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Biswas D, Mahalingam G, Subaschandrabose RK, Priya S, Ramachandran R, Suresh S, Mathivanan TV, Balu NV, Selvaraj K, Nellickal AJ, Christudoss P, Samuel P, Kt RD, Marepally S, Moorthy M. Role of prior immunity in binding to spike of "future" Omicron subvariants. Indian J Med Microbiol 2024; 50:100615. [PMID: 38782260 DOI: 10.1016/j.ijmmb.2024.100615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 04/18/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Throughout the COVID-19 pandemic, virus evolution and large-scale vaccination programs have caused multiple exposures to SARS CoV-2 spike protein, resulting in complex antibody profiles. The binding of these to spike protein of "future" variants in the context of such heterogeneous exposure has not been studied. METHODS We tested archival sera (Delta and Omicron period) stratified by anti-spike antibody (including IgG) levels for reactivity to Omicron-subvariants(BA.1, BA.2,BA.2.12.1, BA.2.75, BA.4/5 and BF.7) spike protein. Assessed antigenic distance between groups using Antigenic Cartography and performed hierarchical clustering of antibody data in a Euclidean distance framework. RESULTS Antibody (including IgG) antibody reactivity to Wild-type (CLIA) and subvariants (ELISA) spike protein were similar between periods (p > 0.05). Both 'High S' and 'Low S' of Delta and Omicron periods were closely related to "future" subvariants by Antigenic Cartography. Sera from different S groups clustered together with 'Low S' interspersed between 'High S' on hierarchical clustering, suggesting common binding sites. Further, anti-spike antibodies (including IgG) to Wild-type (S1/S2 and Trimeric S) clustered with Omicron-subvariant binding antibodies. CONCLUSIONS Hybrid immunity caused by cumulative virus exposure in Delta or Omicron periods resulted in equivalent binding to "future" variants, which might be due to binding to conserved regions of spike protein of future variants. A prominent finding is that the 'Low S' antibody demonstrates similar binding.
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Affiliation(s)
- Deepayan Biswas
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Gokulnath Mahalingam
- Centre for Stem Cell Research (CSCR) (a unit of InStem, Bengaluru), Christian Medical College, Vellore, Pin: 632002, Tamil Nadu, India.
| | | | - Sangeetha Priya
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Rohini Ramachandran
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Sevanthy Suresh
- Centre for Stem Cell Research (CSCR) (a unit of InStem, Bengaluru), Christian Medical College, Vellore, Pin: 632002, Tamil Nadu, India.
| | - Tamil Venthan Mathivanan
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Nelson Vijaykumar Balu
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Kavitha Selvaraj
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Arun Jose Nellickal
- Department of Clinical Biochemistry, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Pamela Christudoss
- Department of Clinical Biochemistry, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
| | - Prasanna Samuel
- Department of Biostatistics, Christian Medical College, Vellore, Tamil Nadu, Pin: 632002, India.
| | - Ramya Devi Kt
- Department of Biotechnology, SRM Institute of Science and Technology, Kanchipuram, Tamil Nadu, Pin: 603203, India.
| | - Srujan Marepally
- Centre for Stem Cell Research (CSCR) (a unit of InStem, Bengaluru), Christian Medical College, Vellore, Pin: 632002, Tamil Nadu, India.
| | - Mahesh Moorthy
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, Pin: 632004, India.
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Kumar A, Kaushal R, Sharma H, Sharma K, Menon MB, P V. Mapping of long stretches of highly conserved sequences in over 6 million SARS-CoV-2 genomes. Brief Funct Genomics 2024; 23:256-264. [PMID: 37461194 DOI: 10.1093/bfgp/elad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/15/2023] [Accepted: 06/26/2023] [Indexed: 05/18/2024] Open
Abstract
We identified 11 conserved stretches in over 6.3 million SARS-CoV-2 genomes including all the major variants of concerns. Each conserved stretch is ≥100 nucleotides in length with ≥99.9% conservation at each nucleotide position. Interestingly, six of the eight conserved stretches in ORF1ab overlapped significantly with well-folded experimentally verified RNA secondary structures. Furthermore, two of the conserved stretches were mapped to regions within the S2-subunit that undergo dynamic structural rearrangements during viral fusion. In addition, the conserved stretches were significantly depleted for zinc-finger antiviral protein (ZAP) binding sites, which facilitated the recognition and degradation of viral RNA. These highly conserved stretches in the SARS-CoV-2 genome were poorly conserved at the nucleotide level among closely related β-coronaviruses, thus representing ideal targets for highly specific and discriminatory diagnostic assays. Our findings highlight the role of structural constraints at both RNA and protein levels that contribute to the sequence conservation of specific genomic regions in SARS-CoV-2.
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Affiliation(s)
- Akhil Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Rishika Kaushal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Himanshi Sharma
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Khushboo Sharma
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Manoj B Menon
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Vivekanandan P
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
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3
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Cornejo A, Franco C, Rodriguez-Nuñez M, García A, Belisario I, Mayora S, Garzaro DJ, Zambrano JL, Jaspe RC, Hidalgo M, Parra-Giménez N, Claro FE, Liprandi F, de Waard JH, Rangel HR, Pujol FH. Humoral Immunity across the SARS-CoV-2 Spike after Sputnik V (Gam-COVID-Vac) Vaccination. Antibodies (Basel) 2024; 13:41. [PMID: 38804309 PMCID: PMC11130906 DOI: 10.3390/antib13020041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/21/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
SARS-CoV-2 vaccines have contributed to attenuating the burden of the COVID-19 pandemic by promoting the development of effective immune responses, thus reducing the spread and severity of the pandemic. A clinical trial with the Sputnik-V vaccine was conducted in Venezuela from December 2020 to July 2021. The aim of this study was to explore the antibody reactivity of vaccinated individuals towards different regions of the spike protein (S). Neutralizing antibody (NAb) activity was assessed using a commercial surrogate assay, detecting NAbs against the receptor-binding domain (RBD), and a plaque reduction neutralization test. NAb levels were correlated with the reactivity of the antibodies to the spike regions over time. The presence of Abs against nucleoprotein was also determined to rule out the effect of exposure to the virus during the clinical trial in the serological response. A high serological reactivity was observed to S and specifically to S1 and the RBD. S2, although recognized with lower intensity by vaccinated individuals, was the subunit exhibiting the highest cross-reactivity in prepandemic sera. This study is in agreement with the high efficacy reported for the Sputnik V vaccine and shows that this vaccine is able to induce an immunity lasting for at least 180 days. The dissection of the Ab reactivity to different regions of S allowed us to identify the relevance of epitopes outside the RBD that are able to induce NAbs. This research may contribute to the understanding of vaccine immunity against SARS-CoV-2, which could contribute to the design of future vaccine strategies.
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Affiliation(s)
- Alejandro Cornejo
- Laboratorio de Bioquímica Celular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela;
| | - Christopher Franco
- Laboratorio de Virología Celular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (C.F.); (J.L.Z.)
| | - Mariajose Rodriguez-Nuñez
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
| | - Alexis García
- Instituto de Inmunología, Universidad Central de Venezuela (UCV), Caracas 1040A, Venezuela; (A.G.); (I.B.); (S.M.)
| | - Inirida Belisario
- Instituto de Inmunología, Universidad Central de Venezuela (UCV), Caracas 1040A, Venezuela; (A.G.); (I.B.); (S.M.)
| | - Soriuska Mayora
- Instituto de Inmunología, Universidad Central de Venezuela (UCV), Caracas 1040A, Venezuela; (A.G.); (I.B.); (S.M.)
| | - Domingo José Garzaro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
| | - José Luis Zambrano
- Laboratorio de Virología Celular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (C.F.); (J.L.Z.)
| | - Rossana Celeste Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
| | - Mariana Hidalgo
- Laboratorio de Inmunoparasitología, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela;
| | - Nereida Parra-Giménez
- Laboratorio de Fisiología de Parásitos, Centro Biofísica y Bioquímica, IVIC, Caracas 1020A, Venezuela;
| | - Franklin Ennodio Claro
- Departamento de Tuberculosis, Servicio Autónomo Instituto de Biomedicina “Dr. Jacinto Convit”, UCV, Caracas 1010A, Venezuela; (F.E.C.); (J.H.d.W.)
| | - Ferdinando Liprandi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela;
| | - Jacobus Henri de Waard
- Departamento de Tuberculosis, Servicio Autónomo Instituto de Biomedicina “Dr. Jacinto Convit”, UCV, Caracas 1010A, Venezuela; (F.E.C.); (J.H.d.W.)
- Laboratorios de Investigación, Facultad de Ciencias de Salud, Universidad de Las Américas (UDLA), Quito 170125, Ecuador
| | - Héctor Rafael Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
| | - Flor Helene Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
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Kim JW, Lee JH, Kim HJ, Heo K, Lee Y, Jang HJ, Lee HY, Park JW, Cho YB, Shin HG, Yang HR, Lee HE, Song JY, Lee S. Empowering SARS-CoV-2 variant neutralization with a bifunctional antibody engineered with tandem heptad repeat 2 peptides. J Med Virol 2024; 96:e29506. [PMID: 38445718 DOI: 10.1002/jmv.29506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/28/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
With the global pandemic and the continuous mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the need for effective and broadly neutralizing treatments has become increasingly urgent. This study introduces a novel strategy that targets two aspects simultaneously, using bifunctional antibodies to inhibit both the attachment of SARS-CoV-2 to host cell membranes and viral fusion. We developed pioneering IgG4-(HR2)4 bifunctional antibodies by creating immunoglobulin G4-based and phage display-derived human monoclonal antibodies (mAbs) that specifically bind to the SARS-CoV-2 receptor-binding domain, engineered with four heptad repeat 2 (HR2) peptides. Our in vitro experiments demonstrate the superior neutralization efficacy of these engineered antibodies against various SARS-CoV-2 variants, ranging from original SARS-CoV-2 strain to the recently emerged Omicron variants, as well as SARS-CoV, outperforming the parental mAb. Notably, intravenous monotherapy with the bifunctional antibody neutralizes a SARS-CoV-2 variant in a murine model without causing significant toxicity. In summary, this study unveils the significant potential of HR2 peptide-driven bifunctional antibodies as a potent and versatile strategy for mitigating SARS-CoV-2 infections. This approach offers a promising avenue for rapid development and management in the face of the continuously evolving SARS-CoV-2 variants, holding substantial promise for pandemic control.
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Affiliation(s)
- Ji Woong Kim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ji Hyun Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Hyun Jung Kim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Kyun Heo
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul, Republic of Korea
| | - Yoonwoo Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Hui Jeong Jang
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Ho-Young Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Jun Won Park
- Division of Biomedical Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Yea Bin Cho
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ha Gyeong Shin
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ha Rim Yang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Hee Eon Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Jin Young Song
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Sukmook Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul, Republic of Korea
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5
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Zhang D, Kukkar D, Kim KH, Bhatt P. A comprehensive review on immunogen and immune-response proteins of SARS-CoV-2 and their applications in prevention, diagnosis, and treatment of COVID-19. Int J Biol Macromol 2024; 259:129284. [PMID: 38211928 DOI: 10.1016/j.ijbiomac.2024.129284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Abstract
Exposure to severe acute respiratory syndrome-corona virus-2 (SARS-CoV-2) prompts humoral immune responses in the human body. As the auxiliary diagnosis of a current infection, the existence of viral proteins can be checked from specific antibodies (Abs) induced by immunogenic viral proteins. For people with a weakened immune system, Ab treatment can help neutralize viral antigens to resist and treat the disease. On the other hand, highly immunogenic viral proteins can serve as effective markers for detecting prior infections. Additionally, the identification of viral particles or the presence of antibodies may help establish an immune defense against the virus. These immunogenic proteins rather than SARS-CoV-2 can be given to uninfected people as a vaccination to improve their coping ability against COVID-19 through the generation of memory plasma cells. In this work, we review immunogenic and immune-response proteins derived from SARS-CoV-2 with regard to their classification, origin, and diverse applications (e.g., prevention (vaccine development), diagnostic testing, and treatment (via neutralizing Abs)). Finally, advanced immunization strategies against COVID-19 are discussed along with the contemporary circumstances and future challenges.
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Affiliation(s)
- Daohong Zhang
- College of Food Engineering, Ludong University, Yantai 264025, Shandong, China; Bio-Nanotechnology Research Institute, Ludong University, Yantai 264025, Shandong, China
| | - Deepak Kukkar
- Department of Biotechnology, Chandigarh University, Gharuan, Mohali 140413, Punjab, India; University Center for Research and Development, Chandigarh University, Gharuan, Mohali 140413, Punjab, India
| | - Ki-Hyun Kim
- Department of Civil & Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Republic of Korea.
| | - Poornima Bhatt
- Department of Biotechnology, Chandigarh University, Gharuan, Mohali 140413, Punjab, India; University Center for Research and Development, Chandigarh University, Gharuan, Mohali 140413, Punjab, India
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6
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Tan S, Zhao J, Hu X, Li Y, Wu Z, Lu G, Yu Z, Du B, Liu Y, Li L, Chen Y, Li Y, Yao Y, Zhang X, Rao J, Gao G, Peng Y, Liu H, Yuan Z, Liu J, Wang Q, Hu H, Gao X, Zhou H, Yu H, Xu Y, Yu W, Feng L, Wang M, Shan C, Lu J, Lin J. Preclinical evaluation of RQ3013, a broad-spectrum mRNA vaccine against SARS-CoV-2 variants. Sci Bull (Beijing) 2023; 68:3192-3206. [PMID: 37993332 DOI: 10.1016/j.scib.2023.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/19/2023] [Accepted: 11/02/2023] [Indexed: 11/24/2023]
Abstract
The global emergence of SARS-CoV-2 variants has led to increasing breakthrough infections in vaccinated populations, calling for an urgent need to develop more effective and broad-spectrum vaccines to combat COVID-19. Here we report the preclinical development of RQ3013, an mRNA vaccine candidate intended to bring broad protection against SARS-CoV-2 variants of concern (VOCs). RQ3013, which contains pseudouridine-modified mRNAs formulated in lipid nanoparticles, encodes the spike (S) protein harboring a combination of mutations responsible for immune evasion of VOCs. Here we characterized the expressed S immunogen and evaluated the immunogenicity, efficacy, and safety of RQ3013 in various animal models. RQ3013 elicited robust immune responses in mice, hamsters, and nonhuman primates (NHP). It can induce high titers of antibodies with broad cross-neutralizing ability against the wild-type, B.1.1.7, B.1.351, B.1.617.2, and the newly emerging Omicron variants. In mice and NHP, two doses of RQ3013 protected the upper and lower respiratory tract against infection by SARS-CoV-2 and its variants. Furthermore, our safety assessment of RQ3013 in NHP showed no observable adverse effects. These results provide strong support for the evaluation of RQ3013 in clinical trials and suggest that it may be a promising candidate for broad protection against COVID-19 and its variants.
