Diagnostic testing and screening for SARS-CoV-2

This section is aimed at assisting public health professionals and is based on an ongoing rapid review of the latest evidence.

(Page last reviewed: 22 March 2022)

Testing for SARS-CoV-2 virus

Case confirmation supports surveillance, rapid and effective contact tracing, implementation of infection prevention and control measures in accordance with national recommendations, and contributes to adequate patient care.

For guidance on testing strategies, see the list of ECDC documents further down on this page.

For recommendations from WHO, the guidance document Laboratory testing strategy recommendations for COVID-19 is available.

Specimens for the diagnosis of SARS-CoV-2 infection

Optimal specimens for the detection of current infection with SARS-CoV-2 are collected from the upper respiratory tract (e.g. nasopharyngeal swab, oropharyngeal swab, nasopharyngeal aspirate, nasal wash) or, if the patient is hospitalised or in intensive care, also from the lower respiratory tract (e.g. bronchoalveolar lavage, endotracheal aspirate, expectorated sputum).

Saliva can also be considered as a specimen when testing for SARS-CoV-2. Available data suggest that assays detecting SARS-CoV-2 RNA should preferably be used for this specimen type as the sensitivity of antigen tests is further reduced and likely not sufficient. For further details, see the ECDC technical reports Considerations for the use of saliva as sample material for COVID-19 testing and Options for the use of rapid antigen tests for COVID-19 in the EU/EEA. The regularly updated common list of rapid antigen detection tests (RADTs) currently includes only RADTs for which their clinical performance was measured based on samples collected from nasal, oropharyngeal or nasopharyngeal specimens and not on alternative sample types like saliva.

Respiratory specimen collection from the upper and especially lower respiratory tract should be performed under strict infection prevention and control measures (to avoid creation of aerosols) in accordance with ECDC guidance on Infection prevention and control and preparedness for COVID-19 in healthcare settings.

Specimens for laboratory testing should be collected early during the infection and within the first five days after onset of symptoms. Viral loads peak in most cases around the time of symptom onset and then gradually decrease. In more severe cases, viral loads are often significantly higher than in mild cases (see also COVID-19 latest evidence from ECDC on viral shedding and viral load).

ECDC has published a guidance for discharge and ending isolation including testing recommendations to end isolation.

Antibody testing

Serological tests cannot be used to detect current infection with SARS-CoV-2. These tests may be used to confirm a past infection with SARS-CoV-2 in clinical care settings or for public health purposes. Antibodies against the spike protein also become detectable after vaccination against SARS-CoV-2; therefore, results from certain serological tests should be interpreted with caution due to high vaccine coverage within the general population.

A negative serological test cannot exclude a previous infection with SARS-CoV-2. Antibody levels are best detected in the serum (or plasma, in some tests) two to four weeks after an acute phase infection or vaccination. ECDC has published a brief technical report on considerations for the use of antibody tests for SARS-COV-2 in the context of Digital Green Certificates.

Storage of specimens

All specimens can be stored at 2-8°C for up to 48 hours after collection. For handling or shipping after 48 hours, storage at -70°C is recommended in WHO’s interim guidance for laboratory testing.

Specimen shipping

According to WHO’s biosafety guidance, patient specimens from suspected or confirmed cases should be transported as UN3373, ‘Biological Substance Category B’. The packaging should be done in accordance with the International Air Transport Association Dangerous Goods Regulations (IATA DGR) – Packing Instruction 650, i.e. it must consist of three components: a primary receptacle, a secondary package, and a rigid outer package. If shipping of specimens is within national borders, it should comply with applicable national regulations. For overnight shipment, use shipment in an ice pack (temp 2-8°C).

If international shipping of specimens is expected, specimens should be stored at -70°C (dry ice) and comply with the UN Model Regulations and any other applicable regulations depending on the mode of transport being used. More information can be found in the Guidance on regulations for the transport of infectious substances 2021–2022.

Available guidance on shipping from WHO: Guidance for laboratories shipping specimens to WHO reference laboratories that provide confirmatory testing for COVID-19 virus

Testing methods

The specific tests currently recommended by WHO for the diagnosis and confirmation of SARS-CoV-2 are described in a dedicated WHO webpage.

Several commercial detection assays for SARS-CoV-2 RNA or antigen, and serological assays for SARS-CoV-2 specific antibodies are available on the market with CE-IVD marking. Information on these assays can be found in the test directory of the Foundation for Innovative New Diagnostics (FIND) and in the JRC COVID-19 In Vitro Diagnostic Devices and Test Methods Database of the European Commission. 

ECDC provides guidance on sequencing methods and alternative methods to detect and identify SARS-CoV-2 variants in two guidance documents:

More information on CE-IVD-marked COVID-19 rapid antigen tests can be found in  ECDC’s technical report Options for the use of rapid antigen tests for COVID-19 in the EU/EEA and the UK.

Genetic characterisation of SARS-CoV-2, detection of variant viruses

If possible, viral sequence information should be generated from representative samples of positive specimens. Regarding the optimal sampling strategy and number of specimens for sequencing, see ECDC’s technical report Guidance for representative and targeted genomic SARS-CoV-2 monitoring.

