Methods for the detection and characterisation of SARS-CoV-2 variants - first update

Technical report

European Centre for Disease Prevention and Control/World Health Organization Regional Office for Europe. Methods for the detection and characterisation of SARS-CoV-2 variants – first update. 20 December 2021. Stockholm/Copenhagen; ECDC/WHO Regional Office for Europe: 2021.

This technical report provides guidance to laboratories, microbiology experts and relevant stakeholders in making decisions on establishing or scaling up capability and capacity to detect and identify circulating SARS-CoV-2 variants. It will also facilitate decision-making on the appropriate technologies to use and for which objective.

Executive summary

What is new in this update

  • The reference list for available assays has been updated.
  • The Delta and Omicron variant assays have been included.
  • The rapid antigen detection test chapter has been updated to include information related to the Health Security Committee’s list of mutually recognised tests in the EU/EEA countries.

Key messages

  • Several SARS-CoV-2 VOCs have emerged in recent months and monitoring their circulation in all countries is of key importance to prevent and control the spread of VOCs.
  • Whole SARS-CoV-2 genome sequencing, or at least complete or partial S-gene sequencing, should be used to confirm infection with a specific variant and characterise the variant.
  • For the early detection and prevalence calculation of VOCs (or when sequencing capacity is limited) alternative methods should be used, such as diagnostic screening NAAT-based assays. To contain or delay introduction of a VOC, positive samples should ideally be screened using a NAAT-based assay that can offer the advantage of rapid results.
  • When employing NAAT-based methods, sequencing should be used to characterise at least a subset of the variants.
  • In the event of low prevalence of a VOC in the population and when the objective is to delay the introduction and spread of the VOC, ideally all NAAT-based results indicative of the VOC should be confirmed by sequencing.
  • Sample and method selection are key and will depend on the objectives (e.g. to assess the circulation of the different SARS-CoV-2 variants using representative samples from the community, or genomic characterisation to monitor the virus evolution and inform vaccine composition decisions or outbreak analyses).
  • Assay validation should be carried out to ensure that the laboratory testing system is performing adequately for the circulating viruses.
  • Laboratories should remain vigilant to ensure that they detect reduction in sensitivity or failure to detect/identify circulating variants by the different PCR or antigen-based assays.
  • If the diagnostic capacity is insufficient, priority should be given to severe cases, fatal cases, and cases with suspected high contagiousness of the pathogen that caused the outbreak, especially among those vaccinated or individuals with a history of COVID-19.
  • SARS-CoV-2 consensus sequences should be submitted to GISAID or other public databases. Raw sequences should also be submitted to the European Nucleotide Archive (ENA).
  • Detection of novel VOCs or outbreaks of currently circulating VOCs should be reported immediately through the Early Warning and Response System (EWRS), while variant detections should be reported to TESSy on a weekly basis.