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Affiliation(s)
- Shudan Tan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Jinghua Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Xue Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yufeng Li
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zihan Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Guoliang Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Zhaoli Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Binhe Du
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Yan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Li Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Yuchen Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Ye Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China
| | - Yanfeng Yao
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xiaoyu Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Juhong Rao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ge Gao
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yun Peng
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Hang Liu
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhiming Yuan
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jia Liu
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qianran Wang
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Hengrui Hu
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xiaobo Gao
- Shanghai RNACure Biopharma Co., Ltd., Shanghai 200438, China
| | - Hui Zhou
- Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China; Shanghai RNACure Biopharma Co., Ltd., Shanghai 200438, China
| | - Hang Yu
- Shanghai RNACure Biopharma Co., Ltd., Shanghai 200438, China
| | - Yingjie Xu
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wei Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China.
| | - Lin Feng
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou 510060, China.
| | - Manli Wang
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Chao Shan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Jing Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China; Shanghai RNACure Biopharma Co., Ltd., Shanghai 200438, China.
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200438, China; Zhangjiang mRNA Innovation and Translation Center, Fudan University, Shanghai 200438, China.
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7
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Mohazzab A, Fallah Mehrabadi MH, Es-Haghi A, Kalantari S, Mokhberalsafa L, Setarehdan SA, Sadeghi F, Rezaei Mokarram A, Haji Moradi M, Razaz SH, Taghdiri M, Ansarifar A, Lotfi M, Khorasani A, Nofeli M, Masoumi S, Boluki Z, Erfanpoor S, Bagheri Amiri F, Esmailzadehha N, Filsoof S, Mohseni V, Ghahremanzadeh N, Safari S, Shahsavan M, Bayazidi S, Raghami Derakhshani M, Rabiee MH, Golmoradi-Zadeh R, Khodadoost B, Solaymani-Dodaran M, Banihashemi SR. Phase II, Safety and Immunogenicity of RAZI Cov Pars (RCP) SARS Cov-2 Vaccine in Adults Aged 18-70 Years; A Randomized, Double-Blind Clinical Trial. J Pharm Sci 2023; 112:3012-3021. [PMID: 37832918 DOI: 10.1016/j.xphs.2023.09.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/30/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND This study explores the safety and immunogenicity of the Razi-Cov-Pars (RCP) SARS Cov-2 recombinant spike protein vaccine. METHOD In a randomized, double-blind, placebo-controlled trial, adults aged 18-70 were randomly allocated to receive selected 10 µg/200 µl vaccine strengths or placebo (adjuvant). It included two intramuscular injections at days 0 and 21, followed by an intranasal dose at day 51. Immediate and delayed solicited local and systemic adverse reactions after each dose up to a week, and specific IgG antibodies against SARS Cov-2 spike antigens two weeks after the 2nd dose were assessed as primary outcomes. Secondary safety outcomes were abnormal laboratory findings and medically attended adverse events (MAAE) over six months follow up. Secondary immunogenicity outcomes were neutralizing antibody activity and cell-mediated immune response. RESULT Between May 27th and July 15th, 2021, 500 participants were enrolled. Participants' mean (SD) age was 37.8 (9.0), and 67.0 % were male. No immediate adverse reaction was observed following the intervention. All solicited local and systemic adverse events were moderate (Grade I-II). Specific IgG antibody response against S antigen in the vaccine group was 5.28 times (95 %CI: 4.02-6.94) the placebo group with a 75 % seroconversion rate. During six months of follow-up, 8 SAEs were reported, unrelated to the study intervention. The participants sustained their acquired humoral responses at the end of the sixth month. The vaccine predominantly resulted in T-helper 1 cell-mediated immunity, CD8+ cytotoxic T-cell increase, and no increase in inflammatory IL-6 cytokine. CONCLUSION RCP vaccine is safe and creates strong and durable humoral and cellular immunity. TRIAL REGISTRATION (IRCT20201214049709N2).
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Affiliation(s)
- Arash Mohazzab
- School of Public Health, Iran University of Medical Sciences, Tehran, Iran; Reproductive Biotechnology Research Center, Avicenna Research Institute Tehran, ACECR, Tehran, Iran
| | - Mohammad Hossein Fallah Mehrabadi
- Department of epidemiology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Ali Es-Haghi
- Department of Physico Chemistry, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Saeed Kalantari
- Departments of Infectious Diseases and Tropical Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ladan Mokhberalsafa
- Department of epidemiology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | | | - Fariba Sadeghi
- Department of epidemiology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Ali Rezaei Mokarram
- Research and Development Department, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Monireh Haji Moradi
- Department of immunology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Seyad Hossein Razaz
- Department of immunology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Maryam Taghdiri
- Department of immunology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Akram Ansarifar
- School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Lotfi
- Department of Quality Control, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Akbar Khorasani
- Research and Development Department, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mojtaba Nofeli
- Research and Development Department, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Safdar Masoumi
- Department of Biostatistics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zahra Boluki
- Knowledge Utilization Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeed Erfanpoor
- School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Fahimeh Bagheri Amiri
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging infectious diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Neda Esmailzadehha
- School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Sara Filsoof
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Vahideh Mohseni
- School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | | | - Shiva Safari
- School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Shahsavan
- School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Shnoo Bayazidi
- School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Raghami Derakhshani
- Department of epidemiology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Hasan Rabiee
- Department Of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Rezvan Golmoradi-Zadeh
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Behnam Khodadoost
- School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Masoud Solaymani-Dodaran
- Clinical Trial Center, Iran University of Medical Science, Tehran, Iran; Minimally Invasive Surgery Research Center, Hazrat-e-Rasool Hospital, Iran University of Medical Science, Tehran, Iran.
| | - Seyed Reza Banihashemi
- Department of immunology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
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8
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Kapingidza AB, Marston DJ, Harris C, Wrapp D, Winters K, Mielke D, Xiaozhi L, Yin Q, Foulger A, Parks R, Barr M, Newman A, Schäfer A, Eaton A, Flores JM, Harner A, Catanzaro NJ, Mallory ML, Mattocks MD, Beverly C, Rhodes B, Mansouri K, Van Itallie E, Vure P, Dunn B, Keyes T, Stanfield-Oakley S, Woods CW, Petzold EA, Walter EB, Wiehe K, Edwards RJ, Montefiori DC, Ferrari G, Baric R, Cain DW, Saunders KO, Haynes BF, Azoitei ML. Engineered immunogens to elicit antibodies against conserved coronavirus epitopes. Nat Commun 2023; 14:7897. [PMID: 38036525 PMCID: PMC10689493 DOI: 10.1038/s41467-023-43638-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Immune responses to SARS-CoV-2 primarily target the receptor binding domain of the spike protein, which continually mutates to escape acquired immunity. Other regions in the spike S2 subunit, such as the stem helix and the segment encompassing residues 815-823 adjacent to the fusion peptide, are highly conserved across sarbecoviruses and are recognized by broadly reactive antibodies, providing hope that vaccines targeting these epitopes could offer protection against both current and emergent viruses. Here we employ computational modeling to design scaffolded immunogens that display the spike 815-823 peptide and the stem helix epitopes without the distracting and immunodominant receptor binding domain. These engineered proteins bind with high affinity and specificity to the mature and germline versions of previously identified broadly protective human antibodies. Epitope scaffolds interact with both sera and isolated monoclonal antibodies with broadly reactivity from individuals with pre-existing SARS-CoV-2 immunity. When used as immunogens, epitope scaffolds elicit sera with broad betacoronavirus reactivity and protect as "boosts" against live virus challenge in mice, illustrating their potential as components of a future pancoronavirus vaccine.
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Affiliation(s)
- A Brenda Kapingidza
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Daniel J Marston
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Caitlin Harris
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Daniel Wrapp
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Kaitlyn Winters
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Dieter Mielke
- Department of Surgery, Duke University, Durham, NC, USA
- Center for Human Systems Immunology, Duke University, Durham, NC, USA
| | - Lu Xiaozhi
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Qi Yin
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Andrew Foulger
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Rob Parks
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amanda Eaton
- Department of Surgery, Duke University, Durham, NC, USA
| | - Justine Mae Flores
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Austin Harner
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael L Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa D Mattocks
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christopher Beverly
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Brianna Rhodes
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | | | - Elizabeth Van Itallie
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Pranay Vure
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Brooke Dunn
- Department of Surgery, Duke University, Durham, NC, USA
| | - Taylor Keyes
- Department of Surgery, Duke University, Durham, NC, USA
| | | | - Christopher W Woods
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
- Center for Infectious Diseases and Diagnostic Innovation, Duke University Medical Center, Durham, NC, USA
| | - Elizabeth A Petzold
- Center for Infectious Diseases and Diagnostic Innovation, Duke University Medical Center, Durham, NC, USA
| | - Emmanuel B Walter
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Robert J Edwards
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | | | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Surgery, Duke University, Durham, NC, USA
- Center for Human Systems Immunology, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Surgery, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Department of Immunology, Duke University, Durham, NC, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
- Department of Immunology, Duke University, Durham, NC, USA
| | - Mihai L Azoitei
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA.
- Department of Medicine, Duke University, Durham, NC, USA.
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9
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Balinsky CA, Jiang L, Jani V, Cheng Y, Zhang Z, Belinskaya T, Qiu Q, Long TK, Schilling MA, Jenkins SA, Corson KS, Martin NJ, Letizia AG, Hontz RD, Sun P. Antibodies to S2 domain of SARS-CoV-2 spike protein in Moderna mRNA vaccinated subjects sustain antibody-dependent NK cell-mediated cell cytotoxicity against Omicron BA.1. Front Immunol 2023; 14:1266829. [PMID: 38077368 PMCID: PMC10702584 DOI: 10.3389/fimmu.2023.1266829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023] Open
Abstract
Vaccination with the primary two-dose series of SARS-CoV-2 mRNA protects against infection with the ancestral strain, and limits the presentation of severe disease after re-infection by multiple variants of concern (VOC), including Omicron, despite the lack of a strong neutralizing response to these variants. We compared antibody responses in serum samples collected from mRNA-1273 (Moderna) vaccinated subjects to identify mechanisms of immune escape and cross-protection. Using pseudovirus constructs containing domain-specific amino acid changes representative of Omicron BA.1, combined with domain competition and RBD-antibody depletion, we showed that RBD antibodies were primarily responsible for virus neutralization and variant escape. Antibodies to NTD played a less significant role in antibody neutralization but acted along with RBD to enhance neutralization. S2 of Omicron BA.1 had no impact on neutralization escape, suggesting it is a less critical domain for antibody neutralization; however, it was as capable as S1 at eliciting IgG3 responses and NK-cell mediated, antibody-dependent cell cytotoxicity (ADCC). Antibody neutralization and ADCC activities to RBD, NTD, and S1 were all prone to BA.1 escape. In contrast, ADCC activities to S2 resisted BA.1 escape. In conclusion, S2 antibodies showed potent ADCC function and resisted Omicron BA.1 escape, suggesting that S2 contributes to cross-protection against Omicron BA.1. In line with its conserved nature, S2 may hold promise as a vaccine target against future variants of SARS-CoV-2.
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Affiliation(s)
- Corey A. Balinsky
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Le Jiang
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Vihasi Jani
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | | | - Zhiwen Zhang
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Tatyana Belinskaya
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Qi Qiu
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | | | - Megan A. Schilling
- Virology and Emerging Infectious Department, U.S. Naval Medical Research Unit SOUTH, Lima, Peru
| | - Sarah A. Jenkins
- Diagnostics and Surveillance Department, Naval Medical Research Command, Silver Spring, MD, United States
| | - Karen S. Corson
- US Naval Medical Research Unit-INDO PACIFIC, Singapore, Singapore
| | | | | | - Robert D. Hontz
- US Naval Medical Research Unit-INDO PACIFIC, Singapore, Singapore
| | - Peifang Sun
- Diagnostics and Surveillance Department, Naval Medical Research Command, Silver Spring, MD, United States
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10
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Keitany GJ, Rubin BER, Garrett ME, Musa A, Tracy J, Liang Y, Ebert P, Moore AJ, Guan J, Eggers E, Lescano N, Brown R, Carbo A, Al-Asadi H, Ching T, Day A, Harris R, Linkem C, Popov D, Wilkins C, Li L, Wang J, Liu C, Chen L, Dines JN, Atyeo C, Alter G, Baldo L, Sherwood A, Howie B, Klinger M, Yusko E, Robins HS, Benzeno S, Gilbert AE. Multimodal, broadly neutralizing antibodies against SARS-CoV-2 identified by high-throughput native pairing of BCRs from bulk B cells. Cell Chem Biol 2023; 30:1377-1389.e8. [PMID: 37586370 PMCID: PMC10659930 DOI: 10.1016/j.chembiol.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/25/2023] [Accepted: 07/23/2023] [Indexed: 08/18/2023]
Abstract
TruAB Discovery is an approach that integrates cellular immunology, high-throughput immunosequencing, bioinformatics, and computational biology in order to discover naturally occurring human antibodies for prophylactic or therapeutic use. We adapted our previously described pairSEQ technology to pair B cell receptor heavy and light chains of SARS-CoV-2 spike protein-binding antibodies derived from enriched antigen-specific memory B cells and bulk antibody-secreting cells. We identified approximately 60,000 productive, in-frame, paired antibody sequences, from which 2,093 antibodies were selected for functional evaluation based on abundance, isotype and patterns of somatic hypermutation. The exceptionally diverse antibodies included RBD-binders with broad neutralizing activity against SARS-CoV-2 variants, and S2-binders with broad specificity against betacoronaviruses and the ability to block membrane fusion. A subset of these RBD- and S2-binding antibodies demonstrated robust protection against challenge in hamster and mouse models. This high-throughput approach can accelerate discovery of diverse, multifunctional antibodies against any target of interest.
