Molecular detection of SARS‐CoV‐2 and differentiation of Omicron and Delta variant strains

• DOI: 10.1111/tbed.14497
• Publication Date: 2022-02-26T19:39:42Z
• Authors: Wai Ning Tiffany ...; Vaughn Hamill; Lance Noll; Nanyan Lu; Elizabeth Poulsen...; Donald Harbidge; Emily Cox; Claire Richardson; Mark Gray; Tesfaalem Sebhatu; Kyle Goerl; Susan Brown; Gregg Hanzlicek; Jamie Retallick; Jianfa Bai
• Keywords: Strain (injury)

The SARS-CoV-2 virus is the causative agent of COVID-19 and has undergone continuous mutations throughout pandemic. more transmissible Omicron variant quickly spread replacing Delta as most prevalent strain globally, including in United States. A new molecular assay that can detect differentiate both variants was developed. collection 660,035 full- or near-full genomes, 169,454 24,202 strains, were used for primer probe designs. In silico data analysis predicted an coverage >99% all strains. differential test designed based on Δ31-33 aa deletion N-gene, which present original B.1.1.529 main genotype, BA.1, well BA.2 BA.3 subtypes. Therefore, should majority Standard curves generated with human clinical samples indicated PCR amplification efficiencies 104%, 90.7% 90.4% Omicron, Delta, non-Delta/non-Omicron wild-type genotypes, respectively. Correlation coefficients standard >0.99. detection limit 14.3, 32.0, 21.5 copies per reaction to specifically SAR-CoV-2 Selected genotypes identified by RT-qPCR also confirmed sequencing. did not any animal coronavirus-positive tested. Human nasal swab previously tested positive (n = 182) negative 42) ThermoFisher TaqPath Combo Kit, produced same result assay. Among samples, 55.5% (101/182), 23.1% (42/182), 21.4% (39/182) non-Omicron/non-Delta