In strain: Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5.
PDZ-binding; required for interaction with human MPP5
Complete loss of binding to the NUP98-RAE1 complex and IFN antagonistic function.
Does not affect repression of reporter protein expression.
In strain: Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4.
Loss of interaction with human NUP98-RAE1 complex which suppresses the down-regulation of protein expression of newly transcribed genes in the host cell.
Loss of interaction with human NUP98-RAE1 complex which suppresses the mRNA accumulation in the nucleus, the down-regulation of protein expression of newly transcribed genes in the host cell and blockade on nuclear import on a broad range of host factors.
Retains interaction with human NUP98-RAE1 complex. Increases down-regulation of protein expression of newly transcribed genes in host cell.
In strain: Alpha/B.1.1.7, Gamma/P.1, Zeta/P.2, Theta/P.3, Lambda/C.37, Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron BA.2.75, Omicron/BA.4, Omicron/BA.5.
In strain: Lambda/C.37, Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron BA.2.75, Omicron/BA.4, Omicron/BA.5.
In strain: Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron BA.2.75, Omicron/BA.4, Omicron/BA.5.
In strain: Omicron/BA.2, Omicron/BA.2.12.1, Omicron BA.2.75, Omicron/BA.4, Omicron/BA.5.
Partial increase of pathogenesis and fitness in vivo. No effect on virus replication ex vivo.
Phosphoserine; by host GSK3-alpha and GSK3-beta
Significant decrease of RNA binding capacity.
Complete loss of N-glycosylation and of secretion.
N-linked (GlcNAc...) (complex) asparagine; by host
About 50% stronger entry efficiency in Vero E6 cells while 30% weaker entry efficiency in hACE2-expressing BHK cells.
Binding to host endocytosis trafficking protein SNX27
Binding to host plasma membrane localising/FERM domain proteins
Complete loss of COPI binding and increase in cell fusion.
Complete loss of O-glycosylation by host GALNT1.
Complete loss of cleavage by host furin.
Decreased HLA binding to NF9 epitope. Increased binding affinity to human ACE2.
Improved COPI binding, reduced cell fusion and reduced levels of S1/S2 cleavage.
In strain: 19B/501Y, Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5.
In strain: 20A.EU2, Iota/B.1.526, Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5.
In strain: Alpha/B.1.1.7, Beta/B.1.351, Gamma/P.1, Delta/B.1.617.2, Epsilon/B.1.427/B.1.429, Eta/B.1.525, Theta/P.3, Iota/B.1.526, Kappa/B.1.617.1, Lambda/C.37, B.1.1.318, Zeta/P.2, Mu/B.1.621, 20A.EU1, 20A.EU2, Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5; common variant; binds to hACE2 more efficiently; produces more infectious particles when cultured in primary human epithelial cells; does not significantly shift SARS-CoV-2 neutralization properties.
In strain: Alpha/B.1.1.7, Beta/B.1.351, Gamma/P.1, Theta/P.3, Mu/B.1.621, 19B/501Y, Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5; May enhance affinity to human ACE2 receptor.
In strain: Alpha/B.1.1.7, Eta/B.1.525, 19B/501T, Omicron/BA.1, Omicron/BA.4, Omicron/BA.5; May compensate for reduced infectivity of RBD escape mutants.
In strain: Alpha/B.1.1.7, Theta/P.3, Mu/B.1.621, B.1.1.318, A23.1, Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5.
In strain: Beta/B.1.351, Eta/B.1.525, Theta/P.3, Iota/B.1.526, B.1.1.318, Gamma/P.1, Zeta/P.2 and Mu/B.1.621; May enhance affinity to human ACE2 receptor.
In strain: Beta/B.1.351, Gamma/P.1, 19B/501Y.
In strain: Beta/B.1.351, Gamma/P.1, Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5; May enhance affinity to human ACE2 receptor.
In strain: Delta/B.1.617.2, Epsilon/B.1.427/B.1.429, Kappa/B.1.617.1, Lambda/C.37, 19B/501Y, Omicron/BA.4, Omicron/BA.5; Contributes to cellular immunity evasion and increases infectivity.
In strain: Delta/B.1.617.2, Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5.
In strain: Delta/B.1.617.2, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5.
In strain: Epsilon/B.1.427/B.1.429; may change signal peptide cleavage to position 16-17.
