Journal: The Journal of Hospital Infection

Article Title: Efficiency and sensitivity optimization of a protocol to quantify indoor airborne SARS-CoV-2 levels

doi: 10.1016/j.jhin.2022.08.011

Figure Lengend Snippet: Reverse transcriptase (RT) efficiency and sensitivity comparison in detection of SARS-CoV-2 genome target by RT–droplet digital polymerase chain reaction. An RNA plasmid solution containing the ORF1ab target was serially diluted and cDNA was synthesized using two RTs. The number of measured ORF1ab target copies was plotted against the expected copies to obtain the slope, from which efficiency was calculated. RTs used were TranscriptMe (green) and SuperScript II (purple). (A) 10 2 –10 5 plasmid copy number range; (B) 1–10 3 plasmid copy number range.

Article Snippet: An RNA plasmid containing the ORF1ab target (TibMolbiol) was used to compare RT efficiencies, that were experimentally calculated by using a known number of plasmid copies.

Techniques: Reverse Transcription, Comparison, Digital PCR, Plasmid Preparation, Synthesized

Journal: The Journal of Hospital Infection

Article Title: Efficiency and sensitivity optimization of a protocol to quantify indoor airborne SARS-CoV-2 levels

doi: 10.1016/j.jhin.2022.08.011

Figure Lengend Snippet: Efficiency comparison between two reverse transcriptases (RT) in airborne SARS-CoV-2 RNA assessment by RT–droplet digital polymerase chain reaction. RNA isolated from air samples collected from COVID-19 patient rooms was reverse-transcribed using TranscriptMe (green) and SuperScript II (purple). (A) Percentage of samples in which SARS-CoV-2 was detected by analysing the ORF1ab and N1 targets (black circle portion). (B) Mean and standard error of target copy number per reaction. N = 30 per group.

Article Snippet: An RNA plasmid containing the ORF1ab target (TibMolbiol) was used to compare RT efficiencies, that were experimentally calculated by using a known number of plasmid copies.

Techniques: Comparison, Digital PCR, Isolation, Reverse Transcription

Journal: The Journal of Allergy and Clinical Immunology

Article Title: Clinical testing for COVID-19

doi: 10.1016/j.jaci.2020.05.012

Figure Lengend Snippet: Companies and laboratories that have received EUA for RT-PCR–based tests

Article Snippet: April 10, 2020 , Atila BioSystems , N/ORF1ab , GAPDH.

Techniques: Control, Luminex

Journal: mBio

Article Title: The Conserved Coronavirus Macrodomain Promotes Virulence and Suppresses the Innate Immune Response during Severe Acute Respiratory Syndrome Coronavirus Infection

doi: 10.1128/mBio.01721-16

Figure Lengend Snippet: The SARS-CoV macrodomain is required but not sufficient to suppress cytokine expression in vitro . (A) Calu-3 2B4 cells were infected with WT or N1040A virus at an MOI of 2 PFU/cell. Cells were collected at the indicated time points, and RNA levels were determined by RT-qPCR with primers specific for each transcript and normalized to HPRT. Data are derived from results of 1 experiment representative of 3 independent experiments. (B) Calu-3 2B4 cells were infected as described for panel A, and cells were collected at 48 hpi. Lysates were analyzed by immunoblotting with the indicated antibodies using a Li-COR Odyssey Imager. (C and D) pcDNA3-GFP, pLKO-MERS-CoV ORF4A, and pcDNA3-sMacro were transfected into HeLa cells. At 24 h later, the cells were either collected for immunoblotting (C) or transfected with 1 μg pI-C or 1 μg dA-dT (D). For panel D, cells were collected at 16 h after transfection and RNA was analyzed by RT-qPCR with primers specific for indicated transcript. HA, hemagglutinin; GAPDH, glyceraldehyde-3-phosphate dehydrogenase. Data are derived from results of 1 experiment representative of 2 independent experiments. *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; #, P = 0.06; n.s., not significant.

Article Snippet: Codon-optimized sMacro (nucleotides 3262 to 3783 of SARS-CoV MA15) and MERS-CoV ORF4a were synthesized and cloned into pUC57 (GenScript).

