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Coronavirus (SARS-CoV-2)

As the coronavirus pandemic (COVID-19) becomes more widespread, the urgency to develop diagnostic tools for viral screening, and the advancement of viral therapeutics and vaccine candidates becomes increasingly apparent. Here at AAT Bioquest we are committed to providing reliable and sensitive solutions for the advancement of COVID-19 research. Browse our comprehensive portfolio of research solutions from virus discovery, pathogen detection and research surveillance to vaccine development.

 



Intro to COVID-19


The coronavirus disease 2019 (COVID-19) is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It was initially discovered in December 2019, in Wuhan, China, and since then COVID-19 has infected more than 103 million people in 185 countries, resulting in over 2.24 million fatalities (as of February 2, 2021). While most infected patients suffer from mild symptoms characterized by fever, cough and shortness of breath, the disease can progress into fatal cases of pneumonia and acute respiratory failure, notably in older males with comorbidities.

SARS-CoV-2 Structure: RNA & Protein Components

Identification and sequencing of the SARS-CoV-2 full-length genome demonstrated that this novel CoV shares a 79.5% sequence identity with the SARS-CoV that occurred in 2002. Similar to SARS-CoV, the SARS-CoV-2 genome encodes four key structural proteins: spike proteins (S), membrane glycoproteins (M), envelope proteins (E) and nucleocaspid proteins (N). The spike protein, which is responsible for facilitating the entry of SARS-CoV-2 into the host cell, utilizes the same host receptor Angiotensin-Converting Enzyme 2(ACE2) as SARS-CoV for cell entry. Such similarities allude to the possibility that therapies developed during the SARS-CoV outbreak could help prevent or serve as a viable treatment for COVID-19.

For more information regarding the functionality of SARS-CoV-2 proteins and its RNA components, please refer to the table below.

SARS-CoV-2 Structure
Figure 1. Illustration of the SARS-CoV-2 structure (figure made in BioRender).

Table 1. Overview of SARS-CoV-2 protein and RNA components.

Component
Function
Spike ProteinsSpike proteins (S-proteins) are large, heavily-glycosylated transmembrane proteins that form the distinctive “corona” or crown-like appearance on the surface of the virus. The ectodomain of S-proteins are comprised of an N-terminal and a C-terminal domain known as the S1 and S2 subunits, respectively. The S1 subunit, which contains the receptor binding domain, is responsible for recognizing and binding to the host cell receptor. The S2 subunit, which contains a fusion peptide and two heptad repeats (HR1 and HR2), are responsible for virus-cell membrane fusion. From a therapeutic stand point, S-proteins are promising targets for SARS-CoV-2 vaccine and anti-viral development of therapies (e.g. antibodies) capable of blocking virus binding and fusion.
Membrane ProteinsMembrane proteins (M-proteins), which are the most abundant of all the structural proteins, define the shape of the viral envelope. M-proteins are considered to be the principal coordinator of SARS-CoV-2 assembly, as it interacts with all of the major coronavirus structural proteins. Interaction of M-proteins with S-proteins promotes retention of S-proteins in the ER-Golgi compartment and its integration into new virions. M-protein and N-protein interactions stabilize the nucleocapsid and facilitate completion of viral assembly. M-protein and E-protein interactions form the viral envelop which assist in the production and release of virus-like particles.
Envelope ProteinsEnvelope proteins (E-proteins) are the smallest of the structural proteins. They are vital for virus production and maturation and facilitate in the release of the virus. A small portion of E-proteins are integrated into the virion envelope, while the majority localizes at the site of intracellular trafficking (e.g. ER-Golgi).
Nucleocapsid ProteinsNucleocapsid proteins (N-proteins), which are heavily phosphorylated, function primarily to bind the SARS-CoV-2 RNA genome and encapsulate it within the viral envelope forming a ribonucleocapsid complex. This capsid is essential for viral self-assembly and replication. N-proteins also affect host cell responses to viral infection.
RNA GenomeRNA is the genome of the virus. Once SARS-CoV-2 enters host cells, it replicates a genomic RNA to produce smaller subgenomic RNA fragments. These fragments are used to synthesize essential proteins (e.g. S-, M-, N- and E-proteins) for viral infection.



