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  1. Article ; Online: Stabilization of the Metastable Pre-Fusion Conformation of the SARS-CoV-2 Spike Glycoprotein through N-Linked Glycosylation of the S2 Subunit.

    Zan, Fuwen / Zhou, Yao / Chen, Ting / Chen, Yahan / Mu, Zhixia / Qian, Zhaohui / Ou, Xiuyuan

    Viruses

    2024  Volume 16, Issue 2

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus responsible for the coronavirus disease 2019 (COVID-19) pandemic, represents a serious threat to public health. The spike (S) glycoprotein of SARS-CoV-2 mediates viral ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus responsible for the coronavirus disease 2019 (COVID-19) pandemic, represents a serious threat to public health. The spike (S) glycoprotein of SARS-CoV-2 mediates viral entry into host cells and is heavily glycosylated. In this study, we systemically analyzed the roles of 22 putative N-linked glycans in SARS-CoV-2 S protein expression, membrane fusion, viral entry, and stability. Using the α-glycosidase inhibitors castanospermine and NB-DNJ, we confirmed that disruption of N-linked glycosylation blocked the maturation of the S protein, leading to the impairment of S protein-mediated membrane fusion. Single-amino-acid substitution of each of the 22 N-linked glycosylation sites with glutamine revealed that 9 out of the 22 N-linked glycosylation sites were critical for S protein folding and maturation. Thus, substitution at these sites resulted in reduced S protein-mediated cell-cell fusion and viral entry. Notably, the N1074Q mutation markedly affected S protein stability and induced significant receptor-independent syncytium (RIS) formation in HEK293T/hACE2-KO cells. Additionally, the removal of the furin cleavage site partially compensated for the instability induced by the N1074Q mutation. Although the corresponding mutation in the SARS-CoV S protein (N1056Q) did not induce RIS in HEK293T cells, the N669Q and N1080Q mutants exhibited increased fusogenic activity and did induce syncytium formation in HEK293T cells. Therefore, N-glycans on the SARS-CoV and SARS-CoV-2 S2 subunits are highly important for maintaining the pre-fusion state of the S protein. This study revealed the critical roles of N-glycans in S protein maturation and stability, information that has implications for the design of vaccines and antiviral strategies.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; COVID-19 ; Spike Glycoprotein, Coronavirus/metabolism ; Glycosylation ; HEK293 Cells ; Severe acute respiratory syndrome-related coronavirus ; Polysaccharides/metabolism ; Virus Internalization
    Chemical Substances spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Polysaccharides
    Language English
    Publishing date 2024-01-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v16020223
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Optimization and Deoptimization of Codons in SARS-CoV-2 and Related Implications for Vaccine Development.

    Wu, Xinkai / Shan, Ke-Jia / Zan, Fuwen / Tang, Xiaolu / Qian, Zhaohui / Lu, Jian

    Advanced science (Weinheim, Baden-Wurttemberg, Germany)

    2023  Volume 10, Issue 23, Page(s) e2205445

    Abstract: The spread of coronavirus disease 2019 (COVID-19), caused by severe respiratory syndrome coronavirus 2 (SARS-CoV-2), has progressed into a global pandemic. To date, thousands of genetic variants have been identified among SARS-CoV-2 isolates collected ... ...

    Abstract The spread of coronavirus disease 2019 (COVID-19), caused by severe respiratory syndrome coronavirus 2 (SARS-CoV-2), has progressed into a global pandemic. To date, thousands of genetic variants have been identified among SARS-CoV-2 isolates collected from patients. Sequence analysis reveals that the codon adaptation index (CAI) values of viral sequences have decreased over time but with occasional fluctuations. Through evolution modeling, it is found that this phenomenon may result from the virus's mutation preference during transmission. Using dual-luciferase assays, it is further discovered that the deoptimization of codons in the viral sequence may weaken protein expression during virus evolution, indicating that codon usage may play an important role in virus fitness. Finally, given the importance of codon usage in protein expression and particularly for mRNA vaccines, it is designed several codon-optimized Omicron BA.2.12.1, BA.4/5, and XBB.1.5 spike mRNA vaccine candidates and experimentally validated their high levels of expression. This study highlights the importance of codon usage in virus evolution and provides guidelines for codon optimization in mRNA and DNA vaccine development.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19/prevention & control ; COVID-19/genetics ; Codon/genetics ; Codon Usage/genetics ; Mutation/genetics
    Chemical Substances Codon
    Language English
    Publishing date 2023-06-02
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2808093-2
    ISSN 2198-3844 ; 2198-3844
    ISSN (online) 2198-3844
    ISSN 2198-3844
    DOI 10.1002/advs.202205445
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Optimization and deoptimization of codons in SARS-CoV-2 and the implications for vaccine development

    Wu, Xinkai / Shan, Kejia / Zan, Fuwen / Tang, Xiaolu / Qian, Zhaohui / Lu, Jian

    bioRxiv

    Abstract: The spread of Coronavirus Disease 2019 (COVID-19), caused by the SARS-CoV-2 coronavirus, has progressed into a global pandemic. To date, thousands of genetic variants have been identified across SARS-CoV-2 isolates from patients. Sequence analysis ... ...

