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Coronavirus Disease (COVID-19): Laboratory Risk Assessments and Lessons Learned

Association of Public Health Laboratories March 12, 2020


Continuing Education Credits

The Association of Public Health Laboratories (APHL) is approved as a provider of continuing education programs in the clinical laboratory sciences by the ASCLS P.A.C.E.® Program. Participants who successfully complete this program will be awarded 1 P.A.C.E. contact hour.

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PresentersMichael Marsico, MS,Association of Public Health Laboratories

Erik Reisdorf, MPH, M(ASCP)CM, Wisconsin State Laboratory of Hygiene

Joey Stringer, BS, BA, Dallas County Health and Human Services

Margie A. Morgan, Ph.D., D(ABMM), Cedars-Sinai, Los Angeles, CA

Drew Fayram, MS, RBP(ABSA), Iowa State Hygienic Laboratory


Agenda

• About APHL • Coronavirus Disease (COVID-19) Response• Overview of the Risk Assessment Process• Risk Assessment in Action• Risk Assessment Examples/Biosafety Guidance for

COVID-19 and Lessons Learned• Questions and Answers


About APHL• Non-profit non-governmental organization

• Over 1000 members from state and local public health laboratories, state environmental and agricultural labs and others federal agencies and academic institutions

• Advocates at the national level in the US to shape public health policy and to secure increased support/resources for member labs

• Provides training, model practices and technical assistance domestically and internationally


COVID-19• Novel virus that emerged in China• Initially called 2019 Novel Coronavirus (2019-nCoV)• Official Name:

– Disease: Coronavirus Disease (COVID-19)– Virus: SARS-CoV-2

• APHL state and local public health laboratories are at the forefront of this response

• Collaborative effort with CDC, FDA, Commercial and other Clinical Laboratories


APHL Activities• Activated/Using its Emergency Operations Center • Shaped/ing Science and Quality of Diagnostics• Secured/ing Private Funding to Support Priority Jurisdictions• Paved the way for Regulatory Changes to meet Testing Demand • Facilitated Data Messaging Solution• Communicated Credible Information at a Rapid Pace• Collaborated with Partners to Educate Congressional Staff and

Policy Makers on Funding Needs


CDC Guidance

www.cdc.gov/coronavirus/2019-ncov/lab

http://www.cdc.gov/coronavirus/2019-ncov/lab


OVERVIEW OF THE RISK ASSESSMENT PROCESSJoey Stringer, BS, BA, Dallas County Health and Human Services


The process of the risk assessment• Hazard Identification • Evaluate and prioritize the risks

– How likely, how severe • Develop a risk strategy

– Determine what controls are needed to reduce the risk (mitigation)• Implement controls • Review the effectiveness of the controls and overall process, adjust if necessary

Need to identify, evaluate and determine levels of risks associated with the hazard present and implement controls to mitigate those risks.


Hazard Identification

Evaluate the risks

Mitigate the risk

Implement controls

Review and adjust

The process of the risk assessment


12

Agent

Place, PPE, Procedures

Host

Source: B. Johnson, Anthology of Biosafety, IV, 2001

Pathogen

Environment People

Interaction of factors


• Once you have identified all hazards of the work to be performed,– Use that information to prioritize and evaluate any risks that exist

• The goal of the risk evaluation:– Determine the likelihood of exposure and consequences of that

exposure– Establish how the likelihood and consequence contribute to the

inherent risk of work performed



Now decide whether the risk is acceptable

• Determine the inherent risk– After all the hazards are identified, decide how much risk a

procedure or situation presents • Establish a risk tolerance

– Once the inherent risk is evaluated, decide whether the level of risk is acceptable

– If not acceptable, then…



Develop a risk strategy

• A risk strategy is developed in order to mitigate the inherent risk to an acceptable level (tolerance)

• Determine what safety precautions and mitigation controls are needed to reduce the risk to an acceptable level


Risk mitigation

• Hazard identification• Risk assessment• Risk management• Risk communication

Credit: Sean Kaufman, MPH, CHES, CPH, CIC, MBTI Certified Provider CEO and Founding Partner of Behavioral-Based Improvement Solutions.

