The joint team of Xie Xiaoliang / Cao Yunlong cracked the evolution trend of the new coronavirus, and broad-spectrum antibodies added new weapons against the epidemic

Abstract: Since the emergence of the new coronavirus Omicron variant, its offspring variants have emerged in a blowout and shown a trend of "convergent evolution", and a large number of neutralizing antibody drugs and convalescent plasma have been "escaped", which has brought a very severe test
to the prevention and control of the new crown epidemic.
The formation mechanism and evolutionary endpoint of the phenomenon of "convergent evolution" need to be deeply explored
.

The research group of Professor Xie Xiaoliang of the Center for Biomedical Frontier Innovation (BIOPIC) of Peking University, Associate Professor Cao Yunlong of Beijing Changping Laboratory and the research group of Wang Youchun of the China Institute of Food and Drug Control published the title "Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD" online in Nature on December 19, 2022 evolution", systematically explores the mechanism of "convergent evolution" of the new coronavirus receptor-binding domain (RBD), and prospectively predicts the future mutation evolution direction of the virus, which provides valuable theoretical and data support
for the design and development of broad-spectrum vaccines and antibody drugs.

The researchers conducted large-scale neutralization assays and escape mapping characterization of antibodies isolated from people with different immune backgrounds, and found that the variants produced by the convergent evolution of the virus escaped the plasma of almost all current neutralizing antibody drugs, vaccinated or recovered patients, including the plasma of
BA.
5 breakthrough infected people.
Moreover, due to the existence of the phenomenon of "western blotting", the diversity of antibodies produced by the Omicron subtype variant after breaking through infection gradually decreased, especially BA.
5 breakthrough infection, which suggested that vaccine booster shots based on BA.
5 variants could not produce good cross-infection protection against
emerging variants.
In addition, based on the data of large-scale neutralization assay and escape pattern characterization of antibodies, the researchers established a computational model to reasonably predict
the evolution direction of the virus 。 Although these new mutant strains, especially the XBB, BQ.
1.
1 and CH.
1.
1 branches, have unprecedented immune evasion capabilities, the broad-spectrum neutralizing antibody drug combination SA55+SA58, especially SA55, previously screened by the author's team, is still potent in neutralizing all major mutant strains and mutant strains that may be circulating in the short term, and can have both therapeutic and preventive effects, and is currently the only clinical-stage drug antibody known to be able to efficiently neutralize all new mutant strains.
The paper was previously published in Cell Reports, a well-known life science journal
, in early December.
The antibody has the characteristics of broad-spectrum neutralization ability, will be difficult to escape by future variants, and has a long half-life, and will be especially suitable for the protection of the elderly and immunodeficient people who are not suitable for vaccination
.

Screenshot of the paper

This study, which was first published online on the bioRxiv preprint platform on September 16, 2022, is the world's first research paper that systematically studies the "convergent evolution" mechanism of the new coronavirus and predicts the direction of virus evolution, which has attracted widespread attention
in the international academic community.

The continuous mutation and evolution of the virus has led to the emergence of a variety of variants with higher growth advantages, including BA.
2.
3.
20, BA.
2.
75.
2 and their branches, and even the recent emergence of BQ.
1.
1 and XBB variants that have higher growth advantages
than BA.
5 。 Although their evolutionary processes are different and they are in different branches of Omicron, mutations in their receptor-binding domains (RBDs) are concentrated in the R346, K356, K444, V445, G446, N450, L452, N460, F486, F490, R493, and S494 alleles, showing a trend of "convergent evolution" (Figure 1).

Fig.
1 Mutations carried by the RBD protein of the Omicron subtype variant

The data of neutralization assays suggest that the variants produced by "convergent evolution" have a strong ability to escape, and the vast majority of neutralizing antibody drugs have been evaded by variants represented by XBB (Figure 2), including AstraZeneca's Evusheld ("Ensade") preventive antibody drugs
, which have previously entered the domestic market.
Due to the prevalence of such new mutant strains, the US FDA also canceled the authorization
of the use of Eli Lilly Bebtelovimab (betrovimab).
The only exception is the SA55 antibody developed by the authors' team, which is currently the only antibody drug that has entered the clinical stage that is still effective against all mutant strains, including XBB and BQ.
1.
1 (Figure 3).

Fig.
2 Escape of Omicron subtype to neutralizing antibody drugs

Figure 3 Broad-spectrum neutralizing antibodies SA55 and SA58

Plasma neutralization and data also show that strains such as XBB, CH.
1.
1, and BQ.
1.
1.
10 (or BQ.
1.
18) not only evade the plasma of three-dose inactivated vaccine recipients, but also almost completely escape Omicron BA.
1/BA.
2/BA.
5 breakthrough plasma samples from infected people, showing great immune evasion ability (Figure 4).