    Abstract The spread of Coronavirus Disease 2019 (COVID-19), caused by the SARS-CoV-2 coronavirus, has progressed into a global pandemic. To date, thousands of genetic variants have been identified across SARS-CoV-2 isolates from patients. Sequence analysis reveals that the codon usage of viral sequences decreased over time but fluctuated from time to time. In this study, through evolution modeling, we found that this phenomenon might result from the virus9 preference for mutations during transmission. Using dual luciferase assays, we further discovered that the deoptimization of codons on viruses might weaken protein expression during the virus evolution, indicating that the choice of codon usage might play important role in virus fitness. Finally, given the importance of codon usage in protein expression and particularly for mRNA vaccine, we designed several omicron BA.2.12.1 and BA.4/5 spike mRNA vaccine candidates based on codon optimization, and experimentally validated their high levels of expression. Our study highlights the importance of codon usage in virus evolution and mRNA vaccine development.
    Keywords covid19
    Language English
    Publishing date 2022-09-05
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2022.09.03.506470
    Database COVID19

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  4. Article: Host susceptibility and structural and immunological insight of S proteins of two SARS-CoV-2 closely related bat coronaviruses.

    Ou, Xiuyuan / Xu, Ge / Li, Pei / Liu, Yan / Zan, Fuwen / Liu, Pan / Hu, Jiaxin / Lu, Xing / Dong, Siwen / Zhou, Yao / Mu, Zhixia / Wu, Zhiqiang / Wang, Jianwei / Jin, Qi / Liu, Pinghuang / Lu, Jian / Wang, Xiangxi / Qian, Zhaohui

    Cell discovery

    2023  Volume 9, Issue 1, Page(s) 78

    Abstract: The bat coronaviruses (CoV) BANAL-20-52 and BANAL-20-236 are two newly identified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) closely related coronaviruses (SC2r-CoV) and the genome of BANAL-20-52 shares the highest homology with SARS- ... ...

    Abstract The bat coronaviruses (CoV) BANAL-20-52 and BANAL-20-236 are two newly identified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) closely related coronaviruses (SC2r-CoV) and the genome of BANAL-20-52 shares the highest homology with SARS-CoV-2. However, the risk of their potential zoonotic transmission has not been fully evaluated. Here, we determined their potential host susceptibility among 13 different bat species and 26 different animal species, and found that both might have extensive host ranges, indicating high zoonotic transmission potential. We also determined the cryo-EM structures of BANAL-20-52 and BANAL-20-236 S proteins at pH 5.5 and the complex of BANAL-20-236 S1 and Rhinolophus affinis ACE2, and found that both trimeric S proteins adopt all three receptor binding domains (RBDs) in "closed" conformation and are more compact than SARS-CoV-2. Strikingly, the unique sugar moiety at N370 of bat SC2r-CoVs acts like a "bolt" and crosses over two neighboring subunits, facilitating the S proteins in the locked conformation and underpinning the architecture stability. Removal of the glycosylation at N370 by a T372A substitution substantially enhances virus infectivity but becomes highly sensitive to trypsin digestion at pH 5.5, a condition roughly mimicking the insectivorous bat's stomach digestion. In contrast, WT S proteins of SC2r-CoVs showed considerable resistance to trypsin digestion at pH 5.5, indicating that the highly conserved T372 in bat CoVs might result from the selective advantages in stability during the fecal-oral transmission over A372. Moreover, the results of cross-immunogenicity among S proteins of SARS-CoV-2, BANAL-20-52, and BANAL-20-236 showed that A372 pseudoviruses are more sensitive to anti-S sera than T372, indicating that immune evasion might also play a role in the natural selection of T372 over A372 during evolution. Finally, residues 493 and 498 of the S protein affect host susceptibility, and residue 498 also influences the immunogenicity of the S protein. Together, our findings aid a better understanding of the molecular basis of CoV entry, selective evolution, and immunogenicity and highlight the importance of surveillance of susceptible hosts of these viruses to prevent potential outbreaks.
    Language English
    Publishing date 2023-07-28
    Publishing country England
    Document type Journal Article
    ISSN 2056-5968
    ISSN 2056-5968
    DOI 10.1038/s41421-023-00581-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Author Correction: Host susceptibility and structural and immunological insight of S proteins of two SARS-CoV-2 closely related bat coronaviruses.

