Tools for COVID-19 Research

Find tools and resources for research on the etiological agent of COVID-19, SARS-CoV-2.

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SARS-CoV-2 Research Resources

SARS-CoV-2 is the etiological agent of COVID-19 and underscores the third instance of a coronavirus induced severe acute respiratory syndrome outbreak since 2002. Similar to SARS-CoV, the identified pathogen of the 2002-2003 outbreak, SARS-CoV-2 is a ~30-kb positive single-stranded RNA virus.


SARS-CoV-2’s genome primarily consists of two large ORFs which encode two polyproteins followed downstream by smaller ORFs which encode several structural proteins.


Genome organization of SARS-CoV-2 is similar to that of SARS-CoV, with both being organized into two main open reading frames (ORFs) and several smaller downstream ORFs. Two large ORFs, ORF1a and ORF1b, encode two polyproteins which are cleaved by viral encoded proteases resulting in several non-structural proteins (nsp). ORF1a encodes a 440-500 kDa polypeptide (pp1a) which is enzymatically processed to generate 11 nsps. The second ORF, ORF1b, encodes a larger polypeptide (pp1ab) of 740-810 kDa which is cleaved to generate 16 nsps.

View Resources by SARS-CoV Target

SARS-CoV-2 is a positive single-stranded RNA virus with four main structural proteins including spike, membrane, envelope, and nucleocapsid proteins.

What are SARS-CoV-2 Structural Proteins?

Four major structural proteins have been identified in SARS-CoV-2 including spike, nucleocapsid, membrane, and envelope proteins, which share significant homology with SARS-CoV. These four structural proteins are encoded by ORF2-10 and are required for viral coat formation and genome encapsidation. Compared to nsps, structural proteins elicit higher immune responses, both humoral and cellular mediated.


SARS-CoV-2 Spike Protein

The spike protein in SARS-CoV-2 (1,273 aa) is a viral surface glycoprotein with two major functional domains, the S1 (14-667 aa) and S2 (668-1255 aa) domains, which mediate cell receptor binding and membrane fusion, respectively. Viral attachment and entry into host cells is dependent on the interaction of the spike’s receptor-binding domain (RBD: 306-527 aa) with specific cellular proteins. The angiotensin converting enzyme 2 (ACE-2) and the protease TMPRSS2 have been identified as the cellular receptor and priming protease required for SARS-CoV-2 cellular entry, respectively. The protease TMPRSS2 and/or cathepsin L cleave the spike protein at the S1-S2 junction, allowing the fusion of viral envelope and cellular membranes required for viral entry. SARS-CoV-2 may also be cleaved by furin which recognizes a four amino acid sequence at the S1-S2 junction. Besides cleavage of the spike protein at the S1-S2 junction, cellular proteases cleave the S2 subunit at a recognized S2’ sequence which is critical for activation of the spike protein and consequent membrane fusion.

How Spike Protein Sequences Compare Between SARS-CoV-2 vs SARS-CoV?

The surface glycoprotein    or spike protein of SARS-CoV-2 shares 76% sequence identity with SARS-CoV's spike protein   . Novus Biologicals offers several antibodies for the detection of SARS-CoV spike protein which are validated in several applications (e.g., ELISA, Flow, ICC/IF, IHC, IHC-P, IP, Simple Western, SPR, WB). Novus Innovator's Reward Program allows you to test some of these available antibodies for the detection of SARS-CoV-2. Additionally, through Novus' 100% guarantee you can test antibodies against SARS-CoV-2 targets sharing 90% or greater homology with proteins in SARS-CoV. Learn more about our 100% guarantee and Innovator's Reward Program.


Antibodies to SARS-CoV Spike Protein

Antibody Catalog Numbers Antibody Clone Immunogen Sequence Immunogen Percent Identity to SARS-CoV-2 Spike Protein Verified Cross-reactivity

NB100-56578

Rabbit Polyclonal Not Available

100% (17/17)
S2

Yes

NBP2-90999

Recombinant Mouse Monoclonal C-QPELDSFKEELDKYFKN
(1124-1140 aa)

100% (17/17)

S2
Yes

NBP2-90980

Recombinant Human Monoclonal (CR3022)

Not Available (SARS-CoV patient derived antibody sequence)

Not Available

Binds to S1 domain (318-510 aa)
Yes

NBP2-90979

Chimeric Recombinant Rabbit Monoclonal (CR3022) Not Available (SARS-CoV patient derived antibody sequence)