Information on variants that ECDC is currently monitoring is available on a dedicated webpage.

ECDC provides guidance on various methods to detect and identify SARS-CoV-2 variants of concern in the two guidance documents mentioned above under ‘Testing for SARS-CoV-2 virus’.

ECDC encourages the timely sharing of sequence data and is supporting sequencing and genetic characterisation in EU/EEA Member States via a sequencing service contract. Please email PHE.Support.Microbiology@ecdc.europa.eu for more information.

The publicly available sequence database GISAID EpiCoV accepts the uploading of SARS-CoV-2 sequences. If available, raw data should be deposited in the COVID-19 data portal through the European Nucleotide Archive (ENA). ECDC analyses all data uploaded to GISAID EpiCoV with the objectives of assessing the proportions and trends of circulating variants as well as detecting and assessing newly emerging variants.

ECDC launched a new online tool, ‘PrimerScan’, for monitoring primer and probe match to published genomes for RT-PCR detection assays. It presents mutation frequencies by primer/probe position and by geographic and temporal distribution. It also describes the assays by genomic position and gene targets.

Neutralisation assays and antigenic characterisation of SARS-CoV-2

To decide if a variant of interest (VOI) might be a variant of concern (VOC) and to inform public health actions, the particular variant needs to be assessed more broadly through a risk assessment process looking into various risk elements (e.g. increased transmissibility, morbidity/mortality, and vaccine escape).

For laboratories to assess the antigenic distance to the currently available vaccine antigen and to main circulating viruses, it is important to perform antigenic characterisation through a neutralisation assay with convalescent sera and/or sera from vaccinated people and standards for anti-SARS-CoV-2 antibody. Multiple laboratory methods to perform virus neutralisation tests have been developed. Some examples are the microneutralisation assay, the pseudovirus neutralisation assay, and the surrogate virus neutralisation test. For further details, see ECDC’s guidance document Methods for the detection and identification of SARS-CoV-2 variants.

WHO has developed an international standard to harmonise and standardise the different serological assays. JRC has developed similar standards. These standards can serve as the basis for the calibration of tests that quantify antibodies. Calibration will need to be performed at the individual laboratories that are using the different commercial antibody tests.

  • WHO/NIBSC WHO International Standard – First WHO International Standard (IS) for anti-SARS-CoV-2 immunoglobulin (human); Instructions for use (Version 2.0, Dated 17/12/2020); NIBSC (Biological reference materials catalogue code): 20/136 (the IS is currently not available, but secondary standards that are calibrated against the IS can be used)
  • JRC – Certified reference materials EURM-017 and EURM-018

Antigenic characterisation of SARS-CoV-2 using neutralisation assays is essential in order to identify variant viruses that may escape natural immunity and/or vaccines. ECDC launched a tender to support the antigenic characterisation of SARS-CoV-2, through which Member States can ship viruses for antigenic characterisation of virus isolates. Laboratories that do not perform virus neutralisation assays are encouraged to send specimens to one of the COVID-19 WHO referral laboratories, especially when a new variant is detected. The list of WHO reference laboratories providing confirmatory testing for COVID-19 can be found on WHO’s website. WHO is facilitating shipment of specimens to these laboratories via a shipping mechanism. Antigenic characterisation results for new VOCs should immediately be shared with the WHO Regional Office for Europe and ECDC. Please email Covid.microbiology@ecdc.europa.eu for more information.

Biosafety

Based on WHO’s document Laboratory biosafety guidance related to coronavirus disease 2019 (COVID-19) (28 January 2021), non-propagative diagnostic laboratory work (for example, sequencing, nucleic acid amplification test (NAAT)) should be conducted at a facility using procedures equivalent to Biosafety Level 2 (BSL-2).

Propagative work (for example, virus culture, isolation, or neutralisation assays) should be conducted at a Biosafety Level 3 (BSL-3) laboratory.

Personal protective equipment

For collecting specimens from patients: ensure healthcare workers wear personal protective equipment (PPE) for preventing contact, droplet and airborne transmission of pathogens and that they adhere to all measures related to reducing the risk of transmission of SARS-CoV-2 in healthcare settings before collecting the patient samples. Please see ECDC’s document Guidance for wearing and removing personal protective equipment in healthcare settings for the care of patients with suspected or confirmed COVID-19.

In the laboratory: see WHO’s biosafety guidance and use laboratory coat, gloves, safety goggles, and appropriate footwear.

Disinfectants

It is important that all clinical laboratories take appropriate measures to properly disinfect surfaces in order to avoid infection of staff handing infectious specimens.

Cleaning of surfaces should be performed using proper PPE. See Guidance for wearing and removing personal protective equipment in healthcare settings for the care of patients with suspected or confirmed COVID-19 for the correct practice for donning and doffing of PPE.

Ethanol-based germicides (71%, 70%, and 62% ethanol) and sodium hypochlorite (bleach, 0.1-1%) are the most effective surface disinfection products and achieve the greatest reduction in viral infectivity. A list of effective cleaning options for different environments and settings can be found in Disinfection of environments in healthcare and non-healthcare settings potentially contaminated with SARS-CoV-2.