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Affiliation(s)
| | | | | | - Andrea Musa
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Jeff Tracy
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Yu Liang
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Peter Ebert
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | - Erica Eggers
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | - Ryan Brown
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Adria Carbo
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | - Austin Day
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | | | | | - Lianqu Li
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Jiao Wang
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Chuanxin Liu
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Li Chen
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Lance Baldo
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | - Bryan Howie
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Mark Klinger
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Erik Yusko
- Adaptive Biotechnologies, Seattle, WA 98109, USA
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11
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de Oliveira DF. In silico identification of five binding sites on the SARS-CoV-2 spike protein and selection of seven ligands for such sites. J Biomol Struct Dyn 2023:1-19. [PMID: 37921757 DOI: 10.1080/07391102.2023.2278077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023]
Abstract
To contribute to the development of products capable of complexing with the SARS-CoV-2 spike protein, and thus preventing the virus from entering the host cell, this work aimed at discovering binding sites in the whole protein structure, as well as selecting substances capable of binding efficiently to such sites. Initially, the three-dimensional structure of the protein, with all receptor binding domains in the closed state, underwent blind docking with 38 substances potentially capable of binding to this protein according to the literature. This allowed the identification of five binding sites. Then, those substances with more affinities for these sites underwent pharmacophoric search in the ZINC15 database. The 14,329 substances selected from ZINC15 were subjected to docking to the five selected sites of the spike protein. The ligands with more affinities for the protein sites, as well as the selected sites themselves, were used in the de novo design of new ligands that were also docked to the binding sites of the protein. The best ligands, regardless of their origins, were used to form complexes with the spike protein, which were subsequently used in molecular dynamics simulations and calculations of ligands affinities to the protein through the molecular mechanics/Poisson-Boltzmann surface area method (MMPBSA). Seven substances with good affinities to the spike protein (-12.9 to -20.6 kcal/mol), satisfactory druggability (Bioavailability score: 0.17 to 0.55), and low acute toxicity to mice (LD50: 751 to 1421 mg/kg) were selected as potentially useful for the future development of new products to manage COVID-19 infections.Communicated by Ramaswamy H. Sarma.
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12
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Boix-Besora A, Gòdia F, Cervera L. Gag Virus-like Particles Functionalized with SARS-CoV-2 Variants: Generation, Characterization and Recognition by COVID-19 Convalescent Patients' Sera. Vaccines (Basel) 2023; 11:1641. [PMID: 38005972 PMCID: PMC10675557 DOI: 10.3390/vaccines11111641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/16/2023] [Accepted: 10/21/2023] [Indexed: 11/26/2023] Open
Abstract
The robustness, safety, versatility, and high immunogenicity of virus-like particles (VLPs) make them a promising approach for the generation of vaccines against a broad range of pathogens. VLPs are recombinant macromolecular structures that closely mimic the native conformation of viruses without carrying viral genetic material. Particularly, HIV-1 Gag-based VLPs are a suitable platform for the presentation of the SARS-CoV-2 Spike (S) protein on their surface. In this context, this work studies the effect of different rationally engineered mutations of the S protein to improve some of its characteristics. The studied variants harbored mutations such as proline substitutions for S stabilization, D614G from the early dominant pandemic form, the elimination of the S1/S2 furin cleavage site to improve S homogeneity, the suppression of a retention motif to favor its membrane localization, and cysteine substitutions to increase its immunogenicity and avoid potential undesired antibody-dependent enhancement (ADE) effects. The influence of the mutations on VLP expression was studied, as well as their immunogenic potential, by testing the recognition of the generated VLP variants by COVID-19 convalescent patients' sera. The results of this work are conceived to give insights on the selection of S protein candidates for their use as immunogens and to showcase the potential of VLPs as carriers for antigen presentation.
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Affiliation(s)
- Arnau Boix-Besora
- Grup d’Enginyeria de Bioprocessos i Biocatàlisi Aplicada ENG4BIO, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain
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13
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Nedaei F, Esmaeili Rastaghi AR, Goodarzi E, Haji Mullah Asadullah H, Mirhadi F, Fateh A. Introduction and effect of natural selection analysis at common mutations of SARS-CoV-2 spike gene in Iran. Virus Res 2023; 336:199202. [PMID: 37595664 PMCID: PMC10491845 DOI: 10.1016/j.virusres.2023.199202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/20/2023]
Abstract
The epidemic of coronavirus disease 2019 (COVID-19) was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike (S) protein of SARS-Cov-2 is composed of two subunits, S1 and S2. This study aimed to describe SARS-CoV-2 haplotypes in Iranians based on the S gene, which plays a key role in the receptor recognition and cell membrane fusion proses. 95 positive saliva samples for SARS-CoV-2 were amplified and sequenced for the S gene. The sequences were classified into 35 haplotypes, which 11 haplotypes were new (H1, H2, H3, H4, H6, H7, H11, H13, H15, H16, H25) and have not been reported so far. Amino acid substitutions were found at 40 positions that 23 were located at S1 subunit and 16 were at S2 subunit and one was at cleavage loop (P681H/R), thus polymorphisms at S1 subunit were found to be higher than S2. The neutrality index (NI) analyses showed a negative departure from the neutral substitution patterns (NI > 1) for S1 and S2 subunit in the studied sequences. The co-occurrence of B-cell epitopes and mutation sites were found in seven positions with more probably to be exposed the immune system pressure. In conclusion, the results provide the significant data to design an effective vaccine based on this protein.
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Affiliation(s)
- Fatemeh Nedaei
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | | | - Esmaeil Goodarzi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Fatemeh Mirhadi
- Department of Medical science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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14
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Mykytyn AZ, Fouchier RA, Haagmans BL. Antigenic evolution of SARS coronavirus 2. Curr Opin Virol 2023; 62:101349. [PMID: 37647851 DOI: 10.1016/j.coviro.2023.101349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023]
Abstract
SARS coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, emerged in China in December 2019. Vaccines developed were very effective initially, however, the virus has shown remarkable evolution with multiple variants spreading globally over the last three years. Nowadays, newly emerging Omicron lineages are gaining substitutions at a fast rate, resulting in escape from neutralization by antibodies that target the Spike protein. Tools to map the impact of substitutions on the further antigenic evolution of SARS-CoV-2, such as antigenic cartography, may be helpful to update SARS-CoV-2 vaccines. In this review, we focus on the antigenic evolution of SARS-CoV-2, highlighting the impact of Spike protein substitutions individually and in combination on immune escape.
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Affiliation(s)
- Anna Z Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ron Am Fouchier
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands.
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15
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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16
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Kapingidza B, Marston DJ, Harris C, Wrapp D, Winters K, Mielke D, Xiaozhi L, Yin Q, Foulger A, Parks R, Barr M, Newman A, Schäfer A, Eaton A, Flores JM, Harner A, Cantazaro NJ, Mallory ML, Mattocks MD, Beverly C, Rhodes B, Mansouri K, Itallie EV, Vure P, Manness B, Keyes T, Stanfield-Oakley S, Woods CW, Petzold EA, Walter EB, Wiehe K, Edwards RJ, Montefiori D, Ferrari G, Baric R, Cain DW, Saunders KO, Haynes BF, Azoitei ML. Engineered Immunogens to Elicit Antibodies Against Conserved Coronavirus Epitopes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530277. [PMID: 36909627 PMCID: PMC10002628 DOI: 10.1101/2023.02.27.530277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Immune responses to SARS-CoV-2 primarily target the receptor binding domain of the spike protein, which continually mutates to escape acquired immunity. Other regions in the spike S2 subunit, such as the stem helix and the segment encompassing residues 815-823 adjacent to the fusion peptide, are highly conserved across sarbecoviruses and are recognized by broadly reactive antibodies, providing hope that vaccines targeting these epitopes could offer protection against both current and emergent viruses. Here we employed computational modeling to design scaffolded immunogens that display the spike 815-823 peptide and the stem helix epitopes without the distracting and immunodominant RBD. These engineered proteins bound with high affinity and specificity to the mature and germline versions of previously identified broadly protective human antibodies. Epitope scaffolds interacted with both sera and isolated monoclonal antibodies with broadly reactivity from individuals with pre-existing SARS-CoV-2 immunity. When used as immunogens, epitope scaffolds elicited sera with broad betacoronavirus reactivity and protected as "boosts" against live virus challenge in mice, illustrating their potential as components of a future pancoronavirus vaccine.
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17
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Stincarelli MA, Quagliata M, Di Santo A, Pacini L, Fernandez FR, Arvia R, Rinaldi S, Papini AM, Rovero P, Giannecchini S. SARS-CoV-2 inhibitory activity of a short peptide derived from internal fusion peptide of S2 subunit of spike glycoprotein. Virus Res 2023; 334:199170. [PMID: 37422270 PMCID: PMC10384657 DOI: 10.1016/j.virusres.2023.199170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/10/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has posed a great concern in human population. To fight coronavirus emergence, we have dissected the conserved amino acid region of the internal fusion peptide in the S2 subunit of Spike glycoprotein of SARS-CoV-2 to design new inhibitory peptides. Among the 11 overlapping peptides (9-23-mer), PN19, a 19-mer peptide, exhibited a powerful inhibitory activity against different SARS-CoV-2 clinical isolate variants in absence of cytotoxicity. The PN19 inhibitory activity was found to be dependent on conservation of the central Phe and C-terminal Tyr residues in the peptide sequence. Circular dichroism spectra of the active peptide exhibited an alpha-helix propensity, confirmed by secondary structure prediction analysis. The PN19 inhibitory activity, exerted in the first step of virus infection, was reduced after peptide adsorption treatment with virus-cell substrate during fusion interaction. Additionally, PN19 inhibitory activity was reduced by adding S2 membrane-proximal region derived peptides. PN19 showed binding ability to the S2 membrane proximal region derived peptides, confirmed by molecular modelling, playing a role in the mechanism of action. Collectively, these results confirm that the internal fusion peptide region is a good candidate on which develop peptidomimetic anti SARS-CoV-2 antivirals.
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Affiliation(s)
- Maria Alfreda Stincarelli
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy
| | - Michael Quagliata
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Andrea Di Santo
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino 50019, Italy
| | - Lorenzo Pacini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Feliciana Real Fernandez
- CNR - Istituto di Chimica dei Composti Organometallici (CNR-ICCOM), Via Madonna del Piano 10, Sesto Fiorentino I-50019, Italy
| | - Rosaria Arvia
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy
| | - Silvia Rinaldi
- CNR - Istituto di Chimica dei Composti Organometallici (CNR-ICCOM), Via Madonna del Piano 10, Sesto Fiorentino I-50019, Italy
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino 50019, Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy.
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18
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Strizzi S, Bernardo L, D'Ursi P, Urbinati C, Bianco A, Limanaqi F, Manconi A, Milanesi M, Macchi A, Di Silvestre D, Cavalleri A, Pareschi G, Rusnati M, Clerici M, Mauri P, Biasin M. An innovative strategy to investigate microbial protein modifications in a reliable fast and sensitive way: A therapy oriented proof of concept based on UV-C irradiation of SARS-CoV-2 spike protein. Pharmacol Res 2023; 194:106862. [PMID: 37479104 DOI: 10.1016/j.phrs.2023.106862] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/04/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023]
Abstract
The characterization of modifications of microbial proteins is of primary importance to dissect pathogen lifecycle mechanisms and could be useful in identifying therapeutic targets. Attempts to solve this issue yielded only partial and non-exhaustive results. We developed a multidisciplinary approach by coupling in vitro infection assay, mass spectrometry (MS), protein 3D modelling, and surface plasma resonance (SPR). As a proof of concept, the effect of low UV-C (273 nm) irradiation on SARS-CoV-2 spike (S) protein was investigated. Following UV-C exposure, MS analysis identified, among other modifications, the disruption of a disulphide bond within the conserved S2 subunit of S protein. Computational analyses revealed that this bond breakage associates with an allosteric effect resulting in the generation of a closed conformation with a reduced ability to bind the ACE2 receptor. The UV-C-induced reduced affinity of S protein for ACE2 was further confirmed by SPR analyses and in vitro infection assays. This comprehensive approach pinpoints the S2 domain of S protein as a potential therapeutic target to prevent SARS-CoV-2 infection. Notably, this workflow could be used to screen a wide variety of microbial protein domains, resulting in a precise molecular fingerprint and providing new insights to adequately address future epidemics.
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Affiliation(s)
- Sergio Strizzi
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Letizia Bernardo
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy
| | - Pasqualina D'Ursi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy
| | - Chiara Urbinati
- Unit of Macromolecular Interaction Analysis, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Andrea Bianco
- Italian National Institute for Astrophysics (INAF) - Brera Astronomical Observatory, Via E. Bianchi, 46, Merate, 23807 Lecco, Italy
| | - Fiona Limanaqi
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy; Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy
| | - Andrea Manconi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy
| | - Maria Milanesi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy; Unit of Macromolecular Interaction Analysis, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Alberto Macchi
- Italian National Institute for Astrophysics (INAF) - Brera Astronomical Observatory, Via E. Bianchi, 46, Merate, 23807 Lecco, Italy
| | - Dario Di Silvestre
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy
| | - Adalberto Cavalleri
- Epidemiology and Prevention Unit, IRCCS Foundation, Istituto Nazionale dei Tumori, Via Giacomo Venezian, 1, 20133 Milan, Italy
| | - Giovanni Pareschi
- Italian National Institute for Astrophysics (INAF) - Brera Astronomical Observatory, Via E. Bianchi, 46, Merate, 23807 Lecco, Italy
| | - Marco Rusnati
- Unit of Macromolecular Interaction Analysis, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy; Don C. Gnocchi Foundation, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Foundation, Via A. Capecelatro 66, 20148 Milan, íItaly
| | - PierLuigi Mauri
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), 20054 Segrate, MI, Italy; Interdisciplinary Research Center "Health Science", Sant'Anna School of Advanced Studies, 56127 Pisa, Italy.