Not Available

Binds to S1 domain (318-510 aa)
Yes

NBP2-90989

Chimeric Recombinant Human Monoclonal (D005) Not Available, Recombinant SARS-CoV Spike RBD Protein

Not Available

RBD sequence identity (74%)
Yes

NBP1-28850

Mouse Monoclonal (4A6C9) Not Available 100% NYD

NBP2-24808

Rabbit Polyclonal Not Available

100% (16/16)

S2
Yes

NB100-56589

Rabbit Polyclonal C-EAEVQIDRLITGRLQS
(970-985 aa)

87% (13/15)

S2
NYD

NB100-56048

Rabbit Polyclonal CSVKSFEIDKGIYQTS
(288-303 aa)

69% (11/16)

S1
NYD

NB100-56684

Rabbit Polyclonal C-RDVSDFTDSVRDPKTSEI
(553-570 aa)

67% (12/18)

S1
NYD

NYD: Not yet determined


Antibodies to SARS-CoV spike protein were developed using immunogens that share from 69 to 100% sequence identity with corresponding SARS-CoV-2 spike protein sequence.

*Solid red line: Immunogen is not known but antibody binds to RBD region (318-510 aa). Dashed red line: Exact immunogen sequence is not known.


SARS-CoV-2 Recombinant Spike Proteins

Recombinant Spike Proteins Region of Full-Length Protein
SARS-CoV-2 Spike S1 (Fc Chimera) NBP2-90983 11-682 aa
SARS-CoV-2 Spike Protein RBD 10499-CV 319-541 aa
SARS-CoV-2 Spike S2 (ECD) NBP2-92990 686-1213 aa
SARS-CoV-2 Spike Protein NBP2-90974 800-1000 aa
SARS-CoV-2 Spike Protein NBP2-90973 1000-1200 aa

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SARS-CoV-2 Nucleocapsid Protein

The nucleocapsid phosphoprotein (419 aa) is located within the core of the SARS-CoV-2 viral particle and interacts with the viral RNA. During viral assembly, the nucleocapsid protein plays a central role in packing the viral RNA genome. This process is dependent on its ability to self-associate as previously determined for the SARS-CoV nucleocapsid protein. SARS-CoV nucleocapsid protein has been implicated in other functions such as the modulation of host cellular processes including cell cycle deregulation, inhibition of IFN production, and induction of proinflammatory factors (e.g., COX-2).


How Nucleocapsid Protein Sequences Compare Between SARS-CoV-2 vs SARS-CoV?

SARS-CoV-2 nucleocapsid protein    shares 91% sequence identity with the SARS-CoV protein   . Novus Biologicals offers several antibodies for the detection of SARS-CoV nucleocapsid protein which are validated in several applications (e.g., ELISA, Flow, ICC/IF, IHC, IHC-P, IP, Simple Western, WB).


Antibodies to SARS-CoV Nucleocapsid Protein

Antibody Catalog Numbers Antibody Clone Immunogen Sequence Immunogen Percent Identity to SARS-CoV-2 Nucleocapsid Protein Verified Cross-reactivity
NB100-56576 Rabbit Polyclonal ADMDDFSRQLQNS-C (399-411 aa) 77% (10/13) Yes
NB100-56683 Rabbit Polyclonal LNKHIDAYKTFPPTEPK-C
(354-370 aa)
100% (17/17) Yes
NBP2-24745 Mouse Monoclonal (18F629.1) LNKHIDAYKTFPPTEPK-C
(354-370 aa)
100% (17/17) Yes
NB100-56049 Rabbit Polyclonal C-QIGYYRRATRRVRGGD (84-99 aa) 94% (15/16) Yes
NBP2-24747 Mouse Monoclonal (Ncap11) Full-length recombinant protein 91% (382/422) NYD
NBP2-90988 Rabbit Monoclonal (001) Full-length recombinant protein 91% (382/422) Yes
NBP2-90339 Rabbit Monoclonal (001) Full-length recombinant protein 91% (382/422) Yes
NBP2-90967

Mouse Monoclonal
(AP201054)

1-49 (C-MSDNGPQSNQRSAPRITFGGPTDST
DNNQNGGRNGARPKQRRPQGLPNN)
84% (41/49) NYD

NYD: Not yet determined


Antibodies to SARS-CoV nucleocapsid protein were developed using immunogens that share from 67 to 100% sequence identity with corresponding SARS-CoV-2 nucleocapsid protein sequences.


