TITLE: Sample reception, unpacking and barcoding
AUTHORS: Leigh Jones, Philip Walker, Robert Goldstone, Simon Caidan

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purpose of examination / Clinical relevance</span></div><div class = "text-block"><div class = "justify" style = "text-align:left">At the end of 2019, several pneumonia cases were reported in Wuhan, China and the pathogen was confirmed as a new viral strain. World Health organization has named the newly identified coronavirus as 2019-nCoV, also known as SARS-Cov-2. The disease developed into a dangerous pandemic, posing major challenges to the NHS. Although more research is necessary to better understand the virus, in response to the emergency, simple and rapid testing is essential to identify the virus in infected individuals. This will aid the implementation of efficient interventions to contain the spread, and distinguish healthcare workers who have been infected, and are required to self-isolate, from those showing similar symptoms but which are not 2019-nCoV associated. The latter category may continue to work, alleviating stress on hard-pressed healthcare resources. 2019-nCoV is an RNA virus, and the diagnostic tests detect viral RNA in swabs from patient airways using a reverse transcriptase PCR assay. Samples are submitted to HSL, an accredited reporting laboratory, and transferred to the Crick for testing. The first step of the process is sample receipt at the Crick. This SOP describes the inactivation of the virus.</div></div></div>

[STEPS]
?. Location of sample receipt and processing area: Clinical samples are delivered by courier and transferred to sample reception area by nominated staff.At the Receipt station, staff will act in the following capacities:Sample Checker (SC)Barcode Operator (BO)Barcode Label Operator (BLO)Sample Sorter (SS) Sample packaging:Incoming sample packs arrive in a UN3373 medical carrier. They are then transferred to a really useful box.  Multiple samples are initially triple baggedEach sample is in 2 sample bags.The sample bags are grouped in a larger outer bag (the sample pack).Sample packaging:Incoming sample packs arrive in a UN3373 medical carrier. They are then transferred to a really useful box.Multiple samples are initially triple baggedEach sample is in 2 sample bags.The sample bags are grouped in a larger outer bag (the sample pack).
?. [Registering Samples on Tube Tracker: Logging into Tube Tracker]
Open up the internet browser (Google Chrome) and search for the designated tube track website.
Tube Tracker is a software system to track the whereabouts of samples from the hospital site to the testing laboratory.
?. [Registering Samples on Tube Tracker: Logging into Tube Tracker]
Click on “Logon” in the top right hand corner of the screen.
?. [Registering Samples on Tube Tracker: Logging into Tube Tracker]
All users must have an individual login for the system; generic accounts must not be used.
?. [Registering Samples on Tube Tracker: Logging into Tube Tracker]
Log in using the username and desgnated password supplied.
?. [Registering Samples on Tube Tracker: Logging into Tube Tracker]
Once a username and password have been entered the relevant location will be visible now click on “Sign In”.
?. [Registering Samples on Tube Tracker: Unpacking the contents from the bag ]
Once samples arrive into the laboratory they will need to be unpacked from each bag received. Click on the icon “Unpack Box” from the main menu on the left hand side of the screen.
?. [Registering Samples on Tube Tracker: Unpacking the contents from the bag ]
Scan the barcode label which should be on the outer bag into the field ‘unpack box’. Always make sure the cursor is inside the field before scanning the bag barcode.
?. [Registering Samples on Tube Tracker: Unpacking the contents from the bag ]
The contents of the box will appear to the right of the screen.
?. [Registering Samples on Tube Tracker: Unpacking the contents from the bag ]
Begin scanning the barcodes of each individual sample to unpack and receive them. This will automatically update the sample audit trail to show when and where each sample has been received, and which user received it.
?. [Registering Samples on Tube Tracker: Unpacking the contents from the bag ]
When all samples have been unpacked from the box, a message will appear to the bottom right of the screen indicating that the box is now empty.
?. [Registering Samples on Tube Tracker: Missing samples]
If there are any missing samples, for example, a sample has been scanned into the bag but is not physically in the bag then this must be marked as “missing”.
?. [Registering Samples on Tube Tracker: Missing samples]
To mark samples as missing click on the following symbol that appears next to each sample number in the list. Please ensure that the correct samples are marked as missing as once this has been clicked it cannot be undone.
?. [Registering Samples on Tube Tracker: Missing samples]
Notify the site that sent this sample so they are able to investigate what has gone wrong.
?. [Registering Samples on Tube Tracker: Missing samples]
If there are any samples that are physically in the bag, but have not been tracked into the bag, the following message will appear:
?. [Registering Samples on Tube Tracker: Missing samples]
Click “Yes” and the system will show on the audit trail for that sample that is has been unpacked. Please ensure you have scanned the correct barcode before selecting yes, especially if there are other barcodes on the sample.
