This standard operating procedure provides instructions for:
Safely handling of human blood
Appropriate waste disposal
Precautions for setting up the CDC-SARS-CoV-2 PCR
Hazards, Safety Controls and Risk
o Exposure to infectious agents
o Dispose of waste correctly
Risk assessments have been undertaken and the risks after the controls are in place are LOW.
We will obtain blood from healthy volunteer from the NYBC and outpatients from HSS who follows the FDA guidelines for collection consisting in checking the body temperature, travel and symptoms history of the donor.
Presence of SARS-CoV-2 in the healthy donor blood will be checked by PCR and the sample used only if tested negative
Many routine laboratory procedures can potentially generate aerosols and droplets that are often undetectable. Laboratory workers may not be aware that such particles can be generated during many laboratory procedures and that these particles could be inhaled or could cross-contaminate work surfaces, materials, and equipment.
The following laboratory procedures have been associated with the generation of infectious aerosols and droplets: centrifugation, pipetting, vortexing, mixing, shaking, removing caps, decanting liquids, loading syringes, manipulating needles, syringes or sharps, aspirating and transferring blood and body fluids, sub-culturing blood culture bottles, spilling specimens, and cleaning up spills. Rotor-sealing lids will be used to reduce the risk of exposure to laboratory personnel. Centrifuging of blood specimens is performed using click seal biocontainment lids that will be loaded and unloaded in a BSL2. Sample vortexing will be performed inside a BSL2.
All technical procedures should be performed in a way that minimizes the generation of aerosols and droplets. For procedures with a high likelihood to generate aerosols or droplets we will use a certified Class II Type A1 Biological Safety Cabinet (BSC) and additional precautions to provide a barrier between the specimen and researchers.
Glass shields (inside and outside of hoods), work surfaces and equipment will be decontaminated with appropriate disinfectants, including sodium hypochlorite (bleach) (e.g. 1,000 ppm (0.1%) for general surface disinfection and 10,000 ppm (1%) for disinfection of blood spills, 62-71% ethanol or 0.5% hydrogen peroxide. This is to be done before and after use by every user.
All generated waste and contaminated materials will be considered biohazardous and will be placed in BSL2 in leak-proof, properly designated and sealed containers. Sealed containers will be placed in biohazard bags for subsequent collection, decontamination and disposal. All dry waste is contained in red hard sided biohazard containers. All waste is then autoclaved before disposal.
In case of a spill, Environmental Health and Safety (EHS) will be contacted and spills will be cleaned up according to the guidelines detailed in section E
o Long-sleeved laboratory gown and closed shoes
o Masks (N95 respirator) only for inactivating of blood samples for presence of SARS-CoV2 virus testing
E. Emergencies (if applicable)
In case of a spill or exposure refer to the EHS EXPOSURE AND SPILL RESPONSE GUIDE, notify your supervisor and call EHS (646-962-7233). In case of emergency always call NYP Security first (212-746-0911)
For biological spills which do not involve injury, are contained, pose little hazard to personnel, and for which you have the proper training and proper protective equipment to do the cleanup, you can clean the spill. For all other biological spill situations, including those for which you have any questions or doubts about your ability to clean up the spill, contact Environmental Health and Safety (EHS) (646-962-7233).
Before aspirating any liquids, be sure that the vacuum tubing is connected to a large flask that contains 1/5 volume of concentrated bleach. Also check that the vacuum flask is connected to a secondary flask, and that both flasks are inside a secondary container large enough to hold the maximum volume of the flasks in case of a spill. The tubing between the secondary flask and the house vacuum system must contain a Vacu-guard filter (0.22um). Make sure the flasks are labeled with a Tissue Culture Waste Label.
If the primary vacuum flask is more than 1/2 full, add 1/3 volume of concentrated bleach and allow it to sit in BSC or fume hood for 1 hour before pouring it down the sink. Obtain a clean vacuum flask for your waste and connect it as is described above in 3.C.i.
Aspirate all liquids from flasks/tubes/plates that will be discarded (no liquids in red bags). Blood must be diluted prior to aspirating so it doesn't clog the tubing.
After aspirating all liquid waste, aspirate an additional 10ml of bleach solution into the vacuum flask to disinfect vacuum tubing.
