The emergence and quick spread of SARS-CoV-2 has pointed at a low capacity response for testing large populations in many countries, in line of material, technical and staff limitations. The traditional RT-qPCR diagnostic test remains the reference method and is by far the most widely used test. These assays are limited to a few probe sets, require large sample PCR reaction volumes, along with an expensive and time-consuming RNA extraction step. Here we describe a quantitative nanofluidic assay that overcomes some of these shortcomings, based on the Biomark TM instrument from Fluidigm. This system offers the possibility of performing 4608 qPCR end-points in a single run, equivalent to 192 clinical samples combined with 12 pairs of primers/probe sets in duplicate, thus allowing the monitoring of SARS-CoV-2 including the detection of specific SARS-CoV-2 variants, as well as the detection other pathogens and/or host cellular responses (virus receptors, response markers, microRNAs). The 10 nL-range volume of Biomark TM reactions is compatible with sensitive and reproducible reactions that can be easily and cost-effectively adapted to various RT-qPCR configurations and sets of primers/probe. Finally, we also evaluated the use of inactivating lysis buffers composed of various detergents in the presence or absence of proteinase K to assess the compatibility of these buffers with a direct reverse transcription enzymatic step and we propose several protocols, bypassing the need for RNA purification. We advocate that the combined utilization of an optimized processing buffer and a high-throughput real-time PCR device would contribute to improve the turn-around-time to deliver the test results to patients and increase the SARS-CoV-2 testing capacities.
【초록키워드】 SARS-CoV-2, diagnostic test, diagnostic, virus, Population, Spread, RNA extraction, clinical samples, RT-qPCR, pathogen, SARS-CoV-2 variants, Real-time PCR, lysis buffer, qPCR, Patient, Pathogens, reverse transcription, receptors, MicroRNAs, Quantitative, Proteinase K, cellular response, protocols, test results, presence or absence, Volume, reaction, this system, proteinase, reference method, RNA purification, compatibility, PCR reaction, large sample, offer, buffer, probe, Host, limitations, IMPROVE, clinical sample, composed, evaluated, contribute, absence, overcome, time-consuming, bypassing, the SARS-CoV-2, 【제목키워드】 SARS-CoV-2, cellular response, qPCR test, nasopharyngeal swab sample, flexible,