Fig.
4 Plasma neutralization of Omicron subtype evasive vaccine recipients and recovered patients

In order to explore the specific mechanism of "convergent evolution" of different Omicron variants, the team enriched antigen-specific memory B cells from BA.
1, BA.
2 or BA.
5 breakthrough infection recovered from infection, and found that most of them cross-bound the original new crown strain and Omicron variant, confirming the "immunoblotting" phenomenon
reported by the author's team in Omicron breakthrough infection 。 Based on high-throughput deep mutation scanning technology, the team conducted mutation escape mapping and cluster analysis on 3051 antibodies that cross-bound the original new crown strain and Omicron variant from different sources (Figure 5a), and found that the types of effective neutralizing antibodies produced by Omicron, especially the BA.
5 variant, were significantly reduced, and mainly antibodies such as E2.
2, E3 and F1 that did not compete for ACE2-binding epitopes and had weak neutralization ability (Figure 5b-d).

Fig.
5 Epitope characterization of Omicron subtype variants stimulated the production of antibodies by breakthrough infection

Based on the data of antibody escape map, antibody neutralization activity, and affinity change of RBD mutation for ACE2, the team established a model and calculated the mutation escape map of BA.
2 and BA.
5 breakthrough infection stimulus to produce antibodies respectively (Figure 6a), and the results showed that the mutation escape sites stimulated by BA.
5 breakthrough infection stimulated the production of antibodies were significantly reduced, indicating that its binding epitope diversity was significantly reduced
.
This suggests that the phenomenon of immunoblotting has reduced the epitope diversity of neutralizing antibodies stimulated by the Omicron variant to break through infection, resulting in concentrated immune pressure, thereby accelerating the convergent evolution
of the virus.
On this basis, based on the mainstream immune status in the real world in August-September 2022, the researchers predicted the evolutionary trend of BA.
2.
75 and BA.
5 based on computational models (Figure 6b), which was verified
in the new strains generated by subsequent convergent evolution.

Fig.
6 Western blot effect accelerates the convergent evolution of antibody escape mutations

Other than that Based on the predicted evolutionary trends of BA.
2.
75 and BA.
5 mutant strains, the researchers designed pseudoviruses carrying different combinations of RBD and NTD prediction mutations (Figure 7a), and determined the neutralization of these pseudoviruses to different neutralizing antibody drugs and plasma samples and ACE2 affinity (Figure 7b-g), and the results showed that introducing at least 5 mutations to BA.
5 or BA.
2.
75 mutant strains can escape almost all plasma samples in different immune states, including BA.
5 breakthrough infected people
。 Moreover, the synthesized pseudoviruses are highly similar to the BQ.
1.
1 clade and CH.
1.
1 clade that are popular in the real world, which verifies the accuracy of
the prediction model.

Fig.
7 The accumulation of convergent escape mutations can almost completely escape the neutralization effect of BA.
1/BA.
2/BA.
5 in infected plasma

This study revealed that the Omicron breakthrough infection caused by "western blotting" stimulates the reduction of antibody epitope diversity, which in turn leads to the concentration of immune pressure, which promotes the convergent evolution of the RBD protein of the new coronavirus, and these viruses that accumulate convergent evolutionary mutations have maintained a high ACE2 affinity while obtaining strong mutation escape ability
.
The prediction methods in this study provide reference materials for predicting the evolution trend of viral mutations and developing broad-spectrum vaccines and antibody drugs, and have the potential
to be extended to other systems.
At the same time, the results also suggest that vaccines developed based on BA.
5 mutant strains are likely to be less than ideal for the cross-protection effect of other variants, and it is important
to further develop and design new vaccines that can overcome immunoblotting and activate broad-spectrum neutralizing antibodies.
The broad-spectrum neutralizing antibody represented by SA55+SA58 antibody combination can not only establish short-term prevention in the respiratory tract conveniently and quickly through nasal spray administration, but also realize the initial treatment and medium and long-term prevention of infection through injection, especially suitable for protecting high-risk medical personnel and immunodeficient people and the elderly
who are not suitable for vaccination.
Preliminary single-blind randomized controlled trials have shown that the immediate protection provided by spray inhalation can be maintained for 6-12 hours, the infection prevention efficiency can reach more than 80%, and the cost is low and convenient to use
.
More rigorous clinical trials are currently underway and are expected to be available
on a large scale in the future.

Yunlong Cao, PhD students Jian Fanchong, Wang Jing, Song Weiliang of Peking University, and Yu Yuanling, China Academy of Food and Drug Control, are co-first authors
of this paper.
Yunlong Cao, Xiaoliang Xie and Youchun Wang are the co-corresponding authors
of this article.
This research was supported
by the Changping Laboratory Fund of the Ministry of Science and Technology and the National Natural Science Foundation of China.