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
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19
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Serra N, Andriolo M, Butera I, Mazzola G, Sergi CM, Fasciana TMA, Giammanco A, Gagliano MC, Cascio A, Di Carlo P. A Serological Analysis of the Humoral Immune Responses of Anti-RBD IgG, Anti-S1 IgG, and Anti-S2 IgG Levels Correlated to Anti-N IgG Positivity and Negativity in Sicilian Healthcare Workers (HCWs) with Third Doses of the mRNA-Based SARS-CoV-2 Vaccine: A Retrospective Cohort Study. Vaccines (Basel) 2023; 11:1136. [PMID: 37514952 PMCID: PMC10384738 DOI: 10.3390/vaccines11071136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/07/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND With SARS-CoV-2 antibody tests on the market, healthcare providers must be confident that they can use the results to provide actionable information to understand the characteristics and dynamics of the humoral response and antibodies (abs) in SARS-CoV-2-vaccinated patients. In this way, the study of the antibody responses of healthcare workers (HCWs), a population that is immunocompetent, adherent to vaccination, and continuously exposed to different virus variants, can help us understand immune protection and determine vaccine design goals. METHODS We retrospectively evaluated antibody responses via multiplex assays in a sample of 538 asymptomatic HCWs with a documented complete vaccination cycle of 3 doses of mRNA vaccination and no previous history of infection. Our sample was composed of 49.44% males and 50.56% females, with an age ranging from 21 to 71 years, and a mean age of 46.73 years. All of the HCWs' sera were collected from April to July 2022 at the Sant'Elia Hospital of Caltanissetta to investigate the immunologic responses against anti-RBD, anti-S1, anti-S2, and anti-N IgG abs. RESULTS A significant difference in age between HCWs who were positive and negative for anti-N IgG was observed. For anti-S2 IgG, a significant difference between HCWs who were negative and positive compared to anti-N IgG was observed only for positive HCWs, with values including 10 (U/mL)-100 (U/mL); meanwhile, for anti-RBD IgG and anti-S1 IgG levels, there was only a significant difference observed for positive HCWs with diluted titers. For the negative values of anti-N IgG, among the titer dilution levels of anti-RBD, anti-S1, and anti-S2 IgG, the anti-S2 IgG levels were significantly lower than the anti-RBD and anti-S1 levels; in addition, the anti-S1 IgG levels were significantly lower than the anti-RBD IgG levels. For the anti-N IgG positive levels, only the anti-S2 IgG levels were significantly lower than the anti-RBD IgG and anti-S1 IgG levels. Finally, a logistic regression analysis showed that age and anti-S2 IgG were negative and positive predictors of anti-N IgG levels, respectively. The analysis between the vaccine type and mixed mRNA combination showed higher levels of antibodies in mixed vaccinated HCWs. This finding disappeared in the anti-N positive group. CONCLUSIONS Most anti-N positive HCWs showed antibodies against the S2 domain and were young subjects. Therefore, the authors suggest that including the anti-SARS-CoV-2-S2 in antibody profiles can serve as a complementary testing approach to qRT-PCR for the early identification of asymptomatic infections in order to reduce the impact of potential new SARS-CoV-2 variants. Our serological investigation on the type of mRNA vaccine and mixed mRNA vaccines shows that future investigations on the serological responses in vaccinated asymptomatic patients exposed to previous infection or reinfection are warranted for updated vaccine boosters.
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Affiliation(s)
- Nicola Serra
- Department of Public Health, University Federico II of Naples, 80131 Napoli, Italy
| | - Maria Andriolo
- Clinical Pathology Laboratory, Provincial Health Authority of Caltanissetta, 93100 Caltanissetta, Italy
| | - Ignazio Butera
- Degree Course in Medicine and Surgery, Medical Scholl of Hypatia, University of Palermo, 93100 Caltanissetta, Italy
| | - Giovanni Mazzola
- Infectious Disease Unit, Provincial Health Authority of Caltanissetta, 93100 Caltanissetta, Italy
| | - Consolato Maria Sergi
- Department of Pathology and Laboratory Medicine, University of Ottawa, 401 Smyth Road, Ottawa, ON K1H 8L1, Canada
| | - Teresa Maria Assunta Fasciana
- Department of Health Promotion, Maternal-Childhood, Internal Medicine of Excellence "G. D'Alessandro", University of Palermo, 90127 Palermo, Italy
| | - Anna Giammanco
- Department of Health Promotion, Maternal-Childhood, Internal Medicine of Excellence "G. D'Alessandro", University of Palermo, 90127 Palermo, Italy
| | - Maria Chiara Gagliano
- Infectious Disease Unit, Department of Health Promotion, Maternal-Childhood, Internal Medicine of Excellence "G. D'Alessandro", University of Palermo, 90127 Palermo, Italy
| | - Antonio Cascio
- Infectious Disease Unit, Department of Health Promotion, Maternal-Childhood, Internal Medicine of Excellence "G. D'Alessandro", University of Palermo, 90127 Palermo, Italy
| | - Paola Di Carlo
- Infectious Disease Unit, Department of Health Promotion, Maternal-Childhood, Internal Medicine of Excellence "G. D'Alessandro", University of Palermo, 90127 Palermo, Italy
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20
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Marcinkevics R, Silva PN, Hankele AK, Dörnte C, Kadelka S, Csik K, Godbersen S, Goga A, Hasenöhrl L, Hirschi P, Kabakci H, LaPierre MP, Mayrhofer J, Title AC, Shu X, Baiioud N, Bernal S, Dassisti L, Saenz-de-Juano MD, Schmidhauser M, Silvestrelli G, Ulbrich SZ, Ulbrich TJ, Wyss T, Stekhoven DJ, Al-Quaddoomi FS, Yu S, Binder M, Schultheiβ C, Zindel C, Kolling C, Goldhahn J, Seighalani BK, Zjablovskaja P, Hardung F, Schuster M, Richter A, Huang YJ, Lauer G, Baurmann H, Low JS, Vaqueirinho D, Jovic S, Piccoli L, Ciesek S, Vogt JE, Sallusto F, Stoffel M, Ulbrich SE. Machine learning analysis of humoral and cellular responses to SARS-CoV-2 infection in young adults. Front Immunol 2023; 14:1158905. [PMID: 37313411 PMCID: PMC10258347 DOI: 10.3389/fimmu.2023.1158905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/09/2023] [Indexed: 06/15/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces B and T cell responses, contributing to virus neutralization. In a cohort of 2,911 young adults, we identified 65 individuals who had an asymptomatic or mildly symptomatic SARS-CoV-2 infection and characterized their humoral and T cell responses to the Spike (S), Nucleocapsid (N) and Membrane (M) proteins. We found that previous infection induced CD4 T cells that vigorously responded to pools of peptides derived from the S and N proteins. By using statistical and machine learning models, we observed that the T cell response highly correlated with a compound titer of antibodies against the Receptor Binding Domain (RBD), S and N. However, while serum antibodies decayed over time, the cellular phenotype of these individuals remained stable over four months. Our computational analysis demonstrates that in young adults, asymptomatic and paucisymptomatic SARS-CoV-2 infections can induce robust and long-lasting CD4 T cell responses that exhibit slower decays than antibody titers. These observations imply that next-generation COVID-19 vaccines should be designed to induce stronger cellular responses to sustain the generation of potent neutralizing antibodies.
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Affiliation(s)
| | | | | | - Charlyn Dörnte
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Sarah Kadelka
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Katharina Csik
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Svenja Godbersen
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Algera Goga
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Lynn Hasenöhrl
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Pascale Hirschi
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Hasan Kabakci
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Mary P. LaPierre
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Johanna Mayrhofer
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | | | - Xuan Shu
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Nouell Baiioud
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Sandra Bernal
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Laura Dassisti
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | | | - Meret Schmidhauser
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Giulia Silvestrelli
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Simon Z. Ulbrich
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Thea J. Ulbrich
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Tamara Wyss
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Daniel J. Stekhoven
- NEXUS Personalized Health Technologies, Zurich & SIB Swiss Institute of Bioinformatics, ETH Zurich, Lausanne, Switzerland
| | - Faisal S. Al-Quaddoomi
- NEXUS Personalized Health Technologies, Zurich & SIB Swiss Institute of Bioinformatics, ETH Zurich, Lausanne, Switzerland
| | - Shuqing Yu
- NEXUS Personalized Health Technologies, Zurich & SIB Swiss Institute of Bioinformatics, ETH Zurich, Lausanne, Switzerland
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Christoph Schultheiβ
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Claudia Zindel
- Department of Health Science, Translational Medicine, ETH Zurich, Zurich, Switzerland
| | - Christoph Kolling
- Department of Health Science, Translational Medicine, ETH Zurich, Zurich, Switzerland
| | - Jörg Goldhahn
- Department of Health Science, Translational Medicine, ETH Zurich, Zurich, Switzerland
| | | | | | - Frank Hardung
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Marc Schuster
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Anne Richter
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Yi-Ju Huang
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Gereon Lauer
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | | | - Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Daniela Vaqueirinho
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Sandra Jovic
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs BioMed SA, a Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Sandra Ciesek
- Institute of Medical Virology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Julia E. Vogt
- Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
- Medical Immunology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Markus Stoffel
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- University Hospital Zurich, Zurich, Switzerland
| | - Susanne E. Ulbrich
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
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21
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Kaplonek P, Deng Y, Shih-Lu Lee J, Zar HJ, Zavadska D, Johnson M, Lauffenburger DA, Goldblatt D, Alter G. Hybrid immunity expands the functional humoral footprint of both mRNA and vector-based SARS-CoV-2 vaccines. Cell Rep Med 2023; 4:101048. [PMID: 37182520 PMCID: PMC10126214 DOI: 10.1016/j.xcrm.2023.101048] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/13/2022] [Accepted: 04/20/2023] [Indexed: 05/16/2023]
Abstract
Despite the successes of current coronavirus disease 2019 (COVID-19) vaccines, waning immunity, the emergence of variants of concern, and breakthrough infections among vaccinees have begun to highlight opportunities to improve vaccine platforms. Real-world vaccine efficacy studies have highlighted the reduced risk of breakthrough infections and diseases among individuals infected and vaccinated, referred to as hybrid immunity. Thus, we sought to define whether hybrid immunity shapes the humoral immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) following Pfizer/BNT162b2, Moderna mRNA-1273, ChadOx1/AZD1222, and Ad26.COV2.S vaccination. Each vaccine exhibits a unique functional humoral profile in vaccination only or hybrid immunity. However, hybrid immunity shows a unique augmentation of S2-domain-specific functional immunity that was poorly induced for the vaccination only. These data highlight the importance of natural infection in breaking the immunodominance away from the evolutionarily unstable S1 domain and potentially affording enhanced cross-variant protection by targeting the more highly conserved S2 domain of SARS-CoV-2.
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Affiliation(s)
- Paulina Kaplonek
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA
| | - Yixiang Deng
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Heather J Zar
- Department of Pediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa; SA MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Dace Zavadska
- Children's Clinical University Hospital, Riga, Latvia
| | - Marina Johnson
- Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London, London, UK
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David Goldblatt
- Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London, London, UK.
| | - Galit Alter
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA.
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22
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Smit WL, van Tol S, Haas LEM, Limonard GJM, Bossink A, Reusken C, Heron M, Thijsen SFT. Differential abundance of IgG antibodies against the spike protein of SARS-CoV-2 and seasonal coronaviruses in patients with fatal COVID-19. Virol J 2023; 20:85. [PMID: 37138352 PMCID: PMC10156070 DOI: 10.1186/s12985-023-02050-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/23/2023] [Indexed: 05/05/2023] Open
Abstract
Infection with the novel pandemic SARS-CoV-2 virus has been shown to elicit a cross-reactive immune response that could lead to a back-boost of memory recall to previously encountered seasonal (endemic) coronaviruses (eCoVs). Whether this response is associated with a fatal clinical outcome in patients with severe COVID-19 remains unclear. In a cohort of hospitalized patients, we have previously shown that heterologous immune responses to eCoVs can be detected in severe COVID-19. Here, we report that COVID-19 patients with fatal disease have decreased SARS-CoV-2 neutralizing antibody titers at hospital admission, which correlated with lower SARS-CoV-2 spike-specific IgG and was paralleled by a relative abundance of IgG against spike protein of eCoVs of the genus Betacoronavirus. Additional research is needed to assess if eCoV-specific back-boosted IgG is a bystander phenomenon in severe COVID-19, or a factor that influences the development of an efficient anti-viral immune response.
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Affiliation(s)
- Wouter L Smit
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Bosboomstraat 1, 3582 KE, Utrecht, The Netherlands.
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
| | - Sophie van Tol
- Centre for Infectious Disease Control, WHO Reference Laboratory for COVID-19, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Lenneke E M Haas
- Department of Intensive Care, Diakonessenhuis Utrecht, Utrecht, The Netherlands
| | - Gijs J M Limonard
- Department of Pulmonary Diseases, Diakonessenhuis Utrecht, Utrecht, The Netherlands
| | - Ailko Bossink
- Department of Pulmonary Diseases, Diakonessenhuis Utrecht, Utrecht, The Netherlands
| | - Chantal Reusken
- Centre for Infectious Disease Control, WHO Reference Laboratory for COVID-19, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Michiel Heron
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Bosboomstraat 1, 3582 KE, Utrecht, The Netherlands
| | - Steven F T Thijsen
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Bosboomstraat 1, 3582 KE, Utrecht, The Netherlands
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23
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Allen JD, Ivory DP, Song SG, He WT, Capozzola T, Yong P, Burton DR, Andrabi R, Crispin M. The diversity of the glycan shield of sarbecoviruses related to SARS-CoV-2. Cell Rep 2023; 42:112307. [PMID: 36972173 PMCID: PMC10015101 DOI: 10.1016/j.celrep.2023.112307] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/16/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023] Open
Abstract
Animal reservoirs of sarbecoviruses represent a significant risk of emergent pandemics, as evidenced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Vaccines remain successful at limiting severe disease and death, but the potential for further coronavirus zoonosis motivates the search for pan-coronavirus vaccines. This necessitates a better understanding of the glycan shields of coronaviruses, which can occlude potential antibody epitopes on spike glycoproteins. Here, we compare the structure of 12 sarbecovirus glycan shields. Of the 22 N-linked glycan attachment sites present on SARS-CoV-2, 15 are shared by all 12 sarbecoviruses. However, there are significant differences in the processing state at glycan sites in the N-terminal domain, such as N165. Conversely, glycosylation sites in the S2 domain are highly conserved and contain a low abundance of oligomannose-type glycans, suggesting a low glycan shield density. The S2 domain may therefore provide a more attractive target for immunogen design efforts aiming to generate a pan-coronavirus antibody response.