Research solutions for virus discovery


Having the right tools is essential for accelerating scientific discovery for COVID-19 and SARS-CoV-2. From genomic tools for viral characterization and vaccine development to immunoassay solutions for the development of rapid diagnostic kits, AAT Bioquest offers comprehensive solutions to advance your research.

Discovering viral genome by Sanger Sequencing

Sanger sequencing by capillary electrophoresis is a chain termination method used to determine the nucleotide order of DNA. Sanger sequencing selectively incorporates chain-terminating dideoxynucleotides (ddNTPs) by DNA polymerase during in vitro DNA replication. The extension products are then separated by capillary electrophoresis and the molecules are injected by an electrical current into a long glass capillary filled with a gel polymer. Although newer NGS technologies are becoming increasingly common in clinical research labs for their higher throughput capabilities and lower costs per sample, Sanger sequencing is still the “gold standard” for clinical research sequencing with 99.99% efficacy rate. In addition to its role in identifying SARS-CoV-2, Sanger sequencing by capillary electrophoresis can be used to verify reverse transcriptase-polymerase chain reaction results and provide accurate discernment of SARS-CoV-2 from other pathogens.

 

Table 2. Available MagaDye™ fluorescent ddNTPs for Sanger sequencing.

Product Name
Nucleotide
Ex (nm)
Em (nm)
Abs(nm)
Unit Size
Cat No.
MagaDye™ 535-ddGTPGuanine503 nm536 nm503 nm5 nmoles17063
MagaDye™ 535-ddGTPGuanine503 nm536 nm503 nm50 nmoles17067
MagaDye™ 561-ddATPAdenine498 nm561 nm498 nm5 nmoles17062
MagaDye™ 561-ddATPAdenine498 nm561 nm498 nm50 nmoles17066
MagaDye™ 588-ddTTPThymine498 nm588 nm498 nm5 nmoles17061
MagaDye™ 588-ddTTPThymine498 nm588 nm498 nm50 nmoles17065
MagaDye™ 613-ddCTPCytosine498 nm614 nm498 nm5 nmoles17060
MagaDye™ 613-ddCTPCytosine498 nm614 nm498 nm50 nmoles17064


Table 3. Specifications for MagaDye™ 4 Color Sanger Sequencing Terminator Kit For Research solutions for virus discovery

Product Name
ddNTPs
Ex (nm)
Em (nm)
Abs (nm)
Unit Size
Cat No.
MagaDye™ 4 Color Sanger Sequencing Terminator KitddGTP
ddATP
ddTTP
ddCTP
488 nm536 nm
561 nm
588 nm
614 nm
498 nm5 nmoles17068



Research solutions for COVID-19 pathogen detection


Nucleic acid analysis by RT-PCR and serologic assays are two techniques extensively used for the detection of SARS-CoV-2. RT-PCR is the most widely used platform and is recommended for screening or diagnosis of early infection by SARS-CoV-2. RT-PCR works to detect the presence of viral RNA prior to seroconversion, the time period during which a specific antibody develops against the pathogen and becomes detectable in the blood. Serological assays such as the enzyme-linked immunosorbent assay (ELISA) and the lateral flow immunoassay (LFIA) detect for the presence of antibodies in serum that are produced in response to viral infection.

For in-depth info about nucleic acid testing and serological assays, click on:

 

RNAstain
Figure 2. Fluorescence images of live and fixed HeLa cells stained with StrandBrite RNA Green. Live HeLa cells were stained using StrandBrite™ RNA Green and co-stained with nuclear dye Hoechst 33342 (Cat No. 17530). HeLa cells fixed in methanol were also stained using StrandBrite RNA Green and co-stained with nuclear dye DAPI (Cat No. 17507).

