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SARS-CoV-2 Variants, Current Vaccines and Therapeutic Implications for COVID-19. Vaccines (Basel) 2022; 10:vaccines10091538. [PMID: 36146616 PMCID: PMC9504858 DOI: 10.3390/vaccines10091538] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Over the past two years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused hundreds of millions of infections, resulting in an unprecedented pandemic of coronavirus disease 2019 (COVID-19). As the virus spreads through the population, ongoing mutations and adaptations are being discovered. There is now substantial clinical evidence that demonstrates the SARS-CoV-2 variants have stronger transmissibility and higher virulence compared to the wild-type strain of SARS-CoV-2. Hence, development of vaccines against SARS-CoV-2 variants to boost individual immunity has become essential. However, current treatment options are limited for COVID-19 caused by the SARS-CoV-2 variants. In this review, we describe current distribution, variation, biology, and clinical features of COVID-19 caused by SARS-CoV-2 variants (including Alpha (B.1.1.7 Lineage) variant, Beta (B.1.351 Lineage) variant, Gamma (P.1 Lineage) variant, Delta (B.1.617.2 Lineage) variant, and Omicron (B.1.1.529 Lineage) variant and others. In addition, we review currently employed vaccines in clinical or preclinical phases as well as potential targeted therapies in an attempt to provide better preventive and treatment strategies for COVID-19 caused by different SARS-CoV-2 variants.
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102
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On the Origins of Omicron's Unique Spike Gene Insertion. Vaccines (Basel) 2022; 10:vaccines10091509. [PMID: 36146586 PMCID: PMC9504260 DOI: 10.3390/vaccines10091509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 01/28/2023] Open
Abstract
The emergence of a heavily mutated SARS-CoV-2 variant (Omicron; Pango lineage B.1.1.529 and BA sublineages) and its rapid spread to over 75 countries raised a global public health alarm. Characterizing the mutational profile of Omicron is necessary to interpret its clinical phenotypes which are shared with or distinctive from those of other SARS-CoV-2 variants. We compared the mutations of the initially circulating Omicron variant (now known as BA.1) with prior variants of concern (Alpha, Beta, Gamma, and Delta), variants of interest (Lambda, Mu, Eta, Iota, and Kappa), and ~1500 SARS-CoV-2 lineages constituting ~5.8 million SARS-CoV-2 genomes. Omicron's Spike protein harbors 26 amino acid mutations (23 substitutions, 2 deletions, and 1 insertion) that are distinct compared to other variants of concern. While the substitution and deletion mutations appeared in previous SARS-CoV-2 lineages, the insertion mutation (ins214EPE) was not previously observed in any other SARS-CoV-2 lineage. Here, we consider and discuss various mechanisms through which the nucleotide sequence encoding for ins214EPE could have been acquired, including local duplication, polymerase slippage, and template switching. Although we are not able to definitively determine the mechanism, we highlight the plausibility of template switching. Analysis of the homology of the inserted nucleotide sequence and flanking regions suggests that this template-switching event could have involved the genomes of SARS-CoV-2 variants (e.g., the B.1.1 strain), other human coronaviruses that infect the same host cells as SARS-CoV-2 (e.g., HCoV-OC43 or HCoV-229E), or a human transcript expressed in a host cell that was infected by the Omicron precursor.
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103
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Wei Z, He J, Wang C, Bao J, Leng T, Chen F. The importance of booster vaccination in the context of Omicron wave. Front Immunol 2022; 13:977972. [PMID: 36159796 PMCID: PMC9498215 DOI: 10.3389/fimmu.2022.977972] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
Omicron (B.1.1.529) was first detected in a sample collected in Botswana on November 11, 2021, and has rapidly replaced Delta as the dominant global variant given the robust transmissibility. Moreover, it displays a lower virulence than other variants. However, the pathogenicity of Omicron appears to be underestimated in view of the increasing levels of herd immunity through natural infection or vaccination. Additionally, the volume of hospitalizations and deaths increase in proportion to the number of cases due to the high transmissibility of Omicron. Therefore, vaccination remains an important public health priority. Notably, a series of important mutations in the Omicron spike protein, especially in the receptor-binding domain and N-terminal domain, appears to be associated with immune escape capacity, reducing the willingness of people to receive vaccines. Herein, we provide an in-depth discussion to assess the effectiveness of the second and third vaccination against Omicron variant. On the one hand, the two-dose vaccination program adopted by many countries is insufficient to prevent Omicron infection given the mutations correlated with immune escape and the decline in vaccine efficacy over time. On the other hand, booster dose significantly increases the protective efficacy against Omicron infection. Most importantly, heterologous third dose vaccination induces a more robust immune response than homologous booster dose. Therefore, under the special background of this pandemic, there is an urgent need to accelerate the third dose of vaccination, especially providing better booster vaccination strategies, to combat emerging Omicron variant.
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104
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Li X, Pan Y, Yin Q, Wang Z, Shan S, Zhang L, Yu J, Qu Y, Sun L, Gui F, Lu J, Jing Z, Wu W, Huang T, Shi X, Li J, Li X, Li D, Wang S, Yang M, Zhang L, Duan K, Liang M, Yang X, Wang X. Structural basis of a two-antibody cocktail exhibiting highly potent and broadly neutralizing activities against SARS-CoV-2 variants including diverse Omicron sublineages. Cell Discov 2022; 8:87. [PMID: 36075908 PMCID: PMC9453709 DOI: 10.1038/s41421-022-00449-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/23/2022] [Indexed: 11/19/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs), especially the latest Omicron, have exhibited severe antibody evasion. Broadly neutralizing antibodies with high potency against Omicron are urgently needed for understanding the working mechanisms and developing therapeutic agents. In this study, we characterized the previously reported F61, which was isolated from convalescent patients infected with prototype SARS-CoV-2, as a broadly neutralizing antibody against all VOCs including Omicron BA.1, BA.1.1, BA.2, BA.3 and BA.4 sublineages by utilizing antigen binding and cell infection assays. We also identified and characterized another broadly neutralizing antibody D2 with epitope distinct from that of F61. More importantly, we showed that a combination of F61 with D2 exhibited synergy in neutralization and protecting mice from SARS-CoV-2 Delta and Omicron BA.1 variants. Cryo-Electron Microscopy (Cryo-EM) structures of the spike-F61 and spike-D2 binary complexes revealed the distinct epitopes of F61 and D2 at atomic level and the structural basis for neutralization. Cryo-EM structure of the Omicron-spike-F61-D2 ternary complex provides further structural insights into the synergy between F61 and D2. These results collectively indicated F61 and F61-D2 cocktail as promising therapeutic antibodies for combating SARS-CoV-2 variants including diverse Omicron sublineages.
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Affiliation(s)
- Xiaoman Li
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yongbing Pan
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Qiangling Yin
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zejun Wang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Sisi Shan
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Laixing Zhang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinfang Yu
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuanyuan Qu
- Institution of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Lina Sun
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fang Gui
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Jia Lu
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Zhaofei Jing
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Wei Wu
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Tao Huang
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuanling Shi
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Jiandong Li
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xinguo Li
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Dexin Li
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- CDC-WIV Joint Research Center for Emerging Diseases and Biosafety, Wuhan, Hubei, China
| | - Shiwen Wang
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- CDC-WIV Joint Research Center for Emerging Diseases and Biosafety, Wuhan, Hubei, China
| | - Maojun Yang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Linqi Zhang
- NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Kai Duan
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China
| | - Mifang Liang
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
- CDC-WIV Joint Research Center for Emerging Diseases and Biosafety, Wuhan, Hubei, China.
| | - Xiaoming Yang
- National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan, Hubei, China.
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
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105
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Kanoi BN, Maina M, Likhovole C, Kobia FM, Gitaka J. Malaria vaccine approaches leveraging technologies optimized in the COVID-19 era. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.988665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Africa bears the greatest burden of malaria with more than 200 million clinical cases and more than 600,000 deaths in 2020 alone. While malaria-associated deaths dropped steadily until 2015, the decline started to falter after 2016, highlighting the need for novel potent tools in the fight against malaria. Currently available tools, such as antimalarial drugs and insecticides are threatened by development of resistance by the parasite and the mosquito. The WHO has recently approved RTS,S as the first malaria vaccine for public health use. However, because the RTS,S vaccine has an efficacy of only 36% in young children, there is need for more efficacious vaccines. Indeed, based on the global goal of licensing a malaria vaccine with at least 75% efficacy by 2030, RTS,S is unlikely to be sufficient alone. However, recent years have seen tremendous progress in vaccine development. Although the COVID-19 pandemic impacted malaria control, the rapid progress in research towards the development of COVID-19 vaccines indicate that harnessing funds and technological advances can remarkably expedite vaccine development. In this review, we highlight and discuss current and prospective trends in global efforts to discover and develop malaria vaccines through leveraging mRNA vaccine platforms and other systems optimized during COVID-19 vaccine studies.
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106
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de Souza A, de Freitas Amorim VM, Guardia GDA, dos Santos FRC, dos Santos FF, de Souza RF, de Araujo Juvenal G, Huang Y, Ge P, Jiang Y, Li C, Paudel P, Ulrich H, Galante PAF, Guzzo CR. Molecular Dynamics Analysis of Fast-Spreading Severe Acute Respiratory Syndrome Coronavirus 2 Variants and Their Effects on the Interaction with Human Angiotensin-Converting Enzyme 2. ACS OMEGA 2022; 7:30700-30709. [PMID: 36068861 PMCID: PMC9437663 DOI: 10.1021/acsomega.1c07240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is evolving with mutations in the spike protein, especially in the receptor-binding domain (RBD). The failure of public health measures in some countries to contain the spread of the disease has given rise to novel viral variants with increased transmissibility. However, key questions about how quickly the variants can spread remain unclear. Herein, we performed a structural investigation using molecular dynamics simulations and determined dissociation constant (K D) values using surface plasmon resonance assays of three fast-spreading SARS-CoV-2 variants, alpha, beta, and gamma, as well as genetic factors in host cells that may be related to the viral infection. Our results suggest that the SARS-CoV-2 variants facilitate their entry into the host cell by moderately increased binding affinities to the human ACE2 receptor, different torsions in hACE2 mediated by RBD variants, and an increased spike exposure time to proteolytic enzymes. We also found that other host cell aspects, such as gene and isoform expression of key genes for the infection (ACE2, FURIN, and TMPRSS2), may have few contributions to the SARS-CoV-2 variant infectivity. In summary, we concluded that a combination of viral and host cell factors allows SARS-CoV-2 variants to increase their abilities to spread faster than the wild type.
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Affiliation(s)
- Anacleto
Silva de Souza
- Department
of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-900, Brazil
| | | | | | - Felipe R. C. dos Santos
- Molecular
Oncology Center, Hospital Sírio Libanes, São Paulo 01308-050, Brazil
- Programa
Interunidades Em Bioinformática, University of São Paulo, São Paulo 05508-900, Brazil
| | - Filipe F. dos Santos
- Molecular
Oncology Center, Hospital Sírio Libanes, São Paulo 01308-050, Brazil
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-900, Brazil
| | - Robson Francisco de Souza
- Department
of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-900, Brazil
| | | | - Yihua Huang
- ACROBiosystems
Inc., 8 N. Hongda Rd.,
Beijing Economic-Technological Development Area, Beijing 100176, China
| | - Pingju Ge
- ACROBiosystems
Inc., 8 N. Hongda Rd.,
Beijing Economic-Technological Development Area, Beijing 100176, China
| | - Yinan Jiang
- ACROBiosystems
Inc., 8 N. Hongda Rd.,
Beijing Economic-Technological Development Area, Beijing 100176, China
| | - Coco Li
- ACROBiosystems
Inc., 8 N. Hongda Rd.,
Beijing Economic-Technological Development Area, Beijing 100176, China
| | - Prajwal Paudel
- ACROBiosystems
Inc., 8 N. Hongda Rd.,
Beijing Economic-Technological Development Area, Beijing 100176, China
| | - Henning Ulrich
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-900, Brazil
| | - Pedro A. F. Galante
- Molecular
Oncology Center, Hospital Sírio Libanes, São Paulo 01308-050, Brazil
| | - Cristiane Rodrigues Guzzo
- Department
of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-900, Brazil
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107
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Laumaea AE, Lewin A, Chatterjee D, Marchitto L, Ding S, Gendron‐Lepage G, Goyette G, Allard M, Simard C, Tremblay T, Perreault J, Duerr R, Finzi A, Bazin R. COVID-19 vaccine humoral response in frequent platelet donors with plateletpheresis-associated lymphopenia. Transfusion 2022; 62:1779-1790. [PMID: 35919021 PMCID: PMC9539235 DOI: 10.1111/trf.17037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Plateletpheresis involves platelet separation and collection from whole blood while other blood cells are returned to the donor. Because platelets are replaced faster than red blood cells, as many as 24 donations can be done annually. However, some frequent apheresis platelet donors (>20 donations annually) display severe plateletpheresis-associated lymphopenia; in particular, CD4+ T but not B cell numbers are decreased. COVID-19 vaccination thereby provides a model to assess whether lymphopenic platelet donors present compromised humoral immune responses. STUDY DESIGN AND METHODS We assessed vaccine responses following 2 doses of COVID-19 vaccination in a cohort of 43 plateletpheresis donors with a range of pre-vaccination CD4+ T cell counts (76-1537 cells/μl). In addition to baseline T cell measurements, antibody binding assays to full-length Spike and the Receptor Binding Domain (RBD) were performed pre- and post-vaccination. Furthermore, pseudo-particle neutralization and antibody-dependent cellular cytotoxicity assays were conducted to measure antibody functionality. RESULTS Participants were stratified into two groups: <400 CD4/μl (n = 27) and ≥ 400 CD4/μl (n = 16). Following the first dose, 79% seroconverted within the <400 CD4/μl group compared to 87% in the ≥400 CD4/μl group; all donors were seropositive post-second dose with significant increases in antibody levels. Importantly differences in CD4+ T cell levels minimally impacted neutralization, Spike recognition, and IgG Fc-mediated effector functions. DISCUSSION Overall, our results indicate that lymphopenic plateletpheresis donors do not exhibit significant immune dysfunction; they have retained the T and B cell functionality necessary for potent antibody responses after vaccination.
