CRISPR has been on the rise to become a new form of COVID-19 detection. 2 of the common labs include one at the Broad Institute led by Feng Zhang and the other by the University of California Berkeley lead by Jennifer Doudna, who had previously fought over patents for CRISPR. Ever since the discovery of the unique specific cutting ability of Cas endonucleases, many diverse applications have been applied with CRISPR. For detection purposes, the design of specific guide RNAs and PAM sequences allow on-site target of viral sequences to cut a fluorescently tagged to emit fluorescence; hence yielding a positive readout. Zhang named this technique SHERLOCK (Specific High Sensitivity Enzymatic Reporter UnLOCKING) using Cas13 while Doudna named it DETECTR (DNA Endonuclease Targeted CRISPR Trans Reporter) using Cas12a. Meanwhile, Addgene, a major facilitator of sharing molecular biology reagents, had constructed a library of COVID-19 plasmids and related CRISPR technologies. Approximately 2100 plasmids were shared where among them, 11 of them were applicable with CRISPR. Plasmids from SHERLOCK and DETECTR were also shared to various research labs and institutions around the world. 

CRISPR Detection

SARS-CoV-2 antigen detection involves identifying viral proteins to diagnose a COVID-19 infection. Unlike nucleic acid tests that detect viral RNA, antigen detection primarily utilizes methods such as Enzyme-Linked Immunosorbent Assay (ELISA) with antibodies selected against specific viral antigens, or lateral flow assays. These rapid testing methods are a critical approach to containing the pathogenicity and spread of the virus.

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Research in the virology of COVID-19 encompasses several primary areas of study. These include understanding the physical structure of SARS-CoV-2, its classification among coronaviruses, and its continuous evolution and mutations. Key focuses also involve the mechanisms of host cell infection, the stability of the virus in various environmental conditions, and the potential for patient reinfection. Furthermore, applied research areas include antigen detection methods, animal studies on the virus, and the development of vaccine candidates to build adaptive immunity.

Areas of Study in COVID-19 Virology

SARS-CoV-2 is comprised of four main structural components: the spike glycoprotein (S), the small envelope glycoprotein (E), the membrane glycoprotein (M), and the nucleocapsid protein (N). There are also several accesory proteins. 

Structure of SARS-CoV-2

- Manipulation of Innate Immune and Pro-inflammatory Response

Methods of Host Cell Infection and Exploitation

A study found that SARS-CoV-2 can be highly sensitive to heat. The virus was still detectable after being left out for 14 days in a 4°C room, while the virus inactive 5 minutes after being left in a 70°C. The study also found a difference in stability on different surfaces, such as paper, plastic, and metal.  At room temperature, the virus is highly stable in a range of pH3 - pH10. However, the standard disinfectant method was still able to affect the virus, with the researchers finding no active infection in different disinfectants after an incubation of 5 minutes (except for hand soap).

Stability of SARS-CoV-2 in different environmental conditions

Investigations are still ongoing in determining the current evolution and mutating nature of SARS-CoV-2, which will aid scientists in understanding more about this virus and in developing effective treatments and vaccines against the disease. 

Evolution and Mutations of SARS-CoV-2

- Application of Rhesus Macaques for Studying SARS-CoV-2 Virology
- Application of Syrian Hamsters for Studying SARS-CoV-2 Virology
- Application of Mosquitoes for Studying SARS-CoV-2 Virology
- Application of African Green Monkeys for Studying SARS-CoV-2 Virology

Animal Studies on SARS-CoV-2 Virology

So far, vaccines consist of either inactivated or weakened versions of antigens or virions. Many pharmaceutical companies like Pfizer and Moderna are developing inactivated antigens in the form of mRNA, DNA, and proteins from the viral envelope or capsid that are often fragmented. 

Vaccine Candidates, Immunogenicity, and Adaptive Immunity

Cases of SARS-CoV-2 reinfection have been documented globally, demonstrating that prior infection does not guarantee permanent immunity. Confirmed instances, verified through whole genome sequencing, have shown that individuals can be reinfected by phylogenetically distinct strains of the virus.

Reinfection of SARS-CoV-2

The coronaviruses belong to the broad viral order Nidovirales within the family, Coronaviridae, notoriously known to be infecting mammals and humans in the recent years. In general, they can be commonly distinguished by their unique morphological structures of spherical or disk-like envelopes embedded with glycoproteins (Burrell et al., 2017). In terms of its genetic composition, it has a large positive sense RNA (33.5 kb) belonging to Group VI in the Baltimore classification. Other shared similarities include highly conserved genomes, Replicase gene upstream of structural and accessory genes as well as the translation of many nonstructural mRNAs from ribosomal frameshift. These viruses are very diverse and can be further subdivided into 4 subfamilies: alpha-, beta-, delta-, and gamma-coronaviruses based on serology (Fehr et al., 2015). 

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