Remember

• There is some risk in everything we do — we can reduce the risk, but not eliminate it

• Risk assessment is an ongoing, continuous cycle

• Evaluate, review and adjust


THANK YOU

Contact InformationJoey Stringer

Dallas County Health and Human ServicesOffice 972-692-2762

[email protected]


RISK ASSESSMENT IN ACTIONApplying concepts of risk assessment to safely test patients with COVID-19

Drew Fayram, MS, RBP(ABSA), Iowa State Hygienic Laboratory


Biosafety Guidance Resources for Laboratories

APHL• Risk assessment best practices

• https://www.aphl.org/programs/preparedness/Documents/APHL%20Risk%20Assessment%20Best%20Practices%20and%20Examples.pdf

CDC• COVID-19 information for laboratories

• February 10, 2020 (New versions coming when updates are approved)• https://www.cdc.gov/coronavirus/2019-ncov/lab/index.html

• COVID-19 information for healthcare providers• https://www.cdc.gov/coronavirus/2019-ncov/hcp/index.html

https://www.aphl.org/programs/preparedness/Documents/APHL%20Risk%20Assessment%20Best%20Practices%20and%20Examples.pdf

https://www.cdc.gov/coronavirus/2019-ncov/lab/index.html

https://www.cdc.gov/coronavirus/2019-ncov/hcp/index.html


Hazard identificationPrimary hazard of concern: virus = SARS-CoV-2

• Note: Laboratory specimens collected from COVID-19 patients may harbor other biological hazards, including but not limited to other respiratory viruses. Non-biological hazards, such as chemical reagents used for diagnostic testing, should also be considered during the site-specific risk assessment process.

Pathogenicity: disease = COVID-19• Currently no known treatment or vaccine• Mild-severe illness, and may cause death• Common symptoms: fever, cough, and shortness of breath• Severe symptoms: pneumonia and severe respiratory disease• Symptom onset 2-14 days post-exposure


Hazard identification continuedCommunicability:

• Human-to-human transmission• Exposure to contaminated surfaces

Primary laboratory hazards:• Droplet exposure of the mucous membranes of the eye, nose, and/or mouth• Exposure to contaminated surfaces

• EPA List N for use against SARS-CoV-2• https://www.epa.gov/sites/production/files/2020-03/documents/sars-cov-2-list_03-03-2020.pdf

• Ingestion

Survival outside the host:• Not specifically known for SARS-CoV-2 at this time

https://www.epa.gov/sites/production/files/2020-03/documents/sars-cov-2-list_03-03-2020.pdf


Risk evaluationDetermine the likelihood and consequence of exposure.

• Note: Determination will vary from facility to facility and group to group.

Consequence: based mostly on the agent. • May cause COVID-19, a novel, mild-to-severe illness that can cause death.• Currently no treatment or vaccines available.• Moderate to Major

Likelihood: based mostly on the procedures.• Different procedures performed by different personnel in different facilities may result in

different levels of likelihood.• Determination must be made based on site-specific discussion.


Example of determining likelihood

Location Task Likelihood

Hospital clinical laboratoryPrepping respiratory specimen for BioFire

FilmArrayLIKELY to be exposed via droplet production during specimen vortexing and

manipulation.Public health or other qualified laboratory

Preparing respiratory specimen for RT-PCR

2019-nCoV assay

Any laboratory Touching contaminated surfaces and instruments

POSSIBLE to be exposed via mucous membranes

after touching contaminated surfaces.