?. [Registering Samples on Tube Tracker: Reporting System issues]
There may be times when the system is slow, or error messages appear such as ‘bad gateway’. This can be due to server issues. In most cases refreshing your browser and/or logging off and logging back on can resolve these. However, if the issue persists, please report using the contacts that have been provided for escalation.
?. [Processing of “correct” clinical nasal or throat swab samples: Receipt (Sample Checker's tasks)]
Sample Checker will:Open the really useful box of incoming samples.
?. [Processing of “correct” clinical nasal or throat swab samples: Receipt (Sample Checker's tasks)]
Without opening a sample pack bag, visually inspect the samples within it for gross leakage.If no leakage seen, proceed to next step.If leakage is observedDo not open the sample pack or remove any sample bagsIf a member of health and safety (H&S) is not already in attendance, contact health and safety immediatelyH&S will spray the sample bags with distel disinfectantPlace the sample pack into a designated really usefull box labelled ‘leaked samples’Place the lid on the really useful boxTransfer the samples to the CL3 facility to disinfect and recover any remaining usable samplesUsable samples will start at receipt stage againUnusable samples will be disposed of via autoclave process
Risk of exposure due to damaged or leaking materials!
?. [Processing of “correct” clinical nasal or throat swab samples: Receipt (Sample Checker's tasks)]
Open a sample pack.
?. [Processing of “correct” clinical nasal or throat swab samples: Receipt (Sample Checker's tasks)]
Working with one sample bag at a time, remove a sample from the sample pack.
?. [Processing of “correct” clinical nasal or throat swab samples: Receipt (Sample Checker's tasks)]
Visually inspect the individual sample bag to ensure appropriate sample.If appropriate sample seen, select case 'Correct Sample'.If incorrect sample is observed, select case 'Incorrect Sample'.
Risk of exposure due to samples eg faeces, urine and blood!
?. [Processing of “correct” clinical nasal or throat swab samples: Receipt (Sample Checker's tasks)]
Visually inspect the individual sample bag for leakage.If no leakage seen, select case 'No Leakage'.If leakage is observed, select case 'Leakage'.
Risk of exposure due to damaged or leaking materials!
?. [Processing of “correct” clinical nasal or throat swab samples: Receipt (Sample Checker's tasks)]
Check that the sample is a clinical nasal or throat swab sample.
It is important that the samples are clinical nasal or throat swab samples
?. [Processing of “correct” clinical nasal or throat swab samples: Receipt (Sample Checker's tasks)]
Check that sample has a barcode label. Note the barcode should start with a two digit number followed by a letter, commonly known as an EDTA number.
?. [Processing of “correct” clinical nasal or throat swab samples: Receipt (Sample Checker's tasks)]
Tell the barocder that it is a correct sample.
?. [Processing of “correct” clinical nasal or throat swab samples: Barcoding (Barcode Operator's tasks)]
The barcode operator will:Scan the barcode though the sample bag twice,On barcode reader 1 to register sample on Clarity softwareOn barcode reader 2 to allow the printing of 2 labels
?. [Processing of “correct” clinical nasal or throat swab samples: Barcoding (Barcode Operator's tasks)]
Barcode reader 1 scan checkIf the barcode has been scanned successfully, the following notification should be received:  If the barcode scanning has failed, the following notification should be received:  Double check correct barcode has been scanned if an EDTA number matching sample ‘force’ the sample through for processingIf non EDTA number entered check sample for an EDTA number anywhere on sample pack, if there is one scan if successful send sample through for processing. If failure ‘force’ sample through for processingIf the barcode scanning has failed, the following notification should be received:  Double check correct barcode has been scanned if an EDTA number matching sample ‘force’ the sample through for processingIf non EDTA number entered check sample for an EDTA number anywhere on sample pack, if there is one scan if successful send sample through for processing. If failure ‘force’ sample through for processingDouble check correct barcode has been scanned if an EDTA number matching sample ‘force’ the sample through for processingIf non EDTA number entered check sample for an EDTA number anywhere on sample pack, if there is one scan if successful send sample through for processing. If failure ‘force’ sample through for processingIf no EDTA number do not force but ‘reset’ and send sample through process for 'Incorrect Sample' .
?. [Processing of “correct” clinical nasal or throat swab samples: Barcoding (Barcode Operator's tasks)]
Barcode reader 2 scan checkEnsure that x2 barcodes (x3 barcodes if sample container has no barcode) have been produced.
?. [Processing of “correct” clinical nasal or throat swab samples: Barcoding (Barcode Operator's tasks)]
Pass the sample to a barcode lable operator.