SARS-CoV-2 Recombinant Nucleocapsid Proteins

Recombinant Nucleocapsid Protein Region of Full-Length Protein
SARS-CoV-2 Nucleocapsid His Protein 10474-CV Full-length recombinant protein

SARS-CoV-2 lysates analyzed by Simple Western to detect nucleocapsid protein with serial dilutions of Rabbit Anti-SARS-CoV nucleocapsid polyclonal antibody. SARS-CoV-2, MERS, OC43, and 229E lysates analyzed by Simple Western to detect SARS-CoV-2 nucleocapsid protein with Rabbit Anti-SARS-CoV nucleocapsid polyclonal antibody, a specific band is only detected in SARS-CoV-2 lysates.

Simple Western analysis of (Left) recombinant SARS-CoV-2 Nucleocapsid Protein (10474-CV) with SARS Nucleocapsid Protein Antibody [NB100-56683]. SARS Nucleocapsid protein was loaded at 20 ng/mL and detected using serial dilutions of the Rabbit Anti-SARS-CoV Nucleocapsid Protein Polyclonal Antibody (NB100-56683) followed by HRP-conjugated Anti-Goat IgG Secondary Antibody. (Right) Simple Western analysis of SARS-CoV-2 (1:50), MERS (1:100), OC43 (1:100), and 229E (1:100) lysates. A specific band was detected for SARS-CoV-2 Nucleocapsid Protein only in the SARS-CoV-2 lysate. Detection was based on the use of Rabbit Anti-SARS-CoV Nucleocapsid Protein Polyclonal Antibody [NB100-56683] followed by HRP-conjugated Anti-Goat IgG Secondary Antibody. Note: some reactivity observed with FL Std 230. SARS-CoV-2 lysate courtesy of University of Maryland. These experiments were conducted under reducing conditions and using the 12-230 kDa separation system.


Publication Highlight: Development of a Rhesus Macaque Model of COVID-19

A recent study developed an animal model of SARS-CoV-2 infection in rhesus macaques (now also published by Nature "Respiratory disease in rhesus macaques inoculated with SARS-CoV-2   ") and utilized the rabbit polyclonal anti SARS-CoV nucleocapsid antibody [NB100-56576] to successfully detect the presence of the SARS-CoV-2 virus in infected tissues.

Newly developed model for COVID19 through SARS-CoV-2 infected rhesus macaques show positive immunostaining for the SARS-CoV nucleocapsid protein.

Pathological changes in rhesus macaques infected with SARS-CoV-2. SARSCoV-2 nucleocapsid antigen is detected by immunohistochemistry in (g) type I pneumocytes, (j) type I pneumocytes (asterisk) and type II pneumocytes (arrow) as well as alveolar macrophages (arrowheads), (k) mediastinal lymph node, and (l) macrophages and lymphocytes in the lamina propria of the cecum. Magnification 400x. Modified from Figure 4: bioRxiv March 21, 2020 //doi.org/10.1101/2020.03.21.001628


Publication Highlight: Pathological Findings in Fatal SARS-CoV-2 Infections

To fully understand the viral cellular and tissue distribution in fatal cases of COVID-19, investigators at the Centers for Disease Control and Prevention (CDC) immunostained pulmonary tissue with SARS-CoV nucleocapsid antibody [NB100-56576]. Investigators were able to confirm the presence of SARS-CoV-2 in upper respiratory tissues and the lungs such as bronchiolar epithelium, submucosal gland epithelium, pneumocytes, and hyaline membranes in the lung. Interestingly, the virus was not detected in other organs including heart, liver, kidney, spleen, or intestinal tissue.

Tissue and cellular distribution of SARS-CoV-2 viral particles analyzed by IHC with Rabbit Anti-SARS-CoV nucleocapsid polyclonal antibody identifying presence of virus in upper respiratory tissues, pneumocytes, macrophages, hyaline membranes from fatal cases.

