N Gene Target Failure (NGTF) for detection of Omicron: a way out for the ‘stealth’ too?
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Abstract
S-gene target failure (SGTF) is neither specific nor accurate for identification of Omicron lineage of SARS-CoV-2. We observed N-gene target failure (NGTF) in 402 out of 412 SARS-CoV2 positive cases from December to mid-January 2022 using a commercially available assay. This phenomenon was not observed with more than 15,000 cases tested previously. We sequenced the genome of five samples with NGTF and compared these results with six cases where NGTF was not seen. We confirm that cases with NGTF were the Omicron lineage while cases with preserved N-gene amplification belonged to Delta lineage. We discovered that the ERS31-33 deletion (nucleotide 28362-28370del) overlaps with N gene probe used, explaining NGTF. As the ‘stealth’ Omicron variant also harbors ERS31-33 deletion, this approach will work for the detection of ‘stealth’ Omicron variant as well. We suggest that NGTF can be used as a low cost, rapid screening strategy for detection of Omicron.
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SciScore for 10.1101/2022.01.28.22269801: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Due approval by Institutional Ethics Committee of Tata Memorial Centre was obtained for this study. 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 Alignment to the reference genome sequence (GenBank: MN908947.3, RefSeq: NC_045512.2; Wuhan-Hu-1 genome) was done using using BWA-MEM algorithm (v.0.7.17) BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)SAM files were processed further using Samtools (v.1.9) and variants were called using iVar (v.1.2) at a minimum alternative frequency of 0.01. Samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)iVarsuggested: NoneResults from O…
SciScore for 10.1101/2022.01.28.22269801: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Due approval by Institutional Ethics Committee of Tata Memorial Centre was obtained for this study. 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 Alignment to the reference genome sequence (GenBank: MN908947.3, RefSeq: NC_045512.2; Wuhan-Hu-1 genome) was done using using BWA-MEM algorithm (v.0.7.17) BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)SAM files were processed further using Samtools (v.1.9) and variants were called using iVar (v.1.2) at a minimum alternative frequency of 0.01. Samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)iVarsuggested: 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: 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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