Tracking SARS-CoV-2: Novel Trends and Diagnostic Strategies

Abstract

The COVID-19 pandemic has had an enormous impact on economies and health systems globally, therefore a top priority is the development of increasingly better diagnostic and surveillance alternatives to slow down the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In order to establish massive testing and contact tracing policies, it is crucial to have a clear view of the diagnostic options available and their principal advantages and drawbacks. Although classical molecular methods such as RT-qPCR are broadly used, diagnostic alternatives based on technologies such as LAMP, antigen, serological testing, or the application of novel technologies such as CRISPR-Cas for diagnostics, are also discussed. The present review also discusses the most important automation strategies employed to increase testing capability. Several serological-based diagnostic kits are presented, as well as novel nanotechnology-based diagnostic methods. In summary, this review provides a clear diagnostic landscape of the most relevant tools to track COVID-19.

Keywords: COVID-19; CRISPR-based diagnostics; antigen testing; automation; nanotechnology-based diagnostics; nucleic acid amplification test.

Figure 1

Structure of SARS-CoV-2 and diagnostic targets: SARS-CoV-2 structure has two components: viral genome (RNA) and viral proteins. Tests based on the detection of nucleic acids (RT-qPCR, RT-LAMP, CRISPR-Cas-based, NGS) target different regions of the viral RNA. Antigen tests aim at the detection of viral proteins such as spike protein (S). Serological tests detect host antibodies produced in response to SARS-COV-2 infection.

Figure 2

Timeline of SARS-CoV-2 detection using nucleic acid-based, antigen and serological tests: Detection of viral nucleic acids is useful from 5 to 15 days after the onset of symptoms. Because many nucleic acid detection tests include nucleic acid amplification, these tests can give positive results for prolonged periods. Due to the nature of antibody production and the variability of immune responses between individuals, serological tests can be used for seroprevalence studies and surveillance from the second week after the onset of symptoms. Antigen tests are useful for the detection of infected individuals from 5 to 15 days after the onset of symptoms.

Figure 3

Nanomaterial tools for fighting future pandemics: (1) diagnostics, (2) vaccine delivery, (3) cell tramps, and (4) microfluidics are the future to fight against the pandemic. Created with BioRender.com (accessed date 15 January 2021).

Figure 4

General RT-qPCR test workflow and comparison of manual and automated nucleic acid extraction in Huo-Yan Lab. The use of MGISP-960 platform to automate nucleic acid extraction increased the testing capacity, simplified the steps for extraction, and reduced the time per test. Adapted from [146,269].

Figure 5

Schematic illustrations of three different diagnostic workflows from patient samples: A thermal cycler device is necessary in the case of RT-qPCR tests, while plate reader or other alternatives are available for measuring the readout in the case of CRISPR-Cas and LAMP tests. Adapted from [277].

Figure 6

ROBOCOV circuit: Run preparation is done by using open-source Python codes. Initial sample setup, sample preparation, and plate filling are performed by OT-2 Station A, B1, and B2, respectively. RNA extraction is processed by KingFisher Flex. Then, qPCR mic preparation is done by OT-2 Station C, and, finally, the qPCR process is run by ABI 7500. The analysis results are exported as a user-friendly R file. Adapted from [280].