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Kuroda M, Halfmann PJ, Uraki R, Yamayoshi S, Kim T, Armbrust TA, Spyra S, Dahn R, Babujee L, Kawaoka Y. SARS-CoV-2 virus lacking the envelope and membrane open-reading frames as a vaccine platform. Nat Commun 2025; 16:4453. [PMID: 40360482 PMCID: PMC12075476 DOI: 10.1038/s41467-025-59533-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 04/25/2025] [Indexed: 05/15/2025] Open
Abstract
To address the need for broadly protective SARS-CoV-2 vaccines, we developed an attenuated a SARS-CoV-2 vaccine virus that lacks the open reading frames of two viral structural proteins: the envelope (E) and membrane (M) proteins. This vaccine virus (ΔEM) replicates in a cell line stably expressing E and M but not in wild-type cells. Vaccination with ΔEM elicits a CD8 T-cell response against the viral spike and nucleocapsid proteins. Two vaccinations with ΔEM provide better protection of the lower respiratory tissues than a single dose against the Delta and Omicron XBB variants in hamsters. Moreover, ΔEM is effective as a booster in hamsters previously vaccinated with an mRNA-based vaccine, providing higher levels of protection in both respiratory tissues compared to the mRNA vaccine booster. Collectively, our data demonstrate the feasibility of a SARS-CoV-2 ΔEM vaccine candidate virus as a vaccine platform.
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Affiliation(s)
- Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA.
| | - Ryuta Uraki
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, 162-8655, Japan
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, 162-8655, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, 162-8655, Japan
| | - Taksoo Kim
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Tammy A Armbrust
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Sam Spyra
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Randall Dahn
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Lavanya Babujee
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA.
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan.
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, 162-8655, Japan.
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2
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Li J, Shuai S. CocoVax: a web server for codon-based deoptimization of viral genes in live attenuated vaccine design. Nucleic Acids Res 2025:gkaf358. [PMID: 40297995 DOI: 10.1093/nar/gkaf358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2025] [Revised: 03/28/2025] [Accepted: 04/17/2025] [Indexed: 04/30/2025] Open
Abstract
Viral infections pose major economic and public health challenges worldwide, with vaccines as a critical tool for prevention. Synonymous recoding of viral genes through codon and codon-pair deoptimization offers a promising approach to design live attenuated vaccines (LAVs) by reducing viral fitness without altering protein sequences. This strategy has been successfully applied to develop vaccines for a range of pathogens affecting human and livestock. To support this approach, we developed CocoVax, the first web server dedicated to codon and codon-pair deoptimization for LAV design. CocoVax features four modules, Virus Database, Gene Recoder, Sequence Evaluator, and Reference Library, guiding users through the entire vaccine development process. With its intuitive interface, CocoVax enables rapid generation of vaccine candidates using only a pathogen's gene sequence, providing a valuable resource for researchers in virology and vaccine development. CocoVax is freely accessible at https://comics.med.sustech.edu.cn/cocovax with no login required.
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Affiliation(s)
- Jiaxuan Li
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Shimin Shuai
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- SUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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3
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Stephens EB, Kunec D, Henke W, Vidal RM, Greishaber B, Saud R, Kalamvoki M, Singh G, Kafle S, Trujillo JD, Ferreyra FM, Morozov I, Richt JA. The Role of the Tyrosine-Based Sorting Signals of the ORF3a Protein of SARS-CoV-2 in Intracellular Trafficking and Pathogenesis. Viruses 2025; 17:522. [PMID: 40284965 PMCID: PMC12031507 DOI: 10.3390/v17040522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2025] [Revised: 03/27/2025] [Accepted: 04/01/2025] [Indexed: 04/29/2025] Open
Abstract
The open reading frame 3a (ORF3a) is a protein important to the pathogenicity of SARS-CoV-2. The cytoplasmic domain of ORF3a has three canonical tyrosine-based sorting signals (160YNSV163, 211YYQL213, and 233YNKI236), and a previous study has indicated that mutation of the 160YNSV163 motif abrogated plasma membrane expression and inhibited ORF3a-induced apoptosis. Here, we have systematically removed all three tyrosine-based motifs and assessed the importance of each motif or combination of motifs in trafficking to the cell surface. Our results indicate that the 160YNSV163 motif alone was insufficient for ORF3a cell-surface trafficking, while the 211YYQL213 motif was the most important. Additionally, an ORF3a with all three YxxΦ motifs disrupted (ORF3a-[ΔYxxΦ]) was not transported to the cell surface, and LysoIP studies indicate that ORF3a but not ORF3a-[ΔYxxΦ] was present in late endosome/lysosome fractions. A growth-curve analysis of different SARS-CoV-2 viruses expressing the different mutant ORF3a proteins revealed no significant differences in virus replication. Finally, the inoculation of K18hACE-2 mice indicated that the SARS-CoV-2 lacking the three YxxΦ motifs was less pathogenic than the unmodified SARS-CoV-2. These results indicate that the tyrosine motifs of ORF3a contribute to cell-surface expression and SARS-CoV-2 pathogenesis.
