POSCOVD – Towards a population-scale Covid-19 diagnostics

One of the major bottle-necks for fighting against the current Covid-19 pandemia is the capacity of a country to count with a large number of diagnostic tests. Currently the use of RT-qPCR assays-driven diagnostics remains the main tool to track the spread of the disease, but this strategy has been limited by the capacity of accessing to reagents. Furthermore, with the current plan to progressively lift confinement restrictions, and in absence of a vaccine, our needs in increasing the number of available tests for tracking infection and controlling its spread remains essential.

In this context, innovative strategies based on the use of massive parallel DNA sequencing for population-scale diagnostics are currently explored by international teams ([1] & [2]), but also within France, as highlighted by the efforts of the Startup SeqOne [3]. While able to address the possibility of analyzing several thousands of patient samples per sequencing run, these strategies require to count with a DNA sequencing platform where large instruments are driven by specialized technical engineers.

Herein I propose to develop a population-scale diagnostics assay using massive parallel DNA sequencing performed With the technology Oxford Nanopore, allowing the advantages of the portability of the instrument as well as its Simplicity of use, such that large number of patients’ samples could be assayed even in remote places on the world Where reagents for RT-qPCR and/or access to large DNA sequencing instruments remains still scarce.

[1] A Massively Parallel COVID-19 Diagnostic Assay for Simultaneous Testing of 19200 Patient Samples; Ayaan Hossain1, Alexander C. Reis2, Sarthok Rahman5, and Howard M. Salis1-4 *

[2] LAMP-Seq: Population-Scale COVID-19 Diagnostics Using a Compressed Barcode Space; Jonathan L. Schmid-Burgk, David Li, David Feldman, Mikołaj Słabicki, Jacob Borrajo, Jonathan Strecker, Brian Cleary, Aviv Regev, Feng Zhang; bioRxv preprint https://doi.org/10.1101/2020.04.06.025635

[3] A French start-up harnesses the power of the latest generation genomic sequencers to dramatically increase COVID 19 testing capacity; 1st May 2020.