Laboratory biosafety guidance related to coronavirus disease (COVID-19): interim

guidance
Annex II: Risk assessment template
Although a qualitative approach to combining likelihood and severity parameters in a risk matrix is provided as a method
for risk evaluation here, it is important to note that quantitative (for example, from simple numerical scoring schemes to
complex mathematical models) and hybrid (semi-quantitative) methods can also be used for risk evaluation. Laboratories
should use a risk-evaluation/assessment method that best meets their unique needs, without excluding the possibility of
developing customized evaluation approaches, scoring methods, and definitions of the parameters.

Although this template was primarily developed for biosafety risk assessment, it can also be used for general safety risk
assessment of laboratory activities, especially when the biosafety and general safety risks are interlinked, for example,
sample collection and transport, where appropriate and applicable.

Institution/Facility name SAN JOSE DISTRICT HOSPITAL

Laboratory name SAN JOSE DISTRICT HOSPITAL-LABORATORY
Laboratory manager/Supervisor CHESTER KYLE D. FERNANDEZ, RMT
Project titles/Relevant standard operating SOPs FOR ANTIGEN COLLECTION AND TESTING
procedures (SOPs) SOPs FOR OPS/ NPS COLLECTION
Date 3-31-2022

If using this template, complete all sections following the instructions in the grey boxes. The instructions and bullet points in the
grey boxes can be copied into the text boxes beneath the instructions and used as prompts to gather and record the necessary site-
specific information. The grey instruction boxes can then be deleted, and the text remaining will form a risk assessment draft. This
draft must be carefully reviewed, edited as necessary, and approved by the members of the risk assessment team.

STEP 1. Gather information (hazard identification)

Instructions: Provide a brief overview of the laboratory work and summarize the laboratory activities to be
conducted that are included in the scope of this risk assessment.
Describe the biological ● Biological agent: COVID-19 VIRUS/ SARS COV 2
agents and other potential
hazards (for example, ● Mode of transmission: Human to human direct contact, via respiratory
transmission, infectious droplets from cough and sneezes, maybe airborne as well with aerosol
dose, treatment/preventive
measures, pathogenicity). potentially being able to transfer virus, indirect contact via contaminated
surfaces

● Predisposing Factors: Pregnant women and those 65 years of age, the

rate exceeds 50%.

● Communicability: It is at its greatest in severely ill patients or those

experiencing rapid clinical deterioration. Transmission usually occurs after
onset of clinical signs and symptoms (on or after the 5th day of illness on
average), which coincides with peak viral load in nasopharyngeal secretions
around day 10 of illness.

● Infectious Dose: The precise infectious dose remains unknown.

