Samples

National Training of Trainers for COVID-19

March 6, 2020

Samples to be collected

• Essential samples:
– Throat swab (oropharyngeal swab).

– Nasal swab (Nasopharyngeal swab)

• Other preferred samples: – Bronchoalveolar lavage

– Tracheal aspirate – Sputum

• In lab confirmed patients: – Blood

– Stool and urine –

Wide mouth sterile plastic containers

Wide mouth sterile plastic containers

Personal protective equipment

WHO interim guidance document for Rational use of personal protective equipmentfor coronavirus disease 2019 (COVID-19)

Collection of OP and NP swabs

• Optimal timing:

– Within 3 days of symptom onset and no later than 7 days.
– Preferably prior to initiation of antimicrobial chemoprophylaxis or therapy.

Collection of Oropharyngeal swab

Materials:

• Sterile Dacron/Nylon flocked swab

• Viral Transport Medium (3 ml sterile VTM)
Procedure:

• Hold the tongue out of the way with a tongue depressor.

• Use a sweeping motion to swab posterior pharyngeal wall and tonsillar pillars

• Have the subject say “aahh” to elevate the uvula.

• Avoid swabbing soft palate and do not touch the tongue with swab tip.

• Put the swab in VTM

 

Collection of Nasopharyngeal swabs

• Materials

• Sterile Dacron/Nylon flocked swab

• Viral Transport Medium (3 ml sterile VTM)
• Procedure

• Tilt patient’s head back 70 degrees

• Insert swab into nostril (Swab should reach depth to distance from nostrils to outer opening of the ear

• Leave swab in place in place for several seconds to absorb secretions

• Slowly remove swab while rotating it

• Place tip of swab into VTM and snap/cut off the applicator stick

Blood collection from positive cases

• Blood sample collection from all positive cases

• Plasma sample collection in EDTA vials

• Resin separator tubes for serum sample collection

 

Guidance for specimen Collection

• A BSL2 containment level is required to handle suspected samples.

• Consider all specimens as POTENTIALLY HAZARDOUS / INFECTIOUS.

• Handle all specimens with gloves in a secure manner.

• Place each specimen into a separate container labeled with the patient’s name and identification number, the collection site, the date of collection and the time of the collection.

• Do not contaminate the outside of the specimen container.

• Do not handle laboratory requisition forms with gloves.

Storage of Specimen

• Keep refrigerated (2-8 °C) if it is to be processed (or sent to a reference laboratory) within 48 hours.

• Keep frozen (-10 to -20 °C) if it is to be processed after the first 48 hours or within 7 days.

• Keep frozen (-70 °C) if it is to be processed after a week. The sample can be preserved for extended periods.

Guidelines followed for sample packaging & transport

• WHO Guidelines for Transport of Infectious Substances:
– Guidance on regulations for the Transport of Infectious Substances

2009–2010.

Click to access WHO_HSE_EPR_2008_10.pdf

• IATA guidelines

Classification of Infectious Substances

• Category A: An infectious substance which is transported in a form that, when exposure to it occurs, is capable of causing permanent disability, life- threatening or fatal disease in otherwise healthy humans or animals.

–  UN 2814 for Infectious substances which cause disease in humans or both in humans and animals.

–  UN 2900 for Infectious substances which cause disease only in animals

Classification of Infectious Substances

• Category B: An infectious substance which does not meet the criteria for inclusion in Category A.

– Infectious substances in Category B shall be assigned to UN 3373 SARS-CoV-2 virus infectious/potentially infectious material falls under category B

Packaging System

• The original samples should be packed, labeled and marked, and documented as Category B.

• Standard triple packing for Category B to be followed.

• Samples to be sent on dry ice (if possible). However using cold packs
is acceptable.

• Sender should provide prior intimation about shipment of samples to the nearest certified laboratory.

 

Triple packaging system

Primary Container

Secondary Container

Outer Container/ Packaging Box

•Watertight and leak proof • Cap correctly and securely closed.
• Keep in upright position during transport

•Watertight
•Several clinical specimens may be placed into one secondary container
• Containers have to be cleansed and disinfected if they are to be re-used E.g.: Disposable, zip-lock plastic bags; Large centrifuge tubes (50 ml) with screw caps

•Made of strong material that can be cleansed and disinfected •Should have the Biohazard warning label

•A content list in a sealed plastic bag inside the transport box may also be included

  

Transport Precautions

• Adequate cushioning materials inside the box to absorb shocks during transport

• Adequate absorbing material to absorb any spillage should it occur

• Do not stick the request form on the specimen

• Specimen request forms should be put into a separate plastic bag

• The outer container, secondary containers and specimen racks for transport should be thoroughly cleansed and disinfected periodically (i.e. at least daily) and when contaminated.

Labeling of Package

• Sender’s, name, address and telephone number
• Whom to contact in case of emergency with telephone number
• Receiver’s name, address and telephone number
• Proper shipping name (e.g. “BIOLOGICAL SUBSTANCE, CATEGORY B”) • UN number e.g. 3373
• Temperature storage requirements
• Quantity of dry ice inside the container
• Arrow mark to indicate upright direction

Responsibility of Sender

• Make advance arrangements with the carrier
-that the shipment will be accepted for appropriate transport

– that the shipment (direct transport if possible) is undertaken by the most direct routing

• Prepare necessary documentation, including permits, dispatch and shipping documents

• Notify the receiver in advance of transportation arrangements and expected date of delivery of shipment

Responsibility of Receiver

• Acknowledge receipt of specimen
• Verify the integrity of packaging
• Box to be opened by personnel wearing adequate PPE. • Open within Biosafety cabinet
• Check the specimens with the data sent
• Apply acceptance and rejection criteria

Types of Tests

• No validated serological tests • Only molecular diagnosis

– PCR based test aims at detection of the virus. • Real time PCR platform is required.

51 VRDLs doing SARS-CoV-2 testing 56 VRDLs as collection sites

                                                                                                            

Tests for SARS-CoV-2

• No validated serological tests are available.

• Only Molecular tests available.

• Laboratory protocols designed on the basis of WHO guidance and sequences available in GISAID.

• First line screening assay: E gene.

• Confirmatory assays: RdRp and ORF 1b.

• SoPs and testing protocol shared with all testing laboratories.

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