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A Review of the SARS-CoV-2 (COVID-19) Genome and Proteome

21-Apr-2020
SARS-CoV-2 (COVID-19) Genome and Protein Functions

 

The SARS-CoV-2 has a ~29.9 kilobase positive-sense RNA genome that contains as many as 29 open reading frames. Though the exact number of functional proteins remains to be established, there are at least 16 nonstructural proteins (nsp), four structural proteins, and at least six or seven accessory proteins. Based on previous work with SARS-CoV and other coronaviruses, scientists have identified functions for the majority of these factors, though work is ongoing. A schematic of the SARS-CoV-2 genome is shown in the figure above, while the known or hypothesized functions of the viral proteins, based on studies of SARS-CoV and other coronaviruses, are summarized below in Table 1.

GeneTex is proud to offer an extensive line of reagents to support the study of SARS-CoV-2 / COVID-19. Please see below to view listings of GeneTex's antibodies (Table 2), recombinant proteins (Table 3), and cell pellet blocks (Table 4) available now to accelerate your SARS-CoV-2 / COVID-19 research.

 

Recombinant Antibodies

SARS-CoV-2 (COVID-19) Spike S1 antibody [HL6]

SARS-CoV-2 (COVID-19) Spike S1 antibody [HL6] (GTX635654)

SARS-CoV-2 (COVID-19) Spike S1 antibody [HL1]

SARS-CoV-2 (COVID-19) Spike S1 antibody [HL1] (GTX635656)

SARS-CoV-2 (COVID-19) nucleocapsid antibody [HL249]

SARS-CoV-2 (COVID-19) nucleocapsid antibody [HL249] (GTX635678)

SARS-CoV-2 (COVID-19) nucleocapsid antibody [HL344]

SARS-CoV-2 (COVID-19) nucleocapsid antibody [HL344] (GTX635679)

SARS-CoV-2 spike and Nucleocapsid protein

 

