Expanding anti-coronavirus arsenal: exploring next generation COVID mRNA vaccine candidate targeting Omicron variant

As a booster to WT spike mRNA vaccinated mice, Omicron-specific mRNA vaccine candidate induces superior Omicron neutralizing antibody titers than WT counterpart

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With its high transmissibility and immune evasion, SARS-CoV-2 Omicron variant rapidly sweeps the globe and replaces Delta variant becoming the dominant variant of concern worldwide. The advent of mRNA vaccine technology1, 2 facilitates the immense success of COVID mRNA vaccine3, 4, which greatly reduces COVID mortality rate and curbs the spread of disease. The widely used COVID mRNA vaccines are designed based on the wild-type (WT) or ancestral spike antigen sequence identified in 2019. Through continuous natural selection, adaptation and evolution, Omicron spike gained over 30 mutations comparing to ancestral spike, many of which mediate strong immune escape from existing preventative vaccines and therapeutic antibodies. The extent of immune evasion of Omicron is unprecedent and makes it easy to crack our immune defense line, leading to breakthrough infections. Because of Omicron’s rapid spread and unprecedent immune evasion, exploring and developing next generation Omicron-specific mRNA vaccine naturally takes the center stage for vaccine makers and science community.


A number of intriguing questions arise when it comes to rapid and efficient evaluation of Omicron-specific mRNA vaccine candidates. The first and most urgent question to address is whether Omicron spike antigen can induce Omicron neutralizing antibodies in the mRNA vaccine system. If it does, then whether the induced antibodies can cross react with other SARS-CoV-2 variants of concerns? As the majority of world population have received two doses of WT mRNA vaccine, whether the Omicron-specific mRNA vaccine candidate can serve as a booster to restore the waning immunity of vaccinees? These questions motivate us to initiate the pre-clinical evaluation of an Omicron-specific mRNA vaccine candidate or lipid nanoparticle (LNP) mRNA, which eventually gets published in Nature Communications on June 6, 20225, Omicron-specific mRNA vaccination alone and as a heterologous booster against SARS-CoV-2 | Nature Communications.


Our study is the result of a highly cooperative team endeavor by members from Drs. Sidi Chen (correspondence), Craig B. Wilen (correspondence), Nathan D. Grubaugh, Albert I. Ko, Chenxiang Lin labs. We found that WT LNP-mRNA induced Omicron neutralizing antibody titers in mice wanes over time and can be drastically enhanced by either WT or Omicron specific LNP-mRNA boosters (third dose). More importantly, the Omicron LNP-mRNA booster shows significantly higher Omicron neutralizing antibody titers and comparable Delta neutralizing titers compared to WT booster.

The Omicron mRNA vaccine candidate in our study was based on the Omicron spike sequence incorporated with six proline substitutions initially reported by Dr. Jason McLellan lab6. Compared to the spike with two proline substitutions (S-2P) used in clinically approved mRNA vaccines, the spike with six proline substitutions (HexaPro) exhibited higher expression and stability. With this HexaPro spike variant, we report that in mice, Omicron LNP-mRNA induced neutralizing antibodies that protect host cells from Omicron live virus infection.


Encouraged by above finding, we further assessed the boosting effect of Omicron vs. WT LNP-mRNA boosters (third dose) in WT LNP-mRNA vaccinated mice. We found the antibody titer against Omicron induced by WT LNP-mRNA was significantly lower than antibody titer against WT and it dropped to near background level after 3 months. The WT and Omicron boosters increased the Omicron neutralizing antibody titers by 10 and 200 fold, respectively. It is worth noting that the Omicron booster elevated an Omicron neutralizing titer that is 10-20 fold higher than that of WT booster and elicited a Delta neutralizing titer comparable to that of WT booster.


In addition, we characterized the cross reactivity of WT and Omicron LNP-mRNA induced antibodies against multiple SARS-CoV-2 variants and coronavirus species. The cross-reactive antibody titers of characterized plasma samples were correlated with sequence identity between ELISA antigen and vaccine antigen, meaning that high titer will be found with cognate ELISA antigen (100% identical to vaccine antigen), and low titer is associated with low-identity ELISA antigen such as MERS spike (~30% identical to SARS-CoV-2). This cross reactivity characterization is associated with the breadth of anti-coronavirus spectrum conferred by WT or Omicron LNP-mRNA vaccination.


Our pre-clinical study comprehensively evaluated immunogenicity of an Omicron specific mRNA vaccine candidate alone and as a heterologous booster, providing data support for the development of next generation COVID mRNA vaccines. The majority of work in our study was completed in February, 2022 and a version of manuscript was uploaded to BioRxiv in the same month. Around the same time, Pfizer/BioNTech and Moderna announced their clinical trials of Omicron-specific boosters. Swift initiation of these clinical trials exemplifies the importance of developing Omicron mRNA vaccines. Our investigation of Omicron LNP-mRNA along with other groups preclinical studies provide unbiased cross validation values and supporting evidence for clinical development of Omicron vaccine candidates. Coincidently, Moderna announced its trial result of bivalent Omicron booster (mRNA-1273.214, mRNA1273 plus Omicron mRNA) on June 8, two days after our paper went online in Nature Communications. This clinical trial has met all prespecified endpoints, including superior neutralizing antibody response against Omicron variant compared to mRNA-1273 (WT). The reported antibody titer difference of mRNA-1273.214 is 8 fold above baseline and it is expected to be available in fall this year (Moderna Announces Omicron-Containing Bivalent Booster Candidate mRNA-1273.214 Demonstrates Superior Antibody Response Against Omicron (modernatx.com)). Meanwhile Pfizer’s COVID-19 vaccine booster addressing Omicron variants is in active development and could be available in this fall (Pfizer may have COVID-19 booster that addresses omicron, other variants by fall - ABC News (go.com)).


Our lab’s effort of evaluating variant-specific COVID mRNA vaccine candidates started in early 2021, when the Beta and Delta variants emerged. Our work about Beta and B.1.617 variant LNP-mRNA prepared ourselves and laid a foundation for the current Omicron vaccine study7. The commercial lipids and microfluidic mixer provided by Precision Nanosystems make it possible to reliably prepare lipid nanoparticle encapsulated mRNA with ease in the lab.




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Zane Zhenhao Fang

Postdoctoral Fellow, Yale University