Research Articles (Centre for Epidemic Response and Innovation (CERI))

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    BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection
    (Springer Nature, 2022-06-17) Cao, Yunlong; Yisimayi, Ayijiang; Jian, Fanchong; Song, Weiliang; Xiao, Tianhe; Wang, Lei; Du, Shuo; Wang, Jing; Li, Qianqian; Chen, Xiaosu; Yu, Yuanling; Wang, Peng; Zhang, Zhiying; Liu, Pulan; An, Ran; Hao, Xiaohua; Wang, Yao; Wang, Jing; Feng, Rui; Sun, Haiyan; Zhao, Lijuan; Zhang, Wen; Zhao, Dong; Zheng, Jiang; Yu, Lingling; Li, Can; Zhang, Na; Wang, Rui; Niu, Xiao; Yang, Sijie; Song, Xuetao; Chai, Yangyang; Hu, Ye; Shi, Yansong; Zheng, Linlin; Li, Zhiqiang; Gu, Qingqing; Shao, Fei; Huang, Weijin; Jin, Ronghua; Shen, Zhongyang; Wang, Youchun; Wang, Xiangxi; Xiao, Junyu; Xie, Xiaoliang Sunney
    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages BA.2.12.1, BA.4 and BA.5 exhibit higher transmissibility than the BA.2 lineage1. The receptor binding and immune-evasion capability of these recently emerged variants require immediate investigation. Here, coupled with structural comparisons of the spike proteins, we show that BA.2.12.1, BA.4 and BA.5 (BA.4 and BA.5 are hereafter referred collectively to as BA.4/BA.5) exhibit similar binding affinities to BA.2 for the angiotensin-converting enzyme 2 (ACE2) receptor. Of note, BA.2.12.1 and BA.4/BA.5 display increased evasion of neutralizing antibodies compared with BA.2 against plasma from triple-vaccinated individuals or from individuals who developed a BA.1 infection after vaccination. To delineate the underlying antibody-evasion mechanism, we determined the escape mutation profiles2, epitope distribution3 and Omicron-neutralization efficiency of 1,640 neutralizing antibodies directed against the receptor-binding domain of the viral spike protein, including 614 antibodies isolated from people who had recovered from BA.1 infection. BA.1 infection after vaccination predominantly recalls humoral immune memory directed against ancestral (hereafter referred to as wild-type (WT)) SARS-CoV-2 spike protein. The resulting elicited antibodies could neutralize both WT SARS-CoV-2 and BA.1 and are enriched on epitopes on spike that do not bind ACE2. However, most of these cross-reactive neutralizing antibodies are evaded by spike mutants L452Q, L452R and F486V. BA.1 infection can also induce new clones of BA.1-specific antibodies that potently neutralize BA.1. Nevertheless, these neutralizing antibodies are largely evaded by BA.2 and BA.4/BA.5 owing to D405N and F486V mutations, and react weakly to pre-Omicron variants, exhibiting narrow neutralization breadths. The therapeutic neutralizing antibodies bebtelovimab4 and cilgavimab5 can effectively neutralize BA.2.12.1 and BA.4/BA.5, whereas the S371F, D405N and R408S mutations undermine most broadly sarbecovirus-neutralizing antibodies. Together, our results indicate that Omicron may evolve mutations to evade the humoral immunity elicited by BA.1 infection, suggesting that BA.1-derived vaccine boosters may not achieve broad-spectrum protection against new Omicron variants.
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    Effects of damping constant of electron and size on quantum-based frequency-dependent dielectric function of small metallic plasmonic devices
    (Elsevier B.V, 2022-07) Akinyemi, Lateef; Oladejo, Sunday; Ekwe, Stephen; Imoize, Agbotiname Lucky; Ojo, Stephen Abiodun
    Electron surface dissipation and quantum-limited size tend to control the material properties of exterior plasmon oscillation as the size of metal nanoparticles goes into the nanoscale domain. The need to examine this characteristic behaviour and its potential becomes imperative. This study explores the effects of the damping constant of electrons and size quantum-based frequency-dependent dielectric function (FDDF) of small metallic materials using an elementary model of electrons in a confined box. The frequency-dependent dielectric function is employed to study quantum size impacts and damping constant in the optical spectra region. The quantum amended frequency-dependent dielectric function and the absorbing spectra of silver-cube geometry for different sizes by adding damping constant and without damping constant are critically examined. The findings reveal that when the damping constant effect is absent, the multiple crests emerge for the quantum-amended frequency-dependent dielectric function and absorbing spectra of the metallic materials, highlighting the electronic discretization levels in the tiny quantum-limited structure. While the damping constant is included, the multiple summits are hidden and vanish owing to a considerable widening of the structures independently. The change in the numerical results from the quantum case to the classical case for growing widths is further illustrated for both cases. The numerical results enhance our knowledge of damping constant dissipation and quantum limited-size impact in small-scaled plasmonic devices.