Our role in this project is to use gargle samples collected from school-aged children and their teachers, to diagnose the virus SARS-CoV-2 using Lampore methodology from Oxford Nanopore Technologies (ONT), a cutting-edge technology high-throughput molecular test. LamPORE, based on isothermal amplification and rapid product sequencing, has been selected by the UK government as one of the main healthcare and population screening approaches, and it is currently undergoing EU/UK/USA/Canada regulatory approval. ONT is currently developing the LamPORE approach to test for multiple pathogens within a single sample, including influenza A (H1N1 and H3N2), influenza B, respiratory syncytial virus (RSV), Rhinovirus and SARS-CoV-2. The assay combines barcoded multi-target amplification, 15-minute barcoded library preparation and real-time nanopore sequencing at a cost similar to the standard qRT-PCR. This provides a rapid way of testing/screening large numbers of samples for the presence or absence of SARS-CoV-2, for particular virus mutations and for other respiratory viruses with sequence as a robust readout. Starting with RNA extracted from nasal swabs or water gargle, results can be obtained from as few as 12 samples or pools in approximately an hour and from multiples of 96 samples or pools in under 2 hours per device. Currently the limit of detection of LamPORE is determined as 7-10 genome copies/μl of extracted RNA. It can detect up to 900-1250 genome copies per milliliter of sample, for a diagnostic sensitivity of 99.1% and a specificity of 99.6% (Peto et al. 2020).
The LamPORE and viral genome sequencing will be processed at the McGill Genome Centre that has a long-standing academic/industry agreement with ONT to interact on technology development and extensive experience with using ONT devices in multiple contexts. The McGill Genome Centre already has the capacity to process > 15,000 samples a day using their available benchtop and palm-sized nanopore devices (PromethION MinION, Flongle etc).
Read more at: MedRxiv
Read a news article on this work: BCCDC
Written by: Caroline Quach
Caroline Quach - CHU Sainte-Justine/UdeM
David L. Buckeridge - EBOH/Mcgill University
Annie-Claude Labbé - Hôpital Maisonneuve-Rosemont/UdeM
Kate Zinszer - ESPUM/UdeM
Marc Desforges, PhD - CHU Sainte-Justine
Yves Petit - Pensionnat du Saint-Nom-de-Marie
Cat Tuong Nguyen - DRSP Montréal
Jean Longtin - CHU de Québec/MSSS
Geneviève Leduc - CHU Sainte-Justine
Lena Li Chun Fong
Sarah Reiling, PhD