Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping
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SciScore for 10.1101/2020.06.03.130591: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Nasopharyngeal swab specimens: NP swab specimens were collected from patients after informed written consent was obtained, under a protocol approved by the local governing human research protection committee.
IRB: The Johns Hopkins Influenza Research and Surveillance (JH-CEIRS) program’s human subjects protocol was approved by the Johns Hopkins School of Medicine Institutional Review Board (IRB): IRB90001667 and NIH Division of Microbiology and Infectious Diseases: Protocol 15-0103Randomization not detected. Blinding Unextracted NP swab specimens (n=9) were de-identified, blinded and provided for further analysis. Power Analysis not detected. Sex as a … SciScore for 10.1101/2020.06.03.130591: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Nasopharyngeal swab specimens: NP swab specimens were collected from patients after informed written consent was obtained, under a protocol approved by the local governing human research protection committee.
IRB: The Johns Hopkins Influenza Research and Surveillance (JH-CEIRS) program’s human subjects protocol was approved by the Johns Hopkins School of Medicine Institutional Review Board (IRB): IRB90001667 and NIH Division of Microbiology and Infectious Diseases: Protocol 15-0103Randomization not detected. Blinding Unextracted NP swab specimens (n=9) were de-identified, blinded and provided for further analysis. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources The Zika virus isolate was from a patient in Cali, Colombia, and was grown in Vero-E6 cells. Vero-E6suggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The cRASL-seq methodology is not without limitations. While we have demonstrated a sensitivity comparable to single-plex RT-qPCR, the limits of detection are governed by overall sequencing depth, which can be reduced by consumption of reads from highly abundant ligation products (due to a high load of a co-infecting virus for example). However, since the ligation products are all amplified with a high degree of uniformity, simple RNA spike-in or PCR spike-in sequences can be used to determine the lower limit of detection sensitivity for each reaction. Analysis of host transcripts can also be used to assess sample acquisition sufficiency, a known source of false negative test results.29 Another important concern for COVID-19 molecular diagnostics is the turnaround time. When NGS is used to read out the cRASL-seq assay, the testing turnaround time is unlikely to be less than ∼24 hours with currently available instrumentation. Per-sample sequencing cost considerations will favor analysis of large sample batches, which could further increase turnaround times. For large-scale regional and national level surveillance purposes however, an occasional one to two days of self-quarantine while awaiting test results may be acceptable, given the costs and limitations associated with alternative methods. Faster, non-NGS-based readouts of cRASL probe ligation products may also be developed. For example, isothermal amplification, followed by array or test-strip hybridization may prove more a...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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