Yunlong Richard Cao Profile picture
Aug 31 7 tweets 3 min read Twitter logo Read on Twitter
Sharing some new experimental data on BA.2.86:
1) BA.2.86 is antigenically distinct compared to XBB.1.5.
2) BA.2.86 can significantly escape XBB-infection/vaccination induced antibodies.
3) However, the infectivity of BA.2.86 may be much lower than XBB.1.5 and EG.5. (1/n) Image
By using pseudovirus neutralization assay and antigenic cartography (based on mRNA immunized mouse serum), we found that BA.2.86 is antigenically distinct from WT, BA.2, BA.5, and XBB.1.5. This means that XBB-induced antibodies cannot well recognize and neutralize BA.2.86. (2/n) Image
Indeed, BA.2.86 can induce significant antibody evasion of plasma isolated from convalescents who experienced XBB breakthrough infection or reinfections. BA.2.86's immune evasion capability even exceeds EG.5 and is comparable to "FLip" variants (XBB.1.5 + L455F & F456L). (3/n) Image
As for monoclonal neutralizing antibody (NAb) drugs, all approved antibodies can't neutralize BA.2.86 well, but SA55 remains effective (clinical phase II-III). Interestingly, the E554K mutation carried by BA.2.86 can escape SD1-targeting NAb, represented by S3H3. (4/n) Image
We also tested a panel of XBB.1.5-effective NAbs against XBB.1.5-based pseudoviruses carrying single BA.2.86 RBD mutations. Results showed that N450D, K356T, L452W, A484K, V483del, V445H are the key mutations responsible for BA.2.86's enhanced immune evasion than XBB.1.5. (5/n) Image
Importantly, we found that BA.2.86 exhibits lower cell infectivity compared to XBB.1.5 and EG.5, which may affect its transmission. The lower infectivity may be contributed by K356T, V483del, and E554K. Note that here the infectivity is measured through pseudovirus assays. (6/n) Image
In sum, we found that BA.2.86 is antigenically distinct from XBB.1.5 and can escape XBB-induced neutralizing antibodies. The updated vaccine's efficacy against BA.2.86 should be closely monitored; however, BA.2.86 may not prevail very fast due to its lower infectivity. (7/n)

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More from @yunlong_cao

Aug 5
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! Image
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. Image
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. Image
Read 4 tweets
May 3
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
Read 33 tweets
Apr 21
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. Image
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. Image
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 Image
Read 8 tweets
Dec 28, 2022
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/ Image
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/ Image
However, the S486P mutation greatly enhanced hACE2 binding, since 486S completely destroyed the local hydrophobic interaction while 486P retained it. 3/ Image
Read 6 tweets
Dec 20, 2022
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.
Read 4 tweets
Oct 31, 2022
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.
Read 10 tweets

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