Risk evaluationRisk = likelihood X consequence

Task Likelihood Consequence RiskPrepping respiratory specimen for

BioFire FilmArray Likely

Moderate

High

Preparing respiratory specimen for RT-PCR Diagnostic Test Likely High

Touching contaminated surfaces and instruments Possible High


Develop a risk strategyBased on agreed-upon risk tolerance. If risk level is unacceptable then develop a risk strategy to reduce risk to acceptable level.

What safety precautions and controls are needed to mitigate the risk?


Identify controlsTask Risk Controls

Prepping respiratory specimen for BioFire

FilmArrayHigh

• Follow CDC guidance for Laboratory Biosafety for COVID-19• Work in a certified BSC* (if possible) in a BSL2 lab• Use Standard Precautions• PPE: gloves, lab coat/gown, and eye protection• Must wash hands after glove removal and prior to exiting the laboratory• Refrain from touching face or mucous membrane prior to washing

hands

Preparing respiratory specimen for RT-PCR 2019-

nCoV assayHigh


hands

Touching contaminated surfaces and instruments High

• Follow CDC guidance for Laboratory Biosafety for COVID-19• Decontaminate work surfaces and equipment with EPA-registered

hospital disinfectants found on the EPA’s List N• PPE: gloves, lab coat/gown, and eye protection• Must wash hands after glove removal and prior to exiting the laboratory• Refrain from touching face or mucous membrane prior to washing

hands


No certified BSC?

* If a certified BSC is not available, precautions can be used to provide a barrier between the specimen and personnel. Examples include using additional PPE (e.g., surgical mask and/or face shield) or other physical barriers (e.g., splash shield, centrifuge safety cups, sealed centrifuge rotors) to reduce the risk of exposure to laboratory personnel.


Identify controlsTask Risk Controls

Prepping respiratory specimen for BioFire

FilmArrayHigh


hands

Preparing respiratory specimen for RT-PCR 2019-

nCoV assayHigh


hands

Touching contaminated surfaces and instruments High

• Follow CDC guidance for Laboratory Biosafety for COVID-19• Decontaminate work surfaces and equipment with EPA-registered

hospital disinfectants found on the EPA’s List N• PPE: gloves, lab coat/gown, and eye protection• Must wash hands after glove removal and prior to exiting the laboratory• Refrain from touching face or mucous membrane prior to washing

hands


Residual risk


Residual riskTask Risk Controls Residual Risk

Prepping respiratory

specimen for BioFire

FilmArray

High

• Follow CDC guidance for Laboratory Biosafety for COVID-19• Work in a certified BSC* (if possible) in a BSL2 lab• Use Standard Precautions• PPE: gloves, lab coat/gown, and eye protection• Must wash hands after glove removal and prior to exiting the

laboratory• Refrain from touching face or mucous membrane prior to

washing hands

Medium

Preparing respiratory

specimen for RT-PCR 2019-nCoV

assay

High

• Follow CDC guidance for Laboratory Biosafety for COVID-19• Work in a certified BSC* (if possible) in a BSL2 lab• Use Standard Precautions• PPE: gloves, lab coat/gown, and eye protection• Must wash hands after glove removal and prior to exiting the


washing hands

Medium

Touching contaminated surfaces and instruments

High

• Follow CDC guidance for Laboratory Biosafety for COVID-19• Decontaminate work surfaces and equipment with EPA-

registered hospital disinfectants found on the EPA’s List N• PPE: gloves, lab coat/gown, and eye protection• Must wash hands after glove removal and prior to exiting the


washing hands

Low


Implement controls and review

Before implementing controls, ask yourself:• Are all identified controls/equipment available?• Is the biosafety cabinet certified and well-maintained?• Are staff trained to properly use, maintain, and dispose of PPE and equipment?• Is additional training needed?• What level of competency have staff demonstrated?

After implementing controls, invite feedback from staff and plan routine reviews to ensure risk assessment is accurate and control strategies are effective.

Every facility must perform its own site- and activity-specific risk assessment to determine if enhanced biosafety precautions are warranted.

Follow CDC guidelines whenever possible and base other decisions on your risk assessment.


