Wednesday, March 18, 2020

National Training of Trainers for COVID-19 (Coronavirus) - India

Samples to be collected for Covid-19 from a person

  • 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

Personal protective equipment


Image 1. Recommended type of personal protective equipment (PPE) to be used in the context of covid-19 disease, according to the setting, personal  and type activity.

Collection of Oropharyngeal (OP) and Nasopharygneal (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

Oropharyngeal swab collection from patient in VRDL
 Image2: Oropharyngeal swab collection from patient in VRDL.

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.

Diagram of the Oropharyngeal collection of the patient for covid-19.

Picture 3: Diagram of the Oropharyngeal collection of the patient for covid-19.

Collection of Nasopharyngeal swabs

Diagram for how to collect Nasopharyngeal Collection for covid-19.
Image 4: Diagram for how to collect Nasopharyngeal Collection for covid-19.

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


Collection of the blood samples into viles for Coronavirus positive Patients

image 5: Collection of the blood samples into viles for Coronavirus positive Patients.
  • 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.

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.

  • 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

Table for the description of the Triple Packaging System of Covid-19 infectious samples
 Image 6: Table for the description of the Triple Packaging System of Covid-19 infectious samples.

Image 7: Individual Part Explanation for triple Package system.


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 Viral Research & Diagnostic Laboratories (VRDL) doing SARS-CoV-2 testing.
Image 8: 51 Viral Research & Diagnostic Laboratories (VRDL) doing SARS-CoV-2 testing.


56 ViralViral Research & Diagnostic Laboratories(VRDL) as collection sites.

Image 9: 56 ViralViral Research & Diagnostic Laboratories(VRDL) 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.




References: 
  1. Indian Council And Medical Research.