Highly sensitive and specific detection of the SARS-CoV-2 Delta variant by double-mismatch allele-specific real time reverse transcription PCR
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SciScore for 10.1101/2021.10.08.21264472: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Clinical samples: Anonymised, residual nose and throat swab samples in virus transport medium were obtained from staff and students at Imperial College London, and from household contacts of individuals with COVID-19 (Research Ethics Committee reference Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Cell cultured virus samples: Purified SARS-CoV-2 RNA extracted from Vero cell supernatants (2 passages) was kindly provided by Professor Wendy Barclay, Department of Infectious Disease, Imperial College London. Verosuggeste…SciScore for 10.1101/2021.10.08.21264472: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Clinical samples: Anonymised, residual nose and throat swab samples in virus transport medium were obtained from staff and students at Imperial College London, and from household contacts of individuals with COVID-19 (Research Ethics Committee reference Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Cell cultured virus samples: Purified SARS-CoV-2 RNA extracted from Vero cell supernatants (2 passages) was kindly provided by Professor Wendy Barclay, Department of Infectious Disease, Imperial College London. Verosuggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)Software and Algorithms Sentences Resources Alignments of SARS-CoV-2 VOC spike gene sequences downloaded from the GISAID database (https://www.gisaid.org/) were performed using MEGA version 7.0.21. MEGAsuggested: (Mega BLAST, RRID:SCR_011920)The primers (Table 1) were checked by in silico PCR (https://genome.ucsc.edu/cgi-bin/hgPcr) to rule out unwanted reactivity with the human genome, and by NCBI BLASTn (https://blast.ncbi.nlm.nih.gov/Blast.cg) to exclude reactivity with other respiratory viruses including human coronaviruses 229E, OC43 and NL63. https://genome.ucsc.edu/cgi-bin/hgPcrsuggested: (In-Silico PCR, RRID:SCR_003089)BLASTnsuggested: (BLASTN, RRID:SCR_001598)Results 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:Resource limitations mean that even in countries where genome sequencing is available it can only be used on a relatively small proportion of positive samples. DMAS-RT-PCR could provide a comparatively inexpensive, simple, rapid, highly sensitive and specific non-commercial alternative to sequencing for epidemiological surveillance of the Delta variant in many settings. An additional advantage of the DMAS-RT-PCR assay is that it appears to be capable of genotyping SARS-CoV-2 when the level of virus in clinical samples is too low for successful sequencing. Counter-intuitively, in countries such as the UK where the Delta variant is already dominant, one might consider using DMAS-RT-PCR for rapidly identifying the small minority of non-Delta cases and subjecting these to genome sequencing in order to increase the chance discovering novel, emergent non-Delta variants. In conclusion, the DMAS-RT-PCR assay that we describe here would be simple to establish in any laboratory that has the ability to conduct PCR assays and should greatly facilitate monitoring of the spread of the SARS-CoV-2 Delta variant globally.
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.
- Thank you for including a protocol registration statement.
Results from scite Reference Check: We found no unreliable references.
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