?. [Processing of “correct” clinical nasal or throat swab samples: Labelling the Sample Bags (Barcode Label Operator's tasks)]
The barcode label operator will:Advance the printer one label and cut using a scissors.
?. [Processing of “correct” clinical nasal or throat swab samples: Labelling the Sample Bags (Barcode Label Operator's tasks)]
Staple through the unbarcoded label onto the sample bag above the zip lock as shown here.
Do not staple through the main compartment of the sample bag.
Risk of exposure through damaging the sample bag integrity!
?. [Processing of “correct” clinical nasal or throat swab samples: Sample Sorting (Sample Sorter's tasks)]
The sample sorter will:Place all correct samples that have been correctly labelled in a really useful box
Sample & the printed barcodes must match to prevent misdiagnosis.
?. [Processing of “correct” clinical nasal or throat swab samples: Sample Sorting (Sample Sorter's tasks)]
Fix the lid of the really useful box once full or all samples accounted for.The samples are now ready for transport into the CL2/3 suite for viral inactivation and a runner will transfer full incoming sample transfer boxes.
?. [Processing of “incorrect” samples: Sample Checking (Sample Checker's tasks)]
Visually inspect the individual sample bag for leakage.If no leakage seen, select case 'No Leakage'.If leakage is observed, select case 'Leakage'.
?. [Processing of “incorrect” samples: Sample Checking (Sample Checker's tasks)]
Identify the sample as an incorrect sample (i.e. the sample is not a clinical nasal or throat swab sample).
Incorrect samples include urine, faeces, blood.
?. [Processing of “incorrect” samples: Sample Checking (Sample Checker's tasks)]
Tell the barcode operator that it is an incorrect sample.
?. [Processing of “incorrect” samples: Barcoding (Barcode Operator's tasks)]
The barcode operator will:Scan the barcode though the sample bag twice,On barcode reader 1 to register sample on Clarity softwareOn barcode reader 2 to allow the printing of 2 labels.
Barcode not readable: If the barcode is unreadable pass to sample sorter for manual input onto paperwork.
?. [Processing of “incorrect” samples: Barcoding (Barcode Operator's tasks)]
Advise the barcode label operator that it is an incorrect sample.
?. [Processing of “incorrect” samples: Barcoding (Barcode Operator's tasks)]
Pass the sample to the barcode label operator.
?. [Processing of “incorrect” samples: Labelling the Sample Bags (Barcode Label Operator's tasks)]
The barcode label operator will:Advance the printer one label and cut using a scissors.
?. [Processing of “incorrect” samples: Labelling the Sample Bags (Barcode Label Operator's tasks)]
Staple through the unbarcoded label onto the sample bag above the zip lock as shown here.
Do not staple through the main compartment of the sample bag.
Risk of exposure through damaging the sample bag integrity!
?. [Processing of “incorrect” samples: Sample Sorting (Sample Sorter's tasks)]
The sample sorter will:Record the details onto the two “Incorrect samples Covid19” form.
Sample & the printed barcodes must match to prevent misdiagnosis.
?. [Processing of “incorrect” samples: Sample Sorting (Sample Sorter's tasks)]
Place one of the printed barcodes onto the first “Incorrect samples Covid19” form.Place the second printed barcode onto the duplicate “Incorrect samples Covid19” form.
?. [Processing of “incorrect” samples: Sample Sorting (Sample Sorter's tasks)]
Place all incorrect samples that have been correctly labelled in a really useful box labelled Return Samples.
?. [Processing of “incorrect” samples: Sample Sorting (Sample Sorter's tasks)]
Fix the lid of the really useful box once full or all samples accounted for.
?. [Processing of “incorrect” samples: Sample Sorting (Sample Sorter's tasks)]
Place the sample into the box marked return/incorrect samples.
?. [Processing of “incorrect” samples: Sample Sorting (Sample Sorter's tasks)]
Rescan the barcode in the sample rejection application to register the sample as rejected.
?. [Recording details of leaked/contaminated samples: Sample Checking (Sample Checker's tasks)  ]
The sample checker will:Identify the sample as a leaked sample (i.e. the sample shows liquid in internal bag).
?. [Recording details of leaked/contaminated samples: Sample Checking (Sample Checker's tasks)  ]
Tell the barcode operator that it is a leaked sample
?. [Recording details of leaked/contaminated samples: Barcoding (Barcode Operator's tasks)]
The barcode operator will:Scan the barcode though the sample bag twice:On barcode reader 1 to register sample on Clarity softwareOn barcode reader 2 to allow the printing of 2 labels
Barcode not readable: If the barcode is unreadable pass to sample sorter for manual input onto paperwork.
