and HCoV 229E RNA levels in the culture supernatant were undetectable by qRT-PCR after inoculation, while viral growth was apparent in the positive control HCoV 229E ATCC type strain (Figure ).

Techniques: Infection, Irradiation, Binding Assay, Reverse Transcription Polymerase Chain Reaction, Control

Journal: NPJ Genomic Medicine

Article Title: Myeloablation-associated deletion of ORF4 in a human coronavirus 229E infection

doi: 10.1038/s41525-017-0033-4

Figure Lengend Snippet: Specimens sequenced in this study

Article Snippet: No CPE was visualized for any of the patient’s four clinical samples and HCoV 229E RNA levels in the culture supernatant were undetectable by qRT-PCR after inoculation, while viral growth was apparent in the positive control HCoV 229E ATCC type strain (Figure ).

Techniques:

Journal: Cell

Article Title: Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks

doi: 10.1016/j.cell.2020.12.006

Figure Lengend Snippet: Genome-wide CRISPR Screens Identify Host Factors Required for SARS-CoV-2 Infection (A) Genome-wide CRISPR screening workflow. Cas9-expressing Huh-7.5 cells are transduced with the Brunello genome-wide CRISPR library, selected with puromycin, and infected with SARS-CoV-2 or one of three seasonal CoVs (HCoV-OC43, HCoV-NL63, or HCoV-229E). Surviving cells and mock controls are then harvested, and sgRNA abundance is determined using next-generation sequencing. (B) Bubble plot of data from SARS-CoV-2 screens at 37°C. Red lines denote z = ±2. (C) Bubble plot of data from SARS-CoV-2 screens at 33°C. Red lines denote z = ±2. (D) Scatterplot comparing Z scores from (B) and (C) for SARS-CoV-2 screens at 37°C and 33°C, respectively. (E) Subset of significantly enriched genes from SARS-CoV-2 screens at 37°C and 33°C.

Article Snippet: HCoV-OC43 , ZeptoMetrix , Cat#0810024CF.

Techniques: Genome Wide, CRISPR, Infection, Expressing, Transduction, Next-Generation Sequencing

Journal: Cell

Article Title: Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks

doi: 10.1016/j.cell.2020.12.006

Figure Lengend Snippet: Analysis of Established and Putative CoV Host Factors and Gene-wise Fitness Scores for SARS-CoV-2 and 3 Seasonal CoVs, Related to and (A) Heatmap of z-scores for known and putative coronavirus host factors. (B-D) Genewise fitness beta scatterplots comparing SARS-CoV-2 at 37°C versus mock (B), SARS-CoV-2 at 33°C versus mock (C), and SARS-CoV-2 at 33°C versus SARS-CoV-2 at 37°C (D). Non-targeting controls and essential control genes are highlighted in blue and red, respectively. (E) HCoV-OC43 versus mock infected. (F) HCoV-NL63 versus mock infected. (G) HCoV-229E versus mock infected.

Article Snippet: HCoV-OC43 , ZeptoMetrix , Cat#0810024CF.

Techniques: Control, Infection

Journal: Cell

Article Title: Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks

doi: 10.1016/j.cell.2020.12.006

Figure Lengend Snippet: Parallel Genome-wide CRISPR Screening against Multiple HCoVs Uncovers Host Factors and Pathways with Pan-CoV and Virus-Specific Functional Roles (A) Bubble plot of data from HCoV-OC43 screens at 33°C. Red lines denote z = ±2. (B) Bubble plot of data from HCoV-NL63 screens at 33°C. Red lines denote z = ±2. (C) Bubble plot of data from HCoV-229E screens at 33°C. Red lines denote z = ±2. (D) UpSet plot showing enriched hits overlapping in screens across all four viruses. Select genes for enriched sgRNAs are indicated.

Article Snippet: HCoV-OC43 , ZeptoMetrix , Cat#0810024CF.

Techniques: Genome Wide, CRISPR, Virus, Functional Assay

Journal: Cell

Article Title: Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks

doi: 10.1016/j.cell.2020.12.006

Figure Lengend Snippet: Expanded CoV-Specific Networks, Related to Figure 3 (A–D) Network diagram of all coronavirus screen hits and the next 100 adjacent interactors, shown in gray. Broad functional categories of highly interconnected gene neighborhoods are indicated. Diagrams are for SARS-CoV-2 (A), HCoV-OC43 (B), HCoV-NL63 (C) and HCoV-229E (D).

Article Snippet: HCoV-OC43 , ZeptoMetrix , Cat#0810024CF.

Techniques: Functional Assay

Journal: Cell

Article Title: Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks

doi: 10.1016/j.cell.2020.12.006

Figure Lengend Snippet: Validation of High-Confidence Coronaviridae Host Factors (A) Candidate validation in Huh-7.5 cells with SARS-CoV-2 infection at 33°C. (B) Candidate validation in Huh-7.5 cells with HCoV-OC43 infection at 33°C. (C) Candidate validation in Huh-7.5 cells with HCoV-NL63 at 33°C. (D) Candidate validation in Huh-7.5 cells with HCoV-229E at 37°C. (E) Heatmap representation of data from (A)–(D). The SARS-CoV-2 and HCoV-NL-63 receptor ( ACE2 ) and the HCoV-229E receptor ( ANPEP ) are shown separately.

Article Snippet: HCoV-OC43 , ZeptoMetrix , Cat#0810024CF.

Techniques: Infection

Journal: Cell

Article Title: Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks

doi: 10.1016/j.cell.2020.12.006

Figure Lengend Snippet: A Majority of Functional CoV Host Factors Are Expressed in the Airway, Related to , , and (A–D) scRNaseq expression dotplot diagrams from select cells in the airway of the average expression and the percent of cells expressing coronavirus host factors for SARS-CoV-2 (A), HCoV-OC43 (B), HCoV-NL63 (C) and HCoV-229E (D). Rows for each diagram are ordered top to bottom from highest to lowest z-score. Data are from Chua et al. (2020) .

Article Snippet: HCoV-OC43 , ZeptoMetrix , Cat#0810024CF.

Techniques: Functional Assay, Expressing

Journal: Cell

Article Title: Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks

doi: 10.1016/j.cell.2020.12.006

Figure Lengend Snippet:

Article Snippet: HCoV-OC43 , ZeptoMetrix , Cat#0810024CF.

Techniques: Virus, Recombinant, SYBR Green Assay, Luciferase, DNA Purification, Plasmid Preparation, CRISPR, Software, Genome Wide, Knock-Out, Inverted Microscopy