Sharing our investigation on the unprecedented convergent RBD evolution of BA.2.75 and BA.5 on sites including 346, 356, 444-446, 450, 460, 486, which have generated highly concerning variants such as BA.2.75.2, BR.1, BJ.1, and BQ.1.1. (1/n) biorxiv.org/content/10.110…
In this paper, we tried to solve the following three questions: 1) How immune evasive could these variants be? 2) Why do they evolve mutations on these converging sites? 3) What could this convergence evolution finally lead to? (2/n) biorxiv.org/content/10.110…
As many have noticed, recent evolution of Omicron has led to numerous subvariants that exhibit high growth advantages over BA.5. Interestingly, mutations on their receptor-binding domain (RBD) converge on several hotspots, including R346, R356, K444, L452, N460 and F486. (3/n)
First, we tested the antibody evasion capability of these variants. Therapeutic antibodies are not very effective against those convergent variants. Bebtelovimab doesn't work against variants carrying K444N/M/T or V445P. Evusheld is also heavily escaped. (4/n)
As for plasma, BA.2.75.2 exhibits the most significant reduction in NT50, even for BA.5 breakthrough-infected convalescents. Almost 10-fold difference compared to BA.5 against plasma from BA.5 convalescents. Will update results on 6~8 new variants, such as BQ.1.1 next week. (5/n)
Proved by pseudovirus neutralization assays using soluble hACE2, we found that all of the tested variants exhibited sufficient hACE2 affinity, higher than that of D614G, indicating they all have a chance to circulate. (6/n)
Next, we investigated why Omicron suddenly started to evolve convergently. In short, we believe this is linked to humoral immune imprinting. Similar to BA.1 breakthrough infection, we showed BA.2/BA.5 breakthrough infection also mainly recalls previous WT-induced memory. (7/n)
We isolated RBD-antibodies from BA.2/5 convalescent plasma, measured their neutralization, determined their epitope and escaping mutations using high-throughput DMS. Integrated with our previous data, we finally got a DMS dataset containing 3051 RBD-reactive antibodies. (8/n)
Importantly, BA.5 breakthrough infection exhibited further enrichment of non-neutralizing epitopes (E2.2/E3/F1, 63%) and less diversified NAb epitopes (less B/D1/E2.2 and more D2). The reduced B/D1/E2.2 antibodies is due to the F486V and L452R mutations. (9/n)
These observation means that due to immune imprinting, BA.5 breakthrough infection mainly recalls previous memory and rarely produces mAbs with new epitopes. This causes a significant reduction of NAb epitope diversity and an increased proportion of non-neutralizing mAbs. (10/n)
To better visualize the above observation, we modified the algorithm by @jbloom_lab and showed the immune presure elicited by BA.2/BA.5 breakthough infection. This strikingly shows the reduced NAb diversity and concentrated immune pressure for BA.5 infection than BA.2. (11/n)
By integrating data of neutralization, ACE2-binding, RBD-stability, and codon-usage (method detailed described in the manuscript), we can accurately identify sites conferring high immune pressure and infer mutations preferred to appear. (12/n)
Check how well this model aligns with the convergent mutations! R346T/S/I, K356T, K444N/T/M, N450D, L452R, N460K, F486S/V/I, and F490S. (13/n)
The above analyses suggest: due to immune imprinting, BA.5 breakthrough infection caused significant reductions of nAb epitope diversity and increased proportion of non-neutralizing mAbs, which in turn concentrated immune pressure and promoted the convergent RBD evolution. (14/n)
Lastely, we want to know if this convergence evolution keeps on going, what would it finally lead to? We started by calculating the convergent RBD evolution trend of BA.2.75 and BA.5. The result fits very well with the emerging variants, such as BA.2.75.2, BR.1, BQ.1.1. (15/n)
We checked whether these indicated mutations could work together. We chose ~200 BA.2-effective NAbs from distinct epitope groups and tested their neutralization against those mutations. Results suggest the mutations synergize very well and could escape almost all RBD-NAbs. (16/n)
Then we constructed pseudoviruses carrying stacked convergent mutations to find the destination of the convergence, and tested the neutralization of plasma and NAb drugs. NAb drugs are escaped as expected, except SA55. All of the mutants exhibit sufficient ACE2-binding. (17/n)
In BA.2.75 derivatives, F486V confers the most striking drop in NT50 for WT/BA.1/BA.2 plasma but R346T for BA.5 plasma. We also found BA.2.75-S4 is enough to eliminate the neutralization of most plasma samples, and NTD mutations are necessary to escape BA.2/5 plasma. (18/n)
Note how close BA.5-S4 (BA.5+R346T+N417T+K444N+N460K) is compared to the recent BQ.1.1. They will have similiar evasion capability and the results already show how evasive BQ.1.1 would be. This also proves our prediction is on track. (19/n)
Together, our results suggest natural infection or vaccine boosters using BA.5 may not provide sufficiently broad protection. Broad-spectrum vaccines and NAb drugs should be developed and our constructed convergent mutants could help examine their effectiveness in advance. (20/n)
We will update information on BA.2.3.20,BN.1,BA.4.6.1,BQ.1,BQ.1.1,BA.2.10.4, BN.2.1 next week. This work is greatly inspired by @jbloom_lab, and we will share all the DMS and neutralization data so everyone could play with it using Jessi’s @jbloom_lab calculator. (21/n)
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Imagine we can identify JN.1-neutralizing mAbs at the start of the pandemic, how revolutionary it would be for COVID mAb drug development. Here we provide a strategy to select potent SARS-CoV-2 broad-spectrum mAbs when we only know the ancestral strain. biorxiv.org/content/10.110…
Many studies have claimed the discovery of “SARS-CoV-2 bnAbs” based on the efficacy against known variants at that time. However, most of these "bnAbs" were rapidly escaped by subsequent viral evolution.