Immunohistochemistry: SARS Nucleocapsid Protein Antibody [NB100-56576] - Immunostaining of severe acute respiratory syndrome coronavirus 2 in pulmonary tissues from fatal coronavirus disease cases. A) P5 (Patient 5): scattered immunostaining of tracheal epithelial cells. B) P5: higher magnification shows immunostaining of ciliated cells. C) P8: immunostaining of desquamated type I pneumocyte in an alveolar lumen. D) P4: colocalization of SARS-CoV-2 viral antigen (red) with type II pneumocyte stained by surfactant (brown; arrow). E) P4: colocalization of SARS-CoV-2 viral antigen (red) with macrophages stained by CD163 (brown; arrows); virus immunostaining within type II pneumocytes is also seen (arrowheads). F) P4: extensive immunostaining of hyaline membranes in a region of exudative DAD. G) P3: scattered immunostaining within macrophage in hilar lymph node; anthracosis is also present. Emerg Infect Dis. 2020 May 21;26(9) 10.3201/eid2609.202095, PMID: 32437316

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SARS-CoV-2 Membrane and Envelope Proteins

The membrane (222 aa) and envelope (75 aa) proteins are integral proteins that function in viral assembly. SARS-CoV’s membrane protein is known to elicit the production of neutralizing antibodies in SARS patients while the envelope protein plays a role in SARS-CoV virulence and functions as an ion channel.


How Membrane and Envelope Protein Sequences Compare Between SARS-CoV-2 vs SARS-CoV?

SARS-CoV-2 membrane protein    shares 91% sequence identity with the SARS-CoV protein   . SARS-CoV-2 envelope protein    shares 95% sequence identity with the SARS-CoV protein   . Novus Biologicals offers several antibodies for the detection of SARS-CoV membrane    and envelope proteins which are validated in several applications (e.g., ELISA, EM, ICC/IF, IP, WB).


Antibodies to SARS-CoV Membrane and Envelope Proteins

Antibody Catalog Numbers Antibody Clone Immunogen Sequence Immunogen Percent Identity to SARS-CoV-2 Proteins Verified Cross-reactivity
Membrane NB100-56569 Rabbit Polyclonal C-YNRYRIGNYKLNTDHA (196-210 aa) 93% (14/15) NYD
Membrane NBP1-28852 Mouse Monoclonal (2H2C4) Not Available 88% NYD
Membrane NBP2-21628 Rabbit Polyclonal C-KLNTDHAGSNDNIALLVQ (204-221 aa) 83% (15/18) NYD
Membrane NBP2-41060 Rabbit Polyclonal (15 aa peptide within last 50 aa of SARS-CoV sequence) 80% Yes
Membrane NBP2-41059 Rabbit Polyclonal (13 aa peptide within first 50 aa of SARS-CoV sequence) 77% NYD
Envelope NB100-56562 Rabbit Polyclonal YSRVKNLNSSEG (59-70 aa) 83% (10/12) NYD

*NYD: Not yet determined


SARS-CoV-2 Recombinant Proteins

Recombinant Proteins and Peptides Region of Full-Length Protein
Envelope  
SARS-CoV-2 Envelope (Avi Epitope Tag) NBP2-90986 Full-length recombinant protein

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What are SARS-CoV-2 Non-structural Proteins?

Non-structural proteins (nsps) serve different functions in the viral replication cycle. Together the encoded nsps (1-16) form a replicase-transcriptase complex.

Non-structural Proteins (nsps) % Identity SARS-CoV vs SARS-CoV-2 Properties and Functions
nsp1 84% Suppression of host gene expression
nsp2 100% Suppression of host gene expression
nsp3 76% Multi-spanning transmembrane protein. Papain-like protease domain. Mediates cleavage of ORF encoded polypeptides.
nsp4 80% Multi-spanning transmembrane protein. Important for membrane rearrangement.
nsp5 96% Papain-like protease domain. Mediates cleavage of ORF encoded polypeptides.
nsp6 88% Multi-spanning transmembrane protein. Associates with nsp3 and nsp4 to form organelle-like structure (double membrane vesicle) for viral replication. Induces autophagy and formation of Atg5 and LC3 containing vesicles.
nsp7-nsp8 96% Primase complex
nsp9 99% / 97% RNA binding protein. Forms dimer important in viral infection.
nsp10 97% Contains two zinc finger domains. Cofactor for the activation of the replicative enzyme.
nsp11 96% RNA-dependent RNA polymerase activity (RdRP). Mediates genome replication.
nsp12 96% Helicase activity/triphosphatase. RNA and DNA unwinding activity. Involved in viral replication.
nsp13 99% Exoribonuclease activity
nsp14 95% Papain-like protease domain. Mediates cleavage of ORF encoded polypeptides.
nsp15 89% Endoribonuclease activity
nsp15 93% Methyltransferase activity

Antibodies to SARS-CoV Non-structural Proteins

Novus offers rabbit polyclonal antibodies to nsp3, nsp5, nsp8, and nsp13 proteins which are validated in several applications (e.g., WB, ICC/IF, ELISA, IP and IM). Novus Innovator's Reward Program allows you to test some of these available antibodies for the detection of SARS-CoV-2. Additionally, through Novus' 100% guarantee you can test antibodies against SARS-CoV-2 targets sharing 90% or greater homology with proteins in SARS-CoV. Learn more about our 100% guarantee and Innovator's Reward Program.

