SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations

Abstract

The unprecedented global pandemic known as SARS-CoV-2 has exercised to its limits nearly all aspects of modern viral diagnostics. In doing so, it has illuminated both the advantages and limitations of current technologies. Tremendous effort has been put forth to expand our capacity to diagnose this deadly virus. In this work, we put forth key observations in the functionality of current methods for SARS-CoV-2 diagnostic testing. These methods include nucleic acid amplification-, CRISPR-, sequencing-, antigen-, and antibody-based detection methods. Additionally, we include analysis of equally critical aspects of COVID-19 diagnostics, including sample collection and preparation, testing models, and commercial response. We emphasize the integrated nature of assays, wherein issues in sample collection and preparation could impact the overall performance in a clinical setting.

Keywords: COVID-19; CRISPR; RT-PCR; SARS-CoV-2; Sequencing; Serological testing.

Fig. 1

Overview of COVID-19 diagnostic workflow—samples are collected and stored in a transport medium, lysed, RNA extracted, reverse transcribed to complementary DNA (cDNA), and then amplified (via PCR or isothermal amplification). The amplified viral sequence is detected/quantified using fluorescent dyes or colorimetric readout. CRISPR-Cas-based detection (SARS-CoV-2 DETECTR) works by the activation of Cas12 due to the presence of a target RNA sequence. The activated Cas12 subsequently cleaves reporter labels generating a fluorescent signal. The sequencing workflow converts the cDNA into a form compatible with the sequencer (library preparation) and then determines the cDNA sequence via digital images (sequencing-by-synthesis) or using electrical signals (Nanopore sequencing). Antigen-based lateral flow assays detect the SARS-CoV-2 antigen using an immunoassay format. Viral antigen forms a sandwich bound by capture and detection antibodies. The presence of the labeled detection antibody indicates the presence of antigen in the sample (image created with BioRender.com)

Fig. 2

Schematic of a CRISPR/Cas-based molecular diagnostic test. Adapted from [37] with permission

Fig. 3

Key factors that could potentially impact each step of the workflow for COVID-19 diagnostic assays

Fig. 4

Schematic of novel COVID-19 diagnostics platforms utilizing nanostructured materials for potential POC use. a A graphene-based FET sensor for SARS-CoV-2 detection. The device consists of the SARS-CoV-2 spike antibody conjugated to graphene sheets. The specific binding of spike antibody to SARS-CoV-2 spike protein causes a change in current (response) between source and drain. (modified with permission from [207]. Copyright © American Chemical Society) b A colorimetric assay based on SPR utilizing thiol-modified antisense oligonucleotides capped on the surface of gold nanoparticles for the detection of isolated SARS-CoV-2 RNA. (modified with permission from [208]. Copyright © American Chemical Society) c A dual-functional LSPR biosensor utilizing gold nanoislands for sensitive detection of target SARS-CoV-2 RNA sequence from a multigene mixture. (modified with permission from [209]. Copyright © American Chemical Society) d A chemi-resistive sensor utilizing array consisting of AuNPs for detection of VOCs from the exhaled breath of COVID-19 patients (reproduced from [210] with permission from the Royal Society of Chemistry)