Stealth Omicron: A Novel SARS-CoV-2 Variant That Is Insensitive to RT-qPCR Using the N1 and N2 Primer-Probes

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that is causing a worldwide pandemic since the spring of 2020. In Osaka, the second biggest prefecture in Japan, we identified a novel SARS-CoV-2 variant from a coronavirus disease 2019 (COVID-19) patient that was detected by polymerase chain reaction (PCR) using E primers, but not by real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) using the N1 and N2 primer-probe sets recommended by CDC. We analyzed the S and N gene regions by reverse-transcription and nested PCR using the S and N specific primers, and DNA sequencing, and found that this BA.5 variant contained point mutations in the probe sequences of both the N1 and N2 primer-probe regions. This finding led us to affirm the importance of monitoring the genome sequence of the SARS-CoV-2 variants continuously.