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Affiliation(s)
- Annemarie Eare Laumaea
- Centre de Recherche du CHUMMontréalCanada
- Département de Microbiologie, Infectiologie et ImmunologieUniversité de MontréalMontréalQuébecCanada
- Héma‐QuébecAffaires Médicales et InnovationQuébecCanada
| | - Antoine Lewin
- Héma‐QuébecAffaires Médicales et InnovationMontréalQuébecCanada
| | | | - Lorie Marchitto
- Centre de Recherche du CHUMMontréalCanada
- Département de Microbiologie, Infectiologie et ImmunologieUniversité de MontréalMontréalQuébecCanada
| | | | | | | | | | - Carl Simard
- Héma‐QuébecAffaires Médicales et InnovationQuébecCanada
| | - Tony Tremblay
- Héma‐QuébecAffaires Médicales et InnovationQuébecCanada
| | | | - Ralf Duerr
- Department of MicrobiologyNew York University School of MedicineNew York CityNew YorkUSA
| | - Andrés Finzi
- Centre de Recherche du CHUMMontréalCanada
- Département de Microbiologie, Infectiologie et ImmunologieUniversité de MontréalMontréalQuébecCanada
| | - Renée Bazin
- Héma‐QuébecAffaires Médicales et InnovationQuébecCanada
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108
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Beeraka NM, Sukocheva OA, Lukina E, Liu J, Fan R. Development of antibody resistance in emerging mutant strains of SARS CoV-2: Impediment for COVID-19 vaccines. Rev Med Virol 2022; 32:e2346. [PMID: 35416390 PMCID: PMC9111059 DOI: 10.1002/rmv.2346] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/28/2022] [Accepted: 03/06/2022] [Indexed: 02/05/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a highly infectious agent associated with unprecedented morbidity and mortality. A failure to stop growth of COVID-19-linked morbidity rates is caused by SARS-CoV-2 mutations and the emergence of new highly virulent SARS-CoV-2 strains. Several acquired SARS-CoV-2 mutations reflect viral adaptations to host immune defence. Mutations in the virus Spike-protein were associated with the lowered effectiveness of current preventive therapies, including vaccines. Recent in vitro studies detected diminished neutralisation capacity of vaccine-induced antibodies, which are targeted to bind Spike receptor-binding and N-terminal domains in the emerging strains. Lower than expected inhibitory activity of antibodies was reported against viruses with E484K Spike mutation, including B.1.1.7 (UK), P.1 (Brazil), B.1.351 (South African), and new Omicron variant (B.1.1.529) with E484A mutation. The vaccine effectiveness is yet to be examined against new mutant strains of SARS-CoV-2 originating in Europe, Nigeria, Brazil, South Africa, and India. To prevent the loss of anti-viral protection in vivo, often defined as antibody resistance, it is required to target highly conserved viral sequences (including Spike protein) and enhance the potency of antibody cocktails. In this review, we assess the reported mutation-acquiring potential of coronaviruses and compare efficacies of current COVID-19 vaccines against 'parent' and 'mutant' strains of SARS-CoV-2 (Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529)).
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Affiliation(s)
- Narasimha M. Beeraka
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
- Department of Human AnatomyI.M. Sechenov First Moscow State Medical University (Sechenov University)MoscowRussian Federation
| | - Olga A. Sukocheva
- Discipline of Health SciencesCollege of Nursing and Health SciencesFlinders University of South AustraliaBedford ParkAustralia
| | - Elena Lukina
- Discipline of BiologyCollege of SciencesFlinders University of South AustraliaBedford ParkAustralia
| | - Junqi Liu
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
| | - Ruitai Fan
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
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109
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Attwood SW, Hill SC, Aanensen DM, Connor TR, Pybus OG. Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic. Nat Rev Genet 2022; 23:547-562. [PMID: 35459859 PMCID: PMC9028907 DOI: 10.1038/s41576-022-00483-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2022] [Indexed: 01/05/2023]
Abstract
Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic and to the design of effective control strategies. Phylogenies (evolutionary trees) have provided key insights into the international spread of SARS-CoV-2 and enabled investigation of individual outbreaks and transmission chains in specific settings. Phylodynamic approaches combine evolutionary, demographic and epidemiological concepts and have helped track virus genetic changes, identify emerging variants and inform public health strategy. Here, we review and synthesize studies that illustrate how phylogenetic and phylodynamic techniques were applied during the first year of the pandemic, and summarize their contributions to our understanding of SARS-CoV-2 transmission and control.
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Affiliation(s)
- Stephen W Attwood
- Department of Zoology, University of Oxford, Oxford, UK.
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.
| | - Sarah C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas R Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK.
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110
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Xu A, Hong B, Lou F, Wang S, Li W, Shafqat A, An X, Zhao Y, Song L, Tong Y, Fan H. Sub-lineages of the SARS-CoV-2 Omicron variants: Characteristics and prevention. MedComm (Beijing) 2022; 3:e172. [PMID: 35992968 PMCID: PMC9380698 DOI: 10.1002/mco2.172] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/07/2022] Open
Abstract
Since the start of the coronavirus disease 2019 (COVID-19) pandemic, new variants of severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) have emerged, accelerating the spread of the virus. Omicron was defined by the World Health Organization in November 2021 as the fifth "variant of concern" after Alpha, Beta, Gamma, and Delta. In recent months, Omicron has become the main epidemic strain. Studies have shown that Omicron carries more mutations than Alpha, Beta, Gamma, Delta, and wild-type, facilitating immune escape and accelerating its transmission. This review focuses on the Omicron variant's origin, transmission, main biological features, subvariants, mutations, immune escape, vaccination, and detection methods. We also discuss the appropriate preventive and therapeutic measures that should be taken to address the new challenges posed by the Omicron variant. This review is valuable to guide the surveillance, prevention, and development of vaccines and other therapies for Omicron variants. It is desirable to develop a more efficient vaccine against the Omicron variant and take more effective measures to constrain the spread of the epidemic and promote public health.
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Affiliation(s)
- Ailan Xu
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
- The First Affiliated Hospital of Jiamusi UniversityJiamusiChina
| | - Bixia Hong
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Fuxing Lou
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Shuqi Wang
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Wenye Li
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Amna Shafqat
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Xiaoping An
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Yunwei Zhao
- The First Affiliated Hospital of Jiamusi UniversityJiamusiChina
| | - Lihua Song
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Yigang Tong
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Huahao Fan
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
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111
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Daher-Nashif S, Al-Anany R, Ali M, Erradi K, Farag E, Abdallah AM, Emara MM. COVID-19 exit strategy during vaccine implementation: a balance between social distancing and herd immunity. Arch Virol 2022; 167:1773-1783. [PMID: 35723757 PMCID: PMC9208258 DOI: 10.1007/s00705-022-05495-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/05/2022] [Indexed: 11/09/2022]
Abstract
Currently, health authorities around the world are struggling to limit the spread of COVID-19. Since the beginning of the pandemic, social distancing has been the most important strategy used by most countries to control disease spread by flattening and elongating the epidemic curve. Another strategy, herd immunity, was also applied by some countries through relaxed control measures that allow the free spread of natural infection to build up solid immunity within the population. In 2021, COVID-19 vaccination was introduced with tremendous effort as a promising strategy for limiting the spread of disease. Therefore, in this review, we present the current knowledge about social distancing, herd immunity strategies, and aspects of their implementation to control the COVID-19 pandemic in the presence of the newly developed vaccines. Finally, we suggest a short-term option for controlling the pandemic during vaccine application.
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Affiliation(s)
- Suhad Daher-Nashif
- Population Medicine Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Rania Al-Anany
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
- Public Health Department, Health Protection and Communicable Diseases, Ministry of Public Health, Doha, Qatar
| | - Menatalla Ali
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Khadija Erradi
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Elmoubasher Farag
- Public Health Department, Health Protection and Communicable Diseases, Ministry of Public Health, Doha, Qatar
| | - Abdallah M Abdallah
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Mohamed M Emara
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar.
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112
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Walls AC, VanBlargan LA, Wu K, Choi A, Navarro MJ, Lee D, Avena L, Berrueta DM, Pham MN, Elbashir S, Kraft JC, Miranda MC, Kepl E, Johnson M, Blackstone A, Sprouse K, Fiala B, O'Connor MA, Brunette N, Arunachalam PS, Shirreff L, Rogers K, Carter L, Fuller DH, Villinger F, Pulendran B, Diamond MS, Edwards DK, King NP, Veesler D. Distinct sensitivities to SARS-CoV-2 variants in vaccinated humans and mice. Cell Rep 2022; 40:111299. [PMID: 35988541 PMCID: PMC9376299 DOI: 10.1016/j.celrep.2022.111299] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/19/2022] [Accepted: 08/09/2022] [Indexed: 11/03/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 has led to the development of a large number of vaccines, several of which are now approved for use in humans. Understanding vaccine-elicited antibody responses against emerging SARS-CoV-2 variants of concern (VOCs) in real time is key to inform public health policies. Serum neutralizing antibody titers are the current best correlate of protection from SARS-CoV-2 challenge in non-human primates and a key metric to understand immune evasion of VOCs. We report that vaccinated BALB/c mice do not recapitulate faithfully the breadth and potency of neutralizing antibody responses elicited by various vaccine platforms against VOCs, compared with non-human primates or humans, suggesting caution should be exercised when interpreting data obtained with this animal model.
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Affiliation(s)
- Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kai Wu
- Moderna Inc., Cambridge, MA, USA
| | | | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | | | | | - Minh N Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | | | - John C Kraft
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth Kepl
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Max Johnson
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Blackstone
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Megan A O'Connor
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA; Washington National Primate Research Center, Seattle, WA 98121, USA
| | - Natalie Brunette
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Lisa Shirreff
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA 70560, USA
| | - Kenneth Rogers
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA 70560, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Deborah H Fuller
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA; Washington National Primate Research Center, Seattle, WA 98121, USA
| | - Francois Villinger
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA 70560, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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113
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SARS-CoV-2 Infections in Vaccinated and Unvaccinated Populations in Camp Lemonnier, Djibouti, from April 2020 to January 2022. Viruses 2022; 14:v14091918. [PMID: 36146724 PMCID: PMC9505681 DOI: 10.3390/v14091918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 12/12/2022] Open
Abstract
The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the disparity between developed and developing countries for infectious disease surveillance and the sequencing of pathogen genomes. The majority of SARS-CoV-2 sequences published are from Europe, North America, and Asia. Between April 2020 and January 2022, 795 SARS-CoV-2-positive nares swabs from individuals in the U.S. Navy installation Camp Lemonnier, Djibouti, were collected, sequenced, and analyzed. In this study, we described the results of genomic sequencing and analysis for 589 samples, the first published viral sequences for Djibouti, including 196 cases of vaccine breakthrough infections. This study contributes to the knowledge base of circulating SARS-CoV-2 lineages in the under-sampled country of Djibouti, where only 716 total genome sequences are available at time of publication. Our analysis resulted in the detection of circulating variants of concern, mutations of interest in lineages in which those mutations are not common, and emerging spike mutations.
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114
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Sinha S, Tam B, Wang SM. Applications of Molecular Dynamics Simulation in Protein Study. MEMBRANES 2022; 12:844. [PMID: 36135863 PMCID: PMC9505860 DOI: 10.3390/membranes12090844] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 05/29/2023]
Abstract
Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study protein function, protein stability, protein-protein interaction, enzymatic reactions and drug-protein interactions, and membrane proteins. In this review, we provide a brief review for the history of MD Simulations application and the current status of MD Simulations applications in protein studies.
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Affiliation(s)
| | | | - San Ming Wang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau SAR, China
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Hill V, Du Plessis L, Peacock TP, Aggarwal D, Colquhoun R, Carabelli AM, Ellaby N, Gallagher E, Groves N, Jackson B, McCrone JT, O’Toole Á, Price A, Sanderson T, Scher E, Southgate J, Volz E, Barclay WS, Barrett JC, Chand M, Connor T, Goodfellow I, Gupta RK, Harrison EM, Loman N, Myers R, Robertson DL, Pybus OG, Rambaut A. The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evol 2022; 8:veac080. [PMID: 36533153 PMCID: PMC9752794 DOI: 10.1093/ve/veac080] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/28/2022] [Accepted: 08/25/2022] [Indexed: 01/06/2023] Open
Abstract
The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organization as Alpha. Originating in early autumn but discovered in December 2020, it spread rapidly and caused large waves of infections worldwide. The Alpha variant is notable for being defined by a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. Alpha genomes comprise a well-supported monophyletic clade within which the evolutionary rate is typical of SARS-CoV-2. The Alpha epidemic continued to grow despite the continued restrictions on social mixing across the UK and the imposition of new restrictions, in particular, the English national lockdown in November 2020. While these interventions succeeded in reducing the absolute number of cases, the impact of these non-pharmaceutical interventions was predominantly to drive the decline of the SARS-CoV-2 lineages that preceded Alpha. We investigate the only two sampled sequences that fall on the branch ancestral to Alpha. We find that one is likely to be a true intermediate sequence, providing information about the order of mutational events that led to Alpha. We explore alternate hypotheses that can explain how Alpha acquired a large number of mutations yet remained largely unobserved in a region of high genomic surveillance: an under-sampled geographical location, a non-human animal population, or a chronically infected individual. We conclude that the latter provides the best explanation of the observed behaviour and dynamics of the variant, although the individual need not be immunocompromised, as persistently infected immunocompetent hosts also display a higher within-host rate of evolution. Finally, we compare the ancestral branches and mutation profiles of other VOCs and find that Delta appears to be an outlier both in terms of the genomic locations of its defining mutations and a lack of the rapid evolutionary rate on its ancestral branch. As new variants, such as Omicron, continue to evolve (potentially through similar mechanisms), it remains important to investigate the origins of other variants to identify ways to potentially disrupt their evolution and emergence.