This is because “neutralization against known variants” is a poor indicator for true bnAbs against fast-evolving pathogens.
Inferred from a retrospective analysis of our SARS-CoV-2 mAb collection, we found that among the potent mAbs available at the early stage of the pandemic, only 1~3% could remain effective for more than two years.
If we could rationally identify bnAbs that remain potent against future variants, it would revolutionize mAb drug development against evolving viruses.
(2/9)
Previously, we showed the possibility of accurately predicting SARS-CoV-2 RBD evolution by aggregating high-throughput antibody DMS results.
Therefore, we hypothesize that if we use constructed pseudoviruses carrying predicted mutations as filters, we could screen for those "true" bnAbs as drug candidates, even when no knowledge of real-world viral evolution was available.
To demonstrate whether this strategy would work, we used the DMS profiles of mAbs elicited by SARS-CoV-2 WT infection/vaccination, which were the only data available early in the pandemic, and constructed pseudoviruses (B.1-S1~S5) harboring mutations on the identified hotspots.
(3/9)nature.com/articles/s4158…
Our paper on JN.1 is now online @TheLancetInfDis!
The manuscript explains how a single RBD mutation L455S could turn BA.2.86 into a heavy immune evasive variant JN.1.
Notably, JN.1 is now approaching worldwide dominance (42% two weeks ago). thelancet.com/journals/lanin…
Two months ago, we warned about JN.1 due to its extreme immune evasion. The reason why we paid attention to JN.1 so early is that we know BA.2.86 is very weak to Class 1 antibodies and L455S is one of the strongest Class 1 antibody escaping mutations. 2/6
Many labs have shown that BA.2.86 is well-neutralized. However, the absolute neutralizing titers cannot tell the full story. Since the majority of BA.2.86-neutralizing Abs are from a single epitope, huge changes in titers could happen when BA.2.86 acquires critical mutations. 3/6
Our research on how repeated Omicron exposure mitigates ancestral strain immune imprinting is finally out in @Nature!
In this paper, we found that multiple Omicron exposures can induce high proportions of Omicron-specific Abs that target new RBD epitopes.
There is an additional burning question following this study. In this paper, we showed that 3 doses of inactivated vaccination + 2 Omicron infection could override immune imprinting. However, multiple studies using mRNA vaccine cohorts did not see this phenomenon.
Updates on BA.2.86. 1) BA.2.86's ACE2 binding affinity is very high. 2) BA.2.86 has lower fusogenicity than XBB.1.5. 3) BA.2.86's infectivity in Vero cells is similar to BA.1, lower than XBB.1.5. 4) Structure analysis shows that BA.2.86's Spike prefers RBD "down" conformation.
BA.2.86's RBD showed a pretty high hACE2 binding affinity measured by SPR, higher than that of XBB.1.5 and EG.5 and is even comparable to "FLip" variants like HK.3. BA.2.86's V483del indeed decreases ACE2 binding, but R403K is just too powerful and makes up for the loss. 2/n
We also measured the cell-cell fusion capability using Spike-transfected 293T cells and 293T-hACE2 cells. BA.2.86 showed a lower fusogenicity than XBB.1.5, despite the fact that BA.2.86's ACE2 binding affinity is much higher. Note this assay is free of pseudoviruses. 3/n
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)
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)
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)
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.