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Affiliation(s)
- Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
| | - Dylan P Ivory
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sophie Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wan-Ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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Yurina V, Rahayu Adianingsih O, Widodo N. Oral and intranasal immunization with food-grade recombinant Lactococcus lactis expressing high conserved region of SARS-CoV-2 spike protein triggers mice's immunity responses. Vaccine X 2023; 13:100265. [PMID: 36712897 PMCID: PMC9869617 DOI: 10.1016/j.jvacx.2023.100265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
The COVID-19 pandemic began at the end of 2019 in Wuhan, China, and has spread throughout the world. Vaccination is still the most effective method of prevention of pathogenic infections, including viral infections. However, there is little evidence that vaccination can protect against SARS-CoV-2 virus for a long time. Thus, regular re-vaccination is necessary to control COVID-19. Vaccination by injection is invasive, and is one of the reasons people refuse to get re-vaccinated. Therefore, we developed a less invasive vaccine based on oral or nasal administration. The gene encoding the high conserved region (HCR) spike protein was inserted into pNZ8149 and expressed in L.lactis NZ3900. Mice were immunized at 3-week intervals with oral or nasal routes. Anti-SARS-CoV2 spike antibody (IgG and IgA) level were measured using ELISA method before and after treatment. Plasma cells population in lymph were analyzed using flowcytometry and the CD4 + and CD8 + cells in lymph and intestine were analyzed using immunofluorescence method. The results of nasal and oral administration in experimental animals showed that L.lactis carrying the HCR gene could induce a humoral immune response, as indicated by increased levels of IgG and IgA against SARS-CoV-2 (IgG/IgA-SARS-CoV-2). The plasma cell population after nasal and oral vaccination in mice were significantly different with control group (p < 0.05). The CD4 + and CD8 + cells in intestine were significantly higher in orally immunized group mice than control group. The CD8 + cells in lymph were significantly higher in intranasal immunized group mice than control group. Our data demonstrate L.lactis expressing spike protein can be developed into a less invasive alternative to nasal and oral vaccination.
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Affiliation(s)
- Valentina Yurina
- Department of Pharmacy, Faculty of Medicine, Universitas Brawijaya, Malang, East Java, Indonesia,Corresponding author at: Department of Pharmacy, Faculty of Medicine, Universitas Brawijaya, Jalan Veteran, Malang 65145, East Java, Indonesia
| | | | - Nashi Widodo
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Malang, East Java, Indonesia
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25
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Study of the Effects of Several SARS-CoV-2 Structural Proteins on Antiviral Immunity. Vaccines (Basel) 2023; 11:vaccines11030524. [PMID: 36992107 DOI: 10.3390/vaccines11030524] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike (S) protein is a critical viral antigenic protein that enables the production of neutralizing antibodies, while other structural proteins, including the membrane (M), nucleocapsid (N) and envelope (E) proteins, have unclear roles in antiviral immunity. In this study, S1, S2, M, N and E proteins were expressed in 16HBE cells to explore the characteristics of the resultant innate immune response. Furthermore, peripheral blood mononuclear cells (PBMCs) from mice immunized with two doses of inactivated SARS-CoV-2 vaccine or two doses of mRNA vaccine were isolated and stimulated by these five proteins to evaluate the corresponding specific T-cell immune response. In addition, the levels of humoral immunity induced by two-dose inactivated vaccine priming followed by mRNA vaccine boosting, two homologous inactivated vaccine doses and two homologous mRNA vaccine doses in immunized mice were compared. Our results suggested that viral structural proteins can activate the innate immune response and elicit a specific T-cell response in mice immunized with the inactivated vaccine. However, the existence of the specific T-cell response against M, N and E is seemingly insufficient to improve the level of humoral immunity.
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26
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Immunogenicity and Safety of a Combined Intramuscular/Intranasal Recombinant Spike Protein COVID-19 Vaccine (RCP) in Healthy Adults Aged 18 to 55 Years Old: A Randomized, Double-Blind, Placebo-Controlled, Phase I Trial. Vaccines (Basel) 2023; 11:vaccines11020455. [PMID: 36851334 PMCID: PMC9961243 DOI: 10.3390/vaccines11020455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
Objectives: This study aimed to determine the safety and immunogenicity of a combined intramuscular/intranasal recombinant spike protein COVID-19 vaccine (RCP). Methods: We conducted a randomized, double-blind, placebo-controlled, phase I trial. Three vaccine strengths were compared with an adjuvant-only preparation. It included two intramuscular and a third intranasal dose. Eligible participants were followed for adverse reactions. Specific IgG, secretory IgA, neutralizing antibodies, and cell-mediated immunity were assessed. Results: A total of 153 participants were enrolled (13 sentinels, 120 randomized, 20 non-randomized open-labeled for IgA assessment). No related serious adverse event was observed. The geometric mean ratios (GMRs) and 95% CI for serum neutralizing antibodies compared with placebo two weeks after the second injection were 5.82 (1.46-23.13), 11.12 (2.74-45.09), and 20.70 (5.05-84.76) in 5, 10, and 20 µg vaccine groups, respectively. The GMR for anti-RBD IgA in mucosal fluid two weeks after the intranasal dose was 23.27 (21.27-25.45) in the 10 µg vaccine group. The humoral responses were sustained for up to five months. All vaccine strengths indicated a strong T-helper 1 response. Conclusion: RCP is safe and creates strong and durable humoral and cellular immunity and good mucosal immune response in its 10 µg /200 µL vaccine strengths. Trial registration: IRCT20201214049709N1.
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27
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Al-Tamimi M, Tarifi AA, Qaqish A, Abbas MM, Albalawi H, Abu-Raideh J, Salameh M, Khasawneh AI. Immunoglobulins response of COVID-19 patients, COVID-19 vaccine recipients, and random individuals. PLoS One 2023; 18:e0281689. [PMID: 36787317 PMCID: PMC9928079 DOI: 10.1371/journal.pone.0281689] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/29/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND The development of specific immunoglobulins to COVID-19 after natural infection or vaccination has been proposed. The efficacy and dynamics of this response are not clear yet. AIM This study aims to analyze the immunoglobulins response among COVID-19 patients, COVID-19 vaccine recipients and random individuals. METHODS A total of 665 participants including 233 COVID-19 patients, 288 COVID-19 vaccine recipients, and 144 random individuals were investigated for anti-COVID-19 immunoglobulins (IgA, IgG, IgM). RESULTS Among COVID-19 patients, 22.7% had detectable IgA antibodies with a mean of 27.3±57.1 ng/ml, 29.6% had IgM antibodies with a mean of 188.4±666.0 BAU/ml, while 59.2% had IgG antibodies with a mean of 101.7±139.7 BAU/ml. Pfizer-BioNTech vaccine recipients had positive IgG in 99.3% with a mean of 515.5±1143.5 BAU/ml while 85.7% of Sinopharm vaccine recipients had positive IgG with a mean of 170.0±230.0 BAU/ml. Regarding random individuals, 54.9% had positive IgG with a mean of 164.3±214 BAU/ml. The peak IgM response in COVID-19 patients was detected early at 15-22 days, followed by IgG peak at 16-30 days, and IgA peak at 0-60 days. IgM antibodies disappeared at 61-90 days, while IgG and IgA antibodies decreased slowly after the peak and remained detectable up to 300 days. The frequency of IgG positivity among patients was significantly affected by increased age, admission department (inpatient or outpatient), symptoms, need for oxygen therapy, and increased duration between positive COVID-19 RT PCR test and serum sampling (p˂0.05). Positive correlations were noted between different types of immunoglobulins (IgG, IgM, and IgA) among patients. CONCLUSIONS Natural infection and COIVD-19 vaccines provide IgG-mediated immunity. The class, positivity, mean, efficacy, and duration of immunoglobulins response are affected by the mechanism of immunity and host related variables. Random community individuals had detectable COVID-19 IgG at ~55%, far from reaching herd immunity levels.
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Affiliation(s)
- Mohammad Al-Tamimi
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Amjed A. Tarifi
- Department of Specialized Surgery, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Arwa Qaqish
- Department of Biology and Biotechnology, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Manal M. Abbas
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
- Pharmacological and Diagnostic Research Lab, Al-Ahliyya Amman University, Amman, Jordan
| | - Hadeel Albalawi
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Jumanah Abu-Raideh
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Muna Salameh
- Department of Basic Medical Sciences, Faculty of Medicine, AlBalqa Applied University, Alsalt, Jordan
| | - Ashraf I. Khasawneh
- Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
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28
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Klose AM, Kosoy G, Miller BL. Arrayed Imaging Reflectometry monitoring of anti-viral antibody production throughout vaccination and breakthrough Covid-19. PLoS One 2023; 18:e0277846. [PMID: 36749755 PMCID: PMC9904502 DOI: 10.1371/journal.pone.0277846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Immune responses to COVID-19 infection and vaccination are individual and varied. There is a need to understand the timeline of vaccination efficacy against current and yet to be discovered viral mutations. Assessing immunity to SARS-CoV-2 in the context of immunity to other respiratory viruses is also valuable. Here we demonstrate the capability of a fully automated prototype Arrayed Imaging Reflectometry system to perform reliable longitudinal serology against a 34-plex respiratory array. The array contains antigens for respiratory syncytial virus, seasonal influenza, common human coronaviruses, MERS, SARS-CoV-1, and SARS-CoV-2. AIR measures a change in reflectivity due to the binding of serum antibodies to the antigens on the array. Samples were collected from convalescent COVID-19 donors and individuals vaccinated with a two-dose mRNA vaccine regimen. Vaccinated samples were collected prior to the first dose, one week after the first dose, one week after the second dose, and monthly thereafter. Information following booster dose and/or breakthrough infection is included for a subset of subjects. Longitudinal samples of vaccinated individuals demonstrate a rise and fall of SARS-CoV-2 spike antibodies in agreement with general knowledge of the adaptive immune response and other studies. Linear Regression analysis was performed to understand the relationship between antibodies binding to different antigens on the array. Our analysis identified strong correlations between closely related influenza virus strains as well as correlations between SARS-CoV-2, SARS-CoV-1, and human coronavirus 229E. A small test of using diluted whole blood from a fingerstick provided clean arrays with antibody binding comparable to serum. Potential applications include assessing immunity in the context of exposure to multiple respiratory viruses, clinical serology, population monitoring to facilitate public health recommendations, and vaccine development against new viruses and virus mutations.
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Affiliation(s)
- Alanna M. Klose
- Department of Dermatology, University of Rochester, Rochester, New York, United States of America
- Program in Materials Science, University of Rochester, Rochester, New York, United States of America
| | - Gabrielle Kosoy
- Department of Dermatology, University of Rochester, Rochester, New York, United States of America
- Department of Biophysics and Biochemistry, University of Rochester, Rochester, New York, United States of America
| | - Benjamin L. Miller
- Department of Dermatology, University of Rochester, Rochester, New York, United States of America
- Program in Materials Science, University of Rochester, Rochester, New York, United States of America
- Department of Biophysics and Biochemistry, University of Rochester, Rochester, New York, United States of America
- Department of Biomedical Engineering, University of Rochester, Rochester, New York, United States of America
- Institute of Optics, University of Rochester, Rochester, New York, United States of America
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29
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Salimian J, Ahmadi A, Amani J, Olad G, Halabian R, Saffaei A, Arabfard M, Nasiri M, Nazarian S, Abolghasemi H, Alishiri G. Safety and immunogenicity of a recombinant receptor-binding domain-based protein subunit vaccine (Noora vaccine™) against COVID-19 in adults: A randomized, double-blind, placebo-controlled, Phase 1 trial. J Med Virol 2023; 95:10.1002/jmv.28097. [PMID: 36029105 PMCID: PMC9539327 DOI: 10.1002/jmv.28097] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/01/2022] [Accepted: 08/25/2022] [Indexed: 11/11/2022]
Abstract
The development of a safe and effective vaccine is essential to protect populations against coronavirus disease 2019 (COVID-19). There are several vaccine candidates under investigation with different mechanisms of action. In the present study, we have evaluated the safety and immunogenicity of a recombinant receptor-binding domain (RBD)-based protein subunit vaccine (Noora vaccine) against COVID-19 in adults. This Phase 1 trial is a randomized, double-blind, placebo-controlled study to evaluate the safety and immunogenicity of the recombinant RBD-based protein subunit vaccine (Noora vaccine) against COVID-19 in healthy adults volunteers. Eligible participants were included in this study after evaluating their health status and considering the exclusion criteria. They were then randomized into three groups and received three doses of vaccine (80 µg, 120 µg, and placebo) on Days 0, 21, and 35. Primary outcomes including solicited, unsolicited, and medically attended adverse events were recorded during this study. Secondary outcomes including the humoral and cellular immunity (including anti-RBD IgG antibody and neutralizing antibody) were measured on Days 0, 21, 28, 35, 42, and 49 by using the ELISA kit and the Virus Neutralization Test (VNT) was performed on day 49. Totally 70 cases were included in this Phase 1 trial and 60 of them completed the study. Safety assessments showed no severe adverse events. Local pain at the vaccine injection site occurred in 80% of the vaccinated volunteers. Induration and redness at the injection site were the other adverse reactions of this vaccine. There was no significant difference between the studied groups regarding adverse reactions. Anti-RBD IgG antibody and neutralizing antibody assessment showed significant seroconversion in comparison to the placebo group (80%, and 100% respectively, p < 0.001). The cellular immunity panel also showed mild to moderate induction of TH1 responses and the VNT showed 78% of seroprotection. The results of this Phase 1 trial showed acceptable safety without serious adverse events and significant seroconversions in the humoral and cellular immunity panel. The dose of 80 µg is an appropriate dose for injection in the next phases of the trial.