SAFE HANDLING OF SARS- COV-2 SPECIMENS IN THE PUBLIC HEALTH LABORATORYExperiences & Lessons Learned

Erik Reisdorf, MPH, M(ASCP)CM, Wisconsin State Laboratory of Hygiene


2019 Novel Coronavirus

Situational Report—January 25

Image Source (WHO, 2020) https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200131-sitrep-11-ncov.pdf?sfvrsn=de7c0f7_4


CDC Interim Lab Biosafety Recommendations

The following activities involving manipulation of potentially infected specimens should be, at a minimum, performed as above and in a certified Class II BSC in a BSL-2 facility. Site- and activity-specific risk assessments should be performed to determine if enhanced biosafety precautions are warranted based on situational needs (e.g. high testing volumes):• Aliquoting and/or diluting specimens• Performing diagnostic tests that do not involve propagation of viral agents

in vitro or in vivo• Nucleic acid extraction procedures involving potentially infected

specimens


Context for Risk Assessment

• Novel virus, knowledge gap.• Limited immunity.• Transmissible, respiratory route.• Severe disease (est. 18%), high mortality in China.• No vaccine.• No antiviral treatments.


Laboratory Practices

• Indicated BSL-2 with *enhancementsPPE

1. N95 respirator (fit tested).2. Impermeable lab gown, back closure.3. Eye protection.4. Double glove.


Laboratory Practices Implemented• Trained, experienced staff knowledgeable of

COVID-19 symptoms.• Completed class 6.2 shipping training. • PUI specimens sent directly to lab (inside bags).• Unpacking performed in a Class II BSC.• Process specimens once per day.• Anyone else present in the lab when processing

SARS-CoV-2 PUI specimens dons N95 respirator.


Laboratory PracticesEngineering controls

1. Sequestered Class II BSC, limit lab access.2. Centrifugation of blood specimens should be

performed using sealed centrifuge rotors or sample cups. These rotors or cups should be loaded and unloaded in a BSC.


Laboratory Practices

Waste handling1. Aliquot preparation.2. Double bag waste.3. All material leaving BSC decontaminated.4. Surface disinfection (bleach 1:10 or 0.525%) and contact time

followed by 70% EtOH.


Laboratory PracticesAdditional best practices

1. Two microbiologists processing and packaging for shipment.

2. Restrict lab access.3. Patient specimens from suspected

cases should be transported as UN3373, “Biological Substance, Category B”


Key Considerations for Risk Assessment Development• Address the “unusual” situations.

1) Leaking specimens.2) Broken specimens.3) Transport between lab areas.4) Small spills.5) Serum.


LABORATORY BIOSAFETY GUIDANCE RELATED TO COVID-19Margie Morgan, PhD D(ABMM)Professor Pathology and Laboratory MedicineMedical Director Microbiology Cedars-Sinai Medical CenterLos Angeles, CA


First case of COVID-19 infection in the United States¹

1. NEJM, Jan 31,2020


Viral Loads in Clinical Samples


Aerosol vs. droplet transmission?• Aerosol transmission:

– Liquid/solid infectious material can be suspended in air for extended period of time, remaining infectious and can be inhaled

• Droplet transmission:– Primary transmission of COVID-19 infection– Larger particles than aerosolized ones, rapidly fall out of air to

contaminate surfaces– Contaminate gloves & immediate work area, could transfer to

mucous membranes from poor hand hygiene


Risk Assessment Best Practices• Identify and mitigate the risks of working in your laboratory environment with the current

facts about COVID-19 infection• Workforce

– Identify personnel that will be affected – Assess competency for necessary procedures

• Risk Characterization– Identify the hazards– Modes of transmission and potential exposure– Identify activities with increased risk

• Risk Mitigations– Identify required appropriate safety practices– Communicate risks and required safety practices to staff – Review safety practices to make sure they were effective


Workforce• Identify personnel that would be affected throughout the workflow in your

laboratory• Assess the training and competency of all personnel• Is additional new training necessary for staff members for the COVID-19 event

– Should additional CLS be trained for test performance – Proper safe packaging for PHD/Ref lab send out testing– Adequate number of personnel with packaging certification– New requirements related to risk assessment

• Laboratory meetings frequently to air concerns and discuss updates to risk assessment/mitigation

• Is an emotional support resource available?