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Affiliation(s)
- Edward B. Stephens
- Department of Microbiology, Molecular Genetics, and Immunology 2000 Cates Hall, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Dusan Kunec
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany; (D.K.)
| | - Wyatt Henke
- Department of Microbiology, Molecular Genetics, and Immunology 2000 Cates Hall, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | | | - Brandon Greishaber
- Department of Microbiology, Molecular Genetics, and Immunology 2000 Cates Hall, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Rabina Saud
- Department of Microbiology, Molecular Genetics, and Immunology 2000 Cates Hall, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Maria Kalamvoki
- Department of Microbiology, Molecular Genetics, and Immunology 2000 Cates Hall, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Gagandeep Singh
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (G.S.); (J.D.T.)
| | - Sujan Kafle
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (G.S.); (J.D.T.)
| | - Jessie D. Trujillo
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (G.S.); (J.D.T.)
| | - Franco Matias Ferreyra
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Igor Morozov
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (G.S.); (J.D.T.)
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (G.S.); (J.D.T.)
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Lu Y, Zeng Y, Luo H, Chen N, Zhao L, Zhang H, Xia J, Ping J. Rapid development of attenuated IBV vaccine candidates through a versatile backbone applicable to variants. NPJ Vaccines 2025; 10:60. [PMID: 40155419 PMCID: PMC11953439 DOI: 10.1038/s41541-025-01114-z] [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: 09/24/2024] [Accepted: 03/17/2025] [Indexed: 04/01/2025] Open
Abstract
The antigen variability of the infectious bronchitis virus (IBV) has hindered vaccine effectiveness and perpetuated its epidemic. We engineered a rapid attenuation method for IBV variants. The strategy involves creating the rH-CPDF7 backbone by recoding a segment of the H120 nonstructural protein (NSP) genome via codon pair deoptimization (CPD), facilitating S gene integration from IBV variants via transformation-associated recombination (TAR) cloning. These recombinant strains exhibited even lower pathogenicity, indicating the effectiveness of CPDF7 in reducing virulence. Importantly, the rH-CPDF7 backbone demonstrated versatility, being applicable to the development of attenuated strains for IBV variants, including the QX-type, TW-type, and GVI-type strains (different genotypes). In conclusion, our method allows for the rapid development of attenuated strains by integrating the S gene of IBV variants into the rH-CPDF7 backbone. These recombinant strains can elicit a strong immune response and provide effective protection against homologous challenges. This strategy is crucial for developing live-attenuated vaccines against emerging IBV strains.
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Affiliation(s)
- Yuanlu Lu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yiran Zeng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, 210095, Nanjing, China
| | - Haowei Luo
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, 210095, Nanjing, China
| | - Na Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, 210095, Nanjing, China
| | - Lingcai Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, 210095, Nanjing, China
| | - Haitao Zhang
- Biotechnology Research Laboratory, Jiangsu Lihua Animal Husbandry Co., Ltd, 213168, Changzhou, China
| | - Jun Xia
- Xinjiang Academy of Animal Sciences Institute of Veterinary Medicine, Key Laboratory for Prevention and Control of Herbivorous Animal Diseases of the Ministry of Agriculture and Rural Affairs & Xinjiang Animal Disease Research Key Laboratory, 830000, Urumchi, China
| | - Jihui Ping
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, 210095, Nanjing, China.
