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This publication is available at https://www.gov.uk/government/publications/wuhan-novel-coronavirus-guidance-for-clinical-diagnostic-laboratories/wuhan-novel-coronavirus-handling-and-processing-of-laboratory-specimens
Knowledge about the pathogenic potential and transmission risks for the novel coronavirus, SARS coronavirus-2 (SARS-CoV-2), and the associated disease it causes, COVID-19, is currently very limited. The World Health Organisation officially named the disease COVID-19 on 11 February 2020. The International Committee for Taxonomy of Viruses named the causative virus SARS-CoV-2 on 7 Feb 2020. This guidance is based on current knowledge of the virus and other coronaviruses. It aims to minimise risks for laboratory staff handling specimens from patients with suspected or laboratory-confirmed COVID-19.
This interim guidance is specific to clinical diagnostic laboratory practice in England and may differ from guidance produced by agencies in other countries, including recommendations about containment levels and control measures. Advice offered here relates to laboratory procedures conducted in clinical diagnostic laboratories; it does not cover virus isolation, research work, or work involving animals infected with SARS-CoV-2.
This guidance may be updated as new information becomes available.
To date, laboratory-acquired infection has not been reported for SARS-CoV-2. Laboratory-acquired infections with the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) have been reported previously but only in laboratories performing virus propagation.
For the related Middle East respiratory syndrome coronavirus (MERS-CoV), tissue tropism appears to be broad in humans and although MERS-CoV infection is a zoonosis, human-to-human transmission of MERS-CoV has occurred in households and healthcare facilities.
There is a human-to-human transmission risk (and an assumed potential zoonotic source) for SARS-CoV-2 infection (COVID-19). As for SARS-CoV and MERS-CoV, SARS-CoV-2 is an ACDP Hazard Group 3 pathogen (ACDP decision 13 February 2020).
Based on knowledge of other coronaviruses, infection with SARS-CoV-2 could occur by inhalation of aerosolised virus or by contact with droplets and contaminated fomites. Exposure to upper and lower respiratory tract specimens in the absence of appropriate biological safety measures is likely to represent the greatest risk of transmission of SARS-CoV-2 in a laboratory setting.
MERS-CoV RNA has been detected in a variety of human specimens, including urine, faeces and blood, and it is reasonable to assume this could be the case for SARS-CoV-2 until more is known about the virus. Human tissue specimens may also pose an infection risk, based on information obtained from studies of infected animals.
It is possible that laboratory workers could become infected if appropriate precautions are not taken when handling biological samples from patients with COVID-19. Since a patient with suspected COVID-19 may present to any healthcare facility, it is important that all clinical diagnostic laboratories take appropriate measures to contain potentially infectious materials, and prevent secondary infections and onward transmission.
3. Risk assessments and awareness
Clinical laboratories must perform their own risk assessments for handling biological specimens from patients with suspected or confirmed COVID-19. Point of care tests, including blood gas analysis, should be avoided unless a local risk assessment has been completed and shows it can be undertaken safely.
Clinical staff should notify laboratory staff when specimens are submitted from a patient with suspected or confirmed COVID-19, through proper completion of request forms or electronic test ordering systems, and by direct communication with the laboratory.
Clinicians may not have considered COVID-19 as a potential diagnosis, prior to sending specimens to the laboratory. Good laboratory practice, including the use of standard biological safety precautions, regular training of staff, and the use of standard operating procedures, will help minimise potential risks.
4. Personal protective equipment
Laboratory staff should wear personal protective equipment (PPE) appropriate to the biological containment level for the work being conducted and consistent with the risk assessment. PPE must always be removed on leaving the laboratory and hygiene practices rigorously maintained.
This must include disposable gloves and a laboratory coat or gown as a minimum, and may also include eye protection and other equipment, as identified by risk assessment. Respiratory protective equipment such as masks or respirators are not necessary when respiratory tract, urine, faecal or tissue samples are handled inside a microbiological safety cabinet (MSC).
If a local risk assessment deems that masks or respirators should be used, these should be FFP3 (conforming to BS EN149:2001) and fit-testing and training should be undertaken prior to use.
Masks or respirators are not an appropriate substitute for processing samples in an MSC when there is a risk of aerosols being generated.
5. Containment levels
Any procedure that involves potentially infectious material and is associated with a risk of generating aerosols, droplets or splashes, should always be performed within a MSC at containment level 3 (CL3) as defined in the Approved Code of Practice and Guidance for the Control of Substances Hazardous to Health (COSHH) Regulations 2002 (as amended).
Routine laboratory blood tests can be carried out in auto-analysers using standard practices and procedures at containment level 2 (CL2) but only after a suitable and sufficient risk assessment has been conducted which considers the potential for the generation of infectious aerosols. Auto-analysers should be disinfected following local procedures after sample processing and before scheduled maintenance.