● Incubation Period: It ranges from 2-16 days, with maximum of 10 days

● Pathogenicity: Chest examinations typically show ground-glass opacities

and focal consolidations. Diarrhea is the most common extrapulmonary
manifestation, followed by hepatic dysfunction, dizziness, abnormal
urinalysis, myositis, petechiae, epileptic fits. The case fatality is 9.6%
however, in patients over 65 years of age, the rate exceeds 50%. Disease
severity classification with probable and confirmed cases.
 Laboratory biosafety guidance related to coronavirus disease (COVID-19): interim
guidance
● Signs/ symptoms:
1. Mild: symptomatic presenting with fever, cough, fatigue, anorexia,
myalgias; other non-specific symptoms such as sore throat, nasal
congestion, headache, diarrhea, nausea and vomiting; loss of
smell) or loss of taste (ageusia) preceding the onset of respiratory
symptoms with no signs of pneumonia or hypoxia
2. Moderate: Adult with clinical signs of non-severe (fever, cough,
dyspnea, respiratory rate = 21-30 breaths/minute, peripheral
capillary oxygen saturation >92% on room air
Moderate: Child with signs of non severe pneumonia (e.g. cough
or difficulty breathing and fast breathing <2 months: >60; 2-11
months>50; 1-5 years: >40; and chest in drawing
3. Severe: Adult with clinical signs of severe pneumonia or severe
acute respiratory infection as follows: fever, cough, dyspnea,
RR>30 breaths/ minute, severe respiratory distress <92% on room
air
Severe: Child with clinical signs of pneumonia plus at least one of
the ff: central cyanosis < 90%; severe respiratory distress (e.g. fast
breathing, grunting, very severe chest in drawing); general danger
sign: inability to breastfeed or drink, lethargy or unconsciousness,
or convulsions. Fast breathing: <2 months: >60 in breaths/ min; 2-
11 months: >50; 1-5 yr: >40
4. Critical: Acute Respiratory Distress Syndrome patient with onset
within 1 week of known clinical insult (pneumonia) or new or
worsening respi. Symptoms, progressing infiltrates on chest x-ray
or ct scan, with respiratory failure not fully explained by cardiac
failure
5. Sepsis: Adults with life threatening organ dysfunction caused by a
dysregulated host response to suspected or proven infection. Signs
of organ dysfunction include altered mental status, difficult or fast
breathing, low oxygen saturation, reduced urine output, fast heart
rate, weak pulse, cold extremities or low blood pressure, skin
mottling, or laboratory evidence of coagulopathy,
thrombocytopenia, acidosis, high lactate or hyperbilirubinemia
6. A. Children with suspected or proven infection and >2 age-based
systemic inflammatory response syndrome criteria (abnormal temp
> 38.5 or <36 OC; tachycardia for age or bradycardia for age if <1
yr; tachypnea for age or need for mechanical ventilation; abnormal
wbc count for age or > 10% bands, of which one must be abnormal
temperature or wbc count
Septic shock: Adults with persistent hypotension despite volume
resuscitation, requiring vasopressor to maintain MAP> 65 mmHg
and serum lactate >2 mmol/L
B. Children with any hypotension (SBP <5th centile or > 2 SD below
normal for age) or two or three of the following: altered mental
status; bradycardia or tachycardia (HR <90bpm or > 160 bpm in
infants and heart rate <70 bpm or 150 bpm in children); prolonged
capillary refill >2 sec or weak pulse; fast breathing; mottled or cool
skin or petechial or purpuric rash; high lactate; reduced urine
output; hyperthermia or hypothermia.

Describe the laboratory 1. Direct interview with patients & filling out CIFs
procedures to be used (for 2. Packing of complete PPEs
example, culturing, 3. Antigen testing & OPS/NPS collection
centrifugation, work with 4. Proper waste handling and disposal
sharps, waste handling, 5. Triple packaging
frequency of performing the 6. Linelist encoding
laboratory 7. Sorting and transporting of samples
activity). 8. Decontamination of equipment
9. Frequency of performing lab activity: every 24 hours

Describe the types of 1. PPE

equipment to be used 2. OPS/ NPS KIT
(personal protective 3. ANTIGEN KIT
equipment [PPE], 4. Cool packs
centrifuges, autoclaves, 5. Waste bags

biological safety cabinets
[BSCs]).
Describe the type and
condition of the facility
where work is conducted.
Describe relevant human
factors (for example,
competency, training,
experience and attitude of
personnel).
Describe any other factors
that may affect laboratory
operations (for example,
legal, cultural,
socioeconomic).
Laboratory biosafety guidance related to coronavirus disease (COVID-19): interim
guidance
6. VTM
7. Disinfectant: 3-5%Lysol, 70% alcohol, 10% bleach
8. Refrigerator
9. Ice box container
10. Sharps bin
● The collection site for COVID-19 amongst close contacts, probable,
suspected and random patients is separated from the clinical laboratory. It
has its own waiting area for swabbing and antigen testing. The collection of
samples is done on a swab booth located on Covid Fastlane for close
contact, probable and suspected, which is isolated from the main building
and out-patient department. An interview area is placed beside the swabbing
booth and is fully covered to protect the interviewers from possible
transmission amongst patients.
● San Jose District Hospital Laboratory is a Level-1 hospital based facility with
a secondary laboratory that performs routine tests, blood chemistry, serology
and crossmatching. The covid fastlane is assigned for covid related
procedures like filling out of CIFs, encoding of linelists and doffing of PPEs
are conducted on fastlane. Swab testing is conducted at the swabbing
booth. Samples are properly packaged and stored in refrigerators prior
transportation to OMPH for RT-PCR testing.
● San Jose District Hospital’s Covid Fastlane is not accessible to anyone
besides healthcare personnel and swabbers so as to avoid being infected
and infecting other personnels.
1. The swabber is a licensed medical personnel preferably medical
technologist with training in OPS/ NPS collection
2. The swabber must have basic handling of infectious waste in accordance to
biorisk management training
3. The person for the job must be competent, skilled, knowledgeable, flexible,
good listener and follower.
1. Inadequate supplies of PPEs’ and antigen kits
2. Increased number od Covid-19 cases.
3. Decreasing number of workforce due to health care personnel with Covid-19
infection.
 Laboratory biosafety guidance related to coronavirus disease (COVID-19): interim
guidance
STEP 2. Evaluate the risks

Instructions: Describe how exposure and/or release could occur.