References

[1] Cao, Y.
et al.
Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution.
Nature (2022).

[2] Cao, Y.
et al.
Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies.
Nature (2022).

[3] Cao, Y.
et al.
BA.
2.
12.
1, BA.
4 and BA.
5 escape antibodies elicited by Omicron infection.
Nature (2022).

[4] Cao, Y.
et al.
Rational identification of potent and broad sarbecovirus-neutralizing antibody cocktails from SARS convalescents.
Cell Rep.
(2022)

Expert Reviews:

Professor Qi Hai, School of Medicine, Tsinghua University:

This work delves into the escape of
human herd immunity from the multiple Omicron strains that make up the current pandemic.
The joint team of Yunlong Cao/Xiaoliang Xie found that multiple Omicron subtypes showed the same or similar escape mutations
on receptor-binding proteins.
These mutations, while ensuring that the virus binds to its receptors, evade the inhibition of previous neutralizing antibodies
.
This shows that herd immunity built by sequential vaccination and natural infection in the population is indeed blocking and reducing infection with previous strains; At the same time, this pressure of herd immunity also leaves fewer and fewer potential escape paths
for future virus mutations.
So, can we predict the most likely escape mutations in the future based on the existing herd immunity status and the receptor-binding proteins of existing strains? The Cao Yunlong/Xie team used a high-throughput deep mutation scanning (DMS) method they developed to analyze and identify mutations in BA5 and BA2 that may escape herd immunity
.
Very importantly, the mutations they predicted did appear in
other strains with epidemic potential.
The predictive power provided by the Cao Yunlong/Xie Xiaoliang joint team's study can help us design broad-spectrum anti-coronavirus vaccines more efficiently, and will also make us more likely to prepare "miracle drugs"
for all strains that potentially escape existing herd immunity.

Researcher Wang Xiangxi, Institute of Biophysics, Chinese Academy of Sciences:

The new coronavirus has been continuously evolving, deriving a variety of mutant strains; However, after the emergence of Omicron, the evolution of the new coronavirus accelerated
significantly.
In the past six months, nearly ten new mutant strains such as BA.
5, BF7, BA.
2.
75, BQ, and XBB have become the main epidemic mutant strains
in some countries.
These new mutant strains tend to have increased
infectivity and antibody evasion.
In general, human research on the new coronavirus is to passively follow the virus, and then understand its viral characteristics after a new mutant strain appears, and explore the impact of
the new mutant strain on existing vaccines and drugs.
It is of great strategic significance
to predict the direction of virus evolution in a forward-looking manner and predict in advance the mutant strains that may appear in the future.

On December 19, 2022, the team of Xie Xiaoliang/Cao Yunlong of Peking University and the team of Wang Youchun of the Central People's Inspection Institute published a research paper entitled "Imprinted SARS-CoV-2 humoral immunity induces convergent OmicronRBD evolution" in Nature, which is after the team followed the new crown neutralizing antibodies, the evaluation of the effect of the new crown vaccine, and the tracking of the immune escape characteristics of the new mutant strain.
Another systematic and innovative work
.
The study has five important findings: 1) from the huge database, dozens of new mutant strains have recently surpassed BA.
5 in growth advantages, and these mutant strains have certain commonalities, carrying the same or similar mutations at some specific sites, showing a convergent evolutionary law; 2) these new mutant strains show strong antibody escape characteristics, basically escaping internationally approved antibody drugs; 3) an antibody pair combination SA55/ SA58 (also the team's work) remains highly effective at neutralizing these new mutant strains; The last two points are more exciting: 4) more than 2000 antibodies were isolated from different immune backgrounds such as those who recovered from the original strain infection and those who had broken through the infection such as BA.
1/BA.
2/BA.
5 breakthrough infection, and the characteristics
of the antibody lineage in different immune backgrounds were mapped 。 Compared with the previous immune background, the main neutralizing antibody categories of BA.
5 breakthrough infected patients are relatively single, the proportion of non-neutralizing antibodies is increased, and it is easier to breed virus mutations to escape host immunity; 5) The antibody immune escape map is accurately drawn by using high-throughput yeast display technology, and compared with the immune background of BA.
2 breakthrough infection, the immune escape sites of BA.
5 breakthrough infection neutralizing antibodies are relatively concentrated and mostly appear on recently appeared mutant
strains.
The experimental data is highly consistent
with real-world monitoring results.
This research result can achieve accurate prediction of new mutant strains in the future, and understanding the viral characteristics of these new mutant strains in advance can leave a valuable window
of time for scientific and precise prevention and control.