Techniques: Expressing, In Vitro, Infection, Virus, Quantitative RT-PCR, Derivative Assay, Western Blot, Transfection

Journal: Clinics in Laboratory Medicine

Article Title: An Overview of SARS-CoV-2 Molecular Diagnostics in Europe

doi: 10.1016/j.cll.2022.02.005

Figure Lengend Snippet: An overview of stand-alone RT-PCR suppliers and kits available in the EU. Details are taken from company websites and/or accompanying literature

Article Snippet: Euroimmun , EuroRealTime SARS-CoV-2 , Orf1ab , N , , Manufacturer SPC , 25–1000 , Roche LightCycler 480, ABI 7500, Bio-Rad CFX 96, Qiagen Rotor-Gene Q, qTower 3 , 1 copy/ul , .

Techniques: Control, Virus, Real-time Polymerase Chain Reaction, CDC Assay, Quantitative RT-PCR

Journal: Clinics in Laboratory Medicine

Article Title: An Overview of SARS-CoV-2 Molecular Diagnostics in Europe

doi: 10.1016/j.cll.2022.02.005

Figure Lengend Snippet: An overview of low- to mid-throughput end-to-end testing platforms for SARS-CoV-2

Article Snippet: Euroimmun , EuroRealTime SARS-CoV-2 , Orf1ab , N , , Manufacturer SPC , 25–1000 , Roche LightCycler 480, ABI 7500, Bio-Rad CFX 96, Qiagen Rotor-Gene Q, qTower 3 , 1 copy/ul , .

Techniques: Control

Journal: Clinics in Laboratory Medicine

Article Title: An Overview of SARS-CoV-2 Molecular Diagnostics in Europe

doi: 10.1016/j.cll.2022.02.005

Figure Lengend Snippet: An overview of high-throughput molecular diagnostic platforms for SARS-CoV-2

Article Snippet: Euroimmun , EuroRealTime SARS-CoV-2 , Orf1ab , N , , Manufacturer SPC , 25–1000 , Roche LightCycler 480, ABI 7500, Bio-Rad CFX 96, Qiagen Rotor-Gene Q, qTower 3 , 1 copy/ul , .

Techniques: Diagnostic Assay, Control

Journal: The Journal of Allergy and Clinical Immunology

Article Title: Clinical testing for COVID-19

doi: 10.1016/j.jaci.2020.05.012

Figure Lengend Snippet: Companies and laboratories that have received EUA for RT-PCR–based tests

Article Snippet: March 20, 2020 , Primerdesign Ltd , ORF1ab , None.

Techniques: Control, Luminex

Journal: The Journal of Allergy and Clinical Immunology

Article Title: Clinical testing for COVID-19

doi: 10.1016/j.jaci.2020.05.012

Figure Lengend Snippet: Examples of companies offering tests that are packaged in cartridges and POC tests

Article Snippet: March 20, 2020 , Primerdesign Ltd , ORF1ab , None.

Techniques:

Journal: The Journal of Allergy and Clinical Immunology

Article Title: Clinical testing for COVID-19

doi: 10.1016/j.jaci.2020.05.012

Figure Lengend Snippet: EUAs for RT-PCR tests

Article Snippet: March 20, 2020 , Primerdesign Ltd , ORF1ab , None.

Techniques: Control, Diagnostic Assay

Journal: The Journal of Allergy and Clinical Immunology

Article Title: Clinical testing for COVID-19

doi: 10.1016/j.jaci.2020.05.012

Figure Lengend Snippet: SARS-CoV-2 genome and RT-PCR primer/amplicon sites: Schematic of SARS-CoV-2 genome with localization of various published RT-PCR amplicons in ORF1ab/b, S, E, and N genes. Primer/amplicon sequences aligned with 2 highly similar viral consensus sequences (EPI_ISL_412026 [BetaCoV/Hefei/2/2020] and MT106052.1 [2019-nCoV/USA-CA7/2020]) using NCBI BLAST program. E , Envelope; ORF , Open Reading Frame; RdRp , RNA-dependent RNA polymerase; UTR , untranslated region. Primer sequences from referenced publications. , , US CDC primers (N1, N2, N3) as reported in Udugama et al.

Article Snippet: March 20, 2020 , Primerdesign Ltd , ORF1ab , None.

Techniques: Reverse Transcription Polymerase Chain Reaction, Amplification