From: Evolutionary trajectory of SARS-CoV-2 and emerging variants
Gene | Protein | Putative function | References |
---|---|---|---|
Nsp1 | Leader protein/host translation inhibitor | Inhibits translation of host mRNAs and promotes expression of viral genes | [320] |
Nsp2 | Non-structural protein 2 | Modulates host cell survival signalling pathways | [321] |
Nsp3 | Papain-like protease | Proteolytic cleavage of polyprotein to generate Nsps 1–3, and inhibition of host IFN responses | |
Nsp4 | Non-structural protein 4 | Interacts with Nsp3 and host proteins to induce cytoplasmic autophagosomes for viral replication | |
Nsp5 | Chymotrypsin-like protease | Proteolytic cleavage of polyprotein to generate Nsps 4–16 and mediation of Nsp maturation | |
Nsp6 | Non-structural protein 6 | Interferes with delivery of viral factors to host lysosomes and inhibits IFN-1 responses | |
Nsp7 | Primase complex | Forms a complex with Nsp8 which interacts with RdRp (Nsp12) to transcribe viral genome | [120] |
Nsp8 | Primase complex | Forms a complex with Nsp7 which interacts with RdRp (Nsp12) to transcribe viral genome | [120] |
Nsp9 | ssRNA-binding protein | Binds to viral ssRNA and promotes replication | [328] |
Nsp10 | Non-structural protein 10 | Interacts with 3′–5′ exoribonuclease (Nsp14) and 2′ O-ribose methyltransferase (Nsp16) and promotes methylation of viral mRNA caps | [328] |
Nsp11 | Non-structural protein 11 | Released from cleavage of pp1a and forms N-terminal sequence of Nsp12 in pp1ab frameshift product. No known function | [328] |
Nsp12 | RNA-dependent RNA polymerase (RdRp) | Replicates and transcribes viral genome | [326] |
Nsp13 | Helicase | Unwinds dsRNA and dsDNA in viral replication | |
Nsp14 | 3′–5′ exoribonuclease/N7-guanine methyltransferase | Proofreading during RNA replication (exoribonuclease) and viral mRNA capping (methyltransferase). Interacts with Nsp10 | [330] |
Nsp15 | Nidoviral uridylate-specific endoribonuclease | RNA processing and inhibition of host IFN responses | [331] |
Nsp16 | 2′ O-ribose methyltransferase | Activated by Nsp10 for methylation of viral mRNA caps | [332] |
S | Spike glycoprotein | Cleaved into S1 and S2 subunits. S1 binds host receptor (ACE2) while S2 mediates viral and host membrane fusion | [333] |
ORF3a | Orf3a viroporin | Activates NF-kB and NLRP3 inflammasome to contribute to cytokine storm. Promotes viral release and may induce necrotic cell death | |
ORF3b | Accessory protein ORF3b | IFN-1 antagonist | [337] |
E | Envelope protein | A viroporin involved in viral assembly, budding, and pathogenesis. Forms CoV envelope | |
M | Membrane protein | Forms viral membrane and induces N and S localization to the ER-Golgi-Intermediate compartment for virion assembly and budding | [340] |
ORF6 | Accessory protein ORF6 | IFN-1 antagonist | [144] |
ORF7a | Accessory protein ORF7a | SARS-CoV ortholog inhibits bone marrow stromal antigen 2 mediated tethering of virions to host plasma membrane | [341] |
ORF7b | Accessory protein ORF7b | SARS-CoV ortholog attenuates viral replication | [342] |
ORF8 | Accessory protein ORF8 | Inhibits IFN-1 activity and downregulates MHC-1 expression to evade host immunity | |
N | Nucleocapsid | Involved in immune evasion through IFN-1 antagonism, nucleocapsid formation, viral RNA replication, and virion assembly | |
ORF9b | Accessory protein ORF9b | Suppresses IFN-1 responses through inhibition of TOM70 | [343] |
ORF9c | Accessory protein ORF9c | Interferes with IFN signalling, antigen presentation, and complement signalling. Induces IL-6 signalling | [344] |
ORF10 | Accessory protein ORF10 | Interacts with a Cullin 2 RING E3 ligase complex to potentially modulate ubiquitination | [345] |