Oxford Nanopore Technologies announces advanced development of LamPORE, for rapid, highly scalable, low-cost COVID-19 detection
Fri 22nd May 2020
LamPORE is designed for use in both high-throughput labs or decentralised locations-
Oxford Nanopore Technologies is in advanced development of a new generation of end-to-end test (assay) for the detection of SARS-CoV-2, the virus that causes COVID-19.
The LamPORE assay is designed to be rapid, low cost, and scalable to cater to on-demand analysis of smaller sample numbers, to very large numbers of samples. Hardware and reagents sit outside current, squeezed supply chains for other molecular tests.
LamPORE is based on Oxford Nanopore’s DNA/RNA sequencing technology, in combination with a simple, sample-preparation method (loop-mediated isothermal amplification, plus Oxford Nanopore’s ‘rapid kit’). It seeks to understand whether a sample currently contains the SARS-CoV-2 virus (rather than detecting antibodies that may indicate a previous infection).
Since the first emergence of the virus, Oxford Nanopore’s rapid, portable sequencing technology has been used extensively for COVID-19 epidemiology and scientific research.
LamPORE is the first assay that the Company has developed in-house with intended use in diagnostic applications, subject to relevant authorisations 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 be made openly available for research use on any Oxford Nanopore device.
Oxford Nanopore’s vision is to support wide efforts to identify, track, trace and isolate cases. LamPORE is designed to enable rapid detection of SARS-CoV-2, whether in a high- throughput centralised lab processing thousands of samples, or for on-demand analysis in decentralised locations, so that analysis can be performed in more community settings.
LamPORE is designed to enable:
- Very high throughput, centralised lab-based analyses: for example, to support routine screening of workforces - whether on the frontline or to support a general return to work. This might include regular screening of healthcare workers/other public sector employees, or businesses’ employees, whether symptomatic or asymptomatic.
- Near-community: Also designed to be deployable in decentralised environments, LamPORE opens up potential opportunities for rapid, local testing as restrictions are eased, for example in care homes, transport networks, businesses or other community settings. Decentralisation supports rapid turnaround of testing, which is important to enable rapid, precise isolation and therefore prevent onwards transmission of the virus.
The LamPORE method can also be used to analyse environmental samples to assess for the presence of the SARS-CoV-2 virus. This has the potential to be used for swabbing surfaces, or systems such as water treatment.
LamPORE does not rely on reagents used in traditional COVID-19 tests, which could ease pressure on current supply chains and expand access.
“This year we have gained extensive experience supporting customers using our sequencing technology for COVID-19 epidemiology, and we have also been directing our own powerful innovation and development engine at COVID-19,” said Dr Gordon Sanghera, CEO of Oxford Nanopore. “We designed our first nanopore sequencing device to be used by any scientist, anywhere. Now, with LamPORE, we want to bring the accessibility and scalability of nanopore sequencing into the area of rapid testing,”
Oxford Nanopore is collaborating with scientists in multiple institutions for rapid optimisation and validation of the LamPORE method for SARS-CoV-2 detection.
The LamPORE method provides certain advantages in the detection of SARS-CoV-2:
- Simple materials for precise results: With simple hardware requirements, LamPORE combines the established, rapid, low cost LAMP method for initial amplification of the virus with Oxford Nanopore sequencing for a precise, digital result. LAMP alone has been used for the detection of virus with a colour based readout, but interpretation of colour-based results can be challenging at scale; sequencing provides a digital ‘readout’
- Available materials: The reagents required are low-cost and are detached from the supply chains that currently serve RT-PCR testing systems, where devices and reagents are in global short supply
- Scalability and rapid results: Scaling-up of sample numbers is performed using molecular barcodes to run multiple samples at the same time.
- When used on the smallest sequencing device, MinION, 96 samples can be analysed in around an hour or 1,152 samples in around 4.5 hours. Smaller numbers can be analysed on-demand if required
- Where there is a requirement to process much larger numbers of samples, a single desktop GridION sequencing device allowed five times this number (480 samples in just over an hour, or 5,760 samples in 4-5 hours), in the same timeframe
- Sample type: The assay is being developed for compatibility with swabs or saliva samples.
- Analysis of other pathogens: The LamPORE method also has the potential to be developed for the simultaneous analysis of multiple pathogens including SAR-CoV-2. This has potential utility when the prevalence of COVID-19 has fallen, and that of other respiratory pathogens is high, in order to screen for SARS-CoV-2 when it is less common in a population
LamPORE at scale for population-scale COVID screening
LamPORE can be scaled to process very large sample numbers (a single desktop GridION device can process up to 20,000 samples a day). Additional ultra-high throughput capacity to existing testing programmes has the potential to expand testing from key workers or those with symptoms, to enable broader, regular screening of communities and support an easing of COVID restrictions for the benefit of broad populations.
In UAE, Oxford Nanopore is working to develop and optimise LamPORE for ultra-high throughput screening with our technology partner G42. G42 has been a scientific and engineering partner in the conceptualisation and creation of ultra-high throughput nanopore sequencing capabilities, and is bringing to bear extensive field experience in processing of high sample numbers. An unprecedented national-scale infrastructure project is now starting, with the goal of bringing these benefits to the UAE population and beyond.