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Affiliation(s)
- Jafar Salimian
- Applied Microbiology Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
- Chemical Injuries Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Ali Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - Jafar Amani
- Applied Microbiology Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - Gholamreza Olad
- Applied Biotechnology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Raheleh Halabian
- Applied Microbiology Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - Ali Saffaei
- Department of Clinical Pharmacy, School of PharmacyShahid Beheshti University of Medical SciencesTehranIran
- Student Research CommitteeShahid Beheshti University of Medical SciencesTehranIran
- Skull Base Research Center, Loghman Hakim HospitalShahid Beheshti University of Medical SciencesTehranIran
| | - Masoud Arabfard
- Chemical Injuries Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Mojtaba Nasiri
- Clinical Trial CenterTehran University of Medical SciencesTehranIran
| | - Shahram Nazarian
- Department of Biology, Faculty of ScienceImam Hossein UniversityTehranIran
| | - Hassan Abolghasemi
- Applied Microbiology Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
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30
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Nejat R, Torshizi MF, Najafi DJ. S Protein, ACE2 and Host Cell Proteases in SARS-CoV-2 Cell Entry and Infectivity; Is Soluble ACE2 a Two Blade Sword? A Narrative Review. Vaccines (Basel) 2023; 11:vaccines11020204. [PMID: 36851081 PMCID: PMC9968219 DOI: 10.3390/vaccines11020204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/07/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
Since the spread of the deadly virus SARS-CoV-2 in late 2019, researchers have restlessly sought to unravel how the virus enters the host cells. Some proteins on each side of the interaction between the virus and the host cells are involved as the major contributors to this process: (1) the nano-machine spike protein on behalf of the virus, (2) angiotensin converting enzyme II, the mono-carboxypeptidase and the key component of renin angiotensin system on behalf of the host cell, (3) some host proteases and proteins exploited by SARS-CoV-2. In this review, the complex process of SARS-CoV-2 entrance into the host cells with the contribution of the involved host proteins as well as the sequential conformational changes in the spike protein tending to increase the probability of complexification of the latter with angiotensin converting enzyme II, the receptor of the virus on the host cells, are discussed. Moreover, the release of the catalytic ectodomain of angiotensin converting enzyme II as its soluble form in the extracellular space and its positive or negative impact on the infectivity of the virus are considered.
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Affiliation(s)
- Reza Nejat
- Department of Anesthesiology and Critical Care Medicine, Laleh Hospital, Tehran 1467684595, Iran
- Correspondence:
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31
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Acharjee A, Ray A, Salkar A, Bihani S, Tuckley C, Shastri J, Agrawal S, Duttagupta S, Srivastava S. Humoral Immune Response Profile of COVID-19 Reveals Severity and Variant-Specific Epitopes: Lessons from SARS-CoV-2 Peptide Microarray. Viruses 2023; 15:248. [PMID: 36680289 PMCID: PMC9866125 DOI: 10.3390/v15010248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
The amaranthine scale of the COVID-19 pandemic and unpredictable disease severity is of grave concern. Serological diagnostic aids are an excellent choice for clinicians for rapid and easy prognosis of the disease. To this end, we studied the humoral immune response to SARS-CoV-2 infection to map immunogenic regions in the SARS-CoV-2 proteome at amino acid resolution using a high-density SARS-CoV-2 proteome peptide microarray. The microarray has 4932 overlapping peptides printed in duplicates spanning the entire SARS-CoV-2 proteome. We found 204 and 676 immunogenic peptides against IgA and IgG, corresponding to 137 and 412 IgA and IgG epitopes, respectively. Of these, 6 and 307 epitopes could discriminate between disease severity. The emergence of variants has added to the complexity of the disease. Using the mutation panel available, we could detect 5 and 10 immunogenic peptides against IgA and IgG with mutations belonging to SAR-CoV-2 variants. The study revealed severity-based epitopes that could be presented as potential prognostic serological markers. Further, the mutant epitope immunogenicity could indicate the putative use of these markers for diagnosing variants responsible for the infection.
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Affiliation(s)
- Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Arka Ray
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Surbhi Bihani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Chaitanya Tuckley
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai 400076, India
| | | | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Mumbai 400011, India
| | - Siddhartha Duttagupta
- Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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32
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Dacon C, Peng L, Lin TH, Tucker C, Lee CCD, Cong Y, Wang L, Purser L, Cooper AJR, Williams JK, Pyo CW, Yuan M, Kosik I, Hu Z, Zhao M, Mohan D, Peterson M, Skinner J, Dixit S, Kollins E, Huzella L, Perry D, Byrum R, Lembirik S, Murphy M, Zhang Y, Yang ES, Chen M, Leung K, Weinberg RS, Pegu A, Geraghty DE, Davidson E, Doranz BJ, Douagi I, Moir S, Yewdell JW, Schmaljohn C, Crompton PD, Mascola JR, Holbrook MR, Nemazee D, Wilson IA, Tan J. Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses. Cell Host Microbe 2023; 31:97-111.e12. [PMID: 36347257 PMCID: PMC9639329 DOI: 10.1016/j.chom.2022.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/04/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
Humanity has faced three recent outbreaks of novel betacoronaviruses, emphasizing the need to develop approaches that broadly target coronaviruses. Here, we identify 55 monoclonal antibodies from COVID-19 convalescent donors that bind diverse betacoronavirus spike proteins. Most antibodies targeted an S2 epitope that included the K814 residue and were non-neutralizing. However, 11 antibodies targeting the stem helix neutralized betacoronaviruses from different lineages. Eight antibodies in this group, including the six broadest and most potent neutralizers, were encoded by IGHV1-46 and IGKV3-20. Crystal structures of three antibodies of this class at 1.5-1.75-Å resolution revealed a conserved mode of binding. COV89-22 neutralized SARS-CoV-2 variants of concern including Omicron BA.4/5 and limited disease in Syrian hamsters. Collectively, these findings identify a class of IGHV1-46/IGKV3-20 antibodies that broadly neutralize betacoronaviruses by targeting the stem helix but indicate these antibodies constitute a small fraction of the broadly reactive antibody response to betacoronaviruses after SARS-CoV-2 infection.
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Affiliation(s)
- Cherrelle Dacon
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ting-Hui Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Courtney Tucker
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu Cong
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren Purser
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Andrew J R Cooper
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | | | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ivan Kosik
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhe Hu
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming Zhao
- Protein Chemistry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Divya Mohan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Mary Peterson
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Jeff Skinner
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Saurabh Dixit
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Erin Kollins
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Louis Huzella
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Donna Perry
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Russell Byrum
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Sanae Lembirik
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Michael Murphy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rona S Weinberg
- New York Blood Center, Lindsley F. Kimball Research Institute, New York, NY 10065, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan Moir
- B Cell Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Connie Schmaljohn
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joshua Tan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA.
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Kim JW, Cho AH, Shin HG, Jang SH, Cho SY, Lee YR, Lee S. Development and Characterization of Phage Display-Derived Monoclonal Antibodies to the S2 Domain of Spike Proteins of Wild-Type SARS-CoV-2 and Multiple Variants. Viruses 2023; 15:174. [PMID: 36680213 PMCID: PMC9862430 DOI: 10.3390/v15010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/07/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
The rapid emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has resulted in the ongoing global coronavirus disease 2019 (COVID-19) pandemic. Thus, the rapid development of a platform to detect a broad range of SARS-CoV-2 variants is essential for successful COVID-19 management. In this study, four SARS-CoV-2 spike protein-specific single-chain variable fragments (scFvs) were isolated from a synthetic antibody library using phage display technology. Following the conversion of these scFvs into monoclonal antibodies (mAbs) (K104.1-K104.4) and production and purification of the mAbs, the antibody pair (K104.1 and K104.2) that exhibited the highest binding affinity (K104.1 and K104.2, 1.3 nM and 1.9 nM) was selected. Biochemical analyses revealed that this antibody pair specifically bound to different sites on the S2 subunit of the spike protein. Furthermore, we developed a highly sensitive sandwich immunoassay using this antibody pair that accurately and quantitatively detected the spike proteins of wild-type SARS-CoV-2 and multiple variants, including Alpha, Beta, Gamma, Delta, Kappa, and Omicron, in the picomolar range. Conclusively, the novel phage display-derived mAbs we have developed may be useful for the rapid and efficient detection of the fast-evolving SARS-CoV-2.
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Affiliation(s)
- Ji Woong Kim
- Department of Applied Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Ah Hyun Cho
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Ha Gyeong Shin
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Sung Hoon Jang
- Department of Applied Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Su Yeon Cho
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Ye Rim Lee
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Sukmook Lee
- Department of Applied Chemistry, Kookmin University, Seoul 02707, Republic of Korea
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seoul 02707, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul 02707, Republic of Korea
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Rümke LW, Smit WL, Bossink A, Limonard GJM, Muilwijk D, Haas LEM, Reusken C, van der Wal S, Thio BJ, van Os YMG, Gremmels H, Beekman JM, Nijhuis M, Wensing AMJ, Heron M, Thijsen SFT. Impaired SARS-CoV-2 specific T-cell response in patients with severe COVID-19. Front Immunol 2023; 14:1046639. [PMID: 37168853 PMCID: PMC10165493 DOI: 10.3389/fimmu.2023.1046639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/28/2023] [Indexed: 05/13/2023] Open
Abstract
Cellular immune responses are of pivotal importance to understand SARS-CoV-2 pathogenicity. Using an enzyme-linked immunosorbent spot (ELISpot) interferon-γ release assay with wild-type spike, membrane and nucleocapsid peptide pools, we longitudinally characterized functional SARS-CoV-2 specific T-cell responses in a cohort of patients with mild, moderate and severe COVID-19. All patients were included before emergence of the Omicron (B.1.1.529) variant. Our most important finding was an impaired development of early IFN-γ-secreting virus-specific T-cells in severe patients compared to patients with moderate disease, indicating that absence of virus-specific cellular responses in the acute phase may act as a prognostic factor for severe disease. Remarkably, in addition to reactivity against the spike protein, a substantial proportion of the SARS-CoV-2 specific T-cell response was directed against the conserved membrane protein. This may be relevant for diagnostics and vaccine design, especially considering new variants with heavily mutated spike proteins. Our data further strengthen the hypothesis that dysregulated adaptive immunity plays a central role in COVID-19 immunopathogenesis.
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Affiliation(s)
- Lidewij W. Rümke
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Utrecht, Netherlands
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Wouter L. Smit
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Utrecht, Netherlands
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ailko Bossink
- Department of Pulmonary Diseases, Diakonessenhuis Utrecht, Utrecht, Netherlands
| | - Gijs J. M. Limonard
- Department of Pulmonary Diseases, Diakonessenhuis Utrecht, Utrecht, Netherlands
| | - Danya Muilwijk
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, Utrecht, Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center, Utrecht University, Utrecht, Netherlands
| | - Lenneke E. M. Haas
- Department of Intensive Care, Diakonessenhuis Utrecht, Utrecht, Netherlands
| | - Chantal Reusken
- Centre for Infectious Disease Control, WHO Reference Laboratory for COVID-19, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Sanne van der Wal
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Utrecht, Netherlands
| | - Bing J. Thio
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Utrecht, Netherlands
| | - Yvonne M. G. van Os
- Occupational Health Office, Department of Human Resources, University Medical Center Utrecht, Utrecht, Netherlands
| | - Hendrik Gremmels
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Utrecht, Netherlands
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Jeffrey M. Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, Utrecht, Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center, Utrecht University, Utrecht, Netherlands
| | - Monique Nijhuis
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Annemarie M. J. Wensing
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Michiel Heron
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Utrecht, Netherlands
- *Correspondence: Michiel Heron,
| | - Steven F. T. Thijsen
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Utrecht, Netherlands
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Wang X, Hu M, Liu B, Xu H, Jin Y, Wang B, Zhao Y, Wu J, Yue J, Ren H. Evaluating the effect of SARS-CoV-2 spike mutations with a linear doubly robust learner. Front Cell Infect Microbiol 2023; 13:1161445. [PMID: 37153142 PMCID: PMC10154619 DOI: 10.3389/fcimb.2023.1161445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
Driven by various mutations on the viral Spike protein, diverse variants of SARS-CoV-2 have emerged and prevailed repeatedly, significantly prolonging the pandemic. This phenomenon necessitates the identification of key Spike mutations for fitness enhancement. To address the need, this manuscript formulates a well-defined framework of causal inference methods for evaluating and identifying key Spike mutations to the viral fitness of SARS-CoV-2. In the context of large-scale genomes of SARS-CoV-2, it estimates the statistical contribution of mutations to viral fitness across lineages and therefore identifies important mutations. Further, identified key mutations are validated by computational methods to possess functional effects, including Spike stability, receptor-binding affinity, and potential for immune escape. Based on the effect score of each mutation, individual key fitness-enhancing mutations such as D614G and T478K are identified and studied. From individual mutations to protein domains, this paper recognizes key protein regions on the Spike protein, including the receptor-binding domain and the N-terminal domain. This research even makes further efforts to investigate viral fitness via mutational effect scores, allowing us to compute the fitness score of different SARS-CoV-2 strains and predict their transmission capacity based solely on their viral sequence. This prediction of viral fitness has been validated using BA.2.12.1, which is not used for regression training but well fits the prediction. To the best of our knowledge, this is the first research to apply causal inference models to mutational analysis on large-scale genomes of SARS-CoV-2. Our findings produce innovative and systematic insights into SARS-CoV-2 and promotes functional studies of its key mutations, serving as reliable guidance about mutations of interest.
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Affiliation(s)
| | | | | | | | | | | | | | - Jun Wu
- *Correspondence: Hongguang Ren, ; Junjie Yue, ; Jun Wu,
| | - Junjie Yue
- *Correspondence: Hongguang Ren, ; Junjie Yue, ; Jun Wu,
| | - Hongguang Ren
- *Correspondence: Hongguang Ren, ; Junjie Yue, ; Jun Wu,
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Li E, Han Q, Bi J, Wei S, Wang S, Zhang Y, Liu J, Feng N, Wang T, Wu J, Yang S, Zhao Y, Liu B, Yan F, Xia X. Therapeutic equine hyperimmune antibodies with high and broad-spectrum neutralizing activity protect rodents against SARS-CoV-2 infection. Front Immunol 2023; 14:1066730. [PMID: 36875106 PMCID: PMC9981790 DOI: 10.3389/fimmu.2023.1066730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
The emergence of SARS-CoV-2 variants stresses the continued need for broad-spectrum therapeutic antibodies. Several therapeutic monoclonal antibodies or cocktails have been introduced for clinical use. However, unremitting emerging SARS-CoV-2 variants showed reduced neutralizing efficacy by vaccine induced polyclonal antibodies or therapeutic monoclonal antibodies. In our study, polyclonal antibodies and F(ab')2 fragments with strong affinity produced after equine immunization with RBD proteins produced strong affinity. Notably, specific equine IgG and F(ab')2 have broad and high neutralizing activity against parental virus, all SARS-CoV-2 variants of concern (VOCs), including B.1.1,7, B.1.351, B.1.617.2, P.1, B.1.1.529 and BA.2, and all variants of interest (VOIs) including B.1.429, P.2, B.1.525, P.3, B.1.526, B.1.617.1, C.37 and B.1.621. Although some variants weaken the neutralizing ability of equine IgG and F(ab')2 fragments, they still exhibited superior neutralization ability against mutants compared to some reported monoclonal antibodies. Furthermore, we tested the pre-exposure and post-exposure protective efficacy of the equine immunoglobulin IgG and F(ab')2 fragments in lethal mouse and susceptible golden hamster models. Equine immunoglobulin IgG and F(ab')2 fragments effectively neutralized SARS-CoV-2 in vitro, fully protected BALB/c mice from the lethal challenge, and reduced golden hamster's lung pathological change. Therefore, equine pAbs are an adequate, broad coverage, affordable and scalable potential clinical immunotherapy for COVID-19, particularly for SARS-CoV-2 VOCs or VOIs.
