Diagnostic testing and screening for SARS-CoV-2

(Page last reviewed: 8 September 2021)

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 (BAL), endotracheal aspirate (ETA), expectorated sputum).

Saliva can also be considered as a specimen when testing for SARS-CoV-2. Available data suggests that only assays detecting SARS-CoV-2 RNA should be used for this specimen type as the sensitivity of antigen tests is not sufficient. For further details, see the ECDC technical report Considerations for the use of saliva as sample material for COVID-19 testing.

Respiratory specimen collection from the upper and in particular lower respiratory tract should be performed under heightened infection prevention and control measures (airborne precautions) 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 in the infection. High viral loads have been detected at or shortly after symptom onset and they tend to decrease afterwards. In more severe cases viral load is significantly higher (see also COVID-19 latest evidence from ECDC on viral shedding and viral load).

ECDC has published a guidance for discharge and ending isolation in the context of widespread community transmission of COVID-19 including testing recommendations to end isolation.

Antibody testing

Serological tests should not be used to detect current infection with SARS-CoV-2. These tests may be used to confirm past infection with SARS-CoV-2 in clinical care or for public health purposes. A negative serological test, however, cannot exclude a previous infection with SARS-CoV-2. Optimal specimens for antibody testing are acute and convalescent (possibly two to four weeks after acute phase) serum (or for some tests also plasma). ECDC has published a brief technical report on 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 the WHO interim guidance for laboratory testing.

Specimen shipping

Based on the WHO 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, then 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 may 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-marked COVID-19 rapid tests can also be found in the ECDC 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 the ECDC 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 sequencing methods and alternative methods to detect and identify the 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 scaling up of sequencing and genetic characterisation in EU/EEA Member States via a sequencing service contract. Please contact PHE.Support.Microbiology@ecdc.europa.eu for more information.

The publicly-available sequence database GISAID EpiCoV accepts the upload of SARS-CoV-2 sequences. Nextstrain offers genomic evolution analysis and phylogenetic visualisation of SARS-CoV-2. ECDC analyses all data uploaded to GISAID EpiCoV with the objectives to assess the proportions and trends of circulating variants as well as to detect and assess 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 is a variant of concern, the particular variant would need to be assessed more broadly through a risk assessment process looking into various risk elements (e.g. increased transmissibility, morbidity/mortality or vaccine escape).

For laboratories to assess at least the antigenic distance to the currently available vaccine antigen and to main circulating viruses, it would be important to perform antigenic characterisation through neutralisation assay with convalescent sera and standards. Multiple laboratory methods to perform virus neutralisation test have been developed. Some examples are the microneutralisation assay, the pseudovirus neutralisation assay and the surrogate virus neutralisation test. For further details, see the ECDC guidance 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 for detection of neutralising antibodies. JRC has also 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.

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. Please contact PHE.Support.Microbiology@ecdc.europa.eu for more information.

Biosafety

Based on WHO 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 PPE for preventing contact, droplet and airborne transmission of pathogens and they adhere to all measures related for reducing the risk of transmission of SARS-CoV-2 in healthcare settings before collecting the patient samples. Please see ECDC 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 biosafety guidance and use laboratory coat, gloves, 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 the staff handing infectious specimens.

Cleaning of the surfaces should be performed using proper personal protective equipment (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 correct practise of 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