?. [Recording details of leaked/contaminated samples: Barcoding (Barcode Operator's tasks)]
Advise the barcode label operator that it is an incorrect sample.
?. [Recording details of leaked/contaminated samples: Barcoding (Barcode Operator's tasks)]
Pass the sample to the barcode label operator.
?. [Recording details of leaked/contaminated samples: Labelling the Sample Bags (Barcode Label Operator's tasks)]
The barcode label operator will:Advance the printer one label and cut using a scissors.
?. [Recording details of leaked/contaminated samples: Labelling the Sample Bags (Barcode Label Operator's tasks)]
Staple through the unbarcoded label onto the sample bag above the zip lock as shown here.
Do not staple through the main compartment of the sample bag.
Risk of exposure through damaging the sample bag integrity!
?. [Recording details of leaked/contaminated samples: Sample Sorting (Sample Sorter's tasks)]
The sample sorter will:Record the details onto the two “Incorrect samples Covid19” form.
Sample & the printed barcodes must match to prevent misdiagnosis.
?. [Recording details of leaked/contaminated samples: Sample Sorting (Sample Sorter's tasks)]
Place one of the printed barcodes onto the first “Incorrect samples Covid19” form.Place the second printed barcode onto the duplicate “Incorrect samples Covid19” form.
?. [Recording details of leaked/contaminated samples: Sample Sorting (Sample Sorter's tasks)]
Place all leaked samples that have been correctly labelled in a really useful box labelled Leaked Samples.
?. [Recording details of leaked/contaminated samples: Sample Sorting (Sample Sorter's tasks)]
Fix the lid of the really useful box once full or all samples accounted for.
?. [Recording details of leaked/contaminated samples: Sample Sorting (Sample Sorter's tasks)]
Place the sample into the box marked leaked samples.
?. [Recording details of leaked/contaminated samples: Sample Sorting (Sample Sorter's tasks)]
Rescan the barcode in the sample rejection application to register the sample as rejected.
?. [Recording details of leaked/contaminated samples: Sample Checking (Sample Checker's tasks)]
The sample checker will:Identify the sample as a leaked sample (i.e. the sample shows liquid in internal bag).
?. [Recording details of leaked/contaminated samples: Sample Checking (Sample Checker's tasks)]
Tell the barcode operator that it is a leaked sample
?. [Recording details of leaked/contaminated samples: Barcoding (Barcode Operator's tasks)]
The barcode operator will:Scan the barcode though the sample bag twice:On barcode reader 1 to register sample on Clarity softwareOn barcode reader 2 to allow the printing of 2 labels
Barcode not readable: If the barcode is unreadable pass to sample sorter for manual input onto paperwork.
?. [Recording details of leaked/contaminated samples: Barcoding (Barcode Operator's tasks)]
Advise the barcode label operator that it is an incorrect sample.
?. [Recording details of leaked/contaminated samples: Barcoding (Barcode Operator's tasks)]
Pass the sample to the barcode label operator.
?. [Recording details of leaked/contaminated samples: Labelling the Sample Bags (Barcode Label Operator's tasks)]
The barcode label operator will:Advance the printer one label and cut using a scissors.
?. [Recording details of leaked/contaminated samples: Labelling the Sample Bags (Barcode Label Operator's tasks)]
Staple through the unbarcoded label onto the sample bag above the zip lock as shown here.
Do not staple through the main compartment of the sample bag.
Risk of exposure through damaging the sample bag integrity!
?. [Recording details of leaked/contaminated samples: Sample Sorting (Sample Sorter's tasks)]
The sample sorter will:Record the details onto the two “Incorrect samples Covid19” form.
Sample & the printed barcodes must match to prevent misdiagnosis.
?. [Recording details of leaked/contaminated samples: Sample Sorting (Sample Sorter's tasks)]
Place one of the printed barcodes onto the first “Incorrect samples Covid19” form.Place the second printed barcode onto the duplicate “Incorrect samples Covid19” form.
?. [Recording details of leaked/contaminated samples: Sample Sorting (Sample Sorter's tasks)]
Place all leaked samples that have been correctly labelled in a really useful box labelled Leaked Samples.
?. [Recording details of leaked/contaminated samples: Sample Sorting (Sample Sorter's tasks)]
Fix the lid of the really useful box once full or all samples accounted for.
?. [Recording details of leaked/contaminated samples: Sample Sorting (Sample Sorter's tasks)]
Place the sample into the box marked leaked samples.
?. [Recording details of leaked/contaminated samples: Sample Sorting (Sample Sorter's tasks)]
Rescan the barcode in the sample rejection application to register the sample as rejected.