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Affiliation(s)
- Entao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Qiuxue Han
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Veterinary Medicine, Jilin Agriculture University, Changchun, China
| | - Jinhao Bi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,Institute of Laboratory Animal Science, Chinese Academy of Medical Science and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Shimeng Wei
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,Institute of Laboratory Animal Science, Chinese Academy of Medical Science and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Shen Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Ying Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Wildlife and Protected Area, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Jun Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Na Feng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Tiecheng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jun Wu
- Department of Microorganism Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Songtao Yang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yongkun Zhao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Bo Liu
- Department of Microorganism Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Feihu Yan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xianzhu Xia
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
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Ko SH, Chen WY, Su SC, Lin HT, Ke FY, Liang KH, Hsu FF, Kumari M, Fu CY, Wu HC. Monoclonal antibodies against S2 subunit of spike protein exhibit broad reactivity toward SARS-CoV-2 variants. J Biomed Sci 2022; 29:108. [PMID: 36550570 PMCID: PMC9774083 DOI: 10.1186/s12929-022-00891-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harbor diverse spike (S) protein sequences, which can greatly influence the efficacies of therapeutics. Therefore, it would be of great value to develop neutralizing monoclonal antibodies (mAbs) that can broadly recognize multiple variants. METHODS Using an mRNA-LNP immunization strategy, we generated several mAbs that specifically target the conserved S2 subunit of SARS-CoV-2 (B-S2-mAbs). These mAbs were assessed for their neutralizing activity with pseudotyped viruses and binding ability for SARS-CoV-2 variants. RESULTS Among these mAbs, five exhibited strong neutralizing ability toward the Gamma variant and also recognized viral S proteins from the Wuhan, Alpha, Beta, Gamma, Delta and Omicron (BA.1, BA.2 and BA.5) variants. Furthermore, we demonstrated the broad reactivities of these B-S2-mAbs in several different applications, including immunosorbent, immunofluorescence and immunoblotting assays. In particular, B-S2-mAb-2 exhibited potent neutralization of Gamma variant (IC50 = 0.048 µg/ml) in a pseudovirus neutralization assay. The neutralizing epitope of B-S2-mAb-2 was identified by phage display as amino acid residues 1146-1152 (DSFKEEL) in the S2 subunit HR2 domain of SARS-CoV-2. CONCLUSION Since there are not many mAbs that can bind the S2 subunit of SARS-CoV-2 variants, our set of B-S2-mAbs may provide important materials for basic research and potential clinical applications. Importantly, our study results demonstrate that the viral S2 subunit can be targeted for the production of cross-reactive antibodies, which may be used for coronavirus detection and neutralization.
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Affiliation(s)
- Shih-Han Ko
- grid.28665.3f0000 0001 2287 1366Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529 Taiwan
| | - Wan-Yu Chen
- grid.28665.3f0000 0001 2287 1366Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529 Taiwan
| | - Shih-Chieh Su
- grid.28665.3f0000 0001 2287 1366Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529 Taiwan
| | - Hsiu-Ting Lin
- grid.28665.3f0000 0001 2287 1366Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529 Taiwan
| | - Feng-Yi Ke
- grid.28665.3f0000 0001 2287 1366Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529 Taiwan
| | - Kang-Hao Liang
- grid.28665.3f0000 0001 2287 1366Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529 Taiwan
| | - Fu-Fei Hsu
- grid.28665.3f0000 0001 2287 1366Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529 Taiwan
| | - Monika Kumari
- grid.28665.3f0000 0001 2287 1366Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529 Taiwan
| | - Chi-Yu Fu
- grid.28665.3f0000 0001 2287 1366Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529 Taiwan
| | - Han-Chung Wu
- grid.28665.3f0000 0001 2287 1366Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529 Taiwan ,grid.28665.3f0000 0001 2287 1366Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529 Taiwan
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38
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Challenges and developments in universal vaccine design against SARS-CoV-2 variants. NPJ Vaccines 2022; 7:167. [PMID: 36535982 PMCID: PMC9761649 DOI: 10.1038/s41541-022-00597-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had become a global concern because of its unexpectedly high pathogenicity and transmissibility. SARS-CoV-2 variants that reduce the immune protection elicited from previous vaccination or natural infection raise challenges in controlling the spread of the pandemic. The development of universal vaccines against these variants seems to be a practical solution to alleviate the physical and economic effects caused by this disease, but it is hard to achieve. In this review, we describe the high mutation rate of RNA viruses and dynamic molecular structures of SARS-CoV-2 variants in several major neutralizing epitopes, trying to answer the question of why universal vaccines are difficult to design. Understanding the biological basis of immune evasion is crucial for combating these obstacles. We then summarize several advancements worthy of further study, including heterologous prime-boost regimens, construction of chimeric immunogens, design of protein nanoparticle antigens, and utilization of conserved neutralizing epitopes. The fact that some immunogens can induce cross-reactive immune responses against heterologous coronaviruses provides hints for universal vaccine development. We hope this review can provide inspiration to current universal vaccine studies.
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Is the Stalk of the SARS-CoV-2 Spike Protein Druggable? Viruses 2022; 14:v14122789. [PMID: 36560795 PMCID: PMC9786045 DOI: 10.3390/v14122789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/28/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
The spike protein is key to SARS-CoV-2 high infectivity because it facilitates the receptor binding domain (RBD) encounter with ACE2. As targeting subunit S1 has not yet delivered an ACE2-binding inhibitor, we have assessed the druggability of the conserved segment of the spike protein stalk within subunit S2 by means of an integrated computational approach that combines the molecular docking of an optimized library of fragments with high-throughput molecular dynamics simulations. The high propensity of the spike protein to mutate in key regions that are responsible for the recognition of the human angiotensin-converting enzyme 2 (hACE2) or for the recognition of antibodies, has made subunit S1 of the spike protein difficult to target. Despite the inherent flexibility of the stalk region, our results suggest two hidden interhelical binding sites, whose accessibility is only partially hampered by glycan residues.
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40
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Song S, Kim H, Jang EY, Jeon H, Diao H, Khan MRI, Lee M, Lee YJ, Nam J, Kim S, Kim Y, Sohn E, Hwang I, Choi J. SARS-CoV-2 spike trimer vaccine expressed in Nicotiana benthamiana adjuvanted with Alum elicits protective immune responses in mice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2298-2312. [PMID: 36062974 PMCID: PMC9538723 DOI: 10.1111/pbi.13908] [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] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/30/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic has spurred rapid development of vaccines as part of the public health response. However, the general strategy used to construct recombinant trimeric severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) proteins in mammalian cells is not completely adaptive to molecular farming. Therefore, we generated several constructs of recombinant S proteins for high expression in Nicotiana benthamiana. Intramuscular injection of N. benthamiana-expressed Sct vaccine (NSct Vac) into Balb/c mice elicited both humoral and cellular immune responses, and booster doses increased neutralizing antibody titres. In human angiotensin-converting enzyme knock-in mice, two doses of NSct Vac induced anti-S and neutralizing antibodies, which cross-neutralized Alpha, Beta, Delta and Omicron variants. Survival rates after lethal challenge with SARS-CoV-2 were up to 80%, without significant body weight loss, and viral titres in lung tissue fell rapidly, with no infectious virus detectable at 7-day post-infection. Thus, plant-derived NSct Vac could be a candidate COVID-19 vaccine.
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Affiliation(s)
- Shi‐Jian Song
- Department of Life SciencePohang University of Science and TechnologyPohangKorea
| | - Heeyeon Kim
- Division of Acute Viral Disease, Center for Emerging Virus ResearchNational Institute of Infectious Diseases, Korea National Institute of HealthCheongjuKorea
| | - Eun Young Jang
- Division of Vaccine Research, Vaccine Research CenterNational Institute of Infectious Diseases, Korea National Institute of HealthCheongjuKorea
| | - Hyungmin Jeon
- Department of Life SciencePohang University of Science and TechnologyPohangKorea
| | - Hai‐Ping Diao
- Department of Life SciencePohang University of Science and TechnologyPohangKorea
| | - Md Rezaul Islam Khan
- Department of Life SciencePohang University of Science and TechnologyPohangKorea
| | - Mi‐Seon Lee
- Division of Infectious Diseases InspectionJeju Special Self‐Governing Province Institute of Environment ResearchJejuKorea
| | - Young Jae Lee
- Division of Vaccine Research, Vaccine Research CenterNational Institute of Infectious Diseases, Korea National Institute of HealthCheongjuKorea
| | - Jeong‐hyun Nam
- Division of Vaccine Research, Vaccine Research CenterNational Institute of Infectious Diseases, Korea National Institute of HealthCheongjuKorea
| | - Seong‐Ryeol Kim
- Division of Acute Viral Disease, Center for Emerging Virus ResearchNational Institute of Infectious Diseases, Korea National Institute of HealthCheongjuKorea
| | - Young‐Jin Kim
- Department of Life SciencePohang University of Science and TechnologyPohangKorea
| | - Eun‐Ju Sohn
- BioApplications Inc.Pohang Technopark ComplexPohangSouth Korea
| | - Inhwan Hwang
- Department of Life SciencePohang University of Science and TechnologyPohangKorea
| | - Jang‐Hoon Choi
- Division of Acute Viral Disease, Center for Emerging Virus ResearchNational Institute of Infectious Diseases, Korea National Institute of HealthCheongjuKorea
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Mutational escape prevention by combination of four neutralizing antibodies that target RBD conserved regions and stem helix. Virol Sin 2022; 37:860-873. [PMID: 36414178 PMCID: PMC9674564 DOI: 10.1016/j.virs.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/16/2022] [Indexed: 11/20/2022] Open
Abstract
New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appear rapidly every few months. They have showed powerful adaptive ability to circumvent the immune system. To further understand SARS-CoV-2's adaptability so as to seek for strategies to mitigate the emergence of new variants, herein we investigated the viral adaptation in the presence of broadly neutralizing antibodies and their combinations. First, we selected four broadly neutralizing antibodies, including pan-sarbecovirus and pan-betacoronavirus neutralizing antibodies that recognize distinct conserved regions on receptor-binding domain (RBD) or conserved stem-helix region on S2 subunit. Through binding competition analysis, we demonstrated that they were capable of simultaneously binding. Thereafter, a replication-competent vesicular stomatitis virus pseudotyped with SARS-CoV-2 spike protein was employed to study the viral adaptation. Twenty consecutive passages of the virus under the selective pressure of individual antibodies or their combinations were performed. It was found that it was not hard for the virus to adapt to broadly neutralizing antibodies, even for pan-sarbecovirus and pan-betacoronavirus antibodies. The virus was more and more difficult to escape the combinations of two/three/four antibodies. In addition, mutations in the viral population revealed by high-throughput sequencing showed that under the selective pressure of three/four combinational antibodies, viral mutations were not prone to present in the highly conserved region across betacoronaviruses (stem-helix region), while this was not true under the selective pressure of single/two antibodies. Importantly, combining neutralizing antibodies targeting RBD conserved regions and stem helix synergistically prevented the emergence of escape mutations. These studies will guide future vaccine and therapeutic development efforts and provide a rationale for the design of RBD-stem helix tandem vaccine, which may help to impede the generation of novel variants.
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Novel chimeric proteins mimicking SARS-CoV-2 spike epitopes with broad inhibitory activity. Int J Biol Macromol 2022; 222:2467-2478. [PMID: 36220405 PMCID: PMC9546781 DOI: 10.1016/j.ijbiomac.2022.10.031] [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: 07/28/2022] [Revised: 09/29/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022]
Abstract
SARS-CoV-2 spike (S) protein mediates virus attachment to the cells and fusion between viral and cell membranes. Membrane fusion is driven by mutual interaction between the highly conserved heptad-repeat regions 1 and 2 (HR1 and HR2) of the S2 subunit of the spike. For this reason, these S2 regions are interesting therapeutic targets for COVID-19. Although HR1 and HR2 have been described as transiently exposed during the fusion process, no significant antibody responses against these S2 regions have been reported. Here we designed chimeric proteins that imitate highly stable HR1 helical trimers and strongly bind to HR2. The proteins have broad inhibitory activity against WT B.1 and BA.1 viruses. Sera from COVID-19 convalescent donors showed significant levels of reactive antibodies (IgG and IgA) against the HR1 mimetic proteins, whereas these antibody responses were absent in sera from uninfected donors. Moreover, both inhibitory activity and antigenicity of the proteins correlate positively with their structural stability but not with the number of amino acid changes in their HR1 sequences, indicating a conformational and conserved nature of the involved epitopes. Our results reveal previously undetected spike epitopes that may guide the design of new robust COVID-19 vaccines and therapies.
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43
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Focus on Marine Animal Safety and Marine Bioresources in Response to the SARS-CoV-2 Crisis. Int J Mol Sci 2022; 23:ijms232315136. [PMID: 36499463 PMCID: PMC9737530 DOI: 10.3390/ijms232315136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
SARS-CoV-2 as a zoonotic virus has significantly affected daily life and social behavior since its outbreak in late 2019. The concerns over its transmission through different media directly or indirectly have evoked great attention about the survival of SARS-CoV-2 virions in the environment and its potential infection of other animals. To evaluate the risk of infection by SARS-CoV-2 and to counteract the COVID-19 disease, extensive studies have been performed to understand SARS-CoV-2 biogenesis and its pathogenesis. This review mainly focuses on the molecular architecture of SARS-CoV-2, its potential for infecting marine animals, and the prospect of drug discovery using marine natural products to combat SARS-CoV-2. The main purposes of this review are to piece together progress in SARS-CoV-2 functional genomic studies and antiviral drug development, and to raise our awareness of marine animal safety on exposure to SARS-CoV-2.
