Dec 16, 2024

Public workspaceREDI-NET SW-3 SWAB STORAGE V.2

DOI
dx.doi.org/10.17504/protocols.io.n2bvj3j6plk5/v2
  • REDI-NET Consortium1
  • 1REDI-NET Consortium
  • Remote Emerging Disease Intelligence - NETwork (REDI-NET)
REDI-NET Consortium
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DOI: dx.doi.org/10.17504/protocols.io.n2bvj3j6plk5/v2
Protocol Citation: REDI-NET Consortium 2024. REDI-NET SW-3 SWAB STORAGE. protocols.io https://dx.doi.org/10.17504/protocols.io.n2bvj3j6plk5/v2Version created by REDI-NET Consortium
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: November 17, 2023
Last Modified: December 16, 2024
Protocol Integer ID: 110570
Keywords: STORAGE PROCEDURE FOR UNTREATED SAMPLE, STORAGE PROCEDURE FOR TOTAL NUCLEIC ACID
Funders Acknowledgements:
USAMRAA
Grant ID: HT9425-23-C-0059
USAMRAA
Grant ID: W81XWH-22-C-0093
USAMRAA
Grant ID: W81XWH-21-C-0001
USAMRAA
Grant ID: HT9425-24-C-0072
Disclaimer
This work is supported by the US Army Medical Research and Development Command under Contract No.W81XWH-21-C-0001, W81XWH-22-C-0093, HT9425-23-C-0059 and HT9425-24-C-0072. The views, opinions and/or findings contained in this report are those of the author(s) and should not be construed as an official Department of the Army or Navy position, policy or decision unless so designated by other documentation.
Abstract
This protocol describes swab storage.
Guidelines
OBJECTIVE

To outline steps for properly storing swab samples and nucleic acid samples purified from these samples.

SUMMARY/SCOPE

The overarching aim of the REDI-NET is to develop a collaborative laboratory network between domestic and international partnering institutions to address disease surveillance needs in order to effectively detect, predict and contain potentially emergent zoonosis. This SOP provides guidance on storage of swab samples and their purified nucleic acid to preserve their integrity for downstream nucleic acid extraction and/or sequencing library preparation


MAINTENANCE OF EQUIPMENT

Decontaminate a PCR workstation by keeping the UV light on for Duration00:15:00 .

Materials
EQUIPMENT AND MATERIALS
Note
NOTE: If product number is listed, please ensure use of this or equivalent product.
ABC
Equipment / MaterialDescriptionMfg / Product #
–80°C freezerFor sample storageLocally sourced
ForcepsClean, stainlessLocally sourced
IceTo maintain cold chain during sample handlingLocally sourced
96-Well Microfuge tube racks with coverTo hold microplatesLocally sourced
KingFisher™ 96 KF microplateTo store the sampleThermoFisher, 97002540
PCR WorkstationPCR cabinet with UV lightLocally sourced
Clear Adhesive FilmTo seal the KingFisher™ 96 KF microplateThermoFisher, 4306311
Adjustable micropipettesTo handle the samplesLocally sourced
Multi-channel micropipettes8- or 12- channel; to handle the sampleLocally sourced
Nuclease-free filter tips low-retentionTo ensure appropriate sample handlingLocally sourced
Nuclease free microfuge tubes1.5 mLLocally sourced
Saran wrapPlastic wrap; to seal rack holding sampleLocally sourced
Permanent markersTo label tubes and microplatesLocally sourced
Data sheetREDI-NET DCS T-3 Tick StorageREDI-NET Data Portal
Safety warnings
RISKS AND PERSONAL PROTECTION:

Gloves should be worn all the time when handling samples.
Ethics statement
The protocols.io team notes that research involving animals and humans, including tissues or samples collected directly from specimens or participants, must be conducted according to internationally-accepted standards and should always have prior approval from an Institutional Ethics Committee or Board.
STORAGE PROCEDURE FOR UNTREATED SAMPLE
STORAGE PROCEDURE FOR UNTREATED SAMPLE

Note
NOTES:
  • Swab samples need to be kept on cold chain all the time to prevent RNA degradation. The following procedure will apply only where Temperature-80 °C storage is feasible.
  • If Temperature-80 °C storage is not possible, temporarily store the swab samples in a Temperature-20 °C freezer and follow swab sample processing SOP (REDI-NET SOP SW-2 Swab Processing) as soon as possible for total nucleic acid extraction. Subsequently, use a portion of the total nucleic acid and reverse- transcribe RNA into cDNA for Temperature-20 °C storage. To do this, follow the initial steps of the swab sample testing SOP (REDI-NET SOP SW-4 Swab Testing) cDNA Synthesis, until finishing step 40.

Precool 96-well microfuge tube racks TemperatureOn ice .

Using preprinted adhesive labels or permanent markers, label Amount1.5 mL microfuge tubes.

Transfer swab sample into the corresponding pre-labeled Amount1.5 mL microfuge tubes, cut and discard the swab shaft and keep the tip portion only, close the cap and put it onto the microfuge tube rack TemperatureOn ice sequentially.

Once the rack is full or all swab samples have been completed, label the rack with a unique rack ID.
Close the rack lid tightly, secure with clear Saran wrap and immediately transfer to Temperature-80 °C freezer.
Update the freezer inventory so samples can be tracked properly.
STORAGE PROCEDURE FOR TOTAL NUCLEIC ACID
STORAGE PROCEDURE FOR TOTAL NUCLEIC ACID

Note
NOTES:
  • The following procedure is to properly store total nucleic acid extracted from swab samples (including negative controls) using the KingFisher nucleic acid purification system. The eluted total nucleic acid will be in either 96-well microplate (Flex model) or elution strip (Duo Prime model).
  • Total nucleic acid samples need to be kept TemperatureOn ice all the time to minimize RNA degradation.

In the clean PCR workstation, carefully transfer the eluted total nucleic acid to a 96-well PCR microplate, make sure to keep samples in the exact same locations corresponding to the rack where the original blood were stored.

Note
IMPORTANT: Mark the “A1” position of the 96-well microplate to prevent any mistakes on plate orientation.

Critical
Cover the 96-well PCR microplate with adhesive film to prevent spill over or contamination.
Label the film with a unique plate ID.
Immediately transfer the 96-well PCR microplate to Temperature-80 °C freezer.
Update the freezer inventory so samples can be tracked properly.
Protocol references