F456L-carrying XBB*, like EG.5, is rapidly rising. Meanwhile, XBB*+L455F+F456L is also growing fast. Some updates explaining their advantages: 1) F456L evades serum neutralization, even after XBB infection. 2) L455F+F456L combo adds on evasion and could also boost ACE2 binding!
The L455F+F456L RBD mutation combo is a very smart move by the virus (it's actually an LF->FL shift). Note that both individual L455F or F456L actually lose ACE2 binding, but together, the LF->FL shift somehow strengthened ACE2 interaction while destroying most antibody binding.
The emergence of 455 & 456 mutations is well-predicted half-year ago by our model built on DMS. Interestingly, we recently found that F456L is much more well-tolerated on the XBB.1.5 backbone instead of BA.2, which may explain why F456L only started to rise just now.
It can be highly expected that this winter, we will be facing XBB offspring that carry mutation combos like L455F+F456L+K478R, or even additional evasive mutations since the high ACE2 affinity could give a large buffering room for strong antibody-evading mutations to appear.
• • •
Missing some Tweet in this thread? You can try to
force a refresh
Sharing our latest work on SARS-CoV-2 immune imprinting.
Main finding:
Repeated Omicron infection/boosting alleviates WT vaccine-induced immune imprinting by generating many potent XBB-neutralizing Omicron-specific antibodies that target new RBD epitopes. biorxiv.org/content/10.110…
First, let's revisit the major concept of SARS-CoV-2 immune imprinting:
When we experience a variant-vaccine boosting or breakthrough infection, our immune system will mainly recall WT vaccination-induced memory B cells and rarely produces variant-specific antibodies. 2/n
The problem caused by this concept is that when the boosting/infecting variant has a long antigenic distance to WT, the majority of memory B cells recalled will be those that target conserved and non-neutralizing epitopes, which will greatly hinder the antibody response. 3/n
Recently, many fast-growing XBB lineages have gained RBD mutations on K478, such as VOI XBB.1.16 (K478R), XBB.2.3.5 (K478N), XBB.2.3.4 (K478Q). Also, many XBB* have independently obtained F456L, like FD.1.1, FE.1, XBB.1.5.10. In this thread I'll briefly discuss these mutations.
Like the results by Kei @SystemsVirology, we found XBB.1.16 and XBB.1.5 have comparable immune evasion capabilities in the serum tested. The ACE2 binding affinity of XBB.1.16 and XBB.1.5 is also similar. In contrast, F456L brings additional immune evasion but lowers ACE2 binding.
F456L escapes XBB.1.5-effective class I mAbs. These mAbs are quite abundant in various immune backgrounds, such as people who experienced BA.5 breakthrough infections or repeated Omicron infections. Those that are developing RBD-targeting mAb drugs should pay attention to F456L
The superior growth advantage of XBB.1.5 has been well-documented by many colleagues @JPWeiland@LongDesertTrain@EricTopol. Here I'll add some experimental data: 1) XBB.1.5 is equally immune evasive as XBB.1, but 2) XBB.1.5 has a much higher hACE2 binding affinity. 1/
Notably, even BF.7 breakthrough infection doesn't induce high neutralization against XBB.1 and XBB.1.5. The S486P mutation only caused a slight reduction in immune evasion capability. mRNA breakthrough infection samples (n=9) here all received at least 2-dose mRNA vac. 2/
However, the S486P mutation greatly enhanced hACE2 binding, since 486S completely destroyed the local hydrophobic interaction while 486P retained it. 3/
Our paper regarding Omicron convergent evolution is out on @Nature.
In this story, we analyzed the immune evasion capability of ~50 convergent variants and explained how RBD mutations suddenly emerged convergently due to a more focused immune pressure. nature.com/articles/s4158…
Moreover, in this paper, we proved that by accurately mapping the immune pressure elicited by our humoral immunity, we can predict future immune-evasive RBD mutations of the virus! This is a big step to help us better prepare new variant-specific vaccines and antibody drugs.
The details of this paper have been extensively covered in my old tweets, which are attached here for those that are interested.
Latest update on some new convergent variants.
Summary: 1. XBB, XBB.1, CH.1.1, BA.4.6.3, and BQ.1.1.10 (BQ.1.1+Y144del) are currently the most immune-evasive strains to monitor. 2. BQ.1*+NTD mutations, such as Y144del, makes them much more immune evasive. biorxiv.org/content/10.110…
Like @LongDesertTrain@JosetteSchoenma@CorneliusRoemer have mentioned, recently there has been a rapid increase of Y144del proportion in the BQ.1* lineages. This NTD deletion is observed in many worrisome BA.5 sublineages such as BQ.1.1.10, BQ.1.18, as well as BA.4.6.3.
The appearance of Y144del in those BA.5 sublineages is a really bad sign since we know this mutation is extremely good at escaping NTD-neutralizing antibodies. See below, Y144 is located at the epitope center of a specific group of NTD NAbs that are potent against BA.5.
Updating results regarding convergent variants BU.1, BR.2, BM.1.1.1, CA.1, and XBB.
XBB is currently the most antibody-evasive strain tested, and BR.2, BM.1.1.1, CA.1 are more immune evasive than BA.2.75.2 and BQ.1.1. biorxiv.org/content/10.110…
Similar to BQ.1.1, XBB also escapes Evusheld and Bebtelovimab. BU.1, BR.2, BM.1.1.1, CA.1, and XBB all displayed sufficient hACE2 binding capability.
XBB is significantly more immune evasive than BA.2.75.2 and BQ.1.1 against plasma from all breakthrough infections, comparable to or even exceeding SARS-CoV-1 level escaping capability. BR.2, BM.1.1.1 and CA.1 also exhibit very strong immune evasion, but less compared to XBB.