The Sci Transl Med Lanke/Xu Ke team traced the evolution of the virus lineage and proposed a new strategy for the design of a broad-spectrum new crown vaccine

The epidemic caused by the new coronavirus (SARS-CoV-2) is still ongoing, and so far more than 640 million people have been infected with the new coronavirus and more than 6.
6 million people have died (according to the official website of the World Health Organization)
。 With the longer the virus spreads and circulates, the virus continues to accumulate and mutate, coupled with the selection pressure of human immunity and vaccine immunity, the new coronavirus has evolved from the original original strain to a multi-lineage variant strain
.
The World Health Organization names some variants as variants of concern (VOCs) and variants of interest (VOIs) based on their transmissibility, virulence, disease severity, and impact on existing drugs and vaccines
。 Among them, there are 5 types of VOCs: Alpha, Beta, and Gamma ), Delta and Omicron
.
Different VOCs have been replaced since the epidemic of the new coronavirus, and the main VOC strain currently circulating in the world is the Omicron strain and its subline (Figure 1).

Figure 1 Frequency of SARS-CoV-2 mutant strains as of December 2022

However, what does not match the speed of virus mutation is that vaccine research and development requires a long cycle, and most of the vaccines currently on the market (inactivated vaccines, subvaccines, nucleic acid vaccines, viral vector vaccines, etc.
) still use the new coronavirus prototype strain as the antigen, and its neutralization ability against Omicron and its sublineage has decreased
to varying degrees.
Even when vaccine companies can update vaccines based on changes in epidemic strains, they tend to lag behind the emergence
of variant viruses.
Therefore, how to develop a relatively broad-spectrum vaccine that can fight both the current epidemic strains and the possible variants of the future is an important scientific question
.

The team of Professor Lan Ke and Professor Xu Ke, State Key Laboratory of Virology of Wuhan University, proposed a new broad-spectrum vaccine design strategy of "optimizing the design of vaccine immunogens based on viral evolution consensus sequence" by tracking the evolution and mutation law of the new coronavirus spike protein (S protein), which was achieved as early as 2021 Published on preprint platform bioRxiv on December 23 style="font-size:12.
0pt;line-height:150%;font-family:;color:#222222;background:white" _istranslated="1">), and on January 4, 2023 Nikkei peer-reviewed and officially published in the prestigious academic journal SCIENCE Translational Medicine (Science.
).
Translational Medicine").

The study is based on "Vaccinatio n with S _pan, an antigen guided by SARS-CoV-2 S protein evolution, protects against challenge with viral variants in mice.
" ", a broad-spectrum vaccine immunogen S pan (pan-novel coronavirus S antigen) covering "common mutations" was developed, which can induce the production of antibodies against alpha ( Alpha), Beta, Gamma, Eta, Kappa, Delta Broad-spectrum neutralizing antibodies, including Delta, Lambda and Omicron and their sublineages, protect lab mice against Omicron Lethal attack
of multiple coronavirus variants, including them.

[S1] [S2] 

The study, which reported for the first time the evolutionary path of the new coronavirus, found that mutations in the spike (S) protein in virus isolates that survived in the population were not completely random, but evolved
along three directional pathways.
One path is that mutations lead to high cellular infectivity while maintaining weak immune evasion (such as Delta and Lambda strains), and the second path It is the mutation that leads to low cell infectivity while acquiring strong immune evasion ability (such as the Gamma strain), and the number of variants of the third path is relatively small, and their cell infectivity and immune evasion ability are enhanced at the same time (such as the Beta strain) (Figure 2）
。 This shows that in most cases, the regulation of function by mutations in S protein needs to be coordinated, rather than simply enhanced or weakened
.
The Omicron strain, which is now widely prevalent, has the strongest immune evasion ability, and the comprehensive escape ability of most existing antibodies is more than 3 times that of the original strain, but its ability to avoid A549 (human lung cancer epithelial cells) and Caco-2 The infectivity of susceptible cells such as (human colorectal cancer cells) has not increased, indicating that the Omicron strain is still balancing the different functions of S protein and needs to be continuously observed and evaluated
.

