From Delta to Omicron SARS-CoV-2 variant: Switch to saliva sampling for higher detection rate
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SciScore for 10.1101/2022.03.17.22272538: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: Informed consent and questionnaire (assessing eating, drinking, chewing or smoking 30 minutes before test and test indication) were completed under the guidance of the researcher.
Field Sample Permit: Based on the Belgian Sciensano guidelines for saliva collection [6], the participant collected the saliva sample in a CE-labeled sterile buffer-free recipient by spitting.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources In brief: WGS was performed using the Research Use Only AmpliSeq for Illumina SARS-CoV-2 Research Panel on Illumina MiSeq (80 samples on V2 flow … SciScore for 10.1101/2022.03.17.22272538: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: Informed consent and questionnaire (assessing eating, drinking, chewing or smoking 30 minutes before test and test indication) were completed under the guidance of the researcher.
Field Sample Permit: Based on the Belgian Sciensano guidelines for saliva collection [6], the participant collected the saliva sample in a CE-labeled sterile buffer-free recipient by spitting.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources In brief: WGS was performed using the Research Use Only AmpliSeq for Illumina SARS-CoV-2 Research Panel on Illumina MiSeq (80 samples on V2 flow cell) according to the manufacturer’s standard protocol: 8 µl RNA extract was reverse transcribed using Lunascript RT SuperMix Kit (New England Biolabs, MA, USA), followed by amplification of 237 virus specific amplicons covering > 99% of the 30kb reference genome aiming at a median coverage above 500x, minimal coverage for mutation calling of 10x and variant allele frequency > 90% and a minimum of 30,000 reads per sample and a maximum of 1kb bases below minimal coverage. WGSsuggested: NoneA consensus sequence was constructed using an in-house pipeline containing Trimomatic for trimming, alignment by BWA, mutation calling by Freebayes and inspection of sequence quality by IGV. BWAsuggested: (BWA, RRID:SCR_010910)Freebayessuggested: (FreeBayes, RRID:SCR_010761)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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.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.
Results from scite Reference Check: We found no unreliable references.
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