Oct 22, 2021

Public workspaceStep 1: Swab sample collection V.2

This protocol is a draft, published without a DOI.
  • Peter H L Krijger1,
  • Tim A Hoek1,
  • Sanne Boersma1,
  • Lieke I P M Donders2,
  • Maaike M C Broeders2,
  • Mark Pieterse1,
  • Pim W Toonen1,
  • Ive Logister1,
  • Bram M P Verhagen1,
  • Marjon J A M Verstegen1,
  • Thomas W van Ravesteyn1,
  • Rene J T M Roymans2,
  • Francesca Mattiroli1,
  • Jo Vandesompele3,
  • Monique Nijhuis4,
  • Stefan Meijer5,
  • Anton van Weert5,
  • Edwin Dekker6,
  • Fred J Dom7,
  • Rob Ruijtenbeek8,
  • Lieven B J van der Velden2,
  • Jeroen H B van de Bovenkamp2,
  • Martijn Bosch8,
  • Wouter de Laat1,
  • Marvin E Tanenbaum1
  • 1Oncode Institute, Hubrecht Institute–KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.;
  • 2Laboratory of Medical Microbiology, Stichting PAMM, Veldhoven, the Netherlands.;
  • 3InActiv Blue, Beernem, Belgium. Biogazelle, Zwijnaarde, Belgium.;
  • 4Dept of Medical Microbiology, University Medical Center, Utrecht, the Netherlands.;
  • 5Tecan labwerx, Tecan Trading AG, Männedorf, Switzerland.;
  • 6Bodegro B.V., Breda, the Netherlands.;
  • 7HiFiBio Therapeutics, Saint-Jacques, France.;
  • 8Department of Laboratory Automation, Genmab B.V., Utrecht, the Netherlands.
Peter Krijger
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Protocol Citation: Peter H L Krijger, Tim A Hoek, Sanne Boersma, Lieke I P M Donders, Maaike M C Broeders, Mark Pieterse, Pim W Toonen, Ive Logister, Bram M P Verhagen, Marjon J A M Verstegen, Thomas W van Ravesteyn, Rene J T M Roymans, Francesca Mattiroli, Jo Vandesompele, Monique Nijhuis, Stefan Meijer, Anton van Weert, Edwin Dekker, Fred J Dom, Rob Ruijtenbeek, Lieven B J van der Velden, Jeroen H B van de Bovenkamp, Martijn Bosch, Wouter de Laat, Marvin E Tanenbaum 2021. Step 1: Swab sample collection. protocols.io https://protocols.io/view/step-1-swab-sample-collection-bzecp3awVersion created by Peter Krijger
Manuscript citation:
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it’s working
Created: October 22, 2021
Last Modified: October 22, 2021
Protocol Integer ID: 54436
Disclaimer
J.V. is co-founder and CSO of InActiv Blue; S.M. is an employee of Tecan Trading AG; L.M.P.D., M.M.C.B., R.J.T.M.R., L.B.J.V. and J.H.B.B. are employees of Stichting PAMM Veldhoven; A.vW. is an employee of Sanquin;, E.D. is a founder and employee of Bodegro; and F.J.D. is CEO and co-founder HiFIBiO France.
Abstract
One of the most critical innovations within STRIP is the collection of samples in small tubes (0.8 ml compared with 5–15 ml in standard diagnostics) with virus-inactivating and RNA-stabilizing lysis buffer (InActiv Blue) spiked with a control RNA (PDV). The use of small tubes enables the collection of sample tubes in small 96-tube boxes at sample collection sites. These 96-tube boxes are directly compatible with automated sample processing in the lab without slow and often laborious transfer of samples from collection tubes to plates that are compatible with robotics.





Materials
Sample collection tubes
  • 0.8 ml 2D Data-Matrix coded tube with external thread, Micronic, #MP52720.
  • Micronic tube rack: Micronic, #MP51207.
  • Micronic tube manual recapper: Micronic, #MP35480.
  • Micronic tube barcode scanner: Single TUBE HQ SCANNER, HQ healthcare, #268821.
  • InActiv Blue, virus inactivating and RNA stabilizing transport medium. InActiv Blue (https://www.inactivblue.com), #IB1000.
  • Virus transport buffer: InActiv Blue mixed with a spike-in control RNA (We use home-made Phocine Distemper Virus, PDV).

0.8 ml Micronic tubes are filled by Micronic with 0.4 ml virus transport buffer and can be stored at RT for at least 8 months. Before shipment to the collection sites the tubes are centrifuged (1 min 500G).




Safety warnings
InActiv Blue contains Guanidine thiocyanate. Guanidine thiocyanate is harmful if inhaled, swallowed or if it comes into contact with skin and causes severe skin burns and eye damage. In addition, never clean up InActiv Blue with bleach as Guanidine thiocyanate reacts with bleach to produce cyanide gas.
Before start
Collection personnel should be trained in the proper collection procedure.
Sample collection
Sample collection
Person 1 scans the 2D barcode at the bottom of a 0.8 ml Micronic tube prefilled with 0.4 ml virus transport buffer ( InActiv Blue mixed with a spike-in control RNA) and places it in a Micronic tube rack (tube rack A).
Person 1 removes cap from the Micronic tube using the manual recapping device (cap stays on the recapping device).
After instructing the patient to blow their nose, the naso- oropharyngeal swab specimen is collected by person 2 using 1 flocked swab using standard procedures. Importantly: Make sure no mucus is attached. Repeat swab collection when needed.
Person 2 places the swap in the tube placed in tube rack A, rotates the swab 10 times between thumb and index finger, and trashes the swab.
Person 1 close the tube with the cap and transfers the tube to a new tube collection rack (tube rack B).
Store at room temperature until shipment to the RNA extraction site. Samples are processed as soon as possible after arrival at the lab. Samples are regularly processed within 24h but can be stored up to 72h if required.