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Li L, Feng T, Shen Q, Shi X, Wei Z, Chen W, Yang F, Zhu Y, Zhang C, Zhang S, Zhang Q, Fu S, Wang N, Tian WX, Liu J, Si L. Natural Infection of Omicron BA.5.2 in Patients Provides Broad Immune Responses Against SARS-CoV-2. Microorganisms 2025; 13:746. [PMID: 40284583 PMCID: PMC12029644 DOI: 10.3390/microorganisms13040746] [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: 03/13/2025] [Revised: 03/22/2025] [Accepted: 03/23/2025] [Indexed: 04/29/2025] Open
Abstract
The implementation of COVID-19 policy and the rapid development of SARS-CoV-2 vaccines in the early pandemic significantly contained numerous outbreaks and reduced the severity and mortality of COVID-19. However, the population immunity induced by existing vaccines was insufficient to prevent SARS-CoV-2 outbreaks. The host immunity induced by the wide spread of Omicron variants and its influence on emerging SARS-CoV-2 variants are attracting broad attention. In this study, a clinical data analysis of the patients indicated that pre-vaccination reduced inflammatory responses and mitigated the severity of COVID-19 cases caused by natural infection with Omicron BA.5.2. The analysis of adaptive immune responses indicated that natural infection with BA.5.2 induced robust and broad immune responses, including both humoral and T cell-mediated immune responses (IFN-γ) against highly conserved viral antigens, and provided cross-reactive neutralization against various viral variants. Collectively, we report that the natural infection with Omicron BA.5.2 induced broad cross-reactive immunity against SARS-CoV-2 variants, which suggests that the development of a live attenuated SARS-CoV-2 vaccine with desired safety, high efficacy, broad spectrum, and long-term immune persistence is feasible. Therefore, we suggest that herd immunity, achieved through vaccination with attenuated vaccines, combined with booster doses of existing vaccines and antiviral therapy for people with high viral loads, may contribute to the eradication of this virus.
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Affiliation(s)
- Le Li
- State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Tang Feng
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Quan Shen
- State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoshan Shi
- State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigong Wei
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wanze Chen
- State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fan Yang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yueting Zhu
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chengxin Zhang
- State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shuang Zhang
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qisi Zhang
- State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shengwei Fu
- State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ning Wang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wen-xia Tian
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Jiyan Liu
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Longlong Si
- State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Suzuki Okutani M, Okamura S, Gis T, Sasaki H, Lee S, Kashiwabara A, Goto S, Matsumoto M, Yamawaki M, Miyazaki T, Nakagawa T, Ikawa M, Kamitani W, Takekawa S, Yamanishi K, Ebina H. Immunogenicity and safety of a live-attenuated SARS-CoV-2 vaccine candidate based on multiple attenuation mechanisms. eLife 2025; 13:RP97532. [PMID: 39932490 PMCID: PMC11813227 DOI: 10.7554/elife.97532] [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] [Indexed: 02/13/2025] Open
Abstract
mRNA vaccines against SARS-CoV-2 were rapidly developed and were effective during the pandemic. However, some limitations remain to be resolved, such as the short-lived induced immune response and certain adverse effects. Therefore, there is an urgent need to develop new vaccines that address these issues. While live-attenuated vaccines are a highly effective modality, they pose a risk of adverse effects, including virulence reversion. In the current study, we constructed a live-attenuated vaccine candidate, BK2102, combining naturally occurring virulence-attenuating mutations in the NSP14, NSP1, spike, and ORF7-8 coding regions. Intranasal inoculation with BK2102 induced humoral and cellular immune responses in Syrian hamsters without apparent tissue damage in the lungs, leading to protection against a SARS-CoV-2 D614G and an Omicron BA.5 strains. The neutralizing antibodies induced by BK2102 persisted for up to 364 days, which indicated that they confer long-term protection against infection. Furthermore, we confirmed the safety of BK2102 using transgenic (Tg) mice expressing human ACE2 (hACE2) that are highly susceptible to SARS-CoV-2. BK2102 did not kill the Tg mice, even when virus was administered at a dose of 106 plaque-forming units (PFUs), while 102 PFU of the D614G strain or an attenuated strain lacking the furin cleavage site of the spike was sufficient to kill mice. These results suggest that BK2102 is a promising live-vaccine candidate strain that confers long-term protection without significant virulence.