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Martin MA, Keith M, Pace RM, Williams JE, Ley SH, Barbosa-Leiker C, Caffé B, Smith CB, Kunkle A, Lackey KA, Navarrete AD, Pace CDW, Gogel AC, Eisenberg DT, Fehrenkamp BD, McGuire MA, McGuire MK, Meehan CL, Brindle E. SARS-CoV-2 specific antibody trajectories in mothers and infants over two months following maternal infection. Front Immunol 2022; 13:1015002. [PMID: 36304449 PMCID: PMC9596287 DOI: 10.3389/fimmu.2022.1015002] [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: 08/09/2022] [Accepted: 09/22/2022] [Indexed: 12/15/2022] Open
Abstract
Infants exposed to caregivers infected with SARS-CoV-2 may have heightened infection risks relative to older children due to their more intensive care and feeding needs. However, there has been limited research on COVID-19 outcomes in exposed infants beyond the neonatal period. Between June 2020 - March 2021, we conducted interviews and collected capillary dried blood spots from 46 SARS-CoV-2 infected mothers and their infants (aged 1-36 months) for up to two months following maternal infection onset (COVID+ group, 87% breastfeeding). Comparative data were also collected from 26 breastfeeding mothers with no known SARS-CoV-2 infection or exposures (breastfeeding control group), and 11 mothers who tested SARS-CoV-2 negative after experiencing symptoms or close contact exposure (COVID- group, 73% breastfeeding). Dried blood spots were assayed for anti-SARS-CoV-2 S-RBD IgG and IgA positivity and anti-SARS-CoV-2 S1 + S2 IgG concentrations. Within the COVID+ group, the mean probability of seropositivity among infant samples was lower than that of corresponding maternal samples (0.54 and 0.87, respectively, for IgG; 0.33 and 0.85, respectively, for IgA), with likelihood of infant infection positively associated with the number of maternal symptoms and other household infections reported. COVID+ mothers reported a lower incidence of COVID-19 symptoms among their infants as compared to themselves and other household adults, and infants had similar PCR positivity rates as other household children. No samples returned by COVID- mothers or their infants tested antibody positive. Among the breastfeeding control group, 44% of mothers but none of their infants tested antibody positive in at least one sample. Results support previous research demonstrating minimal risks to infants following maternal COVID-19 infection, including for breastfeeding infants.
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Affiliation(s)
- Melanie A. Martin
- Department of Anthropology, University of Washington, Seattle, WA, United States,Center for Studies in Demography and Ecology, University of Washington, Seattle, WA, United States,*Correspondence: Melanie A. Martin,
| | - Monica Keith
- Department of Anthropology, University of Washington, Seattle, WA, United States,Center for Studies in Demography and Ecology, University of Washington, Seattle, WA, United States
| | - Ryan M. Pace
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, United States
| | - Janet E. Williams
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
| | - Sylvia H. Ley
- Department of Epidemiology, Tulane University School of Public Health, New Orleans, LA, United States
| | - Celestina Barbosa-Leiker
- College of Nursing, Washington State University Health Sciences Spokane, Spokane, WA, United States
| | - Beatrice Caffé
- Department of Anthropology, Washington State University, Pullman, WA, United States
| | - Caroline B. Smith
- Department of Anthropology, Washington State University, Pullman, WA, United States
| | - Amanda Kunkle
- Department of Anthropology, University of Washington, Seattle, WA, United States
| | - Kimberly A. Lackey
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, United States
| | - Alexandra D. Navarrete
- Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Christina D. W. Pace
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, United States
| | - Alexandra C. Gogel
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, United States
| | - Dan T.A. Eisenberg
- Department of Anthropology, University of Washington, Seattle, WA, United States,Center for Studies in Demography and Ecology, University of Washington, Seattle, WA, United States
| | - Bethaney D. Fehrenkamp
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, United States,Washington, Wyoming, Alaska, Montana and Idaho (WWAMI) Medical Education, University of Idaho, Moscow, ID, United States
| | - Mark A. McGuire
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
| | - Michelle K. McGuire
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, United States
| | - Courtney L. Meehan
- Department of Anthropology, Washington State University, Pullman, WA, United States
| | - Eleanor Brindle
- Center for Studies in Demography and Ecology, University of Washington, Seattle, WA, United States,Maternal, Newborn and Child Health & Nutrition, PATH, Seattle, WA, United States
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45
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Phakaratsakul S, Manopwisedjaroen S, Boonarkart C, Kupatawintu P, Chaiwanichsiri D, Roytrakul T, Auewarakul P, Thitithanyanont A. Dynamics of Neutralizing Antibodies and Binding Antibodies to Domains of SARS-CoV-2 Spike Protein in COVID-19 Survivors. Viral Immunol 2022; 35:545-552. [PMID: 36190505 DOI: 10.1089/vim.2022.0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Neutralizing antibody level is used to predict immune protection against SARS-CoV-2 infection. Spike protein of SARS-CoV-2 is a major target for virus-neutralizing antibody. A number of neutralizing epitopes were mapped on receptor binding domain (RBD) and N-terminal domain (NTD) of S1 subunit of the spike. Anti-SARS-CoV-2 antibody usually decreases over time after recovery. Level of neutralizing antibody and binding antibody to several domains from COVID-19 recovered patients was observed longitudinally in this study. Sequentially collected serum samples from 35 patients demonstrated both similar and different trends of neutralizing antibodies versus binding antibodies to each domain. Twenty-three individuals showed similarly decreasing pattern of neutralizing titer, binding antibodies to RBD, NTD, fusion protein (S2), and nucleocapsid (NP). Interestingly, eight individuals had stably high neutralizing titer (≥320) for 3-12 months, whereas their binding antibodies to RBD, NTD, and NP rapidly decreased. Moreover, their binding antibodies to S2 were stable over time similar to the persistence of neutralizing antibody levels. The long-lasting antibody to S2 suggested an anamnestic response to cross-reactive epitopes from previous infections with other related coronaviruses. These data indicate a difference in kinetics and longevity of antibodies to various domains and epitopes of the SARS-CoV-2 proteins. A better understanding in this difference may help improve vaccine design to induce long-lasting immunity to COVID-19.
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Affiliation(s)
- Supinya Phakaratsakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Chompunuch Boonarkart
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | | | - Thaneeya Roytrakul
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, Thailand.,Dengue Hemorrhagic Fever Research Unit, Office of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Prasert Auewarakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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46
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Costa CFS, Barbosa AJM, Dias AMGC, Roque ACA. Native, engineered and de novo designed ligands targeting the SARS-CoV-2 spike protein. Biotechnol Adv 2022; 59:107986. [PMID: 35598822 PMCID: PMC9119173 DOI: 10.1016/j.biotechadv.2022.107986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 04/29/2022] [Accepted: 05/16/2022] [Indexed: 01/27/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the deadly coronavirus disease 2019 (Covid-19) and is a concerning hazard to public health. This virus infects cells by establishing a contact between its spike protein (S-protein) and host human angiotensin-converting enzyme 2 (hACE2) receptor, subsequently initiating viral fusion. The inhibition of the interaction between the S-protein and hACE2 has immediately drawn attention amongst the scientific community, and the S-protein was considered the prime target to design vaccines and to develop affinity ligands for diagnostics and therapy. Several S-protein binders have been reported at a fast pace, ranging from antibodies isolated from immunised patients to de novo designed ligands, with some binders already yielding promising in vivo results in protecting against SARS-CoV-2. Natural, engineered and designed affinity ligands targeting the S-protein are herein summarised, focusing on molecular recognition aspects, whilst identifying preferred hot spots for ligand binding. This review serves as inspiration for the improvement of already existing ligands or for the design of new affinity ligands towards SARS-CoV-2 proteins. Lessons learnt from the Covid-19 pandemic are also important to consolidate tools and processes in protein engineering to enable the fast discovery, production and delivery of diagnostic, prophylactic, and therapeutic solutions in future pandemics.
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Affiliation(s)
- Carlos F S Costa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Arménio J M Barbosa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Margarida G C Dias
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Cecília A Roque
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
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47
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Abdelhafiz AS, Ali A, Kamel MM, Ahmed EH, Sayed DM, Bakry RM. Sinopharm's BBIBP-CorV Vaccine and ChAdOx1 nCoV-19 Vaccine Are Associated with a Comparable Immune Response against SARS-CoV-2. Vaccines (Basel) 2022; 10:vaccines10091462. [PMID: 36146540 PMCID: PMC9502803 DOI: 10.3390/vaccines10091462] [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: 07/25/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 11/20/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has affected millions of people worldwide. During the early stages of vaccination in Egypt, the ChAdOx1 nCoV-19 and BBIBP-CorV vaccines were the most distributed. The aim of this study was to compare the immune responses and short-term efficacies of these two vaccines. We recruited adults who received two doses of either vaccine. Samples were collected after the first dose of ChAdOx1 nCoV-1 and after the second dose of both vaccines. Antibodies against SARS-CoV-2 antigens were measured using LABScreen™ COVID Plus kits, and cell-mediated immune responses were assessed using flow cytometry. Of the 109 recruited subjects, 60 (55%) received the ChAdOx1 nCoV-19 vaccine, and the remainder received the BBIBP-CorV vaccine. The total antibody level did not significantly differ between the two groups. The level of the anti-spike subunit 2 (S2) antibody was significantly higher in the ChAdOx1 nCoV-19 group. The percentages of both total T cells and B cells were unaffected by the type of vaccination. However, the ChAdOx1 nCoV-1 vaccine was significantly associated with a higher percentage of CD8+ cells. The vaccines did not significantly differ in the number or severity of infections postvaccination. None of the participants were admitted to the hospital or died of COVID-19 infection. In conclusion, the BBIBP-CorV vaccine is associated with an immune response and protection against infection that is comparable to that of the ChAdOx1 nCoV-1 vaccine. Follow-up is needed to study the long-term protective effects of both vaccines. Inactivated vaccines are easier to manufacture in developing countries and their limited side effects may lead to better economic benefits by limiting the number of absences from work.
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Affiliation(s)
- Ahmed Samir Abdelhafiz
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Kasr Al-Aini Street, El-Khalig Square, Cairo 11796, Egypt
| | - Asmaa Ali
- Department of Pulmonary Medicine, Abbassia Chest Hospital, MOH, Cairo 11517, Egypt
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Mahmoud M. Kamel
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Kasr Al-Aini Street, El-Khalig Square, Cairo 11796, Egypt
- Correspondence: ; Tel.: +201-000-219-408
| | - Eman Hasan Ahmed
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut 71515, Egypt
| | - Douaa M. Sayed
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut 71515, Egypt
| | - Rania M. Bakry
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut 71515, Egypt
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48
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Preclinical study of a DNA vaccine targeting SARS-CoV-2. Curr Res Transl Med 2022; 70:103348. [PMID: 35489099 PMCID: PMC9020527 DOI: 10.1016/j.retram.2022.103348] [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: 08/10/2021] [Revised: 03/09/2022] [Accepted: 04/16/2022] [Indexed: 01/31/2023]
Abstract
To fight against the worldwide COVID-19 pandemic, the development of an effective and safe vaccine against SARS-CoV-2 is required. As potential pandemic vaccines, DNA/RNA vaccines, viral vector vaccines and protein-based vaccines have been rapidly developed to prevent pandemic spread worldwide. In this study, we designed plasmid DNA vaccine targeting the SARS-CoV-2 Spike glycoprotein (S protein) as pandemic vaccine, and the humoral, cellular, and functional immune responses were characterized to support proceeding to initial human clinical trials. After intramuscular injection of DNA vaccine encoding S protein with alum adjuvant (three times at 2-week intervals), the humoral immunoreaction, as assessed by anti-S protein or anti-receptor-binding domain (RBD) antibody titers, and the cellular immunoreaction, as assessed by antigen-induced IFNγ expression, were up-regulated. In IgG subclass analysis, IgG2b was induced as the main subclass. Based on these analyses, DNA vaccine with alum adjuvant preferentially induced Th1-type T cell polarization. We confirmed the neutralizing action of DNA vaccine-induced antibodies by a binding assay of RBD recombinant protein with angiotensin-converting enzyme 2 (ACE2), a receptor of SARS-CoV-2, and neutralization assays using pseudo-virus, and live SARS-CoV-2. Further B cell epitope mapping analysis using a peptide array showed that most vaccine-induced antibodies recognized the S2 and RBD subunits. Finally, DNA vaccine protected hamsters from SARS-CoV-2 infection. In conclusion, DNA vaccine targeting the spike glycoprotein of SARS-CoV-2 might be an effective and safe approach to combat the COVID-19 pandemic.
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49
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Allen JD, Ivory D, Ge Song S, He WT, Capozzola T, Yong P, Burton DR, Andrabi R, Crispin M. The diversity of the glycan shield of sarbecoviruses closely related to SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.24.505118. [PMID: 36052375 PMCID: PMC9435400 DOI: 10.1101/2022.08.24.505118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The animal reservoirs of sarbecoviruses represent a significant risk of emergent pandemics, as evidenced by the impact of SARS-CoV-2. Vaccines remain successful at limiting severe disease and death, however the continued emergence of SARS-CoV-2 variants, together with the potential for further coronavirus zoonosis, motivates the search for pan-coronavirus vaccines that induce broadly neutralizing antibodies. This necessitates a better understanding of the glycan shields of coronaviruses, which can occlude potential antibody epitopes on spike glycoproteins. Here, we compare the structure of several sarbecovirus glycan shields. Many N-linked glycan attachment sites are shared by all sarbecoviruses, and the processing state of certain sites is highly conserved. However, there are significant differences in the processing state at several glycan sites that surround the receptor binding domain. Our studies reveal similarities and differences in the glycosylation of sarbecoviruses and show how subtle changes in the protein sequence can have pronounced impacts on the glycan shield.
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Affiliation(s)
- Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Dylan Ivory
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Sophie Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wan-Ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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50
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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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