RE: Question: Omicron detection vs identification28 Nov 2021 12:57
From said WHO document:
Testing and sequencing
Genomic surveillance is of crucial importance for early detection of the presence and monitoring of epidemiological
trends of specific VOCs, VOIs and variants under monitoring, and will provide important information to guide
response for this new variant [16]. This includes regular testing of representative samples but also strengthening
targeted sampling from persons coming from high-risk areas.
The presence of the deletion ?69-70 means that S-gene target failure (SGTF) for the Thermo Fischer TaqPath
assay can be used as a screening method for Omicron. In a setting with the Delta variant dominating, this can be
used as a proxy for Omicron after confirmation of a subset of samples by sequencing. Currently there is no further
information available on any effect on sensitivity for other RT-PCR assays or for rapid antigen tests. Countries
could consider retrospective SGTF screening of SARS-CoV-2 positive samples from recently returned travellers from
Southern African countries to rapidly assess whether cases may have been recently introduced.
Rapid antigen tests should be unaffected based on the analysis of the mutations in the nucleocapsid (N gene) of
Omicron viruses, however, verification of this is underway [13].