G. Solid (non-sharps) Waste
All used flasks, tubes and plates must be rinsed with bleach (at least 10% concentration) and discarded in a red biohazard bag. Disposable funnels should sit in bleach filter side down, for one minute before discarding.
All biohazard waste shall be double bagged and decontaminated by autoclaving
New York State requires that all red bags be marked with the name and address of the facility where the regulated medical waste is generated. Only use approved pre-printed red bags. Pre-printed red bags are available from the Housekeeping department servicing your area.
Standard red bags are not suitable for autoclaving. Generators must purchase autoclave-safe red bags. Once autoclaving is complete, allow autoclave bags to cool and then place the autoclave bag into the approved red bag to satisfy the facility name and address requirements.
H. Training and Competency:
Any person handling human blood must undergo training.
Read and discuss documentation (appropriate SOPs)
Observation of a competent trainer demonstrating the correct procedure
Trainer to observe trainee performing procedure
Refresher training when required ie. Change to SOP
Competency must be demonstrated
Spills within the Biosafety Cabinet
A. Clean up of a small spill (<25 ml):
Make sure the cabinet continues to operate. Wait 5 min. to allow aerosols to be pulled through the HEPA filter.
Decontaminate the surfaces within the cabinet, wearing protective clothing, gently cover the spill with absorbent paper towel soaked with 15% bleach, starting at the perimeter and working towards the centre; allow sufficient contact time (20 min) before clean up.
Discard soaked paper towels in a biohazard bag. Wipe up residual mess.
B. Clean up of a large spill (>25 ml):
Make sure the cabinet continues to operate. Wait 30 min. to allow aerosols to be pulled through the HEPA filter.
Wait 30 min. for aerosols to settle. Meanwhile, notify the University Biosafety Officer, Lab Head and Departmental Safety Officer. If the spill has escaped the BSC, proceed as for a spill outside the BSC II.
Cover split liquid with Virkon-S powder, leave for 20 min. and use paper towels to clean up, starting at the perimeter and working towards the centre; decontaminate all equipment supplies, or surfaces that were potentially contaminated.
If a large quantity is spilled, the entire cabinet, including fans, filters, airflow plenums, will need to be formaldehyde decontaminated.
An incident report must be submitted to PI.
Spills outside of containment
Avoid inhalation of any airborne material by holding your breath, immediately remove and discard contaminated disposable protective equipment and dispose in the biohazard waste, and leave the laboratory. Warn others in the area. Ask a coworker for help if needed, so as to prevent spreading the hazardous material even further.
Seek medical attention if needed.
Re-entry into the laboratory should be delayed for a period of at least 30 minutes to allow aerosol generated by the spill to settle.
Applicable personal protective clothing should be worn when entering the laboratory to clean the spill area.
Utilize a biological spill kit to clean up the spill; this should be prepared prior in anticipation of an incident.
Place paper towels or other absorbent material on the spill to absorb liquids.
Without splashing, carefully pour disinfectant (10% bleach or 70% Isopropanol) over the wet towels in the spill area and cover with a second layer of paper towels to absorb all disinfectant.
Disinfect all other materials near the spill area that may have been affected.
Let sit 30 minutes before discarding wet paper towels and affected materials in biohazard bag (careful not to drip onto other surfaces).
Work area must be fully disinfected before resuming work.
Report all incidents to lab manager.
Variables that effect RNA yields during Whole Blood RNA purification
Whole blood, plasma, and sera represent, by far, the most commonly used sample types in the diagnostic field. Because PCR inhibitors in blood samples ~ have been described, generally, it is accepted that a careful purification of nucleic acids is required from such samples before PCR analysis can be performed. Cellular or viral RNA, present in vivo in a protected form in cells or virus, is not readily accessible to all PCR reagents. This barrier is overcome by lysing the cells or virus.
Erythrocytes lysis: Since whole blood contains a high number of non-nucleated erythrocytes, purifying total RNA from whole blood without the removal of erythrocytes results in low RNA yields and clogging of purification columns. The depletion of abundant erythrocytes is therefore a key step in the purification of whole blood total RNA and is performed by selective lysis of erythrocytes using hypotonic shock. The erythrocytes are resuspended in a hypotonic buffer that causes an influx of water into erythrocytes and ruptures the erythrocyte cell membranes. Leukocytes are not affected by the hypotonic shock and are easily separated from lysed erythrocytes by centrifugation.