Figure 2 Evolutionary law of S protein of the new coronavirus (containing 11,650,487 sequences).

The x-axis indicates the immune evasion ability of the SARS-CoV-2 variant, and the y-axis represents the cellular infectivity
of the SARS-CoV-2 variant.
The sector color marks the separation time
of the shown variant documented in the GISAID database.
The size of the area per sector represents the number of
individual variants isolated as of July 2022 (each month).
Shades of gray indicate evolutionary pathways
.

The different paths of S protein mutations lead to changes
in antigenicity.
Therefore, the vaccine components of a single strain cannot effectively protect the population against other variants along different evolutionary pathways
.
To obtain a broad-spectrum immunogen that can cover the vast majority of variants, the research team analyzed 2675 new coronavirus S protein sequences in the NCBI database, clustered by evolution (Figure 3A).
The frequency of occurrence of all mutation sites is calculated (Figure 3B), and finally a fitted neoantigen (S_pan) covering the common mutation is designed (Figure 3C ）
。 The results show that the _Span sequence is centrally located in the S protein phylogenetic tree (Figure 3D).

Figure 3.
S_pan is located at the center of the phylogenetic tree

Interestingly, S_pan was designed before the Delta and Omicron outbreaks, but it covered evolutionarily calculated common mutations and responded The law of convergence of S protein mutations, and therefore the later emergence of Omicron clustering, suggests that S_pan has the potential to cover future variants (Figure 3E）
。 Further analysis showed that the above six common mutation sites obtained by the research team were retained in the Omicron subline strains that later broke out, showing strong common regularity and predictability (Figure 4).

The above common mutation sites and broad-spectrum vaccine antigen design scheme have been authorized by China invention patent on August 5, 2022 (patent name: novel coronavirus mutant strain S protein and its subvaccine; Patent No.
: ZL 2021 1 1181856.
X).

Figure 4 The 6 common mutation sites (transverse markers) identified by the research team were largely preserved in later outbreaks of Omicron epidemic strains (longitudinal markers) (red indicates that the site was preserved).

In line with design expectations, the research team found that S _pan immunogen showed a clear broad-spectrum neutralization advantage over the prototype strain immunogen (S_wt): it was immune to the 2-shot prototype strain After S protein is strengthened with 1 shot of S _pan protein, compared with immunization with 3 shots of prototype S protein, S_pan induced targets for WT, Beta, Delta, Omicron The strain and its sublines are more efficient and broadly neutralizing antibodies (Figure 5A, Figure 5B) and can protect mice 100% from Omicron Lethal attack of the strain (Figure 5C).

This suggests that S_pan provides broad-spectrum protection
as a booster shot.
Even a simple 2-shot S_pan immunization can provide cross-immune protection across lineages while resisting WT, Lethal attacks
by the Beta and Delta strains.
The researchers also observed that the prototype immunogen (S_wt) was unable to provide effective cross-protection across beta strains
.

Interestingly, S_pan was designed before the advent of Delta (February 2021), but it was efficient to induce targeting Delta and broad-spectrum neutralizing antibodies of Omicron and its variants, indicating that the immunogen design strategy proposed in this study is prospective
.
Therefore, the pan-novel coronavirus S protein immunogen (S_pan) designed based on the common evolutionary mutation of the new crown is expected to become a broad-spectrum vaccine candidate for the prevention of existing and potential future epidemic strains of the new coronavirus (Figure 6).

This work conducted a Proof of Concept for this innovative broad-spectrum vaccine design concept with excellent results
.

Figure 5 S_pan vaccine immunity provides broad-spectrum immunoprotection in mice
.

