En COVID 19 Laboratory Diagnosis 3

Laboratory diagnosis of COVID-19 in suspected cases
Intended use: The laboratory tests that intended to be used for upper and lower respiratory
samples collected from suspected cases who meet case definition for COVID-19 based on the
updated national guidelines.
Laboratories to perform diagnostic testing:
 Testing is limited to qualified laboratories with a certified Biological Safety Cabinet

Class II (BSC-II ) in a Biosafety level 2 facility (BSL-2) with negative pressure room and
those approved by Saudi CDC.
 To provide diagnostic testing for COVID-19, the laboratory should use nucleic acid-
based detection system, and testing using at least one confirmatory target in addition to
the screening targets.
 In the current time laboratories should NOT attempt viral isolation and culture from
samples collected from patients suspected to have COVID-19
Samples type and collection
A. Lower respiratory tract

Bronchoalveolar lavage, tracheal aspirate
2-3 mL in a sterile, leak-proof, screw-cap container.
Sputum
Sputum collected directly into a sterile, leak-proof, screw-cap container.
B. Upper respiratory tract

Nasopharyngeal swab and oropharyngeal swab.
For collection of Nasopharyngeal and oropharyngeal, synthetic fiber swabs with

plastic shafts should be used. It is not recommended to use swabs with wooden
shafts or calcium alginate swabs, which might have negative impact on PCR
results. Swabs should be immediately placed (separate or combined) into a sterile
tube containing 2-3 ml of viral transport media (VTM).
Storage
Store samples at 2-8°C and ship on ice pack to the designated Laboratory. Samples can be
stored at 2-8°C for ≤48 hours, if longer storage is needed, samples should be stored at –70
°C. If sample is frozen at -70°C, ship on dry ice.
Biosafety guidelines for handling samples from suspected cases of COVID-19
 Sample handling and laboratory work should be in a certified Class II BSC and negative
pressure room in a BSL-2 facility
 Laboratory personnel should wear appropriate personal protective equipment (PPE) when
working with infectious materials.
 For Laboratory, procedures that might generate aerosols or droplets should be always
performed in a Class II Biological Safety Cabinet (BSC-II).
 Goggles, mask, and face shield should be used for eye and face protection during any
procedure.
 For decontamination of work surfaces and equipment with appropriate disinfectants and
laboratory waste management, follow your standard procedures for procedures and
samples collected to testing MERS-CoV.
 All the laboratories should not attempt to do Virus isolation and culture of SARS-CoV-2
at this time.
 Before starting testing, risk assessments should be performed
Results interpretation of Real Time RT-PCR:

 Follow the manufacturer recommendations for the defined cut-off CT value for the
positive results based on the CT value for each target gene.
 Make sure to use internal control (IC). Before reporting results make sure that IC is
positive, if not, you have to repeat the test. If the target gene is positive and the IC is
negative, report the target gene as positive.
 For Samples with high CT values, you have to rule out contamination during extraction.
Carry-over and cross contamination is a problem with some automated nucleic acid
extraction systems.
 In case of inconclusive/ indeterminate results, please send the sample to the National
health laboratory for further testing.
 The lower respiratory tract samples are preferred if patient has signs or symptoms of
lower respiratory tract infection. If lower tract specimens are not possible or clinically
indicated, upper respiratory samples should be collected.
 Repeat testing should be performed if initial testing is negative and there is a high index
of diseases suspicion. Patients should be retested using a lower respiratory sample or, if
not possible, repeat collection of a nasopharyngeal sample.
 A single negative test result, especially from upper respiratory tract sample, does not rule
out the infection.
 Negative RT-PCR results must be interpreted in correlation with clinical findings,
history, and other diagnostic procedures.
 Positive RT-PCR for COVID-19 indicate infection with SARS-CoV-2. However, it does
not rule out co-infection with other viruses.
Notification and Reporting positive cases:
 All laboratories testing for COVID-19 are required to report the number of tested samples
on a daily bases to the public health authorities.
 All laboratories testing for COVID-19 are required to report all positive results
immediately to the public health authorities through HESN portal.
 All samples with positive results from MOH, Governmental non-MOH and private
Sectors should be sent to National Health Laboratory, Saudi CDC for further
confirmation.
 Store respiratory samples at 2-8°C and ship to National health Laboratory, Saudi CDC on
ice pack.
Referral of samples to Saudi CDC Laboratory:
1. Label each specimen container with the patient’s ID number, HESN requisition number,
and the date the sample was collected.
2. In HESN you can register the case and for test requested select COVID-19 and for the
distention you select National Health Laboratory (NHL).
3. Store respiratory samples at 2-8°C and ship to NHL, Saudi CDC on ice pack.
4. Samples can be shipped free of charge via the courier, SMSA, following appropriate
regulations. The courier service is available for sample transportation and pickup
locations throughout the country for collection of samples from MOH hospitals and other
non-MOH Health care facilities. Specimens pick up can be requested from SMSA at the
following number (8006149999)
5. All specimens must be appropriately packaged and transported in accordance with
Category B transportation regulations and the WHO guidance on regulations for the
transport of infectious substances 2019-2020. For shipping, of sample, must follow the
current edition of the International Air Transport Association (IATA) Dangerous Goods
Regulations.

En COVID 19 Laboratory Diagnosis 3

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Laboratory diagnosis of COVID-19 in suspected cases

Laboratories to perform diagnostic testing:

 Testing is limited to qualified laboratories with a certified Biological Safety Cabinet

Samples type and collection

A. Lower respiratory tract

B. Upper respiratory tract

For collection of Nasopharyngeal and oropharyngeal, synthetic fiber swabs with

Results interpretation of Real Time RT-PCR:

Referral of samples to Saudi CDC Laboratory:

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