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MESH Headings
- Animals
- Vaccines, Attenuated/immunology
- Vaccines, Attenuated/adverse effects
- Vaccines, Attenuated/administration & dosage
- Vaccines, Attenuated/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- SARS-CoV-2/pathogenicity
- COVID-19 Vaccines/immunology
- COVID-19 Vaccines/adverse effects
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/genetics
- COVID-19/prevention & control
- COVID-19/immunology
- Mice
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Mesocricetus
- Humans
- Mice, Transgenic
- Immunogenicity, Vaccine
- Cricetinae
- Female
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- Mie Suzuki Okutani
- The Research Foundation for Microbial Diseases of Osaka UniversitySuitaJapan
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka UniversitySuitaJapan
| | - Shinya Okamura
- The Research Foundation for Microbial Diseases of Osaka UniversitySuitaJapan
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka UniversitySuitaJapan
| | - Tang Gis
- The Research Foundation for Microbial Diseases of Osaka UniversitySuitaJapan
| | - Hitomi Sasaki
- The Research Foundation for Microbial Diseases of Osaka UniversitySuitaJapan
| | - Suni Lee
- The Research Foundation for Microbial Diseases of Osaka UniversitySuitaJapan
| | - Akiho Kashiwabara
- The Research Foundation for Microbial Diseases of Osaka UniversitySuitaJapan
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka UniversitySuitaJapan
| | - Simon Goto
- The Research Foundation for Microbial Diseases of Osaka UniversitySuitaJapan
| | - Mai Matsumoto
- The Research Foundation for Microbial Diseases of Osaka UniversitySuitaJapan
| | - Mayuko Yamawaki
- The Research Foundation for Microbial Diseases of Osaka UniversitySuitaJapan
| | - Toshiaki Miyazaki
- The Research Foundation for Microbial Diseases of Osaka UniversitySuitaJapan
| | - Tatsuya Nakagawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka UniversitySuitaJapan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka UniversitySuitaJapan
- Center for Advanced Modalities and DDS (CAMaD), Osaka UniversitySuitaJapan
- Center for Infectious Disease Education and Research (CiDER), Osaka UniversitySuitaJapan
| | - Wataru Kamitani
- Department of Infectious Diseases and Host Defense, Gunma University Graduate School of MedicineMaebashiJapan
| | - Shiro Takekawa
- The Research Foundation for Microbial Diseases of Osaka UniversitySuitaJapan
| | - Koichi Yamanishi
- The Research Foundation for Microbial Diseases of Osaka UniversitySuitaJapan
| | - Hirotaka Ebina
- The Research Foundation for Microbial Diseases of Osaka UniversitySuitaJapan
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka UniversitySuitaJapan
- Center for Advanced Modalities and DDS (CAMaD), Osaka UniversitySuitaJapan
- Center for Infectious Disease Education and Research (CiDER), Osaka UniversitySuitaJapan
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Research institute for Microbial Diseases, Osaka UniversitySuitaJapan
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7
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Meurens F, Renois F, Karniychuk U. Elegant and Innovative Recoding Strategies for Advancing Vaccine Development. Vaccines (Basel) 2025; 13:78. [PMID: 39852857 PMCID: PMC11768987 DOI: 10.3390/vaccines13010078] [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: 12/17/2024] [Revised: 01/10/2025] [Accepted: 01/14/2025] [Indexed: 01/26/2025] Open
Abstract
Recoding strategies have emerged as a promising approach for developing safer and more effective vaccines by altering the genetic structure of microorganisms, such as viruses, without changing their proteins. This method enhances vaccine safety and efficacy while minimizing the risk of reversion to virulence. Recoding enhances the frequency of CpG dinucleotides, which in turn activates immune responses and ensures a strong attenuation of the pathogens. Recent advancements highlight synonymous recoding's potential, offering improved genetic stability and immunogenicity compared to traditional methods. Live vaccines attenuated using classical methods pose a risk of reversion to virulence and can be time-consuming to produce. Synonymous recoding, involving numerous codon alterations, boosts safety and vaccine stability. One challenge is balancing attenuation with yield; however, innovations like Zinc-finger antiviral protein (ZAP) knockout cell lines can enhance vaccine production. Beyond viral vaccines, recoding can apply to bacterial vaccines, as exemplified by modified Escherichia coli and Streptococcus pneumoniae strains, which show reduced virulence. Despite promising results, challenges like ensuring genetic stability, high yield, and regulatory approval remain. Briefly, ongoing research aims to harness these innovations for comprehensive improvements in vaccine design and deployment. In this commentary, we sought to further engage the community's interest in this elegant approach by briefly highlighting its main advantages, disadvantages, and future prospects.