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Affiliation(s)
- Verity Hill
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Louis Du Plessis
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, UK
- Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | - Dinesh Aggarwal
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Rachel Colquhoun
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | | | - Nicholas Ellaby
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Eileen Gallagher
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Natalie Groves
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Ben Jackson
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - J T McCrone
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Áine O’Toole
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Anna Price
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff CF10 AX, UK
| | - Theo Sanderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
| | - Emily Scher
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Joel Southgate
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff CF10 AX, UK
| | - Erik Volz
- MRC Unit for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | - Jeffrey C Barrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Meera Chand
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
- Guy’s and St Thomas’ Hospital NHS Trust, St Thomas’ Hospital, Westminster Bridge Rd, London SE1 7EH, UK
| | - Thomas Connor
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff CF10 AX, UK
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff CF14 4XW, UK
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK
- Africa Health Research Institute, Durban, South Africa
| | - Ewan M Harrison
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Nicholas Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Richard Myers
- UK Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
| | - Oliver G Pybus
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, UK
- Department of Pathobiology and Population Science, The Royal Veterinary College, London, UK
| | - Andrew Rambaut
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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116
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Abstract
Despite effective spike-based vaccines and monoclonal antibodies, the SARS-CoV-2 pandemic continues more than two and a half years post-onset. Relentless investigation has outlined a causative dynamic between host-derived antibodies and reciprocal viral subversion. Integration of this paradigm into the architecture of next generation antiviral strategies, predicated on a foundational understanding of the virology and immunology of SARS-CoV-2, will be critical for success. This review aims to serve as a primer on the immunity endowed by antibodies targeting SARS-CoV-2 spike protein through a structural perspective. We begin by introducing the structure and function of spike, polyclonal immunity to SARS-CoV-2 spike, and the emergence of major SARS-CoV-2 variants that evade immunity. The remainder of the article comprises an in-depth dissection of all major epitopes on SARS-CoV-2 spike in molecular detail, with emphasis on the origins, neutralizing potency, mechanisms of action, cross-reactivity, and variant resistance of representative monoclonal antibodies to each epitope.
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Affiliation(s)
- John M Errico
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States
| | - Lucas J Adams
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States
| | - Daved H Fremont
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States; Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, United States; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, United States.
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117
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Imbrechts M, Maes W, Ampofo L, Van den Berghe N, Calcoen B, Van Looveren D, Kerstens W, Rasulova M, Vercruysse T, Noppen S, Abdelnabi R, Foo C, Hollevoet K, Maes P, Zhang X, Jochmans D, Ven K, Lammertyn J, Vanhoorelbeke K, Callewaert N, De Munter P, Schols D, Thibaut HJ, Neyts J, Declerck P, Geukens N. Potent neutralizing anti-SARS-CoV-2 human antibodies cure infection with SARS-CoV-2 variants in hamster model. iScience 2022; 25:104705. [PMID: 35813873 PMCID: PMC9250818 DOI: 10.1016/j.isci.2022.104705] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/15/2022] [Accepted: 06/28/2022] [Indexed: 12/01/2022] Open
Abstract
Treatment with neutralizing monoclonal antibodies (mAbs) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contributes to COVID-19 management. Unfortunately, SARS-CoV-2 variants escape several of these recently approved mAbs, highlighting the need for additional discovery and development. In a convalescent patient with COVID-19, we identified six mAbs, classified in four epitope groups, that potently neutralized SARS-CoV-2 D614G, beta, gamma, and delta infection in vitro, with three mAbs neutralizing omicron as well. In hamsters, mAbs 3E6 and 3B8 potently cured infection with SARS-CoV-2 Wuhan, beta, and delta when administered post-viral infection at 5 mg/kg. Even at 0.2 mg/kg, 3B8 still reduced viral titers. Intramuscular delivery of DNA-encoded 3B8 resulted in in vivo mAb production of median serum levels up to 90 μg/mL, and protected hamsters against delta infection. Overall, our data mark 3B8 as a promising candidate against COVID-19, and highlight advances in both the identification and gene-based delivery of potent human mAbs.
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Affiliation(s)
- Maya Imbrechts
- KU Leuven, PharmAbs: the KU Leuven Antibody Center, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, Department Pharmaceutical and Pharmacological Sciences, Laboratory for Therapeutic and Diagnostic Antibodies, 3000 Leuven, Belgium
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
| | - Wim Maes
- KU Leuven, PharmAbs: the KU Leuven Antibody Center, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven Campus Kortrijk, IRF Life Sciences, Laboratory for Thrombosis Research, 3000 Leuven, Belgium
| | - Louanne Ampofo
- KU Leuven, PharmAbs: the KU Leuven Antibody Center, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
| | - Nathalie Van den Berghe
- KU Leuven, Department Pharmaceutical and Pharmacological Sciences, Laboratory for Therapeutic and Diagnostic Antibodies, 3000 Leuven, Belgium
| | - Bas Calcoen
- KU Leuven Campus Kortrijk, IRF Life Sciences, Laboratory for Thrombosis Research, 3000 Leuven, Belgium
| | - Dominique Van Looveren
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Translational Platform Virology and Chemotherapy (TPVC), KU Leuven, Leuven, Belgium
| | - Winnie Kerstens
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Translational Platform Virology and Chemotherapy (TPVC), KU Leuven, Leuven, Belgium
| | - Madina Rasulova
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Translational Platform Virology and Chemotherapy (TPVC), KU Leuven, Leuven, Belgium
| | - Thomas Vercruysse
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Translational Platform Virology and Chemotherapy (TPVC), KU Leuven, Leuven, Belgium
| | - Sam Noppen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Rana Abdelnabi
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
- GVN, Global Virus Network
| | - Caroline Foo
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
- GVN, Global Virus Network
| | - Kevin Hollevoet
- KU Leuven, PharmAbs: the KU Leuven Antibody Center, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, Department Pharmaceutical and Pharmacological Sciences, Laboratory for Therapeutic and Diagnostic Antibodies, 3000 Leuven, Belgium
| | - Piet Maes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
- GVN, Global Virus Network
| | - Xin Zhang
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
- GVN, Global Virus Network
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
- GVN, Global Virus Network
| | - Karen Ven
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, Department of Biosystems, Biosensors Group, 3000 Leuven, Belgium
| | - Jeroen Lammertyn
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, Department of Biosystems, Biosensors Group, 3000 Leuven, Belgium
| | - Karen Vanhoorelbeke
- KU Leuven, PharmAbs: the KU Leuven Antibody Center, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven Campus Kortrijk, IRF Life Sciences, Laboratory for Thrombosis Research, 3000 Leuven, Belgium
| | - Nico Callewaert
- AZ Groeninge Hospital Clinical Laboratory, 8500 Kortrijk, Belgium
| | - Paul De Munter
- Department of Internal Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical Infectious and Inflammatory Disorders, 3000 Leuven, Belgium
| | - Dominique Schols
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Translational Platform Virology and Chemotherapy (TPVC), KU Leuven, Leuven, Belgium
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
- Molecular Vaccinology and Vaccine Discovery, 3000 Leuven, Belgium
- GVN, Global Virus Network
| | - Paul Declerck
- KU Leuven, PharmAbs: the KU Leuven Antibody Center, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, Department Pharmaceutical and Pharmacological Sciences, Laboratory for Therapeutic and Diagnostic Antibodies, 3000 Leuven, Belgium
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
| | - Nick Geukens
- KU Leuven, PharmAbs: the KU Leuven Antibody Center, Herestraat 49 box 820, 3000 Leuven, Belgium
- KU Leuven, MabMine: KU Leuven Single B Cell Mining Platform, Herestraat 49 box 820, 3000 Leuven, Belgium
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118
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Chen C, Saville JW, Marti MM, Schäfer A, Cheng MH, Mannar D, Zhu X, Berezuk AM, Banerjee A, Sobolewski MD, Kim A, Treat BR, Da Silva Castanha PM, Enick N, McCormick KD, Liu X, Adams C, Hines MG, Sun Z, Chen W, Jacobs JL, Barratt-Boyes SM, Mellors JW, Baric RS, Bahar I, Dimitrov DS, Subramaniam S, Martinez DR, Li W. Potent and broad neutralization of SARS-CoV-2 variants of concern (VOCs) including omicron sub-lineages BA.1 and BA.2 by biparatopic human VH domains. iScience 2022; 25:104798. [PMID: 35875685 PMCID: PMC9296231 DOI: 10.1016/j.isci.2022.104798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/08/2022] [Accepted: 07/14/2022] [Indexed: 12/24/2022] Open
Abstract
The emergence of SARS-CoV-2 variants of concern (VOCs) requires the development of next-generation biologics with high neutralization breadth. Here, we characterized a human VH domain, F6, which we generated by sequentially panning large phage-displayed VH libraries against receptor binding domains (RBDs) containing VOC mutations. Cryo-EM analyses reveal that F6 has a unique binding mode that spans a broad surface of the RBD and involves the antibody framework region. Attachment of an Fc region to a fusion of F6 and ab8, a previously characterized VH domain, resulted in a construct (F6-ab8-Fc) that broadly and potently neutralized VOCs including Omicron. Additionally, prophylactic treatment using F6-ab8-Fc reduced live Beta (B.1.351) variant viral titers in the lungs of a mouse model. Our results provide a new potential therapeutic against SARS-CoV-2 variants including Omicron and highlight a vulnerable epitope within the spike that may be exploited to achieve broad protection against circulating variants.
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Affiliation(s)
- Chuan Chen
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - James W. Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Michelle M. Marti
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Xing Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Alison M. Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Anupam Banerjee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michele D. Sobolewski
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Andrew Kim
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Benjamin R. Treat
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Nathan Enick
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kevin D. McCormick
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Xianglei Liu
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Cynthia Adams
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Margaret Grace Hines
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Zehua Sun
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | | | - Jana L. Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Simon M. Barratt-Boyes
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - John W. Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Abound Bio, Pittsburgh, PA, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dimiter S. Dimitrov
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
- Abound Bio, Pittsburgh, PA, USA
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Gandeeva Therapeutics, Inc., Vancouver, BC, Canada
| | - David R. Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Wei Li
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
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Bowen JE, Addetia A, Dang HV, Stewart C, Brown JT, Sharkey WK, Sprouse KR, Walls AC, Mazzitelli IG, Logue JK, Franko NM, Czudnochowski N, Powell AE, Dellota E, Ahmed K, Ansari AS, Cameroni E, Gori A, Bandera A, Posavad CM, Dan JM, Zhang Z, Weiskopf D, Sette A, Crotty S, Iqbal NT, Corti D, Geffner J, Snell G, Grifantini R, Chu HY, Veesler D. Omicron spike function and neutralizing activity elicited by a comprehensive panel of vaccines. Science 2022; 377:890-894. [PMID: 35857529 PMCID: PMC9348749 DOI: 10.1126/science.abq0203] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/12/2022] [Indexed: 12/23/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern comprises several sublineages, with BA.2 and BA.2.12.1 having replaced the previously dominant BA.1 and with BA.4 and BA.5 increasing in prevalence worldwide. We show that the large number of Omicron sublineage spike mutations leads to enhanced angiotensin-converting enzyme 2 (ACE2) binding, reduced fusogenicity, and severe dampening of plasma neutralizing activity elicited by infection or seven clinical vaccines relative to the ancestral virus. Administration of a homologous or heterologous booster based on the Wuhan-Hu-1 spike sequence markedly increased neutralizing antibody titers and breadth against BA.1, BA.2, BA.2.12.1, BA.4, and BA.5 across all vaccines evaluated. Our data suggest that although Omicron sublineages evade polyclonal neutralizing antibody responses elicited by primary vaccine series, vaccine boosters may provide sufficient protection against Omicron-induced severe disease.
