COVID-19 Guidance for sampling and laboratory investigations Version 7.2

Publication date: 17/04/ 2020

Health Protection Scotland

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Version history

Version Date Summary of changes

v0.2 23/01/2020 First publication

v2.0 01/02/2020

Additional information added to introduction

Removed line stating that CL3 facilities are available in all microbiology laboratories

Updated to align with PHE guidance

Added information about laboratory reporting of results to HPS

Throughout text: limited changes to wording for clarification

New nomenclature and new case definition

V3.0 02/02/2020 Updated contact details (appendix 1)

V4.0 04/02/2020 Updated information about POCT in line with PHE guidance

Updated PHE Colindale packaging requirements

V5.0 07/02/20 Amended to align with updated case definition and contact definition issued by PHE on 06/02/20

V5.1 07/02/20 Small amendment to contact definition

V6.0 10/02/20 Updated to align sample types and with PHE guidance issued by PHE 06/02/20

Amended throughout to clarify correct processes due to the roll out of laboratory testing in Scotland

V6.1 15/02/2020 Changes to formatting of results section to improve clarity

Link to request form for WOSSVC added

Amendment to epidemiological criteria in possible case definition to include transit through an at risk area

HPS number removed from local HPT contact list

Links to relevant HPS guidance documents added

Added comment that pneumatic tubes should not be used for sample transport

Updated nomenclature to SARS-CoV-2 for the virus and COVID-19 for the disease

Updated PHE hyperlinks in line with updated nomenclature.

Added link to PHE packaging video.

V6.2 26/02/2020 Updated reporting results section to include reporting of presumptive positive information

Removed Actions for WOSSVC/Edinburgh SVC from reporting results section

Updated link to PHE packaging video

V6.3 11/03/2020 Change to case definition

Removed information about confirmation of positives at Colindale, including change from presumptive positive to confirmed positive.

Changed information about containment level in line with updated PHE guidance

V7.1 26/03/2020 Remove case definition and insert link to HPT guidance, Primary care guidance and Secondary Care guidance where this information can be found

Changes to align with changes to where samples will be tested

Update which samples will be tested to be clearer

Update IPC guidance link

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Version Date Summary of changes

Update transport requirements

Include request to add epidemiology codes to clinical details

Add link to PHE prioritisation document

Added contact details for laboratories.

V7.2 17/04/20 Testing in care home settings

Link added to IPC step down criteria

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Contents

Introduction .............................................................................................................................. 4

Case definition ......................................................................................................................... 4

Approach to sampling .............................................................................................................. 5

Sample requirements for COVID-19 testing ......................................................................... 6

Additional samples which may be required .......................................................................... 6

Requirements for the request form ....................................................................................... 7

Requirements for sample transport ...................................................................................... 7

Results of testing ..................................................................................................................... 8

Actions for the microbiology laboratory................................................................................. 8

Actions for local Health Protection team ............................................................................... 8

Guidance for microbiologists/virologists ................................................................................... 9

Samples for routine microbiology testing .............................................................................. 9

Samples for SARS-CoV-2 testing ......................................................................................... 9

Appendix 1 – Contacts in local Health Protection teams ........................................................ 10

Appendix 2 – Contacts in local microbiology laboratories ...................................................... 11

Health Protection Scotland

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Introduction

Novel coronavirus (COVID-19) is a new strain of coronavirus first identified in Wuhan, China.

Clinical presentation may range from mild-to-moderate illness to pneumonia or severe acute

respiratory infection.

It has been announced by the UK/Scottish Government that as of 16 March anyone

developing symptoms consistent with COVID-19, however mild, should stay at home for 7

days from the onset of symptoms as per existing advice. In addition, it is now recommended

that anyone living in the same household as a symptomatic person should self-isolate for 14

days. Information on COVID-19, including advice for people who are symptomatic and their

households, can be found on NHS Inform.

Additional measures are recommended to help reduce the spread of COVID-19 and to

protect people at increased risk of severe illness. Information on these can be found on NHS

Inform.

Case definition

For the most updated case definition please refer to the following document: HPS Guidance

for Secondary Care.

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Approach to sampling

Sampling should be arranged for individuals admitted to hospital with suspected

COVID-19. Further information can be found in the HPS Secondary Care Guidance.

Samples may also be taken for other reasons, for example occupational health or to

inform health protection management e.g. for an outbreak within a closed setting.

