Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing
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Abstract
LamPORE is a novel diagnostic platform for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA combining loop-mediated isothermal amplification with Nanopore sequencing, which could potentially be used to analyze thousands of samples per day on a single instrument. We evaluated the performance of LamPORE against reverse transcriptase PCR (RT-PCR) using RNA extracted from spiked respiratory samples and stored nose and throat swabs collected at two UK hospitals.
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SciScore for 10.1101/2020.09.18.20195370: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding LamPORE: LamPORE is described in detail in James, et al.5, and was performed identically at each site using a GridION instrument with operators blinded to sample identity. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our evaluation has several limitations. It was conducted after the …
SciScore for 10.1101/2020.09.18.20195370: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding LamPORE: LamPORE is described in detail in James, et al.5, and was performed identically at each site using a GridION instrument with operators blinded to sample identity. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our evaluation has several limitations. It was conducted after the first wave of COVID-19 in the UK, when there were few incident cases, so we were unable to prospectively collect samples and instead relied on frozen transport media, which could differ from fresh material. Positives were defined by a positive RT-PCR at the time of initial sample collection and by repeat positive RT-PCR simultaneously with LamPORE, but although RT-PCR is used as a reference test for SARS-CoV-2, there are many reports of its suboptimal sensitivity in clinical infection18. This early evaluation of LamPORE compared its performance against RT-PCR using extracted RNA, as this is the standard material used for detection of SARS-CoV-2. However, the requirement for viral inactivation and RNA extraction in a clinical laboratory produces bottlenecks that mitigate the potential benefit of LamPORE for high-throughput or mobile testing. LAMP reactions are reported to be more robust than RT-PCR to inhibitors present in clinical samples so may have superior performance with extraction-free protocols19,20. This could greatly streamline the workflow, but further evaluation is required. We also did not evaluate how the throughput and turnaround time of LamPORE would compare to RT-PCR during routine use in a clinical laboratory or centralised testing centre. Using LamPORE for high-throughput testing of tens or hundreds of thousands of samples per day would be dependent on an streamlined workflow, including autom...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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