Figure 6 S_pan vaccine effect science map

Broad-spectrum vaccine immunogens (S_pan) are like fortified castles against multiple coronavirus variants

Zhao Yongliang, postdoctoral fellow at the State Key Laboratory of Virology, Wuhan University, doctoral students Ni Wenjia, Liang Simeng, Dong Lianghui, Xiang Min, Niu Danping, experimentalist Dr.
Cai Zeng, etc.
are co-authors of the paper, and Professor Lan Ke and Professor Xu Ke are co-corresponding authors
.
Wuhan Institute of Biological Products provided technical support
in the process of antigen purification.
The work was completed by the State Key Laboratory of Virology of Wuhan University, the Animal Tertiary Biosafety Laboratory/Vaccine Research Institute, and the Taikang Life Medical Center, and the research was funded by the National Natural Science Foundation of China, the Hubei Provincial Innovation Team, the Wuhan University New Crown Pneumonia Special Research Fund, and the Beijing Taikang Yicai Public Welfare Foundation
.

Paper Link:

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About the corresponding author:

Professor Lan Ke, Director of the State Key Laboratory of Virology, Director of the Animal Level III Biosafety Laboratory of Wuhan University, Professor of the School of Life Sciences, Wuhan University, PI of Taikang Life Medical Center, Wuhan University; Mainly engaged in the research of viral infection and pathogenic mechanism, he has made systematic and original research work in Kaposi's sarcoma virus (KSHV) and new coronavirus (SARS-CoV-2), in Nature and New England Journal of Medicine、Molecular Cell、Nature Ecology Evolution、Science Translational Medicine 、Science Advances、PLoS Pathogens、Journal of Virology、Cell Host Microbe, PNAS, Cell Research, Cancer Research and other academic journals published 120 papers Remainder; Selected as a Clarivate Global Highly Cited Scholar; Academic part-time jobs include: Journal of Virology, Viruses editorial board, Journal of Medical Virology, Virologica Sinica, Deputy Editor of Science Bulletin, Executive Editor of Cell Insight, Vice Chairman of the Virus Special Committee of the Chinese Society of Microbiology, Chairman of Hubei Bioengineering Society, etc
.

Professor Xu Ke, a national excellent youth, is engaged in the research
of pathogenic mechanisms and drug vaccines of respiratory RNA viruses such as new crown and influenza.
He has won the nomination award of the China Association for Science and Technology Powerful Young Science Award (2021), the ESWI (European Scientific Working Group on Influenza) Young Scientist Award, the Newton Foundation Young Talent Award of the United Kingdom, and Sanofi in France Aventis Young Scientific and Technological Talents and other awards
.
Published SCI papers in scientific journals such as Science Translational Medicine, Cell Research, Nature Communications, PLoS Pathogens, etc The remaining papers, a number of corresponding authors' achievements were selected as ESI highly cited papers, and were awarded cover papers and highlight articles in Science China, Protein & Cell, and Journal of Virology.
Obtained 9 national invention patent authorizations, and realized the transfer of antiviral candidate new drug patents as the first inventor
.
Since joining the State Key Laboratory of Virology/College of Life Sciences, Wuhan University in January 2019, he has made a series of progress in respiratory RNA virus research.
A new host factor target broad-spectrum antiviral and anti-inflammatory double-action inhibitor was discovered (Protein & Cell 2020, cover paper), and one old drug was promoted into the clinical trial of multi-country new crown treatment and obtained the British "Life Love" "Fully funded by the LifeArc Foundation (Virol Sin.
2020, Special Recommendation Paper); The molecular mechanism of influenza virus promoting new crown infection was reported, suggesting that influenza virus is the focus of prevention and control of epidemic superposition (Cell Research 2021, reviewed by journals); discovered the new coronavirus-specific sensitive polypeptide and developed the "light detection" antibody rapid detection technology for quantum dot materials (Viruses 2022, authorized by Chinese invention patent); A broad-spectrum new crown vaccine antigen based on the virus evolutionary lineage law was designed to cope with virus mutation, and the process development of the vaccine prototype product (Sci Transl Med 2022) was completed, which provided a theoretical basis and candidate strategy
for the prevention and control of the new crown epidemic and clinical treatment.