Warnings and Precautions related PCR assays
Amplification technologies such as PCR are sensitive to accidental introduction of PCR product from previous amplifications reactions. Incorrect results could occur if either the clinical specimen or the real-time reagents used in the amplification step become contaminated by accidental introduction of amplification product (amplicon). Workflow in the laboratory should proceed in a unidirectional manner.
Maintain separate areas for assay setup and handling of nucleic acids.
Always check the expiration date prior to use. Do not use expired reagent. Do not substitute or mix reagent from different kit lots or from other manufacturers.
Change aerosol barrier pipette tips between all manual liquid transfers.
During preparation of samples, compliance with good laboratory techniques is essential to minimize the risk of cross-contamination between samples, and the inadvertent introduction of nucleases into samples during and after the extraction procedure. Proper aseptic technique should always be used when working with nucleic acids.
Maintain separate, dedicated equipment (e.g., pipettes, microcentrifuges) and supplies (e.g., microcentrifuge tubes, pipette tips) for assay setup and handling of extracted nucleic acids.
Wear a clean lab coat and powder-free disposable gloves (not previously worn) when setting up assays.
Change gloves between samples and whenever contamination is suspected.
Keep reagent and reaction tubes capped or covered as much as possible.
Primers, probes (including aliquots), and enzyme master mix must be thawed and maintained on cold block at all times during preparation and use.
Work surfaces, pipettes, and centrifuges should be cleaned and decontaminated with cleaning products such as 10% bleach, “DNAZap™” or “RNase AWAY®” to minimize risk of nucleic acid contamination. Residual bleach should be removed using 70% ethanol.
RNA should be maintained on cold block or on ice during preparation and use to ensure stability.
Dispose of unused kit reagents and human specimens according to local, state, and federal regulations.
Reagent Storage, Handling, and Stability
Store all dried primers and probes and the positive control, nCoVPC, at 2-8°C until re-hydrated for use.
Store liquid HSC control materials at ≤ -20°C.
Always check the expiration date prior to use. Do not use expired reagents.
Protect fluorogenic probes from light.
Primers, probes (including aliquots), and enzyme master mix must be thawed and kept on a cold block at all times during preparation and use.
Do not refreeze probes.
Controls and aliquots of controls must be thawed and kept on ice at all times during preparation and use.
Primer and Probe Preparation:
Upon receipt, store dried primers and probes at 2-8°C.
Precautions: These reagents should only be handled in a clean area and stored at appropriate temperatures (see below) in the dark. Freeze-thaw cycles should be avoided. Maintain cold when thawed.
Using aseptic technique, suspend dried reagents in 1.5 mL of nuclease-free water (50X working concentration) and allow to rehydrate for 15 min at room temperature in the dark.
Mix gently and aliquot primers/probe in 300 μL volumes into 5 pre-labeled tubes. Store a single aliquot of primers/probe at 2-8oC in the dark. Do not refreeze (stable for up to 4 months). Store remaining aliquots at ≤ -20oC in a non-frost-free freezer.
2019-nCoV Positive Control (nCoVPC) Preparation:
Precautions: This reagent should be handled with caution in a dedicated nucleic acid handling area to prevent possible contamination. Freeze-thaw cycles should be avoided. Maintain on ice when thawed.
Resuspend dried reagent in each tube in 1 mL of nuclease-free water to achieve the proper concentration. Make single use aliquots (approximately 30 μL) and store at ≤ -70oC.
Thaw a single aliquot of diluted positive control for each experiment and hold on ice until adding to plate. Discard any unused portion of the aliquot.
No Template Control (NTC) (not provided)
Sterile, nuclease-free water
Aliquot in small volumes
Used to check for contamination during specimen extraction and/or plate set-up
Clean and decontaminate all work surfaces, pipettes, centrifuges, and other equipment prior to use. Decontamination agents should be used including 10% bleach, 70% ethanol, and DNAzap™ or RNase AWAY® to minimize the risk of nucleic acid contamination.