Reflex (genotyping) assays for identification of priority SARS-CoV-2 variants of concern
Updated 20 April 2022
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Reflex (genotyping) assays comprise of nucleotide primers and probes to identify the presence of specific mutations in SARS-CoV-2 positive samples. The detection of mutations is indicative of infection with a variant of concern (VOC).
The use of genotyping assays is not a substitute for the detailed identification of VOC lineages and mutations that is achieved by whole genome sequencing (WGS). Instead, the 2 technical approaches are performed in parallel for all suitable positive samples identified via the public sector.
Reflex testing results are available more quickly than WGS and facilitate more rapid public health responses, including surge testing and strategic decision-making. In parallel, WGS is performed on every suitable positive sample to confirm the reflex testing result and to identify variants that cannot be detected or monitored using reflex testing alone. If a sample is insufficient in volume for both reflex testing and WGS, WGS takes priority.
A strategy for reflex assay testing in England has been established. All public provider laboratories can access a quality-assured, equitable reflex testing service to identify priority mutations of concern via regional network laboratories. Samples that are positive for SARS-COV-2 are referred to regional reflex testing laboratories.
The selection of priority mutations is determined by risk assessment of new variants using a risk assessment framework. The reflex assay results are reported to UK Health Security Agency (UKHSA) via the Second-Generation Surveillance System (SGSS) and analysed to give an inferred (mutation) lineage.
When the corresponding WGS results become available, they are matched to the reflex assay results. This provides confirmation of lineage and enables monitoring of the sensitivity and specificity of the reflex assay for inferred lineage calling.
Prospective suppliers can access the current mutation target details via updates that will be published here. Currently, a single mutation target ‘Q493R’ is used within genotyping assays, which infers Omicron lineages (BA.1.529, BA.1, BA.2, BA.3).