 

Table 4. RNA quantification and PCR reagents

Product Name
Ex (nm)
Em (nm)
Unit Size
Cat No.
StrandBrite™ Green Fluorimetric RNA Quantitation Kit *High Selectivity*490 nm540 nm100 Tests17657
StrandBrite™ Green RNA Quantifying Reagent490 nm525 nm1 mL17610
StrandBrite™ Green RNA Quantifying Reagent490 nm525 nm10 mL17611
Portelite™ Fluorimetric RNA Quantitation Kit490 nm525 nm100 Tests17658
Portelite™ Fluorimetric RNA Quantitation Kit490 nm525 nm500 Tests17659
Cyber Green™ [Equivalent to SYBR® Green] *20X Aqueous PCR Solution*498 nm522 nm5 x 1 mL Tests17591
Cyber Green™ [Equivalent to SYBR® Green] *20X Aqueous PCR Solution*498 nm522 nm1 mL17592
Cyber Green™ Nucleic Acid Gel Stain [Equivalent to SYBR® Green]498 nm522 nm100 µL17604
Cyber Green™ Nucleic Acid Gel Stain [Equivalent to SYBR® Green]498 nm522 nm1 mL17590



Research solutions for COVID-19 vaccine development


Proteases play essential roles in protein activation, cell regulation and cell signaling, as well as, in the generation of amino acids for protein synthesis or utilization in other metabolic pathways. The inhibition of viral proteases necessary for proteolytic processing of polyproteins has been a successful strategy in the treatment of human immunodeficiency virus (HIV) and hepatitis C respectively, proving the potential of protease inhibitors for the treatment of viral infections. Similarly, the main protease of SARS-CoV-2 (Mpro or 3CLpro) is thought to be essential for viral gene expression and replication and, therefore, is regarded as a major target for anti-CoV drug design. AAT Bioquest offers a variety of dark-FRET peptide substrates and fluorogenic substrates which can be effectively used to screen for inhibitors of coronavirus proteases, papain-like proteases and more.

Assay Principle for Dark-FRET Protease Substrates

FRETmechanism
Figure 3. FRET mechanisms of Covidyte™ and Covipyte™ COVID-19 peptide substrates (figure made in BioRender). FRET protease substrates are widely used for detecting protease activities, in particular, for virus protease that often require a long peptide sequence for optimal binding such as coronavirus, HIV and HCV proteases. The internally quenched FRET peptide substrate is digested by a protease to generate the highly fluorescent peptide fragment. The fluorescence increase is proportional to the protease activity (figure drawn in BioRender).

Covidyte™ SARS-CoV-2 substrates

Covidyte™ dark-FRET peptide substrates are robust high throughput screening tools for determining inhibitors of coronavirus proteases. Covidyte™ substrates contain either a 12 or 14 amino acid sequence that can be cleaved by coronavirus proteases. Modified to the terminal ends of each amino acid sequence is a fluorescent EDANS donor dye and non-fluorescent DABCYL quencher dye. In its intact conformation, substrate fluorescence is quenched by the two dyes being in close proximity of one another. When the internally quenched Covidyte™ substrate is hydrolyzed by coronavirus proteases, a highly fluorescent peptide fragment is produced, and the fluorescence increase is proportional to the coronavirus proteases activity.

Covidyte Structure
Figure 4. Chemical structure for Covidyte™ EN450.

 

Table 5. Covidyte™ substrates for screening coronavirus protease inhibitors.

