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.
• 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.