A combination of current single gene target failure (SGTF) capability and the current genotyping assay coverage, there are rapid ‘proxy’ ways to detect the Omicron variant in 75-80% of all samples processed by lighthouse laboratories. At present, all samples of interest are being directed to laboratories which can report SGTF and are being prioritised for sequencing.
A genotyping assay capable of detecting Delta variant with more than 90% accuracy and Omicron with 88% accuracy is already in place in eight lighthouse laboratories providing approximately 15%, or 30,000 samples per day, coverage of positive viable samples. All pillar 1 positive samples are tested via the current genotyping assay and capable of detecting Delta variant with more than 90% accuracy and Omicron with 88% accuracy. Most pillar 1 labs are not able to detect SGTF. There are plans to implement the assays in the final two lighthouse laboratories in the coming weeks.