Table 1. Putative Functions of SARS-CoV-2 Proteins

Protein Functions   References
Spike (S) Spike full-length (~1273 a.a. in SARS-CoV-2) protein precursor is cleaved into glycosylated subunits, S1 and S2 (S2’). S1 binds to the host’s receptor, ACE2, while S2 mediates viral and host membrane fusion.   1
Nucleocapsid (N) Nucleocapsid (~419 a.a. in SARS-CoV-2) binds viral genomic RNA and forms a helical ribonucleocapsid. Involved in genome protection, viral RNA replication, virion assembly, and immune evasion. Interacts with M and nsp3 proteins.   2
Membrane (M) Membrane/matrix protein (~222 a.a. in SARS-CoV-2) is the most abundant structural component of the virion, and very conserved. Mediates assembly and budding of viral particles through recruitment of other structural proteins to “ER-Golgi-intermediate compartment (ERGIC)”. Interaction with N for RNA packaging into virion. Interacts with accessory proteins 3a and 7a. Mitigation of immune response?   3
Envelope (E) Envelope small membrane protein (~75 a.a. in SARS-CoV-2) is a single-pass type III membrane protein involved in viral assembly, budding, and pathogenesis. Localizes to ERGIC. Forms a homopentameric ion channel and is a viroporin. Interacts with M, N, 3a, and 7a.   4
nsp1 Nonstructural protein 1 (nsp1; ~180 a.a. in SARS-CoV-2) likely inhibits host translation by interacting with 40S ribosomal subunit, leading to host mRNA degradation through cleavage near their 5’UTRs. Promotes viral gene expression and immunoevasion in part by interfering with interferon-mediated signaling.   5
nsp2 nsp2 (~638 a.a. in SARS-CoV-2) interacts with host factors prohibitin 1 and prohibitin 2, which are involved in many cellular processes including mitochondrial biogenesis. It appears that nsp2 may change the intracellular milieu and perturb host intracellular signaling.   6
nsp3 nsp3 (~1945 a.a. in SARS-CoV-2) is a papain-like protease (PLpro) and multi-pass membrane protein that processes the viral polyprotein to release nsp1, nsp2, and nsp3. It also exhibits deubiquitinating and deISGylating activities. Interacts with nsp4 and nsp6.   7
nsp4 nsp4 (~500 a.a. in SARS-CoV-2) is required for viral replication by inducing (with nsp3) assembly of, and localizing to, double-membrane cytoplasmic vesicles. Multi-pass membrane protein.   8
nsp5 nsp5 (3CLpro; ~306 a.a. in SARS-CoV-2) cleaves at 11 sites in the polyprotein to release nsp4-nsp16. It is also responsible for nsp maturation.   9
nsp6 nsp6 (~290 a.a. in SARS-CoV-2) is a multi-pass membrane protein that induces double-membrane vesicles in infected cells with nsp 3 and nsp4. It also limits autophagosome expansion and interferes with autophagosome delivery of viral factors to lysosomes for destruction.   10,11
nsp7 nsp7 (~83 a.a. in SARS-CoV-2) forms a hexadecamer with nsp8 as a cofactor for the RNA-dependent RNA polymerase nsp12. May have processivity or RNA primase function.   12
nsp8 nsp8 (~198 a.a. in SARS-CoV-2) forms a hexadecamer with nsp7 as a cofactor for the RNA-dependent RNA polymerase nsp12. May have processivity or RNA primase function. Mutation of certain residues in nsp8 is lethal to SARS-CoV by impacting RNA synthesis.   13
nsp9 nsp9 (~113 a.a. in SARS-CoV-2) functions in viral replication as a dimeric ssRNA-binding protein.   13
nsp10 nsp10 (~139 a.a. in SARS-CoV-2) forms a dodecamer and interacts with both nsp14 and nsp16 to stimulate their respective 3’-5’ exoribonuclease and 2’-O-methyltransferase activities in the formation of the viral mRNA capping machinery.   13
nsp11 nsp11 (~13-23 a.a., depending on the CoV species) is a pp1a cleavage product at the nsp10/11 boundary. For pp1ab, it is a frameshift product that becomes the N-terminal of nsp12. Its function, if any, is unknown.   13
nsp12 nsp12 (~932 a.a. in SARS-CoV-2) is the RNA-dependent RNA polymerase (RdRp) performing both replication and transcription of the viral genome. It has >95% identity to the SARS-CoV polymerase and is inhibited by the nucleoside analogue Remdesivir.   13
nsp13 nsp13 (~601 a.a. in SARS-CoV-2) is a multifunctional superfamily 1 helicase capable of using both dsDNA and dsRNA as substrates with 5’-3’ polarity. In addition to working with nsp12 in viral genome replication, it is also involved in viral mRNA capping. It associates with nucleoprotein in membranous complexes.   14
nsp14 nsp14 (~527 a.a. in SARS-CoV-2) has both 3’-5’ exoribonuclease (proofreading during RNA replication) and N7-guanine methyltransferase (viral mRNA capping) activities. Interacts with nsp10.   13
nsp15 nsp15 (~346 a.a. in SARS-CoV-2) is an endoribonuclease that favors cleavage of RNA at the 3’-ends of uridylates. Loss of nsp15 affects both viral replication and pathogenesis. It is also required for evasion of host cell dsRNA sensors.   15
nsp16 nsp16 (~298 a.a. in SARS-CoV-2) interacts with and is activated by nsp10. Its 2’-O-methyltransferase activity is essential for viral mRNA capping. It may also work against host cell antiviral sensors.   13
ORF3a ORF3a (~275 a.a. in SARS-CoV-2) is a multi-pass membrane protein that forms a homotetrameric viroporin in SARS-CoV. It interacts with accessory protein 7a, M, S and E. May be involved in viral release. Importantly, it also activates both NF-kB and NLRP3 inflammasome and contributes to the generation of cytokine storm.   16
ORF6 ORF6 (~61 a.a. in SARS-CoV-2) appears to be a virulence factor in SARS-CoV. It was shown to be an antagonist of type I interferons (IFNs) and is involved in viral escape from the host innate immune system.   17
ORF7a ORF7a (~121 a.a. in SARS-CoV-2) is a type I membrane protein that interacts with bone marrow stromal antigen 2 (BST-2) in SARS-CoV. BST-2 tethers virions to the host’s plasma membrane. ORF7a binding inhibits BST-2 glycosylation and interferes with this restriction activity. ORF7a also interacts with S, M, E, and ORF3a in SARS-CoV.   18
ORF7b ORF7b (~43 a.a. in SARS-CoV-2) is a type III integral transmembrane protein in the Golgi apparatus. In SARS-CoV, it appears to be a viral attenuation factor.   19
ORF8 ORF8 (~121 a.a. in SARS-CoV-2) has only 30% identity to the intact ORF8 of SARS-CoV and might be a luminal ER membrane-associated protein. It may trigger ATF6 activation and affect the unfolded protein response (UPR).   20,21,22
ORF9b ORF9b (~97 a.a. in SARS-CoV-2) is coded for in an alternative ORF within the N gene. No function is known, though the SARS-CoV protein interacts with nsp5, nsp14, and ORF6. There is limited evidence it may bind to lipids.   23
ORF10 ORF10 (~38 a.a. in SARS-CoV-2) has no known function but might have a regulatory role involving interaction with another factor(s).   24

 