What potential situations
are there in which exposure
or release could occur?
1. Improper Donning and Doffing of PPEs’.
2. Biological spill while collecting NPS/OPS samples.
3. Lack of knowledge on Proper Good Microbiological Procedures and
Practices (GMPP) among swabbers/personnel.
4. Not decontaminating the equipment used and the working area (collection
area and swabbing booth)
5. Sorting of samples with bare hands
6. Interviewing with possible carriers in a close space area.
7. Wearing of masks only when a patient possibly carrying SARS-COV2
coughs thus producing droplets.

What is the likelihood of an 1. Improper Donning and Doffing of PPEs’. =Possible

exposure/release 2. Biological spill while collecting NPS/OPS samples. =Possible
occurring? 3. Lack of knowledge on Proper Good Microbiological Procedures and
● Unlikely: not very Practices (GMPP) among swabbers/personnel. =Possible
possible to occur in 4. Not decontaminating the equipment used and the working area (collection
the near future. area and swabbing booth)= Likely
● Possible: feasible 5. Sorting of samples with bare hands = Unlikely
to occur in the near 6. Interviewing with possible carriers in a close space area. =Likely
future 7. Wearing of masks only when a patient possibly carrying SARS-COV2
● Likely: very coughs thus producing droplets. =Likely
possible to occur in
the near future.
What is the severity of the ● Moderate to Severe
consequences of an
exposure/release
(negligible, moderate,
severe)?

Instructions: Evaluate the risk and prioritize the implementation of risk control measures. Circle the initial (inherent)
risk of the laboratory activities before additional risk control measures have been put in place.
Note:
● When assigning priority, other factors may need to be considered, for example, urgency,
feasibility/sustainability of risk control measures, delivery and installation time and training availability.
● To estimate the overall risk, take into consideration the risk ratings for the individual laboratory
activities/procedures, separately or collectively as appropriate for the laboratory.
Likelihood of exposure/release
Unlikely Possible Likely
1. Improper Donning and Doffing of
PPEs’. =Possible ✔️
2. Biological spill while collecting ✔️
NPS/OPS samples. =Possible
3. Lack of knowledge on Proper Good
Microbiological Procedures and ✔️
Practices (GMPP) among
swabbers/personnel. =Possible
4. Not decontaminating the equipment
used and the working area (collection
✔️
area and swabbing booth)= Likely
5. Sorting of samples with bare hands =
✔️
Unlikely
6. Interviewing with possible carriers in
✔️
a close space area. =Likely
7. Wearing of masks only when a ✔️
patient possibly carrying SARS-
COV2 coughs thus producing
droplets. =Likely
 Laboratory biosafety guidance related to coronavirus disease (COVID-19): interim
guidance
Consequence of Severe ✔️ High Very high
exposure/release Medium
Moderat Low ✔️ High
e Medium
Negligibl Very low Low ✔️
e Medium
Laboratory activity/procedure Initial risk Is the initial risk Priority (high/
(very low, low, above the medium/ low)
medium, high, very tolerance level?
high) (yes/ no)
● Direct interview with patients & filling Low No Medium
out CIFs
● Packing of complete PPEs Very Low No Low
● Antigen testing & OPS/NPS Medium Yes High
collection
● Proper waste handling and disposal High Yes High
● Triple packaging High Yes Medium
● Linelist encoding Low No Low
● Sorting and transporting of samples High Yes Medium
● Decontamination of used equipment Medium No Low
Select the overall initial risk. ☐ ☐ ✔️ ☐ ☐
Very Low High Very
Medium
low high
Should work proceed without additional risk
control measures? ☐ Yes ✔️No