Outbreak guidance states that the first 5 symptomatic residents in a care home setting should be tested to provide confirmation of an outbreak of COVID-19. On 15 April 2020 the Scottish Government announced the expansion of testing to include all care home residents who develop symptoms. Therefore Scotland will move to a system where any symptomatic patient in a care home will be clinically assessed and, where appropriate, offered testing for COVID-19. Samples may also be taken for other reasons, for example occupational health or to inform health protection management e.g. for an outbreak within a closed setting other than a care home.

Sampling for Key Workers should be performed according to the testing approach laid out by

your health board, based on Scottish Government Guidance for Health Boards: Testing

for COVID-19 Infection to Enable Key Workers to Return to Work.

Regular liaison with local virology/microbiology departments is important to ensure that

appropriate specimens are taken to establish the diagnosis and sufficient capacity is

available. The local laboratory will process and refer these samples to a referral laboratory by

category B transport if required.

All samples should be collected and processed in line with:

4 Nations Guidance: COVID-19: Guidance for Infection Prevention and Control in Healthcare settings

PHE Guidance: COVID-19: safe handling and processing for laboratories

HPS Guidance: COVID-19: Obtaining an upper respiratory diagnostic sample

Point of care tests, including blood gas analysis, should only be undertaken if a local

risk assessment has been completed and shows it can be undertaken safely.

Where clinically indicated, samples for routine microbiology and virology testing should be

collected and tested according to local protocols. It is essential to inform the laboratory

before samples are sent, and ensure that specimen request forms are clearly marked with

the relevant clinical and epidemiological history.

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There are currently no additional sample storage requirements beyond local laboratory

practice.

Sample requirements for COVID-19 testing

Upper respiratory tract sample(s):

o a viral nose swab AND a viral throat swab in one collection tube OR

o single swab used for throat then nose in one collection tube OR

o a nasopharyngeal aspirate in a universal transport pot.

Lower respiratory tract sample, if obtainable i.e. sputum in a universal container.

If the patient is admitted to hospital, a sample for serology should be collected at the

same time as other samples collected for primary diagnostic testing for COVID-19. A 5

ml serum tube is required. For children <12 years, 1mL is acceptable. Where a

baseline serum sample is collected a convalescent sample will be required 14-

60 days following the acute sample. Clarification is being sought on the

collection of the convalescent sample, and further update will follow when

available.

Additional samples which may be required

Samples for repeat testing

o In certain circumstances, repeat sampling may be required; the testing laboratory will contact the requesting clinician if this is indicated.

Samples for monitoring confirmed COVID-19

o Sequential sampling may be required to monitor the progress of confirmed SARS-CoV-2 infection in secondary care, decided on a case-by-case basis. This should be performed in line with HPS COVID-19 - guidance for stepdown of infection control precautions and discharging COVID-19 patients from hospital to residential settings

Samples for outbreaks in closed and residential settings

o The name of the facility/ward and the date of the first case must be added to the clinical details in order to identify this as an outbreak sample (the date is required in order to differentiate between potential sequential outbreaks)

o In large outbreaks, in non-care home settings it may not be possible to test all samples. The testing laboratory will therefore test the first 5 samples submitted under each incident log as routine. Any further testing within the outbreak would be by discussion with the duty virologist at the laboratory only.

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Requirements for the request form

Please ensure that the category code listed below is included in the clinical details section of

the request form for the sample types below. Codes are not required for other sample types.

COVID Cat: SER GP sentinel samples.

COVID Cat: OCH Samples from individuals being tested for occupational reasons e.g. health care worker or household index case of a health care worker.

COVID Cat: ICU Patients receiving level 3 care.

Important points about sample-labelling and request forms:

each sample must be labelled with ID, date of birth and type of sample;

paperwork (request forms) should NOT be placed in the bag with the sample container

request form must include a contact phone number for sharing of results

samples without appropriate paperwork will not be tested

Requirements for sample transport

All samples should be packaged and transported in accordance with Category B

transportation regulations. UN 3373 packaging must be used for sample transport. If

required, transport requirements should be discussed with the specialist virology laboratory.

Specific requirements for sample packaging can be accessed at: COVID-19: packaging of

COVID-19 samples for referral to regional testing labs.

If moving samples within the same hospital, it is sufficient to double bag samples, which

should be transported by an appropriate person who is aware of the nature of the sample.

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Results of testing

Results of testing will be provided by the testing laboratory.

Patient management and public health action (as required) should be taken as soon as

a confirmed positive or presumptive positive result is available.

If another pathogen is identified, this does not rule out SARS-CoV-2 co-infection.

Actions for the microbiology laboratory

Positive results should be shared urgently with the requesting clinician and the local Health Protection team. In a secondary care setting positive results should also be urgently shared with the infection prevention and control team.