In strain: Epsilon/B.1.427/B.1.429; when coupled with S13I induces resistance to NTD antibodies by changing disulfid bond in positions 15-136 to 136-152.
In strain: Gamma/P.1, 19B/501T, 19B/501Y, Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5.
In strain: Gamma/P.1, Theta/P.3, Zeta/P.2.
In strain: Kappa/B.1.617.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5.
In strain: Omicron/BA.1, Omicron/BA.2 Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5.
In strain: Omicron/BA.1, Omicron/BA.2 Omicron/BA.2.12.1.
In strain: Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.4, Omicron/BA.5.
In strain: Omicron/BA.1, Omicron/BA.2.75.
In strain: Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5.
In strain: Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.4, Omicron/BA.5.
Increase of pseudotyped VSV particle production ex vivo. Increase of viral load in hamster upper respiratory tract. Produces more infectious particles when cultured in primary human epithelial cells; increases replication and transmissibility in hamsters and ferrets.
Increased binding affinity to human ACE2.
Increased incorporation of cleaved spike into virions.
Increased resistance to human covalescent sera neutralization.
Increased resistance to neutralizing antibodies and human covalescent sera neutralization.
Increased resistance to neutralizing antibodies.
Increased resistance to neutralizing antibodies. Decreases HLA binding to NF9 epitope. Increased binding affinity to human ACE2.
N-linked (GlcNAc...) (high mannose) asparagine; by host
N-linked (GlcNAc...) (hybrid) asparagine; by host
No effect on O-glycosylation by host GALNT1.
O-linked (GlcNAc...) threonine; by host GALNT1
Partial improvement of cleavage by host furin.
Partial loss of O-glycoslyation by host GALNT1.
Reduced host ACE2-binding affinity in vitro.
S-palmitoyl cysteine; by host ZDHHC20; partial
Stabilization in prefusion state (in vaccine Ad26.COV2.S/Janssen Pharmaceutical).
Stabilization in prefusion state (in vaccine BNT162b2/Pfizer-Biontech, vaccine mRNA-1273/Moderna, vaccine Ad26.COV2.S/Janssen Pharmaceutical).
In strain: Beta/B.1.351, Epsilon/B.1.429, Iota/B.1.526 and Mu/B.1621.
In strain: Delta/B.1.617.2 and Kappa/B.1.617.1.
Partial loss of Ca(2+) and NMDG(+) permeability.
Partial loss of Ca(2+) and NMDG(+) permeability. Increased localization at host plasma membrane.
Complete loss of 3C-like proteinase nsp5 cleavage.
Complete loss of NSP15 endonuclease activity.
Complete loss of RNA guanylyltransferase activity.
Complete loss of ribosome binding and cellular translation inhibition.
For uridylate-specific endoribonuclease nsp15 activity
In strain: Alpha/B.1.1.7, Beta/B.1.351, Gamma/P.1, Delta/B.1.617.2 Iota/B.1.526, Kappa/B.1.617.1, Lambda/C.7, Epsilon/B.1.427/B.1.429, Theta/P.3, Zeta/P.2, Mu/B.1.621, Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5.
In strain: Alpha/B.1.1.7, Beta/B.1.351, Gamma/P.1, Eta/B.1.525, Iota/B.1.526 and Lambda/C.37.
In strain: Delta/B.1.617.2, Omicron/BA.2.75.
In strain: Iota/B.1.526, Lambda/C.37 and Theta/P.3.
In strain: Lambda/C.37, Mu/B.1.621, Omicron/BA.1, Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75, Omicron/BA.4, Omicron/BA.5.
In strain: Omicron/BA.2, Omicron/BA.2.12.1, Omicron/BA.2.75.
Increased cleavage of ubiquitin in vitro; no effect on ISG15 cleavage in vitro.
Partial loss of ISG15 cleavage in vitro.
Partial loss of ubiquitin cleavage in vitro; no effect on ISG15 cleavage in vitro.
Proton acceptor; for uridylate-specific endoribonuclease nsp15 activity
Proton donor; for uridylate-specific endoribonuclease nsp15 activity
Unable to remove host IFIH1 (MDA5) ISGylation.
Uridylate-specific endoribonuclease nsp15
Complete loss of ubiquitination. Partial loss of interferon pathway inhibition.
Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)
In strain: Eta/B.1.525 and Delta/B.1.617.2.
N-linked (GlcNAc...) asparagine; by host