Table 2. Antibodies for SARS-CoV-2 / COVID-19 Research

Cat. No. Product Name Clonality Applications
GTX635654 SARS-CoV-2 (COVID-19) Spike S1 antibody [HL6] Rb mAb WB, ICC/IF, ELISA, sELISA
GTX635656 SARS-CoV-2 (COVID-19) Spike S1 antibody [HL1] Rb mAb WB, ICC/IF, ELISA, ,sELISA
GTX635672 SARS-CoV-2 (COVID-19) Spike S1 antibody [HL263] Rb mAb WB, ICC/IF, ELISA
GTX635671 SARS-CoV-2 (COVID-19) Spike S1 antibody [HL134] Rb mAb WB, ICC/IF, ELISA
GTX635678 SARS-CoV-2 (COVID-19) nucleocapsid antibody [HL249] Rb mAb WB, ELISA, ICC/IF
GTX635679 SARS-CoV-2 (COVID-19) nucleocapsid antibody [HL344] Rb mAb WB, ELISA
GTX635680 SARS-CoV-2 (COVID-19) nucleocapsid antibody [HL146] Rb mAb WB, ICC/IF
GTX632604 SARS-CoV / SARS-CoV-2 (COVID-19) spike antibody [1A9] Ms mAb WB, ICC/IF, FACS, IP, ELISA, sELISA
GTX01555 SARS-CoV / SARS-CoV-2 (COVID-19) spike antibody [CR3022] Hu mAb ELISA, Neutralizing/Blocking
GTX632269 SARS-CoV / SARS-CoV-2 (COVID-19) nucleocapsid antibody [6H3] Ms mAb WB, ICC/IF, ELISA, sELISA, IP
GTX632696 SARS-CoV / SARS-CoV-2 (COVID-19) NSP8 antibody [5A10] Ms mAb WB
GTX632602 SARS-CoV / SARS-CoV-2 (COVID-19) ORF7a antibody [3C9] Ms mAb WB, ICC/IF
GTX135356 SARS-CoV-2 (COVID-19) spike antibody Rb pAb WB, ICC/IF, ELISA
GTX135360 SARS-CoV-2 (COVID-19) spike antibody Rb pAb WB, ICC/IF, ELISA
GTX135384 SARS-CoV-2 (COVID-19) Spike S1 antibody Rb pAb WB, ICC/IF
GTX135385 SARS-CoV-2 (COVID-19) Spike RBD antibody Rb pAb WB, ICC/IF
GTX135386 SARS-CoV-2 (COVID-19) Spike S2 / S2' antibody Rb pAb ICC/IF, ELISA, sELISA
GTX135357 SARS-CoV-2 (COVID-19) nucleocapsid antibody Rb pAb WB, ICC/IF, ELISA, sELISA
GTX135361 SARS-CoV-2 (COVID-19) nucleocapsid antibody Rb pAb WB, ICC/IF, ELISA, sELISA
GTX101395 ACE2 antibody [N1N2], N-term Rb pAb WB, IHC-P, FACS
GTX100743 TMPRSS2 antibody [N2C3] Rb pAb WB, IHC-P

 

Table 3. Recombinant Proteins for SARS-CoV-2 / COVID-19 Research

Cat. No. Product Name Expression System
GTX01548-pro SARS-CoV-2 (COVID-19) Spike S1 protein, His and Avi tag (active) HEK293
GTX01554-pro SARS-CoV-2 (COVID-19) Spike S1 protein, His tag (active) HEK293
GTX01559-pro SARS-CoV-2 (COVID-19) Spike S2 (ECD) protein, human IgG Fc tag HEK293
GTX01546-pro SARS-CoV-2 (COVID-19) Spike RBD protein, His tag (active) HEK293
GTX01547-pro SARS-CoV-2 (COVID-19) Envelope protein, His and Avi tag E. coli.
GTX135592-pro SARS-CoV-2 (COVID-19) nucleocapsid protein, His tag HEK293
GTX135357-pro SARS-CoV-2 (COVID-19) nucleocapsid protein, His tag E. coli.
GTX135648-pro SARS-CoV-2 (COVID-19) 3C-like Proteinase protein, His tag E. coli.
GTX01557-pro SARS-CoV-2 (COVID-19) 3C-like Proteinase protein, His and Avi tag E. coli.
GTX135683-pro Human ACE2 protein, mouse IgG Fc tag HEK293
GTX01550-pro Human ACE2 protein, His and Avi tag HEK293

 

Table 4. Cell Pellet Blocks for SARS-CoV-2 / COVID-19 Research

Cat. No. Product Name Expression System
GTX435640 SARS-CoV-2 (COVID-19) Spike FFPE Cell Pellet Block HEK293
GTX435643 SARS-CoV-2 (COVID-19) Spike (S1) FFPE Cell Pellet Block HEK293
GTX435644 SARS-CoV-2 (COVID-19) Spike (S2) FFPE Cell Pellet Block HEK293
GTX435641 SARS-CoV-2 (COVID-19) Nucleocapsid FFPE Cell Pellet Block HEK293
GTX435642 SARS-CoV-2 (COVID-19) Envelope FFPE Cell Pellet Block HEK293
GTX435645 SARS-CoV-2 (COVID-19) Membrane FFPE Cell Pellet Block HEK293

 

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