Antibody Catalog Numbers Antibody Clone Immunogen Sequence Immunogen Percent Identity to SARS-CoV-2 nsps Protein Verified Cross-reactivity
nsp3 NBP1-78109 Rabbit Polyclonal (834-943 aa) of polyprotein 1a (ADRP domain), (1208-1557 aa) of polyprotein 1a (SARS-Unique Domain), and (1558-2040 aa) of polyprotein 1a (Papain-like proteinase domain) 79%, 75%, 82% NYD
nsp5 (SARS 3C-like proteinase) NBP1-78110 Rabbit Polyclonal Full-length recombinant protein 96% (294/306) NYD
nsp8 NBP2-89180 Rabbit Polyclonal Full-length SARS-Coronavirus nsp8 97% (193/198) NYD
nsp13 nbp2-89168 Rabbit Polyclonal KLQFTSLEIPRRNVATLQ (584-601 aa) 100% (18/18) NYD
SARS RDRP NBP2-50258 Mouse Monoclonal Full-length recombinant protein 96% NYD

SARS-CoV-2 Recombinant Proteins

Recombinant Proteases Region of Full-Length Protein

Papain-like Protease E-611-050

746-1060 aa

SARS-CoV-2 3CL Protease (Avi Epitope Tag) NBP2-92992 1-306 aa

 

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Select References

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Ashour, H. M., Elkhatib, W. F., Rahman, M. M., & Elshabrawy, H. A. (2020). Insights into the recent 2019 novel coronavirus (Sars-coV-2) in light of past human coronavirus outbreaks. Pathogens. https://doi.org/10.3390/pathogens9030186

Cárdenas-Conejo, Y., Liñan-Rico, A., García-Rodríguez, D. A., Centeno-Leija, S., & Serrano-Posada, H. (2020). An exclusive 42 amino acid signature in pp1ab protein provides insights into the evolutive history of the 2019 novel human-pathogenic coronavirus (SARS-CoV-2). Journal of Medical Virology. https://doi.org/10.1002/jmv.25758

Groneberg, D. A., Hilgenfeld, R., & Zabel, P. (2005). Molecular mechanisms of severe acute respiratory syndrome (SARS). Respiratory Research. https://doi.org/10.1186/1465-9921-6-8

Hoffmann, M., Kleine-Weber, H., Krüger, N., Müller, M., Drosten, C., & Pöhlmann, S. (2020). The novel coronavirus 2019 (2019-nCoV) uses the SARS-coronavirus receptor ACE2 and the cellular protease TMPRSS2 for entry into target cells. BioRxiv. https://doi.org/10.1101/2020.01.31.929042

Kim, D., Lee, J.-Y., Yang, J.-S., Kim, J. W., Kim, V. N., & Chang, H. (2020). The architecture of SARS-CoV-2 transcriptome. BioRxiv. https://doi.org/10.1101/2020.03.12.988865

Liu, J., Sun, Y., Qi, J., Chu, F., Wu, H., Gao, F., … Gao, G. F. (2010). The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Acts as a Dominant Immunogen Revealed by a Clustering Region of Novel Functionally and Structurally Defined Cytotoxic T‐Lymphocyte Epitopes. The Journal of Infectious Diseases. https://doi.org/10.1086/656315

Millet, J. K., & Whittaker, G. R. (2015). Host cell proteases: Critical determinants of coronavirus tropism and pathogenesis. Virus Research. https://doi.org/10.1016/j.virusres.2014.11.021

Munster, V., Feldmann, F., Williamson, B., Doremalen, N. van, Lizzette Perez-Perez, Schultz, J., … Wit, E. de. (2020). Respiratory disease and virus shedding in rhesus macaques inoculated with SARS-CoV-2. BioRxiv. https://doi.org/10.1101/2020.03.21.001628

Ortega, J. T., Serrano, M. L., Pujol, F. H., & Rangel, H. R. (2020). Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: An in silico analysis. EXCLI J. https://doi.org/10.17179/excli2020-1167

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