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Affiliation(s)
- John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Ha V. Dang
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jack T. Brown
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - William K. Sharkey
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin R. Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Ignacio G. Mazzitelli
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Facultad de Medicina, Buenos Aires C1121ABG, Argentina
| | - Jennifer K. Logue
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Nicholas M. Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | | | | | | | - Kumail Ahmed
- Departments of Paediatrics and Child Health and Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Asefa Shariq Ansari
- Departments of Paediatrics and Child Health and Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Andrea Gori
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Alessandra Bandera
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Christine M. Posavad
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jennifer M. Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Zeli Zhang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Najeeha Talat Iqbal
- Departments of Paediatrics and Child Health and Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Jorge Geffner
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Facultad de Medicina, Buenos Aires C1121ABG, Argentina
| | | | - Renata Grifantini
- INGM, Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi,” Milan, Italy
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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120
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Meng B, Datir R, Choi J, Bradley JR, Smith KGC, Lee JH, Gupta RK. SARS-CoV-2 spike N-terminal domain modulates TMPRSS2-dependent viral entry and fusogenicity. Cell Rep 2022; 40:111220. [PMID: 35963244 PMCID: PMC9346021 DOI: 10.1016/j.celrep.2022.111220] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/30/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike N-terminal domain (NTD) remains poorly characterized despite enrichment of mutations in this region across variants of concern (VOCs). Here, we examine the contribution of the NTD to infection and cell-cell fusion by constructing chimeric spikes bearing B.1.617 lineage (Delta and Kappa variants) NTDs and generating spike pseudotyped lentivirus. We find that the Delta NTD on a Kappa or wild-type (WT) background increases S1/S2 cleavage efficiency and virus entry, specifically in lung cells and airway organoids, through use of TMPRSS2. Delta exhibits increased cell-cell fusogenicity that could be conferred to WT and Kappa spikes by Delta NTD transfer. However, chimeras of Omicron BA.1 and BA.2 spikes with a Delta NTD do not show more efficient TMPRSS2 use or fusogenicity. We conclude that the NTD allosterically modulates S1/S2 cleavage and spike-mediated functions in a spike context-dependent manner, and allosteric interactions may be lost when combining regions from more distantly related VOCs.
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Affiliation(s)
- Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Rawlings Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jinwook Choi
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK; NIHR Bioresource, Cambridge, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Joo Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Africa Health Research Institute, Durban, South Africa.
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121
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Patel RS, Agrawal B. Heterologous immunity induced by 1 st generation COVID-19 vaccines and its role in developing a pan-coronavirus vaccine. Front Immunol 2022; 13:952229. [PMID: 36045689 PMCID: PMC9420909 DOI: 10.3389/fimmu.2022.952229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome virus-2 (SARS-CoV-2), the causative infectious agent of the COVID-19 pandemic, has led to multiple (4-6) waves of infections worldwide during the past two years. The development of vaccines against SARS-CoV-2 has led to successful mass immunizations worldwide, mitigating the worldwide mortality due the pandemic to a great extent. Yet the evolution of new variants highlights a need to develop a universal vaccine which can prevent infections from all virulent SARS-CoV-2. Most of the current first generation COVID-19 vaccines are based on the Spike protein from the original Wuhan-hu-1 virus strain. It is encouraging that they still protect from serious illnesses, hospitalizations and mortality against a number of mutated viral strains, to varying degrees. Understanding the mechanisms by which these vaccines provide heterologous protection against multiple highly mutated variants can reveal strategies to develop a universal vaccine. In addition, many unexposed individuals have been found to harbor T cells that are cross-reactive against SARS-CoV-2 antigens, with a possible protective role. In this review, we will discuss various aspects of natural or vaccine-induced heterologous (cross-reactive) adaptive immunity against SARS-CoV-2 and other coronaviruses, and their role in achieving the concept of a pan-coronavirus vaccine.
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Affiliation(s)
| | - Babita Agrawal
- Department of Surgery, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB, Canada
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122
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Gao X, Tian H, Zhu K, Li Q, Hao W, Wang L, Qin B, Deng H, Cui S. Structural basis for Sarbecovirus ORF6 mediated blockage of nucleocytoplasmic transport. Nat Commun 2022; 13:4782. [PMID: 35970938 PMCID: PMC9376891 DOI: 10.1038/s41467-022-32489-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/02/2022] [Indexed: 11/09/2022] Open
Abstract
The emergence of heavily mutated SARS-CoV-2 variants of concern (VOCs) place the international community on high alert. In addition to numerous mutations that map in the spike protein of VOCs, expression of the viral accessory proteins ORF6 and ORF9b also elevate; both are potent interferon antagonists. Here, we present the crystal structures of Rae1-Nup98 in complex with the C-terminal tails (CTT) of SARS-CoV-2 and SARS-CoV ORF6 to 2.85 Å and 2.39 Å resolution, respectively. An invariant methionine (M) 58 residue of ORF6 CTT extends its side chain into a hydrophobic cavity in the Rae1 mRNA binding groove, resembling a bolt-fitting-hole; acidic residues flanking M58 form salt-bridges with Rae1. Our mutagenesis studies identify key residues of ORF6 important for its interaction with Rae1-Nup98 in vitro and in cells, of which M58 is irreplaceable. Furthermore, we show that ORF6-mediated blockade of mRNA and STAT1 nucleocytoplasmic transport correlate with the binding affinity between ORF6 and Rae1-Nup98. Finally, binding of ORF6 to Rae1-Nup98 is linked to ORF6-induced interferon antagonism. Taken together, this study reveals the molecular basis for the antagonistic function of Sarbecovirus ORF6, and implies a strategy of using ORF6 CTT-derived peptides for immunosuppressive drug development. Sarbecovirus ORF6 binds to the Rae1-Nup98 complex, a component of the cytoplasmic face of the nuclear pore complex, and has been shown to suppress interferon responses. Here, the authors provide structures of Rae1-Nup98 in complex with the C-terminal tails of SARS-CoV-2 and SARS-CoV ORF6 and provide insights into ORF6-mediated blockade of mRNA and STAT1 nucleocytoplasmic transport.
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Affiliation(s)
- Xiaopan Gao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Huabin Tian
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kaixiang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Qing Li
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Hao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Linyue Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Hongyu Deng
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China. .,Sanming Project of Medicine in Shenzhen, National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China.
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123
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Design and Immunoinformatic Assessment of Candidate Multivariant mRNA Vaccine Construct against Immune Escape Variants of SARS-CoV-2. Polymers (Basel) 2022; 14:polym14163263. [PMID: 36015519 PMCID: PMC9414445 DOI: 10.3390/polym14163263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 12/12/2022] Open
Abstract
To effectively counter the evolving threat of SARS-CoV-2 variants, modifications and/or redesigning of mRNA vaccine construct are essentially required. Herein, the design and immunoinformatic assessment of a candidate novel mRNA vaccine construct, DOW-21, are discussed. Briefly, immunologically important domains, N-terminal domain (NTD) and receptor binding domain (RBD), of the spike protein of SARS-CoV-2 variants of concern (VOCs) and variants of interest (VOIs) were assessed for sequence, structure, and epitope variations. Based on the assessment, a novel hypothetical NTD (h-NTD) and RBD (h-RBD) were designed to hold all overlapping immune escape variations. The construct sequence was then developed, where h-NTD and h-RBD were intervened by 10-mer gly-ala repeat and the terminals were flanked by regulatory sequences for better intracellular transportation and expression of the coding regions. The protein encoded by the construct holds structural attributes (RMSD NTD: 0.42 Å; RMSD RBD: 0.15 Å) found in the respective domains of SARS-CoV-2 immune escape variants. In addition, it provides coverage to the immunogenic sites of the respective domains found in SARS-CoV-2 variants. Later, the nucleotide sequence of the construct was optimized for GC ratio (56%) and microRNA binding sites to ensure smooth translation. Post-injection antibody titer was also predicted (~12000 AU) to be robust. In summary, the construct proposed in this study could potentially provide broad spectrum coverage in relation to SARS-CoV-2 immune escape variants.
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124
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Rochman ND, Wolf YI, Koonin EV. Molecular adaptations during viral epidemics. EMBO Rep 2022; 23:e55393. [PMID: 35848484 PMCID: PMC9346483 DOI: 10.15252/embr.202255393] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 07/20/2023] Open
Abstract
In 1977, the world witnessed both the eradication of smallpox and the beginning of the modern age of genomics. Over the following half-century, 7 epidemic viruses of international concern galvanized virologists across the globe and led to increasingly extensive virus genome sequencing. These sequencing efforts exerted over periods of rapid adaptation of viruses to new hosts, in particular, humans provide insight into the molecular mechanisms underpinning virus evolution. Investment in virus genome sequencing was dramatically increased by the unprecedented support for phylogenomic analyses during the COVID-19 pandemic. In this review, we attempt to piece together comprehensive molecular histories of the adaptation of variola virus, HIV-1 M, SARS, H1N1-SIV, MERS, Ebola, Zika, and SARS-CoV-2 to the human host. Disruption of genes involved in virus-host interaction in animal hosts, recombination including genome segment reassortment, and adaptive mutations leading to amino acid replacements in virus proteins involved in host receptor binding and membrane fusion are identified as the key factors in the evolution of epidemic viruses.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Yuri I Wolf
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Eugene V Koonin
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
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125
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Clinical and genomic signatures of SARS-CoV-2 Delta breakthrough infections in New York. EBioMedicine 2022; 82:104141. [PMID: 35906172 PMCID: PMC9323230 DOI: 10.1016/j.ebiom.2022.104141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 12/20/2022] Open
Abstract
Background In 2021, Delta became the predominant SARS-CoV-2 variant worldwide. While vaccines have effectively prevented COVID-19 hospitalization and death, vaccine breakthrough infections increasingly occurred. The precise role of clinical and genomic determinants in Delta infections is not known, and whether they contributed to increased rates of breakthrough infections compared to unvaccinated controls. Methods We studied SARS-CoV-2 variant distribution, dynamics, and adaptive selection over time in relation to vaccine status, phylogenetic relatedness of viruses, full genome mutation profiles, and associated clinical and demographic parameters. Findings We show a steep and near-complete replacement of circulating variants with Delta between May and August 2021 in metropolitan New York. We observed an increase of the Delta sublineage AY.25 (14% in vaccinated, 7% in unvaccinated), its spike mutation S112L, and AY.44 (8% in vaccinated, 2% in unvaccinated) with its nsp12 mutation F192V in breakthroughs. Delta infections were associated with younger age and lower hospitalization rates than Alpha. Delta breakthrough infections increased significantly with time since vaccination, and, after adjusting for confounders, they rose at similar rates as in unvaccinated individuals. Interpretation We observed a modest adaptation of Delta genomes in breakthrough infections in New York, suggesting an improved genomic framework to support Delta's epidemic growth in times of waning vaccine protection despite limited impact on vaccine escape. Funding The study was supported by NYU institutional funds. The NYULH Genome Technology Center is partially supported by the Cancer Center Support Grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center.
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126
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Chen KWK, Tsung-Ning Huang D, Huang LM. SARS-CoV-2 variants - Evolution, spike protein, and vaccines. Biomed J 2022; 45:573-579. [PMID: 35526825 PMCID: PMC9072773 DOI: 10.1016/j.bj.2022.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/09/2022] [Accepted: 04/29/2022] [Indexed: 12/11/2022] Open
Abstract
Despite the rising natural and vaccines mediated immunity, several countries have experienced a resurgence of the Coronavirus disease of 2019 (COVID-19) due to the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. From Alpha to Omicron, the variants of concern (VOC) have evolved several spike protein mutations that may have an impact on virus characteristics, such as transmissibility and antigenicity. In this review, we describe the evolution of SARS-CoV-2, summarize current knowledge of epidemiological and clinical features of the variants, and discuss the response strategies in terms of vaccines to reduce the burden of COVID-19.
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Affiliation(s)
- Kai-Wei K Chen
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Daniel Tsung-Ning Huang
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan; Department of Medicine, MacKay Medical College, Taipei, Taiwan
| | - Li-Min Huang
- Department of Pediatrics, National Taiwan University Children's Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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127
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Wilhelm A, Widera M, Grikscheit K, Toptan T, Schenk B, Pallas C, Metzler M, Kohmer N, Hoehl S, Marschalek R, Herrmann E, Helfritz FA, Wolf T, Goetsch U, Ciesek S. Limited neutralisation of the SARS-CoV-2 Omicron subvariants BA.1 and BA.2 by convalescent and vaccine serum and monoclonal antibodies. EBioMedicine 2022; 82:104158. [PMID: 35834885 PMCID: PMC9271884 DOI: 10.1016/j.ebiom.2022.104158] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In recent months, Omicron variants of SARS-CoV-2 have become dominant in many regions of the world, and case numbers with Omicron subvariants BA.1 and BA.2 continue to increase. Due to numerous mutations in the spike protein, the efficacy of currently available vaccines, which are based on Wuhan-Hu 1 isolate of SARS-CoV-2, is reduced, leading to breakthrough infections. Efficacy of monoclonal antibody therapy is also likely impaired. METHODS In our in vitro study using A549-AT cells constitutively expressing ACE2 and TMPRSS2, we determined and compared the neutralizing capacity of vaccine-elicited sera, convalescent sera and monoclonal antibodies against authentic SARS-CoV-2 Omicron BA.1 and BA.2 compared with Delta. FINDINGS Almost no neutralisation of Omicron BA.1 and BA.2 was observed using sera from individuals vaccinated with two doses 6 months earlier, regardless of the type of vaccine taken. Shortly after the booster dose, most sera from triple BNT162b2-vaccinated individuals were able to neutralise both Omicron variants. In line with waning antibody levels three months after the booster, only weak residual neutralisation was observed for BA.1 (26%, n = 34, 0 median NT50) and BA.2 (44%, n = 34, 0 median NT50). In addition, BA.1 but not BA.2 was resistant to the neutralising monoclonal antibodies casirivimab/imdevimab, while BA.2 exhibited almost a complete evasion from the neutralisation induced by sotrovimab. INTERPRETATION Both SARS-CoV-2 Omicron subvariants BA.1 and BA.2 escape antibody-mediated neutralisation elicited by vaccination, previous infection with SARS-CoV-2, and monoclonal antibodies. Waning immunity renders the majority of tested sera obtained three months after booster vaccination negative in BA.1 and BA.2 neutralisation. Omicron subvariant specific resistance to the monoclonal antibodies casirivimab/imdevimab and sotrovimab emphasizes the importance of genotype-surveillance and guided application. FUNDING This study was supported in part by the Goethe-Corona-Fund of the Goethe University Frankfurt (M.W.) and the Federal Ministry of Education and Research (COVIDready; grant 02WRS1621C (M.W.).