STEP 3. Develop a risk control strategy

Instructions: List any requirements that have been prescribed by international and national regulations, legislation,
guidelines, policies, and strategies on biosafety and biosecurity.
Describe the measures required by national ● Executive No. 430 of October 1990
legislation or regulations (if any). ● “National Committee on Biosafety in the Philippines”

Describe the measures advised by guidelines,
policies and strategies (if any).
1. Laboratory Biosafety Guidance to COVID-19 Interim
Guidelines
2. Biosafety Guidelines for Laboratories Handling and
Testing Respiratory Specimen for Laboratory Diagnosis
of COVID-19 using Rapid Antigen Detection Kit.
3. Interim Guidelines for Sample Collection, Handling,
Storage and Transportation of Clinical Specimens from
Persons Suspected of Coronavirus Disease 2019.
4. Interim Guidelines for Specimen Collection and
Laboratory testing for Case Finding and Investigation of
Severe Respiratory Disease Associated with Novel
Coronavirus.
5. Interim Biosafety Guidelines for Laboratories Handling
and Testing SARS-COVS (COVID 19) Specimens
6. Interim Guidelines for Biosafety and COVID-19 (CDC)
7. Department Memorandum No. 2020-0436
“Minimum Data Requirements of COVID-19 Related
Information Systems”.
 Laboratory biosafety guidance related to coronavirus disease (COVID-19): interim
guidance
Instructions: Describe the resources available for risk control and consider their applicability, availability, and
sustainability in the local context, including management support.
Are resources sufficient to secure and maintain ● No
potential risk control measures?
What factors exist that may limit or restrict any of 1. Lack of PPEs’
the risk control measures? 2. Inadequate supplies of decontaminants.
3. Lack of knowledge on dealing with biohazard materials
and on biosafety.

Will work be able to proceed without any of the ● No. Yes.

risk
control measures; are there alternatives?

STEP 4. Select and implement risk control measures

Instructions: Evaluate the residual risk that remains after risk control measures have been selected, to determine
whether that level of risk is now below the tolerance level and whether work should proceed.
Circle the residual risk of the laboratory activities after risk control measures are in place.
Likelihood of exposure/release
Unlikely Possible Likely
Severe ✔️ High Very high
Consequence of
Medium
exposure/releas
e
Moderate ✔️ Medium High
Low
Negligible Very low Low ✔️
Medium
Overall residual risk: ✔️ ☐ ☐ ☐ ☐
Very Low Medium High Very high
low
 Laboratory biosafety guidance related to coronavirus disease (COVID-19): interim
guidance
If the residual risk is still above the risk tolerance level, further action is necessary, such as additional risk control
measures, based on the initial risk evaluated in STEP 2, redefining the scope of work such that it falls below the risk
tolerance level with existing risk control measures in place, or identifying an alternative laboratory with appropriate risk
control strategies already in place that is capable of conducting the work as planned.
Should work proceed with selected ✔️Yes ☐No
risk control measures?
Approved by (name and title) CHESTER KYLE D. FERNANDEZ, RMT
Approved by (signature)

Date 3/31/2022

Instructions: Describe how to communicate risks and risk mitigation strategies to personnel. Provide a mechanism of
communication within the laboratory. Describe the process and timeline for ensuring all identified risk control measures
and that associated SOPs and training have been completed before starting the laboratory work.
Communication of the hazards, risks, and risk Attending trainings, meetings and updating SOP (Standard
control measures Operating Procedure)
Purchase (and budgeting) of risk control ● Provincial Health Office – Budget Department
measures
Operational and maintenance procedures ● Provincial Health Office – Budget Department
Training of personnel ● Provincial Health Office
 Laboratory biosafety guidance related to coronavirus disease (COVID-19): interim
guidance

STEP 5. Review risks and risk control measures

Instructions: Establish a periodic review cycle to identify: changes in laboratory activities, biological agents,
personnel, equipment or facilities; changes in knowledge of biological agents or processes; and lessons learnt from
audits/inspections, personnel feedback, incidents, or near misses.
Frequency of the review Annually or as needed
Person to conduct the review Biosafety Officer and Laboratory Supervisor
Describe updates/changes Training of personnel, updating PPE usage and practices
Personnel/procedures to implement the changes Unit head
Reviewed by (name and title) CHESTER KYLE D. FERNANDEZ, RMT
Reviewed by (signature)

Date 3-31-22