Laboratory support for COVID-19 in the EU/EEA

Testing for SARS-CoV-2 virus

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

Any person fulfilling the criteria of a suspected case should be tested for SARS-CoV-2 virus, as part of active case finding. However, national authorities may decide to only test subgroups of suspected cases based on the national epidemiological situation, capacity to test or other criteria. The criteria for laboratory testing of patients with acute respiratory tract infection could also include a case-by-case clinical judgement based on national recommendations. The WHO recommendations for testing strategy are available here.

As long as the resources allow, a single positive test should be confirmed by a second RT-PCR assay targeting a different SARS-CoV-2 gene. In situations of large increase of cases and community transmission where a second confirmatory test might not be feasible or delay the confirmation, a single positive laboratory test is sufficient to confirm a suspect COVID-19 case.

A single negative SARS-CoV-2 test (especially if from an upper respiratory tract specimen) or a positive test result for another respiratory pathogen result does not exclude SARS-CoV-2 infection. If the result of the first virus gene test is inconclusive or weakly positive and there is a strong suspicion for SARS-CoV-2 infection, another specimen should be tested with the primary and secondary RT-PCR assays.

To safeguard sampling and testing resources, the following actions can be considered:

  • Use of one swab per patient for oropharynx and nasopharynx
  • Pooling of multiple respiratory specimens from one patient
  • Prioritise hospitalised patients and vulnerable populations

Types of specimens 

The following upper respiratory tract specimens should be considered:

  • nasopharyngeal swab
  • oropharyngeal (throat) swab
  • nasopharyngeal aspirate or nasal wash

If the patient is hospitalised or in intensive care, lower respiratory tract specimens could be considered:

  • bronchoalveolar lavage (BAL)
  • endotracheal aspirate (ETA)
  • expectorated sputum (for patients with productive cough, no induction of sputum is recommended)

Additional specimens to consider for later testing:

  • serum, acute and convalescent (possibly 2 to 4 weeks after acute phase) for when serological testing becomes available
  • faeces

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 technical report on Infection prevention and control for the care of patients with 2019-nCoV in healthcare settings.  

Specimens should be collected as soon as possible. Similar to other viral respiratory infections, it is likely that respiratory specimens collected early after symptom onset yield higher virus concentrations. According to the ECDC technical report on Discharge criteria for confirmed COVID-19 cases – When is it safe to discharge COVID-19 cases from the hospital or end home isolation? the frequency of specimen collection for hospitalised patients should be at least every 2 to 4 days until there are two upper respiratory tract samples negative for SARS-CoV-2, collected at ≥ 24-hour intervals. For symptomatic patients after the resolution of symptoms, samples should be collected at least seven days after the onset of symptoms or after > 3 days without fever. When resources are limited, discharge based on only clinical symptoms is advised.

Storage of specimens

All specimens should be stored at 2-8 oC for up to 48 hours after collection. For handling or shipping after 48 hours, storage at -70 oC is recommended.

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 oC).

If international shipping of specimens is expected, then specimens should be stored at -70 oC (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 2019–2020. Available guidance on shipping:

WHO referral laboratories for COVID-19 testing in the EU and the UK

[Source: Current list of WHO reference laboratories providing confirmatory testing for COVID-19 (Updated 2 March 2020)]

Laboratories offering diagnostic testing support

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.

It is recommended that the specimens of the first five positive cases and the first 10 negative cases that meet the COVID-19 case definition for testing should be shipped for confirmation to the national reference or international referral laboratory for COVID-19. After that, the laboratories can test for SARS-CoV-2 independently but should collaborate with national reference laboratories or WHO referral laboratories to troubleshoot any assay issues.

Virus characterisation

If possible, viral sequence information should be generated from a representative sample of positive specimens. ECDC encourages the timely sharing of sequence data. The publically available sequence database GISAID accepts the upload of SARS-CoV-2 sequences. Nextstrain offers genomic evolution analysis and phylogenetic visualisation of SARS-CoV-2.


Based on WHO Laboratory biosafety guidance related to coronavirus disease 2019 (COVID-19) (uploaded 12 February 2020): 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 neutralization assays) should be conducted at a containment laboratory with inward directional airflow (BSL-3).

Personal protective equipment

For sampling: 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.


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 hypochlorid (bleach, 0.1-1%) are the most effective surface disinfection products and achieve the greatest reduction in viral infectivity. A list of effective antimicrobial agents against coronaviruses can be found in ‘Interim guidance for environmental cleaning in non-healthcare facilities exposed to SARS-CoV-2’.

Commercial assays

Currently there are many commercial tests on the market for molecular and serology testing for SARS-CoV-2. A list can be found on the webpage of the Foundation for Innovative New Diagnostics (FIND) . FIND, together with a third-party, is conducting an independent evaluation of multiple SARS-CoV-2 assays that are currently in use or will become available in the future. 

The primary objective of these studies is to independently verify manufacturer’s claims on the analytical lower limit of detection (LOD). The evaluation will also establish diagnostic accuracy using positive and negative clinical specimens from several affected areas. Results will be shared with the global health community so that countries have objective and independent evidence on the performance of available/eligible SARS-CoV-2 in vitro diagnostics.

A total of 200 submissions for evaluation have been received from test developers of in vitro diagnostics (IVDs) that detect SARS-CoV-2 nucleic acid. These are now being assessed against the inclusion criteria and manufacturers will be contacted by the end of March 2020. There will be multiple rounds of evaluation: tests that detect nucleic acid will be prioritised first, and immunoassays (manual, automated or lateral flow) will be assessed at a later date.

FIND has now launched a second evaluation process for test developers interested in having their immunoassays (machine-based or lateral flow, rapid tests specific for SARS-CoV-2 antigen or antibodies) evaluated using a standardised, independent protocol. Deadline is the 20 March.


Latest updates


Considerations relating to social distancing measures in response to COVID-19 – second update

Publication, Technical report -


Considerations related to the safe handling of bodies of deceased persons with suspected or confirmed COVID-19

Technical report -


Coronavirus disease 2019 (COVID-19) and supply of substances of human origin in the EU/EEA

Technical report -


Communicable disease threats report, 15-21 March 2020, week 12

Publication -


Video on COVID-19: Why social distancing is important

Video -

Read more

Case definition and European surveillance for COVID-19, as of 2 March 2020

Case definition for EU surveillance of COVID-19. A case definition is a set of standard criteria for classifying whether a person has a particular disease, syndrome, or other health condition.

External tools

Research projects

European laboratory networks

Emerging Viral Diseases-Expert Laboratory Network (EVD-LabNet)

European Reference Laboratory Network for Human Influenza (ERLI-Net)

Other useful links

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External quality assessments (EQA)

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Molecular and genomic typing

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