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Affiliation(s)
- Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany.
| | - Katharina Grikscheit
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Tuna Toptan
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Barbara Schenk
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Christiane Pallas
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Melinda Metzler
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Niko Kohmer
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Sebastian Hoehl
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe University, Frankfurt am Main, Germany
| | - Eva Herrmann
- Institute of Biostatistics and Mathematical Modelling, Goethe University Frankfurt, 60596 Frankfurt, Germany
| | - Fabian A Helfritz
- Bürgerhospital Frankfurt, Nibelungenallee 37-41, 60318 Frankfurt am Main, Germany
| | - Timo Wolf
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Udo Goetsch
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; German Centre for Infection Research (DZIF), partner site Frankfurt, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch Translational Medicine and Pharmacology, 60596 Frankfurt am Main, Germany.
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128
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Zhang T, Deng R, Wang Y, Wu C, Zhang K, Wang C, Gong N, Ledesma-Amaro R, Teng X, Yang C, Xue T, Zhang Y, Hu Y, He Q, Li W, Li J. A paper-based assay for the colorimetric detection of SARS-CoV-2 variants at single-nucleotide resolution. Nat Biomed Eng 2022; 6:957-967. [PMID: 35835993 DOI: 10.1038/s41551-022-00907-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 05/29/2022] [Indexed: 02/05/2023]
Abstract
The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need for versatile diagnostic assays that can discriminate among emerging variants of the virus. Here we report the development and performance benchmarking of an inexpensive (approximately US$0.30 per test) assay for the rapid (sample-to-answer time within 30 min) colorimetric detection of SARS-CoV-2 variants. The assay, which we integrated into foldable paper strips, leverages nucleic acid strand-displacement reactions, the thermodynamic energy penalty associated with single-base-pair mismatches and the metal-ion-controlled enzymatic cleavage of urea to amplify the recognition of viral RNAs for the colorimetric readout of changes in pH via a smartphone. For 50 throat swab samples, the assay simultaneously detected the presence of SARS-CoV-2 and mutations specific to the SARS-CoV-2 variants Alpha, Beta and Gamma, with 100% concordance with real-time quantitative polymerase chain reaction and RNA sequencing. Customizable and inexpensive paper-based assays for the detection of viruses and their variants may facilitate viral surveillance.
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Affiliation(s)
- Ting Zhang
- College of Biomass Science and Engineering, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
| | - Yuxi Wang
- College of Biomass Science and Engineering, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Chengyong Wu
- College of Biomass Science and Engineering, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou, China
| | - Chunyan Wang
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Huhhot, China
| | - Ningqiang Gong
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Chunrong Yang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
| | - Ting Xue
- College of Biomass Science and Engineering, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yong Zhang
- College of Biomass Science and Engineering, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yun Hu
- College of Biomass Science and Engineering, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qiang He
- College of Biomass Science and Engineering, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Weimin Li
- College of Biomass Science and Engineering, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China.
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129
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Wines BD, Kurtovic L, Trist HM, Esparon S, Lopez E, Chappin K, Chan LJ, Mordant FL, Lee WS, Gherardin NA, Patel SK, Hartley GE, Pymm P, Cooney JP, Beeson JG, Godfrey DI, Burrell LM, van Zelm MC, Wheatley AK, Chung AW, Tham WH, Subbarao K, Kent SJ, Hogarth PM. Fc engineered ACE2-Fc is a potent multifunctional agent targeting SARS-CoV2. Front Immunol 2022; 13:889372. [PMID: 35967361 PMCID: PMC9369017 DOI: 10.3389/fimmu.2022.889372] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/27/2022] [Indexed: 01/26/2023] Open
Abstract
Joining a function-enhanced Fc-portion of human IgG to the SARS-CoV-2 entry receptor ACE2 produces an antiviral decoy with strain transcending virus neutralizing activity. SARS-CoV-2 neutralization and Fc-effector functions of ACE2-Fc decoy proteins, formatted with or without the ACE2 collectrin domain, were optimized by Fc-modification. The different Fc-modifications resulted in distinct effects on neutralization and effector functions. H429Y, a point mutation outside the binding sites for FcγRs or complement caused non-covalent oligomerization of the ACE2-Fc decoy proteins, abrogated FcγR interaction and enhanced SARS-CoV-2 neutralization. Another Fc mutation, H429F did not improve virus neutralization but resulted in increased C5b-C9 fixation and transformed ACE2-Fc to a potent mediator of complement-dependent cytotoxicity (CDC) against SARS-CoV-2 spike (S) expressing cells. Furthermore, modification of the Fc-glycan enhanced cell activation via FcγRIIIa. These different immune profiles demonstrate the capacity of Fc-based agents to be engineered to optimize different mechanisms of protection for SARS-CoV-2 and potentially other viral pathogens.
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Affiliation(s)
- Bruce D. Wines
- Immune therapies Laboratory, Burnet Institute, Melbourne, VIC, Australia
- Life Sciences, Burnet Institute, Melbourne, VIC, Australia
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Liriye Kurtovic
- Life Sciences, Burnet Institute, Melbourne, VIC, Australia
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Halina M. Trist
- Immune therapies Laboratory, Burnet Institute, Melbourne, VIC, Australia
| | - Sandra Esparon
- Immune therapies Laboratory, Burnet Institute, Melbourne, VIC, Australia
| | - Ester Lopez
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Klasina Chappin
- Immune therapies Laboratory, Burnet Institute, Melbourne, VIC, Australia
| | - Li-Jin Chan
- Infectious Diseases and Immune Defence Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Francesca L. Mordant
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Wen Shi Lee
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Nicholas A. Gherardin
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Sheila K. Patel
- Department of Medicine, Austin Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Gemma E. Hartley
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Phillip Pymm
- Infectious Diseases and Immune Defence Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - James P. Cooney
- Infectious Diseases and Immune Defence Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - James G. Beeson
- Life Sciences, Burnet Institute, Melbourne, VIC, Australia
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
- Department of Microbiology, Monash University, Clayton VIC, Australia
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Louise M. Burrell
- Department of Medicine, Austin Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Menno C. van Zelm
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Allergy, Immunology and Respiratory Medicine, Central Clinical School, Alfred Hospital, Melbourne, VIC, Australia
| | - Adam K. Wheatley
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
- Australian Research Council Centre for Excellence in Convergent Bio-Nano Science and Technology, The University of Melbourne, Melbourne, VIC, Australia
| | - Amy W. Chung
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Wai-Hong Tham
- Infectious Diseases and Immune Defence Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Stephen J. Kent
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
- Australian Research Council Centre for Excellence in Convergent Bio-Nano Science and Technology, The University of Melbourne, Melbourne, VIC, Australia
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - P. Mark Hogarth
- Immune therapies Laboratory, Burnet Institute, Melbourne, VIC, Australia
- Life Sciences, Burnet Institute, Melbourne, VIC, Australia
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
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130
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Scovino AM, Dahab EC, Vieira GF, Freire-de-Lima L, Freire-de-Lima CG, Morrot A. SARS-CoV-2’s Variants of Concern: A Brief Characterization. Front Immunol 2022; 13:834098. [PMID: 35958548 PMCID: PMC9361785 DOI: 10.3389/fimmu.2022.834098] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/13/2022] [Indexed: 12/23/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disclose the variants of concern (VOC) including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P1), Delta (B.1.617.2), and Omicron (B.1.1.529). Its spike protein (S) present on the surface of the virus is recognized by the host cell receptor, the angiotensin-2 converting enzyme (ACE2) which promotes their entry into the cell. The mutations presented by VOCs are found in RBD and the N-terminal region of S protein. Therefore, mutations occurring in RBD can modify the biological and immunogenic characteristics of the virus, such as modifying the spike affinity for ACE2, increasing the virus transmissibility, or conferring the ability to escape the immune responses. The raise of a potential new SARS-CoV-2 variant capable of evading the host defenses at the same time maintaining its fitness justifies the importance of continued genetic monitoring of the pandemic coronavirus.
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Affiliation(s)
- Aline Miranda Scovino
- Instituto de Microbiologia Paulo de Goes, Universidade federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Elizabeth Chen Dahab
- Instituto de Microbiologia Paulo de Goes, Universidade federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Leonardo Freire-de-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Alexandre Morrot
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- *Correspondence: Alexandre Morrot,
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131
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Li H, Hong X, Ding L, Meng S, Liao R, Jiang Z, Liu D. Sequence similarity of SARS-CoV-2 and humans: Implications for SARS-CoV-2 detection. Front Genet 2022; 13:946359. [PMID: 35937998 PMCID: PMC9355506 DOI: 10.3389/fgene.2022.946359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
Detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) needs human samples, which inevitably contain trace human DNA and RNA. Sequence similarity may cause invalid detection results; however, there is still a lack of gene similarity analysis of SARS-CoV-2 and humans. All publicly reported complete genome assemblies in the Entrez genome database were collected for multiple sequence alignment, similarity and phylogenetic analysis. The complete genomes showed high similarity (>99.88% sequence identity). Phylogenetic analysis divided these viruses into three major clades with significant geographic group effects. Viruses from the United States showed considerable variability. Sequence similarity analysis revealed that SARS-CoV-2 has 612 similar sequences with the human genome and 100 similar sequences with the human transcriptome. The sequence characteristics and genome distribution of these similar sequences were confirmed. The sequence similarity and evolutionary mutations provide indispensable references for dynamic updates of SARS-CoV-2 detection primers and methods.
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Affiliation(s)
- Heng Li
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | - Xiaoping Hong
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Liping Ding
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Shuhui Meng
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Rui Liao
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Zhenyou Jiang
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, China
- *Correspondence: Zhenyou Jiang, ; Dongzhou Liu,
| | - Dongzhou Liu
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
- *Correspondence: Zhenyou Jiang, ; Dongzhou Liu,
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132
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Structure-selected RBM immunogens prime polyclonal memory responses that neutralize SARS-CoV-2 variants of concern. PLoS Pathog 2022; 18:e1010686. [PMID: 35862442 PMCID: PMC9302722 DOI: 10.1371/journal.ppat.1010686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/17/2022] [Indexed: 11/19/2022] Open
Abstract
Successful control of the COVID-19 pandemic depends on vaccines that prevent transmission. The full-length Spike protein is highly immunogenic but the majority of antibodies do not target the virus: ACE2 interface. In an effort to affect the quality of the antibody response focusing it to the receptor-binding motif (RBM) we generated a series of conformationally-constrained immunogens by inserting solvent-exposed RBM amino acid residues into hypervariable loops of an immunoglobulin molecule. Priming C57BL/6 mice with plasmid (p)DNA encoding these constructs yielded a rapid memory response to booster immunization with recombinant Spike protein. Immune sera antibodies bound strongly to the purified receptor-binding domain (RBD) and Spike proteins. pDNA primed for a consistent response with antibodies efficient at neutralizing authentic WA1 virus and three variants of concern (VOC), B.1.351, B.1.617.2, and BA.1. We demonstrate that immunogens built on structure selection can be used to influence the quality of the antibody response by focusing it to a conserved site of vulnerability shared between wildtype virus and VOCs, resulting in neutralizing antibodies across variants.
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133
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Modelling the interplay of SARS-CoV-2 variants in the United Kingdom. Sci Rep 2022; 12:12372. [PMID: 35859100 PMCID: PMC9296900 DOI: 10.1038/s41598-022-16147-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 07/05/2022] [Indexed: 12/28/2022] Open
Abstract
Many COVID-19 vaccines are proving to be highly effective to prevent severe disease and to diminish infections. Their uneven geographical distribution favors the appearance of new variants of concern, as the highly transmissible Delta variant, affecting particularly non-vaccinated people. It is important to device reliable models to analyze the spread of the different variants. A key factor is to consider the effects of vaccination as well as other measures used to contain the pandemic like social behaviour. The stochastic geographical model presented here, fulfills these requirements. It is based on an extended compartmental model that includes various strains and vaccination strategies, allowing to study the emergence and dynamics of the new COVID-19 variants. The model conveniently separates the parameters related to the disease from the ones related to social behavior and mobility restrictions. We applied the model to the United Kingdom by using available data to fit the recurrence of the currently prevalent variants. Our computer simulations allow to describe the appearance of periodic waves and the features that determine the prevalence of certain variants. They also provide useful predictions to help planning future vaccination boosters. We stress that the model could be applied to any other country of interest.
