KP.3.1.1 subbranch with Orf9b:S53L on Orf1a:K497I branch (50, 12 countries)

[Over-There-Is]

KP.3.1.1> A1755T(Orf1a:K497I)> T26323C, C28441T(Orf9b:S53L) Query: A1755T, T26323C, C28441T

07-04 Tirol, Austria EPI_ISL_19300318 08-26 Noord-Brabant, Netherlands EPI_ISL_19413485 Netherlands 4, US 3(1 from Spain, 1 from UK), Austria 2, France 2, Switzerland 2, Germany 1, Italy 1, Japan 1, Korea 1, Portugal 1, UK 1

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4162_5e1a90.json?c=country&label=id:node_7121350 EPI_ISL_19289761, EPI_ISL_19293155, EPI_ISL_19300318, EPI_ISL_19324531, EPI_ISL_19326839, EPI_ISL_19327718, EPI_ISL_19327747, EPI_ISL_19338484, EPI_ISL_19342791, EPI_ISL_19349486, EPI_ISL_19357538, EPI_ISL_19369054, EPI_ISL_19380767, EPI_ISL_19381926, EPI_ISL_19382141, EPI_ISL_19390585, EPI_ISL_19413480, EPI_ISL_19413485, EPI_ISL_19413625

[FedeGueli]

Orf1a:K497I is an extremely rare mutation little less than half of them are in this lineage cc @ryhisner

[ryhisner]

ORF9b:S53L is a crucial residue that is very rarely mutated. Nevan Krogan, Lucy Thorne, and others have shown that ORF9b:S53 is phosphorylated in the mid/late stages of infection. This phosphorylation eliminates the ability of ORF9b to bind TOM70, which is a transmembrane protein on the outer mitochondrial membrane responsible for shuttling pre-proteins into the intermembrane space. Binding TOM70 is how ORF9b suppresses the cellular interferon (IFN) response (by making HSP90 unable to bind TOM70, which is an essential step in the type-I IFN signaling cascade).

Why would the virus want ORF9b to stop binding to TOM70 and thereby stop suppressing IFN production? One possibility is that in the later stages of infection, it's somehow beneficial for the virus to stimulate an immune response rather than suppress it. But although the NFkB immune response is essential for successful SARS-CoV-2 infection, I don't think there's any evidence for this for the type-I IFN response.

So I think the more likely explanation is that ORF9b plays two completely different roles during infection. The first it does in its monomeric form, consisting entirely of alpha helices, and which binds to TOM70 to suppress the host IFN response. ORF9b's second role is in virus assembly, and it does this in its alternate, dimer form, which consists entirely of beta strands—completely different from its monomer form. This makes ORF9b a fold-switching protein, of which several others are known.

The exact role of ORF9b in viral assembly is not understood. But Krogan Lab showed that when they suppressed ORF9b, the resulting virus suffered a serious replication defect—even in cells that had no IFN response—showing that ORF9b has an important role besides IFN evasion. In mouse hepatitis virus (MHV), which is the model betacoronavirus used in lab studies, the equivalent of ORF9b is the I protein. A group led by Stanley Perlman recently showed that in the JHMV strain of MHV, the I protein is essential for efficient virus assembly and is also incorporated into virions. They were not able to decipher how ORF9b was involved in assembly, but they convincingly showed thatORF9b plays an important role in assembly.

One study showed that ORF9b:S53A (I think) weakened but didn't eliminate binding to TOM70. I have to think that ORF9b:S53L would interfere with TOM70 binding at least as much as S53A, probably more. I think it's very likely a deleterious mutation, which is why it so rarely appears. If this lineage proves successful, it would call for an explanation of why ORF9b's role has apparently changed.

[FedeGueli]

Thank you Ryan!

[FedeGueli]

+6 from italy 2 different regions

[Over-There-Is]

Veneto+1, Penn+1

[FedeGueli]

One recent sample only for this closing it

[FedeGueli]

31, Spain, only two from September

[FedeGueli]

37 with a small October cluster from Ontario, reopening it please check if it grows then @Over-There-Is

[FedeGueli]

45,

[FedeGueli]

50 now , 16/17 samples in October have also S:M731I but likely just a cluster in Canada