Risk Characterization• Which biosafety level is recommended for handling clinical

specimens from suspected COVID-19 persons of interest (PUIs)? • Viral load is highest in respiratory specimens so these assessed to be the

greatest risk to laboratory personnel– Certified Class II Biosafety Cabinet(BSC) should be used for processing

and testing of all respiratory specimens, with gloves and appropriate lab coat/gown

• Standard Precautions at BSL-2 level is appropriate for personnel handling whole blood, serum, plasma, stool and urine specimens – However, any procedure with the potential to generate aerosols or droplets

(vortexing/pipetting/centrifugation/opening closed centrifugation container) is most safely performed in a certified Class II Biosafety Cabinet (BSC)


Risk Characterization

• Extra barriers must be used to provide a barrier between the respiratory specimen and personnel

• Perform a risk assessment to determine optimal PPE• Extra barriers include such additional protective equipment (PPE)

as:– N95 mask and face shield – Counter top splash shield – Performed in an isolated area away from major traffic area

• Mask availability is becoming an issue– Guidance for optimizing mask use¹

• What if a biosafety cabinet is not available?


Standard Precautions at BSL 2?• Good hand hygiene• Appropriate Personal Protective Equipment

– Laboratory coats/gowns – long sleeved/fitted cuffs/closed/splash resistant cloth

– Disposable gloves/ changed when soiled– Safety glasses/goggles– Proper closed non slip footwear– Respiratory protection if acknowledged as necessary in

COVID-19 risk assessment – https://www.cdc.gov/coronavirus/2019-ncov/lab/lab-biosafety-guidelines.html

https://www.cdc.gov/coronavirus/2019-ncov/lab/lab-biosafety-guidelines.html


What if you have a spill?

• EPA-registered hospital disinfectant with label claims against other respiratory pathogens (Influenza)– Sani-cloth wipes approved in our institution

What disinfectant should be used for disinfection of work areas and for spill clean up?


How do we transport specimens from PUIs around our medical facility?– Adhere to standard procedures in place for other respiratory

pathogens, such as Influenza– In our facility our risk assessment determined:

• Hospitalized PUI specimen(s) packaged in Category B packaging on nursing unit

• Walked to microbiology for storage and send out to DPH• Double check proper packaging/requisition in BSC

– Alternative: To be determined by risk assessment• Specimen(s) placed in individual sealed biohazard bag• Appropriate safe transport to laboratory


Packaging specimens/Category B packaging


Packaging and Storage of Specimens• Check the specimen packaging and storage requirement for the

laboratory that is performing your testing– Public health department (PHD) and reference laboratory

could have different packaging and storage requirements• PHD – Category B boxes placed at 2-8*C• Reference laboratory – One specimen per sealed biohazard bag,

stored in an exclusive closed container within refrigerator (2-8*C) prior to courier pick up

• If delay occurs, storage at -70*C could be suggested, so plan for possible freezer usage


How do we handle waste?• Waste requirements for clinical specimens from suspected

COVID-19 PUIs, uses the same standard precautions as for influenza and other respiratory viruses– Our risk assessment, all gloves used to process respiratory specimens in

virology and specimen processing areas are disposed of in “red bag” biohazardous trash

• Waste should be “red bag” and covered at all times– Risk assessment to use containers with slide closures in our virology

laboratory rather than ones with lids• Secured and closed prior to removal from laboratory• Autoclaved on site / or pack waste in accordance with institutional

policy and procedures

COVID-19 [email protected]

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