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134
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Junker D, Becker M, Wagner TR, Kaiser PD, Maier S, Grimm TM, Griesbaum J, Marsall P, Gruber J, Traenkle B, Heinzel C, Pinilla YT, Held J, Fendel R, Kreidenweiss A, Nelde A, Maringer Y, Schroeder S, Walz JS, Althaus K, Uzun G, Mikus M, Bakchoul T, Schenke-Layland K, Bunk S, Haeberle H, Göpel S, Bitzer M, Renk H, Remppis J, Engel C, Franz AR, Harries M, Kessel B, Lange B, Strengert M, Krause G, Zeck A, Rothbauer U, Dulovic A, Schneiderhan-Marra N. Antibody Binding and Angiotensin-Converting Enzyme 2 Binding Inhibition Is Significantly Reduced for Both the BA.1 and BA.2 Omicron Variants. Clin Infect Dis 2022; 76:e240-e249. [PMID: 35717657 PMCID: PMC9384292 DOI: 10.1093/cid/ciac498] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 06/07/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The rapid emergence of the Omicron variant and its large number of mutations led to its classification as a variant of concern (VOC) by the World Health Organization. Subsequently, Omicron evolved into distinct sublineages (eg, BA.1 and BA.2), which currently represent the majority of global infections. Initial studies of the neutralizing response toward BA.1 in convalescent and vaccinated individuals showed a substantial reduction. METHODS We assessed antibody (immunoglobulin G [IgG]) binding, ACE2 (angiotensin-converting enzyme 2) binding inhibition, and IgG binding dynamics for the Omicron BA.1 and BA.2 variants compared to a panel of VOCs/variants of interest, in a large cohort (N = 352) of convalescent, vaccinated, and infected and subsequently vaccinated individuals. RESULTS While Omicron was capable of efficiently binding to ACE2, antibodies elicited by infection or immunization showed reduced binding capacities and ACE2 binding inhibition compared to wild type. Whereas BA.1 exhibited less IgG binding compared to BA.2, BA.2 showed reduced inhibition of ACE2 binding. Among vaccinated samples, antibody binding to Omicron only improved after administration of a third dose. CONCLUSIONS Omicron BA.1 and BA.2 can still efficiently bind to ACE2, while vaccine/infection-derived antibodies can bind to Omicron. The extent of the mutations within both variants prevents a strong inhibitory binding response. As a result, both Omicron variants are able to evade control by preexisting antibodies.
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Affiliation(s)
| | | | | | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Sandra Maier
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Tanja M Grimm
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Johanna Griesbaum
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Patrick Marsall
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Jens Gruber
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Constanze Heinzel
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Yudi T Pinilla
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Jana Held
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Rolf Fendel
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany,German Center for Infection Research, partner site Tuebingen, Tuebingen, Germany,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Andrea Kreidenweiss
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany,German Center for Infection Research, partner site Tuebingen, Tuebingen, Germany,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Annika Nelde
- Department of Peptide-Based Immunotherapy, University of Tuebingen and University Hospital Tuebingen, Tuebingen, Germany,Department of Internal Medicine, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium, University Hospital Tuebingen, Tuebingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tuebingen, Tuebingen, Germany
| | - Yacine Maringer
- Department of Peptide-Based Immunotherapy, University of Tuebingen and University Hospital Tuebingen, Tuebingen, Germany,Department of Internal Medicine, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium, University Hospital Tuebingen, Tuebingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tuebingen, Tuebingen, Germany
| | - Sarah Schroeder
- Department of Peptide-Based Immunotherapy, University of Tuebingen and University Hospital Tuebingen, Tuebingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Department of Otorhinolaryngology, Head and Neck Surgery, University of Tuebingen, Tuebingen, Germany
| | - Juliane S Walz
- Department of Peptide-Based Immunotherapy, University of Tuebingen and University Hospital Tuebingen, Tuebingen, Germany,Department of Internal Medicine, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium, University Hospital Tuebingen, Tuebingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tuebingen, Tuebingen, Germany
| | - Karina Althaus
- Center for Clinical Transfusion Medicine, Tuebingen, Germany,Institute of Clinical and Experimental Transfusion Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Gunalp Uzun
- Center for Clinical Transfusion Medicine, Tuebingen, Germany
| | - Marco Mikus
- Center for Clinical Transfusion Medicine, Tuebingen, Germany
| | - Tamam Bakchoul
- Center for Clinical Transfusion Medicine, Tuebingen, Germany,Institute of Clinical and Experimental Transfusion Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Katja Schenke-Layland
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Department for Medical Technologies and Regenerative Medicine, Institute of Biomedical Engineering, University of Tuebingen, Tuebingen, Germany,Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Stefanie Bunk
- Infectious Diseases, Department of Internal Medicine I, University Hospital Tuebingen, Tuebingen, Germany
| | - Helene Haeberle
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Siri Göpel
- German Center for Infection Research, partner site Tuebingen, Tuebingen, Germany,Infectious Diseases, Department of Internal Medicine I, University Hospital Tuebingen, Tuebingen, Germany
| | - Michael Bitzer
- Infectious Diseases, Department of Internal Medicine I, University Hospital Tuebingen, Tuebingen, Germany,Center for Personalized Medicine, University of Tuebingen, Tuebingen, Germany
| | - Hanna Renk
- University Children’s Hospital, Tuebingen, Germany
| | | | - Corinna Engel
- University Children’s Hospital, Tuebingen, Germany,Center for Pediatric Clinical Studies, University Hospital Tuebingen, Tuebingen, Germany
| | - Axel R Franz
- University Children’s Hospital, Tuebingen, Germany,Center for Pediatric Clinical Studies, University Hospital Tuebingen, Tuebingen, Germany
| | - Manuela Harries
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Barbora Kessel
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Berit Lange
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Monika Strengert
- Helmholtz Centre for Infection Research, Braunschweig, Germany,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture of Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Gerard Krause
- Helmholtz Centre for Infection Research, Braunschweig, Germany,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture of Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Anne Zeck
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany,Pharmaceutical Biotechnology, University of Tuebingen, Tuebingen, Germany
| | - Alex Dulovic
- Correspondence: A. Dulovic, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, Reutlingen, 72770 Germany ()
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135
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Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2. Nat Microbiol 2022; 7:1180-1188. [PMID: 35836002 PMCID: PMC9352594 DOI: 10.1038/s41564-022-01163-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/24/2022] [Indexed: 11/16/2022]
Abstract
SARS-CoV-2 variants may threaten the effectiveness of vaccines and antivirals to mitigate serious COVID-19 disease. This is of most concern in clinically vulnerable groups such as older adults. We analysed 72 sera samples from 37 individuals, aged 70–89 years, vaccinated with two doses of BNT162b2 (Pfizer–BioNTech) 3 weeks apart, for neutralizing antibody responses to wildtype SARS-CoV-2. Between 3 and 20 weeks after the second vaccine dose, neutralizing antibody titres fell 4.9-fold to a median titre of 21.3 (neutralization dose 80%), with 21.6% of individuals having no detectable neutralizing antibodies at the later time point. Next, we examined neutralization of 21 distinct SARS-CoV-2 variant spike proteins with these sera, and confirmed substantial antigenic escape, especially for the Omicron (B.1.1.529, BA.1/BA.2), Beta (B.1.351), Delta (B.1.617.2), Theta (P.3), C.1.2 and B.1.638 spike variants. By combining pseudotype neutralization with specific receptor-binding domain (RBD) enzyme-linked immunosorbent assays, we showed that changes to position 484 in the spike RBD were mainly responsible for SARS-CoV-2 neutralizing antibody escape. Nineteen sera from the same individuals boosted with a third dose of BNT162b2 contained higher neutralizing antibody titres, providing cross-protection against Omicron BA.1 and BA.2. Despite SARS-CoV-2 immunity waning over time in older adults, booster vaccines can elicit broad neutralizing antibodies against a large number of SARS-CoV-2 variants in this clinically vulnerable cohort. Analysis of the neutralizing antibody activity from sera of vaccinated individuals aged between 70 and 89 reveals a reduction of antibody titres against SARS-CoV-2 wildtype and antigenic escape of various variants of concern that links to specific mutations within the RBD. A booster vaccination helps increasing neutralizing antibody titres against the Omicron BA.1 and BA.2 variants in older adults.
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136
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Genetic Surveillance of SARS-CoV-2 M
pro
Reveals High Sequence and Structural Conservation Prior to the Introduction of Protease Inhibitor Paxlovid. mBio 2022; 13:e0086922. [PMID: 35862764 PMCID: PMC9426535 DOI: 10.1128/mbio.00869-22] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to represent a global health emergency as a highly transmissible, airborne virus. An important coronaviral drug target for treatment of COVID-19 is the conserved main protease (Mpro). Nirmatrelvir is a potent Mpro inhibitor and the antiviral component of Paxlovid. The significant viral sequencing effort during the ongoing COVID-19 pandemic represented a unique opportunity to assess potential nirmatrelvir escape mutations from emerging variants of SARS-CoV-2. To establish the baseline mutational landscape of Mpro prior to the introduction of Mpro inhibitors, Mpro sequences and its cleavage junction regions were retrieved from ~4,892,000 high-quality SARS-CoV-2 genomes in the open-access Global Initiative on Sharing Avian Influenza Data (GISAID) database. Any mutations identified from comparison to the reference sequence (Wuhan-Hu-1) were catalogued and analyzed. Mutations at sites key to nirmatrelvir binding and protease functionality (e.g., dimerization sites) were still rare. Structural comparison of Mpro also showed conservation of key nirmatrelvir contact residues across the extended Coronaviridae family (α-, β-, and γ-coronaviruses). Additionally, we showed that over time, the SARS-CoV-2 Mpro enzyme remained under purifying selection and was highly conserved relative to the spike protein. Now, with the emergency use authorization (EUA) of Paxlovid and its expected widespread use across the globe, it is essential to continue large-scale genomic surveillance of SARS-CoV-2 Mpro evolution. This study establishes a robust analysis framework for monitoring emergent mutations in millions of virus isolates, with the goal of identifying potential resistance to present and future SARS-CoV-2 antivirals.
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137
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Wu CS, Chiang HM, Chen Y, Chen CY, Chen HF, Su WC, Wang WJ, Chou YC, Chang WC, Wang SC, Hung MC. Prospects of Coffee Leaf against SARS-CoV-2 Infection. Int J Biol Sci 2022; 18:4677-4689. [PMID: 35874948 PMCID: PMC9305275 DOI: 10.7150/ijbs.76058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022] Open
Abstract
In the current climate, many countries are in dire need of effective preventive methods to curb the Severe Acute Respiratory Syndrome Coronavirus Type 2 (SARS-CoV-2) pandemic. The purpose of this research is to screen and explore natural plant extracts that have the potential to against SARS-CoV-2 and provide alternative options for SARS-CoV-2 prevention and hand sanitizer or spray-like disinfectants. We first used Spike-ACE2 ELISA and TMPRSS2 fluorescence resonance energy transfer (FRET) assays to screen extracts from agricultural by-products from Taiwan with the potential to impede SARS-CoV-2 infection. Next, the SARS-CoV-2 pseudo-particles (Vpp) infection assay was tested to validate the effectiveness. We identified an extract from coffee leaf (Coffea Arabica), a natural plant that effectively inhibited wild-type SARS-CoV-2, and five Variants of Concern (Alpha, Beta, Gamma, Delta, and Omicron strain) from entering host cells. In an attempt to apply coffee leaf extract for hand sanitizer or spray-like disinfectants, we designed a skin-like gelatin membrane experiment. We showed that the high concentration of coffee leaf extract on the skin surface could block SARS-CoV-2 into cells more potently than 75% Ethanol, a standard disinfectant to inactivate SARS-CoV-2. Finally, LC-HRMS analysis was used to identify compounds such as caffeine, chlorogenic acid (CGA), quinic acid, and mangiferin that are associated with an anti-SARS-CoV-2 activity. Our results demonstrated that coffee leaf extract, an agricultural by-product effectively inhibits SARS-CoV-2 Vpp infection through an ACE2-dependent mechanism and may be utilized to develop products against SARS-CoV-2 infection.
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Affiliation(s)
- Chen-Shiou Wu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
| | - Hsiu-Mei Chiang
- Department of Cosmeceutics, China Medical University, Taichung 406040, Taiwan
| | - Yeh Chen
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- Institute of New Drug Development, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
| | - Chung-Yu Chen
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
| | - Hsiao-Fan Chen
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
| | - Wen-Chi Su
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- International Master's Program of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung 404332, Taiwan
| | - Wei-Jan Wang
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
- Department of Biological Science and Technology, China Medical University, Taichung 406040, Taiwan
| | - Yu-Chi Chou
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei 115024, Taiwan
| | - Wei-Chao Chang
- Center for Molecular Medicine, China Medical University Hospital, China Medical University, Taichung 404332, Taiwan
| | - Shao-Chun Wang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, China Medical University, Taichung 404332, Taiwan
- Department of Biotechnology, Asia University, Taichung, 41354 Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, China Medical University, Taichung 404332, Taiwan
- Department of Biotechnology, Asia University, Taichung, 41354 Taiwan
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138
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Andrade SA, Batalha-Carvalho JV, Curi R, Wen FH, Covas DT, Chudzinski-Tavassi AM, Moro AM. Equine Anti-SARS-CoV-2 Serum (ECIG) Binds to Mutated RBDs and N Proteins of Variants of Concern and Inhibits the Binding of RBDs to ACE-2 Receptor. Front Immunol 2022; 13:871874. [PMID: 35898497 PMCID: PMC9310548 DOI: 10.3389/fimmu.2022.871874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The COVID-19 pandemic caused by the severe acute syndrome virus 2 (SARS-CoV-2) has been around since November 2019. As of early June 2022, more than 527 million cases were diagnosed, with more than 6.0 million deaths due to this disease. Coronaviruses accumulate mutations and generate greater diversity through recombination when variants with different mutations infect the same host. Consequently, this virus is predisposed to constant and diverse mutations. The SARS-CoV-2 variants of concern/interest (VOCs/VOIs) such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (B.1.1.28/P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) have quickly spread across the world. These VOCs and VOIs have accumulated mutations within the spike protein receptor-binding domain (RBD) which interacts with the angiotensin-2 converting enzyme (ACE-2) receptor, increasing cell entry and infection. The RBD region is the main target for neutralizing antibodies; however, other notable mutations have been reported to enhance COVID-19 infectivity and lethality. Considering the urgent need for alternative therapies against this virus, an anti-SARS-CoV-2 equine immunoglobulin F(ab’)2, called ECIG, was developed by the Butantan Institute using the whole gamma-irradiated SARS-CoV-2 virus. Surface plasmon resonance experiments revealed that ECIG binds to wild-type and mutated RBD, S1+S2 domains, and nucleocapsid proteins of known VOCs, including Alpha, Gamma, Beta, Delta, Delta Plus, and Omicron. Additionally, it was observed that ECIG attenuates the binding of RBD (wild-type, Beta, and Omicron) to human ACE-2, suggesting that it could prevent viral entry into the host cell. Furthermore, the ability to concomitantly bind to the wild-type and mutated nucleocapsid protein likely enhances its neutralizing activity of SARS-CoV-2. We postulate that ECIG benefits COVID-19 patients by reducing the infectivity of the original virus and existing variants and may be effective against future ones. Impacting the course of the disease, mainly in the more vulnerable, reduces infection time and limits the appearance of new variants by new recombination.
