Parallel profiling of antigenicity alteration and immune escape of SARS-CoV-2 Omicron and other variants

Sun, Cong; Kang, Yinfeng; Liu, Yuantao; Kong, Xiang-Wei; Xu, Hui-Qin; Xiong, Dan; Xie, Chu; Liu, Yihao; Peng, Sui; Feng, Guokai; Liu, Zheng; Zeng, Mu‐Sheng

doi:10.1038/s41392-022-00910-6

Cited by 27 publications

(23 citation statements)

References 62 publications

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“…However, as SARS-CoV-2 spread and caused a pandemic, new variants, including VOCs, emerged and brought new challenges for global containment of COVID-19, due to their reduced sensitivity to current vaccines based on wild-type antigens 1 , 15 , 18 , 20 , 21 , 43 . Studies have shown that vaccine-induced or convalescent sera manifested reduced neutralization activity against SARS-CoV-2 variants, especially the Beta (B.1.351) 1 , 18 , 43 and Omicron (B.1.1.529) variant 6 , 7 , 46 , indicating that current vaccine design based on wild-type antigen may not elicit sufficient protective antibodies against these variants. Therefore, the value of using mutant spike antigens as vaccine candidates against SARS-CoV-2 variant strains deserves further investigation.…”

Section: Discussionmentioning

confidence: 99%

Quadrivalent mosaic HexaPro-bearing nanoparticle vaccine protects against infection of SARS-CoV-2 variants

Kang

Sun

et al. 2022

Nat Commun

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Emerging SARS-CoV-2 variants of concern (VOCs) harboring multiple mutations in the spike protein raise concerns on effectiveness of current vaccines that rely on the ancestral spike protein. Here, we design a quadrivalent mosaic nanoparticle vaccine displaying spike proteins from the SARS-CoV-2 prototype and 3 different VOCs. The mosaic nanoparticle elicits equivalent or superior neutralizing antibodies against variant strains in mice and non-human primates with only small reduction in neutralization titers against the ancestral strain. Notably, it provides protection against infection with prototype and B.1.351 strains in mice. These results provide a proof of principle for the development of multivalent vaccines against pandemic and potential pre-emergent SARS-CoV-2 variants.

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Section: Discussionmentioning

confidence: 99%

Quadrivalent mosaic HexaPro-bearing nanoparticle vaccine protects against infection of SARS-CoV-2 variants

Kang

Sun

et al. 2022

Nat Commun

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“… 82 – 85 Unprecedented complexity in mutation patterns can alter antigenicity, invalidating the existing immunity. 86 The cryo-electron microscopy (cryo-EM) structure helps to reveal the basis of immune evasion by Omicron. Omicron S-trimer exclusively formed one conformational state with one “up” RBD and two “down” RBDs, while a single-up conformation and all-down conformation were depicted in previous variants.…”

Section: Immune Evasionmentioning

confidence: 99%

“… 15 , 87 Steric clashes, altered interactions at antibody-binding surfaces, and local changes in the spike structure were induced by mutations that interfered with antibody recognition. 86 , 87 …”

Section: Immune Evasionmentioning

confidence: 99%

SARS-CoV-2 Omicron variant: recent progress and future perspectives

Fan

Zhang

et al. 2022

Sig Transduct Target Ther

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Since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic, there have been a few variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), one of which is the Omicron variant (B.1.1.529). The Omicron variant is the most mutated SARS-CoV-2 variant, and its high transmissibility and immune evasion ability have raised global concerns. Owing to its enhanced transmissibility, Omicron has rapidly replaced Delta as the dominant variant in several regions. However, recent studies have shown that the Omicron variant exhibits reduced pathogenicity due to altered cell tropism. In addition, Omicron exhibits significant resistance to the neutralizing activity of vaccines, convalescent serum, and most antibody therapies. In the present review, recent advances in the molecular and clinical characteristics of the infectivity, pathogenicity, and immune evasion of Omicron variant was summarized, and potential therapeutic applications in response to Omicron infection were discussed. Furthermore, we highlighted potential response to future waves and strategies to end the pandemic.

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“…Omicron variant possesses comparable binding affinity to human ACE2 in comparison with the wild type SARS-CoV-2, but much weaker binding affinity than Delta variant [12]. Recent study suggests that new mutations in Omicron variant contribute to transmission advantages, immune escape, and novel spike functionality [13, 14]. As of early February 2022, 8,609,048 SARS-COV-2 virus sequences have been submitted to the GISAID database [15].…”

Section: Introductionmentioning

confidence: 99%

Follow-up investigation and detailed mutational characterization of the SARS-CoV-2 Omicron variant lineages (BA.1, BA.2, BA.3 and BA.1.1)

Abbas

Kusakin

Sharrouf

et al. 2022

Preprint

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Aided by extensive protein mutations, the SARS-CoV-2 Omicron (B.1.1.529) variant overtook the previously dominant Delta variant and rapidly spread around the world. It was shown to exhibit significant resistance to current vaccines and evasion from neutralizing antibodies. It is therefore critical to investigate the Omicron mutations trajectories. In this study, a literature search of published articles and SARS-CoV-2 databases was conducted, We explored the full list of mutations in Omicron BA.1, BA.1.1, BA.2, and BA.3 lineages. We described in detail the prevalence and occurrence of the mutations across variants, and how Omicron differs from them. We used GISAID as our primary data source, which provides open access to genomics data of the SARS-CoV-2 virus, in addition to epidemiological and geographical data. We examined how these mutations interact with each other, their co-occurrence and clustering. Our study offers for the first time a comprehensive description of all mutations with a focus on non-spike mutations and demonstrated that mutations in regions other than the Spike (S) genes are worth investigating further. Our research established that the Omicron variant has retained some mutations reported in other SARS-CoV-2 variants, yet many of its mutations are extremely rare in other variants and unique to Omicron. Some of these mutations have been linked to the transmissibility and immune escape of the virus, and indicate a significant shift in SARS-CoV-2 evolution. The most likely theories for the evolution of the Omicron variant were also discussed.

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Parallel profiling of antigenicity alteration and immune escape of SARS-CoV-2 Omicron and other variants

Cited by 27 publications

References 62 publications

Quadrivalent mosaic HexaPro-bearing nanoparticle vaccine protects against infection of SARS-CoV-2 variants

Quadrivalent mosaic HexaPro-bearing nanoparticle vaccine protects against infection of SARS-CoV-2 variants

SARS-CoV-2 Omicron variant: recent progress and future perspectives

Follow-up investigation and detailed mutational characterization of the SARS-CoV-2 Omicron variant lineages (BA.1, BA.2, BA.3 and BA.1.1)

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