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NWLP extraction free protocol - Using SPS and Non-proprietary buffer with the AusDiagnostics SARS CoV-2 assay

D1: Path Lab Bulletin
D3: Catalogue of Resources

The NWLP Infection and Immunity laboratory has been using the AusDiagnostic COVID19 test in conjunctions with multiple nucleic extraction platforms (AusDiagnostics, Qiagen (EZ1), Magnapure).

However, the supply of reagents and extraction kits has emerged as a significant barrier to increasing (and even maintaining) testing capacity.

In light of these difficulties, alternative strategy was validated including using heat inactivation (rather than a GTC containing lysis buffer) and extraction free protocols.

Initial work identified the Serosep SPS propriety buffer as an acceptable alternative for contingency non-extraction testing and this report is included here.

This validation report has been updated following further work with the substitution of SPS with a non-propriety buffer.

Have you validated this method, if so, how and what were the results of the validation?​

 

Using TE as an alternative to the SPS buffer.

  • Overall there was concordance between extraction and heat inactivation with SPS and TE buffers.
  • As anticipated, the discrepant results were seen at the lower limit of detection of the assay as seen in the initial study using SPS buffer
  • Heat inactivated samples can be rescued and retested by repeating the process without loss of sensitivity.
  • TE can be used as a substitute if SPS buffer is not available.

 Previously we reported that using the SPS buffer heat-inactivation method.

  • SPS Overall the sensitivity and specificity of the heat inactivation with no extraction protocol was 93.33% and 92.86% respectively when compared to the standard testing method for SARS CoV-2.
  • Discrepant results were towards the lower limit of detection of the assay where positive samples are anticipated to less reliably detected owing to stochastic detection at these low copy numbers

In the setting where nucleic acid extraction kits are limited these two alternative methods can be implemented as an alternative for SARS CoV-2 testing using the AusDiagnostics assay

How quickly could this be deployed and what are the dependencies?​

With the Non-proprietary buffer there are no obvious barriers to immediate deployment

What is the likely production volume?​

Production volumes are not an issue with the Non-proprietary buffer

SPS buffer is a proprietary buffer

What are the risks and barriers to using this at scale?​

This method has only been tested with the AusDiagnostics two-step MT-PCR process so far. Extraction-free methods are generally less sensitive than protocols that use an extraction step. This has been mitigated by adding additional cycles in Step 1 of the MT-PCR process.

Who are you already partnering with on this?

This validation work has been carried out by the Infection and Immunity Department of North West London Pathology (NWLP) at Charing Cross Hospital, Imperial College Healthcare NHS Trust, London.

 

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Kyle Beacham 7 months ago

Status label added: D

Kyle Beacham 7 months ago

The idea has been progressed to the next milestone.

Colin Gilchrist 7 months ago

This sounds remarkably similar (if a bit behind the curve) to the tech and systems being used by Circular1 Health: https://circular1.com/health/ see enclosed doc.

Panagiotis Pantelidis 7 months ago

I am afraid the comment may have been attached against the wrong method. The attached protocol does not mention TE or SPS buffers with or without Heat inactivation of the virus. It mentions isothermal reaction at 65C “we used a combination of magnetic bead viral genome capture and optimised RT-LAMP (Reverse Transcriptase Loop-Mediated Isothermal Amplification) for amplification and detection of the SARS-CoV-2 genome” and "Magnetic bead capture and RT-LAMP amplification and testing for SARS-CoV-2 was found to be promising, ….."

Bev Matthews 7 months ago

Status label added: D1

Bev Matthews 7 months ago

Status label removed: D

Tom Jordan 6 months ago

Thank you for sharing this with us Panagiotis. Our champions were keen to share your submission more widely. We have added this page to our weekly Testing Methods bulletin, to encourage labs to consider this in detail, test and scale-up.

You can access the weekly bulletins from the COVID-19 resources hub on the RCPath website: https://www.rcpath.org/profession/coronavirus-resource-hub.html

Kind regards,
Tom Jordan
On behalf of the Testing Methods team

Panagiotis Pantelidis 6 months ago

Thank you for letting me know. I hope it helps the wider community towards the 100,000 goal

Tom Jordan 6 months ago

The idea has been progressed to the next milestone.

Bev Matthews 6 months ago

Links with https://testingmethods.crowdicity.com/post/3163450

Charlotte Cookson 6 months ago

Status label added: Requires more information

Charlotte Cookson 6 months ago

Hi Panagiotis, we are trying to make contact to see if you would like to join a conversation we are planning for next week. Charlotte

Users tagged:

Panagiotis Pantelidis 6 months ago

Hi Charlotte
Happy to join next week
I can see you require further information
Panos

Bev Matthews 5 months ago

Status label added: D3: Catalogue of Resources

Status label removed: More information requested

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