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Affiliation(s)
| | | | - Rui Curi
- Cruzeiro do Sul University, São Paulo, Brazil
- Immunobiological Production Section, Bioindustrial Center, Butantan Institute, São Paulo, Brazil
| | - Fan Hui Wen
- Immunobiological Production Section, Bioindustrial Center, Butantan Institute, São Paulo, Brazil
| | | | - Ana Marisa Chudzinski-Tavassi
- Center of Excellence in New Target Discovery (CENTD), Instituto Butantan, São Paulo, Brazil
- Innovation and Development Laboratory, Instituto Butantan, São Paulo, Brazil
- *Correspondence: Ana Marisa Chudzinski-Tavassi, ; Ana Maria Moro,
| | - Ana Maria Moro
- Biopharmaceuticals Laboratory, Instituto Butantan, São Paulo, Brazil
- Center for Research and Development in Immunobiologicals (CeRDI), Instituto Butantan, São Paulo, Brazil
- *Correspondence: Ana Marisa Chudzinski-Tavassi, ; Ana Maria Moro,
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139
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Takefuji Y. A herd immunity approach to the COVID-19 pandemic? HEALTH AND TECHNOLOGY 2022; 12:1037-1041. [PMID: 35818413 PMCID: PMC9261241 DOI: 10.1007/s12553-022-00676-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/12/2022] [Indexed: 12/03/2022]
Abstract
Viral contamination is one of the most urgent and important topics of environmental pollution. COVID-19 is primarily transmitted from person to person, but can also be transmitted from person to animal. Herd immunity must meet the requirements in order to fulfill the goal of mitigating and ending COVID-19. This paper shows five reasons or conditions why herd immunity is not achieved in the present policies without proposed effective strategies in this paper. Unless one of the five reasons for the herd immunity model is met, the promise of herd immunity will not be fulfilled. Many COVID-19 policies worldwide with current vaccines do not meet the requirements. Policymakers have been relying on unreliable R. The number of daily deaths instead of the number of cases is a good indicator of the pandemic which will be mainly used in this paper. Currently, even in vaccinated countries, resurgences are being observed with new variants with spike mutations and immune escape. This paper proposes an effective multipronged approach such as a pharmacological approach and a non-pharmacological approach including digital fencing. Two tools such as scorecovid and deathdaily were used for justifying the claims. Digital fencing as well as pharmacological approaches may be able to overcome the pandemic. Two tools such as scorecovid and deathdaily showed that the proposed multipronged approach will be effective for mitigating the pandemic.
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Affiliation(s)
- Yoshiyasu Takefuji
- Faculty of Data Science, Musashino University, 3-3-3 Ariake Koto-ku, Tokyo, 135-8181 Japan
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140
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Brandys P, Montagutelli X, Merenkova I, Barut GT, Thiel V, Schork NJ, Trüeb B, Conquet L, Deng A, Antanasijevic A, Lee HK, Valière M, Sindhu A, Singh G, Herold J. A mRNA Vaccine Encoding for a RBD 60-mer Nanoparticle Elicits Neutralizing Antibodies and Protective Immunity Against the SARS-CoV-2 Delta Variant in Transgenic K18-hACE2 Mice. Front Immunol 2022; 13:912898. [PMID: 35874687 PMCID: PMC9299372 DOI: 10.3389/fimmu.2022.912898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Two years into the COVID-19 pandemic there is still a need for vaccines to effectively control the spread of novel SARS-CoV-2 variants and associated cases of severe disease. Here we report a messenger RNA vaccine directly encoding for a nanoparticle displaying 60 receptor binding domains (RBDs) of SARS-CoV-2 that acts as a highly effective antigen. A construct encoding the RBD of the Delta variant elicits robust neutralizing antibody response, and also provides protective immunity against the Delta variant in a widely used transgenic mouse model. We ultimately find that the proposed mRNA RBD nanoparticle-based vaccine provides a flexible platform for rapid development and will likely be of great value in combatting current and future SARS-CoV-2 variants of concern.
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Affiliation(s)
| | - Xavier Montagutelli
- Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, Paris, France
| | | | - Güliz T. Barut
- Institute of Virology and Immunology, University of Bern, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology, University of Bern, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Nicholas J. Schork
- Quantitative Medicine & Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Bettina Trüeb
- Institute of Virology and Immunology, University of Bern, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Laurine Conquet
- Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, Paris, France
| | - Aihua Deng
- BTS Research, San Diego, CA, United States
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | | | | | | | | | - Jens Herold
- Phylex BioSciences, Del Mar, CA, United States
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141
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Maeda R, Fujita J, Konishi Y, Kazuma Y, Yamazaki H, Anzai I, Watanabe T, Yamaguchi K, Kasai K, Nagata K, Yamaoka Y, Miyakawa K, Ryo A, Shirakawa K, Sato K, Makino F, Matsuura Y, Inoue T, Imura A, Namba K, Takaori-Kondo A. A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron. Commun Biol 2022; 5:669. [PMID: 35794202 PMCID: PMC9257560 DOI: 10.1038/s42003-022-03630-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/24/2022] [Indexed: 12/15/2022] Open
Abstract
We are amid the historic coronavirus infectious disease 2019 (COVID-19) pandemic. Imbalances in the accessibility of vaccines, medicines, and diagnostics among countries, regions, and populations, and those in war crises, have been problematic. Nanobodies are small, stable, customizable, and inexpensive to produce. Herein, we present a panel of nanobodies that can detect the spike proteins of five SARS-CoV-2 variants of concern (VOCs) including Omicron. Here we show via ELISA, lateral flow, kinetic, flow cytometric, microscopy, and Western blotting assays that our nanobodies can quantify the spike variants. This panel of nanobodies broadly neutralizes viral infection caused by pseudotyped and authentic SARS-CoV-2 VOCs. Structural analyses show that the P86 clone targets epitopes that are conserved yet unclassified on the receptor-binding domain (RBD) and contacts the N-terminal domain (NTD). Human antibodies rarely access both regions; consequently, the clone buries hidden crevasses of SARS-CoV-2 spike proteins that go undetected by conventional antibodies. A panel of nanobodies are presented that can detect the spike proteins of five SARS-CoV-2 variants of concern and structural analyses show that one clone targets conserved epitopes on the receptor-binding domain and contacts the N-terminal domain.
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142
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Zemaitis L, Alzbutas G, Gecys D, Pautienius A, Ugenskiene R, Sukys M, Lesauskaite V. Determining the International Spread of B.1.1.523 SARS-CoV-2 Lineage with a Set of Mutations Highly Associated with Reduced Immune Neutralization. Microorganisms 2022; 10:1356. [PMID: 35889075 PMCID: PMC9320768 DOI: 10.3390/microorganisms10071356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 02/05/2023] Open
Abstract
Here, we report the emergence of the variant lineage B.1.1.523 that contains a set of mutations including 156_158del, E484K and S494P in the spike protein. E484K and S494P are known to significantly reduce SARS-CoV-2 neutralization by convalescent and vaccinated sera and are considered as mutations of concern. Lineage B.1.1.523 presumably originated in the Russian Federation and spread across European countries with the peak of transmission in April-May 2021. The B.1.1.523 lineage has now been reported from 31 countries. In this article, we analyze the possible origin of this mutation subset and its immune response using in silico methods.
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Affiliation(s)
- Lukas Zemaitis
- Laboratory of Molecular Cardiology, Institute of Cardiology, Lithuanian University of Health Sciences, LT-50162 Kaunas, Lithuania; (D.G.); (V.L.)
| | - Gediminas Alzbutas
- Laboratory of Translational Bioinformatics, Institute for Digestive Research, Lithuanian University of Health Sciences, LT-50162 Kaunas, Lithuania;
| | - Dovydas Gecys
- Laboratory of Molecular Cardiology, Institute of Cardiology, Lithuanian University of Health Sciences, LT-50162 Kaunas, Lithuania; (D.G.); (V.L.)
| | - Arnoldas Pautienius
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, LT-47181 Kaunas, Lithuania;
| | - Rasa Ugenskiene
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania; (R.U.); (M.S.)
| | - Marius Sukys
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania; (R.U.); (M.S.)
| | - Vaiva Lesauskaite
- Laboratory of Molecular Cardiology, Institute of Cardiology, Lithuanian University of Health Sciences, LT-50162 Kaunas, Lithuania; (D.G.); (V.L.)
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143
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Niesen MJM, Murugadoss K, Lenehan PJ, Marchler-Bauer A, Wang J, Connor R, Brister JR, Venkatakrishnan AJ, Soundararajan V. Quantifying the immunological distinctiveness of emerging SARS-CoV-2 variants in the context of prior regional herd exposure. PNAS NEXUS 2022; 1:pgac105. [PMID: 35899067 PMCID: PMC9308564 DOI: 10.1093/pnasnexus/pgac105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/29/2022] [Indexed: 02/05/2023]
Abstract
The COVID-19 pandemic has seen the persistent emergence of immune-evasive SARS-CoV-2 variants under the selection pressure of natural and vaccination-acquired immunity. However, it is currently challenging to quantify how immunologically distinct a new variant is compared to all the prior variants to which a population has been exposed. Here, we define "Distinctiveness" of SARS-CoV-2 sequences based on a proteome-wide comparison with all prior sequences from the same geographical region. We observe a correlation between Distinctiveness relative to contemporary sequences and future change in prevalence of a newly circulating lineage (Pearson r = 0.75), suggesting that the Distinctiveness of emergent SARS-CoV-2 lineages is associated with their epidemiological fitness. We further show that the average Distinctiveness of sequences belonging to a lineage, relative to the Distinctiveness of other sequences that occur at the same place and time (n = 944 location/time data points), is predictive of future increases in prevalence (Area Under the Curve, AUC = 0.88 [95% confidence interval 0.86 to 0.90]). By assessing the Delta variant in India versus Brazil, we show that the same lineage can have different Distinctiveness-contributing positions in different geographical regions depending on the other variants that previously circulated in those regions. Finally, we find that positions that constitute epitopes contribute disproportionately (20-fold higher than the average position) to Distinctiveness. Overall, this study suggests that real-time assessment of new SARS-CoV-2 variants in the context of prior regional herd exposure via Distinctiveness can augment genomic surveillance efforts.
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Affiliation(s)
| | | | | | - Aron Marchler-Bauer
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Jiyao Wang
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Ryan Connor
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - J Rodney Brister
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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144
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Bekliz M, Adea K, Vetter P, Eberhardt CS, Hosszu-Fellous K, Vu DL, Puhach O, Essaidi-Laziosi M, Waldvogel-Abramowski S, Stephan C, L'Huillier AG, Siegrist CA, Didierlaurent AM, Kaiser L, Meyer B, Eckerle I. Neutralization capacity of antibodies elicited through homologous or heterologous infection or vaccination against SARS-CoV-2 VOCs. Nat Commun 2022; 13:3840. [PMID: 35787633 PMCID: PMC9253337 DOI: 10.1038/s41467-022-31556-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/22/2022] [Indexed: 12/30/2022] Open
Abstract
Emerging SARS-CoV-2 variants raise questions about escape from previous immunity. As the population immunity to SARS-CoV-2 has become more complex due to prior infections with different variants, vaccinations or the combination of both, understanding the antigenic relationship between variants is needed. Here, we have assessed neutralizing capacity of 120 blood specimens from convalescent individuals infected with ancestral SARS-CoV-2, Alpha, Beta, Gamma or Delta, double vaccinated individuals and patients after breakthrough infections with Delta or Omicron-BA.1. Neutralization against seven authentic SARS-CoV-2 isolates (B.1, Alpha, Beta, Gamma, Delta, Zeta and Omicron-BA.1) determined by plaque-reduction neutralization assay allowed us to map the antigenic relationship of SARS-CoV-2 variants. Highest neutralization titers were observed against the homologous variant. Antigenic cartography identified Zeta and Omicron-BA.1 as separate antigenic clusters. Substantial immune escape in vaccinated individuals was detected for Omicron-BA.1 but not Zeta. Combined infection/vaccination derived immunity results in less Omicron-BA.1 immune escape. Last, breakthrough infections with Omicron-BA.1 lead to broadly neutralizing sera.