Product Name
Sequence Length
Amino Acid Sequence
Target
Ex (nm)
Em (nm)
ε¹
Unit Size
Cat No.
Covidyte™ EN45014 amino acidsKTSAVLQSGFRKMECoronavirus proteases3364455900100 Tests13535
Covidyte™ EN45014 amino acidsKTSAVLQSGFRKMECoronavirus proteases33644559001000 Tests13536
Covidyte™ ED45012 amino acidsVNSTLQSGLRKMCoronavirus proteases3364455900100 Tests13537
Covidyte™ ED45012 amino acidsVNSTLQSGLRKMCoronavirus proteases33644559001000 Tests13538
Covidyte™ TF67014 amino acidsKTSAVLQSGFRKMECoronavirus proteases649664250,000100 Tests13540
Covidyte™ TF67014 amino acidsKTSAVLQSGFRKMECoronavirus proteases649664250,0001000 Tests13541
Covidyte™ IF67012 amino acidsVNSTLQSGLRKMCoronavirus proteases656670250,000100 Tests13542
Covidyte™ IF67012 amino acidsVNSTLQSGLRKMCoronavirus proteases656670250,0001000 Tests13543
  1. ε = Extinction coefficient at their maximum absorption wavelength. The units of extinction coefficient are cm-1M-1.



Covipyte™ SARS-CoV-2 substrates

The Covipyte™ EN450 dark-FRET peptide substrate contains a 9 amino acid sequence (RELNGGAPI) specific for coronavirus papain-like proteases (PLpro). Conjugated to the N- and C-terminals, respectively, are an EDANS donor molecule and a DABCYL quencher molecule. In its intact conformation, substrate fluorescence is quenched by the donor and quencher molecule being in close proximity of one another. When hydrolyzed by coronavirus PLpro, a highly fluorescent Edans fragment is produced and the fluorescence increase is proportional to the coronavirus proteases activity making it a convenient tool for screening and studying the kinetics of PLpro inhibitors. PLpro of coronaviruses carries out proteolytic maturation of non-structural proteins that play a role in replication of the virus and performs deubiquitination of host cell factors to scuttle antiviral responses.

Additionally, AAT Bioquest offers 3 tetra-peptide substrates, Z-KAGG-AMC, Z-KKAG-AMC, and Z-LRGG-AMC, for screening and evaluating coronavirus PLpro inhibitors. Upon hyrolysis by PLpro, these substrates generate highly fluorescent AMC products (Ex/Em = 341/441 nm).

 

Table 6. Covipyte™ substrates for screening coronavirus protease inhibitors.

Product Name
Sequence Length
Amino Acid Sequence
Target
Ex (nm)
Em (nm)
ε¹
Unit Size
Cat No.
Covipyte™ EN4509 amino acidsRELNGGAPIPapain-like proteases3364455900100 Tests13545
Covipyte™ EN4509 amino acidsRELNGGAPIPapain-like proteases33644559001000 Tests13546
Z-KAGG-AMC4 amino acidsKAGGPapain-like proteases341441190001 mg13552
Z-KKAG-AMC4 amino acidsKKAGPapain-like proteases341441190001 mg13554
Z-LRGG-AMC4 amino acidsLRGGPapain-like proteases341441190001 mg13550
  1. ε = Extinction coefficient at their maximum absorption wavelength. The units of extinction coefficient are cm-1M-1.



ACE2 Receptor Recognition by SARS-CoV-2

The binding of viruses to receptors on the surface of target cells is a critical first step in the infectious viral life cycle as it facilitates the entry of the virus into the host cells. Recently, it has been discovered that the spike protein of SARS-CoV-2 utilizes the ACE2 surface receptor on host cells to promote cellular entry. The significance of this discovery recognizes ACE2 as a promising therapeutic target for SARS-CoV-2. To screen and evaluate ACE2 inhibitors AAT Bioquest offers Mca-APK(Dnp), a fluorogenic ACE2 substrate. Upon enzymatic cleavage at the proline-lysine residue, the Dnp quencher is removed and fluorescence of Mca is restored. Mca-APK(Dnp) ACE2 substrates have an excitation and emission maxima of 322 nm and 381 nm, respectively, and are easily adaptable for high through-put screening.

 

ACE2 Dose Response
Figure 5. ACE2 dose response was measure with Mca-APK(Dnp) substrate.

 

ACE2 substrates for screening ACE2 inhibitors.

Name Ex (nm) Em (nm) Unit Size Cat No.
Mca-APK(Dnp) ACE2 substrate 322 381 1 mg 13555
Mca-APK(Dnp) ACE2 substrate 322 381 10 mg 13556