Guidance on the Regulation of SARS‑CoV/SARS‑CoV-2 Chimeric Viruses: Appendix
| Protein | Virus | Examples of Functions | References* |
|---|---|---|---|
| nsp1 | SARS‑CoV‑2 | Binds to human ribosome machinery & shuts down translation; blocking immune response | (5,3) |
| Interference of JAK/STAT pathway | (1) | ||
| nsp1 | SARS-CoV | Dysregulated IFN production | (1,3) |
| Inhibition of RIG-I like receptors (MDA5, PKR)- mediated IFN-β | |||
| nsp3 | SARS-CoV | Dysregulated IFN production | (1,3) |
| Inhibition of Rig-I like receptors (MDA5, PKR)- mediated IFN-β | |||
| nsp4 | SARS-CoV | Dysregulated IFN production | (1,3) |
| Inhibition of RIG-I like receptors (MDA5, PKR)- mediated IFN-β | |||
| nsp6 | SARS-CoV | Dysregulated IFN production | (1,3) |
| Inhibition of RIG-I like receptors (MDA5, PKR)- mediated IFN-β | |||
| nsp7 | SARS-CoV | Antagonizes type-I IFN | (2,3) |
| nsp15 | SARS-CoV | Antagonizes type-I IFN | (2,3) |
| DMV (double membrane vesicles) | SARS-CoV | Dysregulated IFN production | (1) |
| Inhibition of Rig-I like receptors (MDA5, PKR)- mediated IFN-β | |||
| ORF8b/ab | SARS-CoV | Dysregulated IFN production | (1,3) |
| Inhibition of Rig-I like receptors (MDA5, PKR)- mediated IFN-β | |||
| ORF6 | SARS-CoV | Dysregulated IFN production | (1,3) |
| Inhibition of RIG-I like receptors (MDA5, PKR)- mediated IFN-β | |||
| M protein | SARS-CoV | Dysregulated IFN production | (1) |
| Inhibition of RIG-I like receptors (MDA5, PKR)- mediated IFN-β | |||
| endonuclease | SARS-CoV | Dysregulated IFN production | (1,3) |
| Inhibition of RIG-I like receptors (MDA5, PKR)- mediated IFN-β | |||
| Nsp16 | SARS‑CoV‑2 | Disguises viral mRNA as eukaryotic mRNA that is methylated at the 5’ cap, thereby avoiding recognition by cytoplasmic PRR and MDA5, and downstream type I IFN responses | (3) |
| E protein | SARS-CoV / SARS‑CoV‑2 | Alteration of Ca2+ concentrations | (1,3) |
| ORF3a | SARS-CoV/ SARS‑CoV‑2 |
Interaction with TRAF3 and ASC | (1) |
| Interaction with NLRP3 leading to pyroptosis | (3,4) | ||
| ORF8b | SARS-CoV | Interaction with NLRP3 leading to pyroptosis | (1,3) |
| SUDNsp3c | SARS-CoV | Induction c-Jun/c-Fos pathway | (1) |
| S protein | SARS-CoV/ SARS CoV-2 |
Exhaustion of NK cells | (1) |
| S protein | SARS-CoV | Induces the expression of IL6, IL8, CXCL10 and TNF through NF-kB activation in macrophages | (2) |
| M protein | SARS-CoV | Blocks IFN-B production by impairing the formation of TRAF3-TANK-TBK1/IKK complex | (2,3) |
| N protein | SARS-CoV | Antagonizes type I IFN production by blocking IRF-3 phosphorylation | (2,3) |
| 3a | SARS-CoV | Downregulates the expression of the type I IFN receptor (IFNAR) leading to blockade on IFN signaling | (2) |
| 3b | SARS-CoV | Antagonizes type I IFN production by blocking IRF-3 phosphorylation. Inhibits IFN signaling | (2) |
| 6 | SARS-CoV | Antagonizes type I IFN production by blocking IRF-3 phosphorylation | (2) |
| 7a | SARS-CoV | Activates NF-kB and upregulates the expression of the proinflammatory mediators IL8 and CCL5 | (2) |
1This list is subject to change, including the addition or removal of factors.
*Appendix References
(1) Bouayad A. Innate immune evasion by SARS-CoV-2: Comparison with SARS-CoV. Rev Med Virol. 2020 Nov;30(6):1-9. doi: 10.1002/rmv.2135. Epub 2020 Jul 30. PMID: 32734714.
(2) C = Cysteine residues are all present as disulfides, with the 1st and 3rd Cysteine, and the 2nd and 4th Cysteine forming specific disulfide bridges; The consensus sequence includes known toxins a-MI and a-GI (shown above) as well as a-GIA, Ac1.1a, a-CnIA, a-CnIB; X1 = any amino acid(s) or Des-X; X2 = Asparagine or Histidine; P = Proline; A = Alanine; G = Glycine; X3 = Arginine or Lysine; X4 = Asparagine, Histidine, Lysine, Arginine, Tyrosine, Phenylalanine or Tryptophan; X5 = Tyrosine, Phenylalanine, or Tryptophan; X6 = Serine, Threonine, Glutamate, Aspartate, Glutamine, or Asparagine; X7 = Any amino acid(s) or Des X and; “Des X” = “an amino acid does not have to be present at this position.” For example if a peptide sequence were XCCHPA then the related peptide CCHPA would be designated as Des-X.
(3) A virulent Newcastle disease virus (avian paramyxovirus serotype 1) has an intracerebral pathogenicity index in day-old chicks (Gallus gallus) of 0.7 or greater or has an amino acid sequence at the fusion (F) protein cleavage site that is consistent with virulent strains of Newcastle disease virus. A failure to detect a cleavage site that is consistent with virulent strains does not confirm the absence of a virulent virus.
(4) Select agents that meet any of the following criteria are excluded from the requirements of this part: Any low pathogenic strains of avian influenza virus, South American genotype of eastern equine encephalitis virus, west African clade of Mpox viruses, any strain of Newcastle disease virus which does not meet the criteria for virulent Newcastle disease virus, all subspecies Mycoplasma capricolum except subspecies capripneumoniae (contagious caprine pleuropneumonia), all subspecies Mycoplasma mycoides except subspecies mycoides small colony (Mmm SC) (contagious bovine pleuropneumonia), and any subtypes of Venezuelan equine encephalitis virus except for Subtypes IAB or IC, provided that the individual or entity can verify that the agent is within the exclusion category.
(5) For determining the regulatory status of nucleic acids that are capable of producing infectious forms of select agent viruses, please reference guidance here.