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Affiliation(s)
- Meriem Bekliz
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Kenneth Adea
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Pauline Vetter
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Christiane S Eberhardt
- Center for Vaccinology and Neonatal Immunology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- Division of General Pediatrics, Department of Woman, Child and Adolescent Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Center for Vaccinology, Geneva University Hospitals, Geneva, Switzerland
| | - Krisztina Hosszu-Fellous
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Diem-Lan Vu
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Olha Puhach
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Manel Essaidi-Laziosi
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | | | - Caroline Stephan
- Transfusion Unit, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Arnaud G L'Huillier
- Pediatric Infectious Diseases Unit, Department of Women, Child and Adolescent Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Claire-Anne Siegrist
- Center for Vaccinology and Neonatal Immunology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Arnaud M Didierlaurent
- Center for Vaccinology and Neonatal Immunology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Benjamin Meyer
- Center for Vaccinology and Neonatal Immunology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland.
| | - Isabella Eckerle
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland.
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland.
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145
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Markarian NM, Galli G, Patel D, Hemmings M, Nagpal P, Berghuis AM, Abrahamyan L, Vidal SM. Identifying Markers of Emerging SARS-CoV-2 Variants in Patients With Secondary Immunodeficiency. Front Microbiol 2022; 13:933983. [PMID: 35847101 PMCID: PMC9283111 DOI: 10.3389/fmicb.2022.933983] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
Since the end of 2019, the world has been challenged by the coronavirus disease 2019 (COVID-19) pandemic. With COVID-19 cases rising globally, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, resulting in the emergence of variants of interest (VOI) and of concern (VOC). Of the hundreds of millions infected, immunodeficient patients are one of the vulnerable cohorts that are most susceptible to this virus. These individuals include those with preexisting health conditions and/or those undergoing immunosuppressive treatment (secondary immunodeficiency). In these cases, several researchers have reported chronic infections in the presence of anti-COVID-19 treatments that may potentially lead to the evolution of the virus within the host. Such variations occurred in a variety of viral proteins, including key structural ones involved in pathogenesis such as spike proteins. Tracking and comparing such mutations with those arisen in the general population may provide information about functional sites within the SARS-CoV-2 genome. In this study, we reviewed the current literature regarding the specific features of SARS-CoV-2 evolution in immunocompromised patients and identified recurrent de novo amino acid changes in virus isolates of these patients that can potentially play an important role in SARS-CoV-2 pathogenesis and evolution.
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Affiliation(s)
- Nathan M. Markarian
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
- Swine and Poultry Infectious Diseases Research Center and Research Group on Infectious Diseases in Production Animals, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Gaël Galli
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- CNRS, ImmunoConcEpT, UMR 5164, Université de Bordeaux, Bordeaux, France
- CHU de Bordeaux, FHU ACRONIM, Centre National de Référence des Maladies Auto-Immunes et Systémiques Rares Est/Sud-Ouest, Bordeaux, France
| | - Dhanesh Patel
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
| | - Mark Hemmings
- Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Priya Nagpal
- Department of Pharmacology, McGill University, Montréal, QC, Canada
| | | | - Levon Abrahamyan
- Swine and Poultry Infectious Diseases Research Center and Research Group on Infectious Diseases in Production Animals, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Silvia M. Vidal
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
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146
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Kim Y, Gaudreault NN, Meekins DA, Perera KD, Bold D, Trujillo JD, Morozov I, McDowell CD, Chang KO, Richt JA. Effects of Spike Mutations in SARS-CoV-2 Variants of Concern on Human or Animal ACE2-Mediated Virus Entry and Neutralization. Microbiol Spectr 2022; 10:e0178921. [PMID: 35638818 PMCID: PMC9241865 DOI: 10.1128/spectrum.01789-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 04/15/2022] [Indexed: 12/31/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a zoonotic agent capable of infecting humans and a wide range of animal species. Over the duration of the pandemic, mutations in the SARS-CoV-2 spike (S) protein have arisen, culminating in the spread of several variants of concern (VOCs) with various degrees of altered virulence, transmissibility, and neutralizing antibody escape. In this study, we used pseudoviruses that express specific SARS-CoV-2 S protein substitutions and cell lines that express angiotensin-converting enzyme 2 (ACE2) from nine different animal species to gain insights into the effects of VOC mutations on viral entry and antibody neutralization capability. All animal ACE2 receptors tested, except mink, support viral cell entry for pseudoviruses expressing the ancestral prototype S at levels comparable to human ACE2. Most single S substitutions did not significantly change virus entry, although 614G and 484K resulted in a decreased efficiency. Conversely, combinatorial VOC substitutions in the S protein were associated with increased entry of pseudoviruses. Neutralizing titers in sera from various animal species were significantly reduced against pseudoviruses expressing the S proteins of Beta, Delta, or Omicron VOCs compared to the parental S protein. Especially, substitutions in the S protein of the Omicron variant significantly reduced the neutralizing titers of the sera. This study reveals important insights into the host range of SARS-CoV-2 and the effect of recently emergent S protein substitutions on viral entry, virus replication, and antibody-mediated viral neutralization. IMPORTANCE The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to have devastating impacts on global health and socioeconomics. The recent emergence of SARS-CoV-2 variants of concern, which contain mutations that can affect the virulence, transmission, and effectiveness of licensed vaccines and therapeutic antibodies, are currently becoming the common strains circulating in humans worldwide. In addition, SARS-CoV-2 has been shown to infect a wide variety of animal species, which could result in additional mutations of the SARS-CoV-2 virus. In this study, we investigate the effect of mutations present in SARS-CoV-2 variants of concern and determine the effects of these mutations on cell entry, virulence, and antibody neutralization activity in humans and a variety of animals that might be susceptible to SARS-CoV-2 infection. This information is essential to understand the effects of important SARS-CoV-2 mutations and to inform public policy to create better strategies to control the COVID-19 pandemic.
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Affiliation(s)
- Yunjeong Kim
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - David A. Meekins
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Krishani D. Perera
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Dashzeveg Bold
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Jessie D. Trujillo
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Igor Morozov
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Chester D. McDowell
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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147
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Sun W, He L, Lou H, Fan W, Yang L, Cheng G, Liu W, Sun L. The Cross-Protective Immunity Landscape Among Different SARS-CoV-2 Variant RBDs. Front Immunol 2022; 13:898520. [PMID: 35757743 PMCID: PMC9226324 DOI: 10.3389/fimmu.2022.898520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
Despite the fact that SARS-CoV-2 vaccines have been available in most parts of the world, the epidemic status remains grim with new variants emerging and escaping the immune protection of existing vaccines. Therefore, the development of more effective antigens and evaluation of their cross-protective immunity against different SARS-CoV-2 variants are particularly urgent. In this study, we expressed the wild type (WT), Alpha, Beta, Delta, and Lambda RBD proteins to immunize mice and evaluated their cross-neutralizing activity against different pseudoviruses (WT, Alpha, Beta, Delta, Lambda, and Omicron). All monovalent and pentavalent RBD antigens induced high titers of IgG antibodies against different variant RBD antigens. In contrast, WT RBD antigen-induced antibodies showed a lower neutralizing activity against Beta, Delta, Lambda, and Omicron pseudoviruses compared to neutralization against itself. Interestingly, Beta RBD antigen and multivalent antigen induced broader cross-neutralization antibodies than other variant RBD antigens. These data provide a reference for vaccine strain selection and universal COVID-19 vaccine design to fight the constant emergence of new SARS-CoV-2 variants.
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Affiliation(s)
- Wenqiang Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning, China
| | - Lihong He
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Huicong Lou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning, China
| | - Wenhui Fan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Limin Yang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Gong Cheng
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen, China.,Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Lei Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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148
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Moga E, Lynton-Pons E, Domingo P. The Robustness of Cellular Immunity Determines the Fate of SARS-CoV-2 Infection. Front Immunol 2022; 13:904686. [PMID: 35833134 PMCID: PMC9271749 DOI: 10.3389/fimmu.2022.904686] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/27/2022] [Indexed: 12/11/2022] Open
Abstract
Two years after the appearance of the SARS-CoV-2 virus, the causal agent of the current global pandemic, it is time to analyze the evolution of the immune protection that infection and vaccination provide. Cellular immunity plays an important role in limiting disease severity and the resolution of infection. The early appearance, breadth and magnitude of SARS-CoV-2 specific T cell response has been correlated with disease severity and it has been thought that T cell responses may be sufficient to clear infection with minimal disease in COVID-19 patients with X-linked or autosomal recessive agammaglobulinemia. However, our knowledge of the phenotypic and functional diversity of CD8+ cytotoxic lymphocytes, CD4+ T helper cells, mucosal-associated invariant T (MAIT) cells and CD4+ T follicular helper (Tfh), which play a critical role in infection control as well as long-term protection, is still evolving. It has been described how CD8+ cytotoxic lymphocytes interrupt viral replication by secreting antiviral cytokines (IFN-γ and TNF-α) and directly killing infected cells, negatively correlating with stages of disease progression. In addition, CD4+ T helper cells have been reported to be key pieces, leading, coordinating and ultimately regulating antiviral immunity. For instance, in some more severe COVID-19 cases a dysregulated CD4+ T cell signature may contribute to the greater production of pro-inflammatory cytokines responsible for pathogenic inflammation. Here we discuss how cellular immunity is the axis around which the rest of the immune system components revolve, since it orchestrates and leads antiviral response by regulating the inflammatory cascade and, as a consequence, the innate immune system, as well as promoting a correct humoral response through CD4+ Tfh cells. This review also analyses the critical role of cellular immunity in modulating the development of high-affinity neutralizing antibodies and germinal center B cell differentiation in memory and long-lived antibody secreting cells. Finally, since there is currently a high percentage of vaccinated population and, in some cases, vaccine booster doses are even being administered in certain countries, we have also summarized newer approaches to long-lasting protective immunity and the cross-protection of cellular immune response against SARS-CoV-2.
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Affiliation(s)
- Esther Moga
- Department of Immunology, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant Pau (IIB Sant Pau), Universitat Autònoma de Barcelona, Barcelona, Spain,*Correspondence: Esther Moga,
| | - Elionor Lynton-Pons
- Department of Immunology, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant Pau (IIB Sant Pau), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pere Domingo
- Unidad de enfermedades infecciosas, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
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149
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Inhibitors of Deubiquitinating Enzymes Interfere with the SARS-CoV-2 Papain-like Protease and Block Virus Replication In Vitro. Viruses 2022; 14:v14071404. [PMID: 35891385 PMCID: PMC9324251 DOI: 10.3390/v14071404] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 02/01/2023] Open
Abstract
The ubiquitin proteasome system (UPS), particularly its deubiquitinating enzymes (DUBs), play a key role in the replication cycle of coronaviruses. The SARS-CoV-2 papain-like protease (Plpro) is known to process the viral polyproteins to form the replicase transcriptase complex and to counteract the host viral response. Recently, it was shown that this viral protease can also act as a deubiquitinating enzyme. In this study, we demonstrate that certain DUB-Inhibitors (DIs) interfere with SARS-CoV-2 replication. The DIs PR-619 and HBX41108 restrict SARS-CoV-2 in both Vero B4 and human Calu-3 lung cells where cells were infected with a Multiplicity of Infection (MOI) of 0.02. An in vitro protease assay using recombinant Plpro and Amido-4-methylcoumarin (AMC)-conjugated substrate revealed that PR-619 and HBX41108 are able to block the protease at concentrations where the interventions restricted virus replication. In contrast, DIs that do not inhibit Plpro had no influence on virus replication, which indicated that the protease might be at least one major target. Future vertical studies that would gain more insights into the mechanisms of how DUBs effect the replication of SARS-CoV-2 will further validate them as a potential therapeutic target.
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150
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Tortorici MA, Walls AC, Joshi A, Park YJ, Eguia RT, Miranda MC, Kepl E, Dosey A, Stevens-Ayers T, Boeckh MJ, Telenti A, Lanzavecchia A, King NP, Corti D, Bloom JD, Veesler D. Structure, receptor recognition, and antigenicity of the human coronavirus CCoV-HuPn-2018 spike glycoprotein. Cell 2022; 185:2279-2291.e17. [PMID: 35700730 PMCID: PMC9135795 DOI: 10.1016/j.cell.2022.05.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 04/24/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023]
Abstract
The isolation of CCoV-HuPn-2018 from a child respiratory swab indicates that more coronaviruses are spilling over to humans than previously appreciated. We determined the structures of the CCoV-HuPn-2018 spike glycoprotein trimer in two distinct conformational states and showed that its domain 0 recognizes sialosides. We identified that the CCoV-HuPn-2018 spike binds canine, feline, and porcine aminopeptidase N (APN) orthologs, which serve as entry receptors, and determined the structure of the receptor-binding B domain in complex with canine APN. The introduction of an oligosaccharide at position N739 of human APN renders cells susceptible to CCoV-HuPn-2018 spike-mediated entry, suggesting that single-nucleotide polymorphisms might account for viral detection in some individuals. Human polyclonal plasma antibodies elicited by HCoV-229E infection and a porcine coronavirus monoclonal antibody inhibit CCoV-HuPn-2018 spike-mediated entry, underscoring the cross-neutralizing activity among ɑ-coronaviruses. These data pave the way for vaccine and therapeutic development targeting this zoonotic pathogen representing the eighth human-infecting coronavirus.
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Affiliation(s)
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Anshu Joshi
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rachel T Eguia
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth Kepl
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Annie Dosey
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Terry Stevens-Ayers
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Michael J Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Antonio Lanzavecchia
- Istituto Nazionale Genetica Molecolare, 20122 Milano, Italy; Humabs Biomed SA-a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA-a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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