Some auto-analyser protocols for routine laboratory tests may require specimen tubes to be opened first, or initial processing of the sample to be performed. Evidence suggests that capping and uncapping of samples is not a high-risk aerosol generating procedure. This does, however, depend on the cap and tube design and this must be considered in a suitable and sufficient risk assessment which also considers if the sample needs to be centrifuged, vortexed or pipetted manually. The risk assessment must include consideration of whether a microbiological safety cabinet needs to be used.
5.1 Work to be conducted at Containment Level 3
It is recommended that the following work is conducted in a MSC at CL3:
- division, aliquoting, or diluting of respiratory tract specimens, faecal specimens, urine specimens, and tissue specimens in which virus has not been inactivated1
- inoculation of bacterial or fungal culture media
- preparation of specimens for molecular testing (for example respiratory virus PCR) prior to sample inactivation
- urine antigen testing (such as for detection of Legionella pneumophila or Streptococcus pneumoniae)
- rapid antigen tests of respiratory tract specimens
- processing of any non-inactivated specimen that might result in the generation of aerosols
- preparation and fixing (chemical or heat) of smears for microscopy
5.2 Work that may be conducted at Containment Level 2
The following work may be conducted at CL2 following standard laboratory precautions, as long as it is consistent with the terms of the local risk assessment:
- diagnostic assays using whole blood, serum and plasma, including routine biochemistry and haematology, unless there is a risk of generating aerosols
- assays using virus-inactivated specimens, including molecular testing of inactivated specimens
- examination of bacterial or fungal cultures
- staining and microscopy of heat-fixed or chemically-fixed smears
- rapid diagnostic tests for malaria parasites, as long as they are performed within a MSC at CL2
Manual centrifugation of specimens with infectious potential must be performed using sealed centrifuge rotors or sample cups. Rotors or cups should be loaded and unloaded in a MSC.
7. Movement of samples within the laboratory
Specimen containers and vials should be decontaminated using a disinfectant with proven activity against enveloped viruses, prior to their removal from the MSC in CL3. Care should be taken to avoid accidental contamination of the exterior surfaces of all vessels and containers, regardless of containment level.
8. Packaging and transport of samples
Final packaging of potentially infectious specimens (for example, to send to a reference laboratory) may be performed at CL2, as long as the specimens are already contained within a sealed and decontaminated primary container. All potentially infectious samples must be transported in accordance with Category B transportation regulations, except for cultured samples for research or calibration which should be transported in accordance with Category A transportation regulations.
PHE follows the guidance on regulations for the transport of infectious substances 2019 to 2020, published by the World Health Organization.
|Sample type||Dangerous Goods Classification||Additional External Labelling Required for Samples Sent to PHE||Recommended method of transportation|
|Suspect patient sample||Category B||White label with Priority 10 printed in red||Same Day delivery courier|
|Presumptive positive patient sample||Category B||White label with Priority 20 printed in red||Same Day delivery courier|
|Confirmed positive samples for follow up||Category B||White label with Priority 20 printed in red||Same Day delivery courier|
|Contacts of known positive patients||Category B||White label with Priority 10 printed in red||Same Day delivery courier|
|Cultured samples for research or calibration||Category A||None||Mandatory ADR approved Category A courier|
Ensure the following for all packaged samples being sent to Public Health England (PHE):
- packaging is clearly labelled ‘PRIORITY 10’ or ‘PRIORITY 20’ as specified above per sample type
- contact details for reporting results have been provided on the accompanying request form
- accompanying paperwork is NOT placed inside the packaging with or within the primary container
See specific packaging guidance.
Transport via same day delivery courier is recommended for all sample types, except for cultured samples for research or calibration which must be transported by an approved Category A carrier.
9. Cleaning and handling of waste
Irrespective of the containment level, work surfaces and equipment should be decontaminated after specimens have been processed. Attention must be paid to all surfaces that may have come into contact with specimens or specimen containers.
A disinfectant solution or disinfectant wipe with proven activity against enveloped RNA viruses should be used, in accordance with local policies and following the manufacturer’s instructions.
Clinical waste should be disposed of according to local and national policies appropriate to the categorisation of the waste. Waste from auto-analysers is unlikely to pose a significant risk, due to the low sample volume and dilution steps, therefore special waste disposal precautions are not recommended for auto-analyser waste.
10. Maintaining service delivery
It is recommended that urgent and essential clinical diagnostic tests are not postponed pending the results of SARS-CoV-2 (COVID-19) testing, as long as this is consistent with the local risk assessment for the planned work and that appropriate containment measures are in place.
Inactivation refers to recognised processes that inactivate viral particles and render the virus replication incompetent, for example, addition of nucleic acid extraction buffer containing guanidinium thiocyanate. ↩