LamPORE is a new assay, in advanced development, for the detection of the SARS-CoV-2 virus.
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.
- Scalable; users can run between 1 - 768 samples on a single flow cell (including positive / negative controls)
- Designed to be deployed on MinION Mk1C (one flow cell) or GridION (up to 5 flow cells)
- Simple desktop devices can therefore enable as many as 15,000 tests a day
- On-demand processing rather than a requirement to batch
- Rapid results: under two hours for 1-96 samples on a single flow cell
- 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'
- Assay sequences three genes of the SARS-CoV-2 virus for precise analysis
LamPORE is a rapid, low-cost and highly scalable assay for the detection of SARS-CoV-2, the virus that causes COVID-19. The assay combines nanopore sequencing with loop-mediated isothermal amplification to detect the virus, and uses materials outside of current supply chain limitations.
LamPORE is the first assay that Oxford Nanopore has developed with the intention for future diagnostic use.
Status at 30 July 2020: Oxford Nanopore has spent recent weeks and months collaborating with multiple clinical laboratories in the UK to complete evaluations of analytical performance of LamPORE. This dataset will be released soon. We will keep you informed about the rapid progress of its development here, with future regulatory updates.
Interested in finding out more and staying informed?
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.
1-96 samples can be processed in just over an hour on a single MinION Flow Cell, or using more barcodes can enable the sequencing of 768 samples on a MinION Flow Cell, requiring an additional ~3 hours sequencing time. 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 (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.
Results can be delivered in under two hours for between 1-96 samples, meaning rapid turnaround of results.
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.
The LamPORE protocol will also later be made openly available for research use on any Oxford Nanopore device.
How can I find out more?
Register your interest in LamPORE here to find out more and be kept up to date.