    Ou, Xiuyuan / Xu, Ge / Li, Pei / Liu, Yan / Zan, Fuwen / Liu, Pan / Hu, Jiaxin / Lu, Xing / Dong, Siwen / Zhou, Yao / Mu, Zhixia / Wu, Zhiqiang / Wang, Jianwei / Jin, Qi / Liu, Pinghuang / Lu, Jian / Wang, Xiangxi / Qian, Zhaohui

    Cell discovery

    2023  Volume 9, Issue 1, Page(s) 102

    Language English
    Publishing date 2023-10-09
    Publishing country England
    Document type Published Erratum
    ISSN 2056-5968
    ISSN 2056-5968
    DOI 10.1038/s41421-023-00597-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Effect of polymorphism in Rhinolophus affinis ACE2 on entry of SARS-CoV-2 related bat coronaviruses.

    Li, Pei / Hu, Jiaxin / Liu, Yan / Ou, Xiuyuan / Mu, Zhixia / Lu, Xing / Zan, Fuwen / Cao, Mengmeng / Tan, Lin / Dong, Siwen / Zhou, Yao / Lu, Jian / Jin, Qi / Wang, Jianwei / Wu, Zhiqiang / Zhang, Yingtao / Qian, Zhaohui

    PLoS pathogens

    2023  Volume 19, Issue 1, Page(s) e1011116

    Abstract: Bat coronavirus RaTG13 shares about 96.2% nucleotide sequence identity with that of SARS-CoV-2 and uses human and Rhinolophus affinis (Ra) angiotensin-converting enzyme 2 (ACE2) as entry receptors. Whether there are bat species other than R. affinis ... ...

    Abstract Bat coronavirus RaTG13 shares about 96.2% nucleotide sequence identity with that of SARS-CoV-2 and uses human and Rhinolophus affinis (Ra) angiotensin-converting enzyme 2 (ACE2) as entry receptors. Whether there are bat species other than R. affinis susceptible to RaTG13 infection remains elusive. Here, we show that, among 18 different bat ACE2s tested, only RaACE2 is highly susceptible to transduction by RaTG13 S pseudovirions, indicating that the bat species harboring RaTG13 might be very limited. RaACE2 has seven polymorphic variants, RA-01 to RA-07, and they show different susceptibilities to RaTG13 S pseudovirions transduction. Sequence and mutagenesis analyses reveal that residues 34, 38, and 83 in RaACE2 might play critical roles in interaction with the RaTG13 S protein. Of note, RaACE2 polymorphisms have minimal effect on S proteins of SARS-CoV-2 and several SARS-CoV-2 related CoVs (SC2r-CoVs) including BANAL-20-52 and BANAL-20-236 in terms of binding, membrane fusion, and pseudovirus entry. Further mutagenesis analyses identify residues 501 and 505 in S proteins critical for the recognition of different RaACE2 variants and pangolin ACE2 (pACE2), indicating that RaTG13 might have not been well adapted to R. affinis bats. While single D501N and H505Y changes in RaTG13 S protein significantly enhance the infectivity and minimize the difference in susceptibility among different RaACE2 variants, an N501D substitution in SARS-CoV-2 S protein displays marked disparity in transduction efficiencies among RaACE2 variants with a significant reduction in infectivity on several RaACE2 variants. Finally, a T372A substitution in RaTG13 S protein not only significantly increases infectivity on all RaACE2 variants, but also markedly enhances entry on several bat ACE2s including R. sinicus YN, R. pearsonii, and R. ferrumeiqunum. However, the T372A mutant is about 4-fold more sensitive to neutralizing sera from mice immunized with BANAL-20-52 S, suggesting that the better immune evasion ability of T372 over A372 might contribute to the natural selective advantage of T372 over A372 among bat CoVs. Together, our study aids a better understanding of coronavirus entry, vaccine design, and evolution.
    MeSH term(s) Animals ; Mice ; Humans ; SARS-CoV-2/metabolism ; Chiroptera ; Angiotensin-Converting Enzyme 2 ; COVID-19 ; Spike Glycoprotein, Coronavirus/metabolism
    Chemical Substances spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Spike Glycoprotein, Coronavirus
    Language English
    Publishing date 2023-01-23
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2205412-1
    ISSN 1553-7374 ; 1553-7374
    ISSN (online) 1553-7374
    ISSN 1553-7374
    DOI 10.1371/journal.ppat.1011116
    Database MEDical Literature Analysis and Retrieval System OnLINE

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