A SARS-CoV-2 Delta variant containing mutation in the probe binding region used for RT-qPCR test in Japan exhibited atypical PCR amplification and might induce false negative result

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1. Version published to 10.1016/j.jiac.2022.01.019

   May 1, 2022
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   ScreenIT

   Nov 23, 2021

   SciScore for 10.1101/2021.11.15.21266335: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	IRB: The downstream analyses were performed at the Division of Genomics and Transcriptomics in the Joint Research Center for Human Retrovirus Infection, Kumamoto University [Approved by the Ethics Review Committee of the Faculty of Life Sciences Kumamoto Field Sample Permit: Specimen collection and storage: For this study, sputum and/or nasopharyngeal swab samples were collected from the Kumamoto city area from August 16, 2021, to September 8, 2021, as part of the regular COVID-19 diagnostic service.
   Sex as a biological variable	not detected.
   Randomization	Global genome collections were downloaded from the “Region-specific Auspice source file” of the GISAID database, resulting in 3580 viral …

   SciScore for 10.1101/2021.11.15.21266335: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	IRB: The downstream analyses were performed at the Division of Genomics and Transcriptomics in the Joint Research Center for Human Retrovirus Infection, Kumamoto University [Approved by the Ethics Review Committee of the Faculty of Life Sciences Kumamoto Field Sample Permit: Specimen collection and storage: For this study, sputum and/or nasopharyngeal swab samples were collected from the Kumamoto city area from August 16, 2021, to September 8, 2021, as part of the regular COVID-19 diagnostic service.
   Sex as a biological variable	not detected.
   Randomization	Global genome collections were downloaded from the “Region-specific Auspice source file” of the GISAID database, resulting in 3580 viral genomes (globally distributed random viral strains collected from December 2019 to October 2021) for global phylogenetic tree construction.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   After the adapter trimming step, a cleaning step was performed using the PRINSEQ tool [25] and Read1 with Phred score > 20 were used for downstream analysis.	PRINSEQ suggested: (PRINSEQ, RRID:SCR_005454) Phred suggested: (Phred, RRID:SCR_001017)
   Adapter trimmed and cleaned reads were then aligned to the SARS-CoV-2 reference genome NC_045512 (isolate Wuhan-Hu-1) using the BWA-MEM algorithm [26].	BWA-MEM suggested: (Sniffles, RRID:SCR_017619)
   Subsequently, the Samtools program [27] was used to remove multiple aligned reads, and Freebayes (Version 1.2.0	Samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   Finally, the aligned files and VCF files were visualized using the Integrative Genomics Browser (IGV) [29].	Integrative Genomics Browser suggested: None
   First, the viral sequences were aligned to the SARS-CoV-2 reference genome NC_045512 (isolate Wuhan-Hu-1) using Geneious Prime (version 2020.2.4) (https://www.geneious.com/).	https://www.geneious.com/ suggested: (Geneious, RRID:SCR_010519)
   Then, the aligned sequences were used to construct a maximum-likelihood phylogenetic tree using phyML 3.0 [33] with Smart Model Selection (SMS) [34].	phyML suggested: (PhyML, RRID:SCR_014629)

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   Results from OddPub: Thank you for sharing your data.

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2021.11.15.21266335v1 on medRxiv

   Nov 20, 2021