As a minimum, the laboratory should communicate ALL results to:

o The requesting clinician: If positive result note that screening assay has resulted in SARS-Cov-2 detection and to ensure the patient is being managed in line with COVID-19: Guidance for Infection Prevention and Control in Healthcare settings.

o The local Health Protection team (Appendix 1): Further guidance for HPT is available on the HPS website: HPS Guidance for Health Protection teams.

o Health Protection Scotland

o In a secondary care setting both positive and negative result should also be shared with the infection prevention and control team.

Actions for local Health Protection team

The local Health Protection Team should refer to HPS Guidance for Health Protection

teams.

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Guidance for microbiologists/virologists

Clinical laboratories should perform their own risk assessments for handling biological

specimens from patients with suspected or confirmed COVID-19 taking into account the

guidance outlined in:

COVID-19: Guidance for Infection Prevention and Control in Healthcare settings – 4 Nations Guidance

COVID-19: safe handling and processing for laboratories – PHE guidance

Laboratory algorithm: Algorithm summarising sampling and laboratory investigations for SARS-CoV-2

COVID-19 is a notifiable disease and SARS-CoV-2 is a notifiable organism under the

Public Health etc (Scotland) Act 2008, as outlined in a letter from the CMO.

An overview of the laboratory testing process for diagnostic samples can be seen in the HPS

algorithm: testing for SARS-CoV-2 in Scotland.

Samples for routine microbiology testing

Microbiological samples for tests performed locally will need to be handled at the appropriate

biological containment level. Further information about safe sample handling is available in

the PHE Guidance: COVID-19: safe handling and processing for laboratories specific for

SARS-CoV-2.

Testing should be performed where clinically indicated, in line with local arrangements

including referral where necessary.

Note that it is the responsibility of the treating centre to arrange investigations for pathogens

other than SARS-CoV-2.

Samples for SARS-CoV-2 testing

Please note that during periods of significant demand, samples may be prioritised as

described in PHE Guidance: Priority of SARS-CoV-2 (COVID-19) testing during periods

of significant demand.

These samples may also be tested using a routine respiratory virus panel as per current local

arrangements, however as the epidemic progresses, increasingly laboratories may need to

narrow the repertoire of testing. For patients of clinical concern additional test requirements

should be discussed with your local laboratory.

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Appendix 1 – Contacts in local Health Protection teams

Organisation Office Hours Telephone Number

Out of Hours Telephone Number

Ayrshire and Arran 01292 885858 01563 521 133

Crosshouse Hospital switchboard

Borders 01896 825560 01896 826 000

Borders General switchboard

Dumfries and Galloway 01387 272 724 01387 246 246

Fife 01592 226435 01592 643355

Victoria Hospital switchboard

Forth Valley 01786 457 283 Ask for CPHM on call

01324 566000 Ask for CPHM on call

Grampian 01224 558520 0345 456 6000

Greater Glasgow & Clyde 0141 201 4917 0141 211 3600

Gartnavel switchboard

Highland 01463 704886 01463 704000

Raigmore switchboard

Lanarkshire 01698 858232 01236 748 748

Monklands switchboard

Lothian 0131 465 5429/5422 0131 536 1000

Edinburgh Royal switchboard

Orkney 01856 888034 01856 888 000

Balfour Hospital switchboard

Shetland 01595 743340 01595 743000

Gilbert Bain switchboard

Tayside 01382 596 976/987 01382 660111

Ninewells switchboard

Western Isles 01851 704704 01851 708033

Ayrshire and Arran 01292 885858 01563 521 133

Crosshouse Hospital switchboard

Borders 01896 825560 01896 826 000

Borders General switchboard

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Appendix 2 – Contacts in local microbiology laboratories

Organisation Laboratory contact details

Ayrshire & Arran 01563 827420

Borders 01896 826250 01896 826258

Dumfries & Galloway 01387 241560

Fife 01592 648169

Forth Valley 01324 566692

Grampian 01224 552444

GGC

Virology: 0141 201 8721

Out of hours: 0141 211 4000 (ask for on-call virologist)

Email: west.ssvc@nhs.net

Golden Jubilee 0141 951 5931

Highland 01463 704206

01463 704207

Lanarkshire (Wishaw) 01698 366405

Lothian

Virology: 0131 536 3373 (Option 2)

Out of hours: 0131 536 1000 (ask for on-call virologist)

Email: virologyadvice@nhslothian.scot.nhs.uk

Orkney 01856 888217

Shetland 015950 743011

Tayside 01382 632559

Western Isles 01851 708033

Ayrshire & Arran 01563 827420