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LamPORE is a new assay, in advanced development, for the detection of the SARS-CoV-2 virus.

Status at 7 August 2020: Oxford Nanopore has spent recent weeks collaborating with multiple clinical laboratories in the UK to complete evaluations of analytical performance of LamPORE. Information about this dataset of several hundred samples will be released soon and regulatory submissions are underway. We will keep you informed about the rapid progress of its development here.

LamPORE is a rapid, accurate, low-cost, and highly scalable assay for the detection of SARS-CoV-2, the virus that causes COVID-19. The assay combines nanopore analyses with loop-mediated isothermal amplification to detect the SARS-CoV-2 virus, and uses materials outside of current supply chain limitations.

  • Assay targets three genes of the SARS-CoV-2 virus for increased sensitivity
  • Scalable: users can run 24-96 samples on a single flow cell using LamPORE Small and Medium kits. Additionally, a Large kit will be available imminently enabling up to 768 samples to be run on a single flow cell 
  • Designed to be deployed on MinION Mk1C (one flow cell) or GridION (up to 5 flow cells)
  • A GridION device can enable as many as 20,000 tests a day if running 768 samples per flow cell
  • On-demand processing rather than a requirement to batch
  • Rapid results: RNA to answer in under two hours
  • Near-sample analysis.  Simple hardware requirement enables use in centralised lab environment, or 'pop-up', near-community labs; flexible location is also designed to support rapid turnaround times
  • Control mechanism inbuilt to identify errors in sample collection, a common source of 'false negatives'

LamPORE is also in development for the detection of multiple respiratory pathogens in a single assay, in preparation for a need to detect SARS-CoV-2 in samples that may also contain influenza or other respiratory viruses.

LamPORE is the first assay that Oxford Nanopore has developed with the intention for future diagnostic use.

Interested in finding out more and staying informed?

Register your interest in LamPORE

The LamPORE assay

LamPORE is deployable in both high-throughput, centralised settings as well as smaller, local environments for quick turnaround of a large number of samples, opening up opportunities for future routine screening.

Twenty-four to ninety-six samples or, through the use of additional barcodes, up to 768 samples can be processed on a single MinION Flow Cell, or using more barcodes one flow cell can enable the sequencing of 768 samples on a MinION Flow Cell. The GridION can process up to five times this many samples.

How does it work?

LamPORE leverages LAMP (loop-mediated isothermal amplification) upstream of nanopore sequencing to detect the presence of SARS-CoV-2 in a sample.

Isothermal amplification has been used successfully alongside nanopore sequencing previously for the analysis of malaria parasite Plasmodium, leishmaniasis and dengue virus, providing a simple and fast way to amplify a specific target.

The LamPORE assay can be performed on extracted RNA from swabs, and is also in development to enable working directly from saliva.

In a SARS-CoV-2-positive sample, once the viral target has been amplified via LAMP the sample is then prepared for sequencing using Oxford Nanopore’s rapid sequencing chemistry. By barcoding the samples at both the amplification and library preparation stages, high multiplexing capacity can be achieved for large sample volumes.

As well as targeting three specific genes of the SARS-CoV-2 virus, a control target is included in the assay (human β-actin).  This acts as confirmation of successful sample collection, and is designed to show the user where a negative result is because of sample collection errors rather than the lack of presence of SARS-CoV-2.

The prepared sequencing library is subsequently loaded onto a nanopore sequencing device, such as the GridION Mk1 or MinION Mk1C, and real-time analysis begins. When sequencing reads aligning to the SARS-CoV-2 genome and a control target reach a threshold number per sample, the sample can be classed as positive.

By deploying sequencing as the measuring mechanism, the assay is robust to false positives caused by amplification of spurious material.  By incorporating a control, the assay is robust to false negatives caused by incorrect sampling procedures.

Results can be delivered in under two hours for between 1-96 samples, meaning rapid turnaround of results.

The LamPORE workflow
Figure 1: LamPORE is a simple and fast process comprising of amplification, library preparation and sequencing steps to identify whether the SARS-CoV-2 virus is present in a sample.

Regulatory status

LamPORE is the first assay that the Company has developed in-house with intended use in diagnostic applications, subject to relevant regulatory clearances that the Company is currently pursuing. Oxford Nanopore is planning to deploy LamPORE for COVID-19 in a regulated setting initially on GridION and soon after on the portable MinION Mk1C.

CE-IVD registration of the assay is underway.  

How can I find out more?  

Register your interest in LamPORE here to find out more and be kept up to date.

 

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