N Gene Target Failure (NGTF) for detection of Omicron: a way out for the "stealth" too?

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.