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Affiliation(s)
- François Meurens
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada;
- Department of Veterinary Microbiology and Immunology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada;
| | - Fanny Renois
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| | - Uladzimir Karniychuk
- Department of Veterinary Microbiology and Immunology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada;
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
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8
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Tang Y, Li Y, Cai X, Yin X. Viral Live-Attenuated Vaccines (LAVs): Past and Future Directions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2407241. [PMID: 39639853 PMCID: PMC11744563 DOI: 10.1002/advs.202407241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 11/08/2024] [Indexed: 12/07/2024]
Abstract
Viral infections continue to pose a significant threat to the health of both humans and animals. Currently, live attenuated vaccines (LAVs) remain the most efficacious and widely utilized tool for combating viral infections. Conventional LAVs involve the adaptation of virulent viruses to novel hosts, cell cultures, or suboptimal environments, resulting in a reduction in pathogenicity while retaining immunogenicity. This process entails directed evolution of the virus to enhance its replication efficiency under these modified conditions. In this review, the development of traditional animal-adapted and cold-adapted LAVs is specially discussed. Additionally, the factors that contribute to virus attenuation from a viral lifecycle perspective are summarized. Finally, we propose future directions for next-generation LAVs.
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Affiliation(s)
- Yan‐Dong Tang
- State Key Laboratory for Animal Disease Control and PreventionHarbin Veterinary Research Institute of Chinese Academy of Agricultural SciencesHarbin150069China
- Heilongjiang Provincial Research Center for Veterinary BiomedicineHarbin Veterinary Research Institute of Chinese Academy of Agricultural SciencesHarbin150069China
- Heilongjiang Provincial Key Laboratory of Veterinary ImmunologyHarbin Veterinary Research Institute of Chinese Academy of Agricultural SciencesHarbin150069China
| | - Yuming Li
- School of Public HealthShandong First Medical University & Shandong Academy of Medical SciencesJi'nan250117China
- Key Laboratory of Emerging Infectious Diseases in Universities of ShandongShandong First Medical University & Shandong Academy of Medical SciencesTai'an271000China
| | - Xue‐Hui Cai
- State Key Laboratory for Animal Disease Control and PreventionHarbin Veterinary Research Institute of Chinese Academy of Agricultural SciencesHarbin150069China
| | - Xin Yin
- State Key Laboratory for Animal Disease Control and PreventionHarbin Veterinary Research Institute of Chinese Academy of Agricultural SciencesHarbin150069China
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9
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Schirm S, Nouailles G, Kirsten H, Trimpert J, Wyler E, Teixeira Alves LG, Landthaler M, Ahnert P, Suttorp N, Witzenrath M, Scholz M. A biomathematical model of SARS-CoV-2 in Syrian hamsters. Sci Rep 2024; 14:30541. [PMID: 39695178 DOI: 10.1038/s41598-024-80498-9] [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: 04/12/2024] [Accepted: 11/19/2024] [Indexed: 12/20/2024] Open
Abstract
When infected with SARS-CoV-2, Syrian hamsters (Mesocricetus auratus) develop moderate disease severity presenting key features of human COVID-19. We here develop a biomathematical model of the disease course by translating known biological mechanisms of virus-host interactions and immune responses into ordinary differential equations. We explicitly describe the dynamics of virus population, affected alveolar epithelial cells, and involved relevant immune cells comprising for example CD4+ T cells, CD8+ T cells, macrophages, natural killer cells and B cells. We also describe the humoral response dynamics of neutralising antibodies and major regulatory cytokines including CCL8 and CXCL10. The model is developed and parametrized based on experimental data collected at days 2, 3, 5, and 14 post infection. Pulmonary cell composition and their transcriptional profiles were obtained by lung single-cell RNA (scRNA) sequencing analysis. Parametrization of the model resulted in a good agreement of model and data. The model can be used to predict, for example, the time course of the virus population, immune cell dynamics, antibody production and regeneration of alveolar cells for different therapy scenarios or after multiple-infection events. We aim to translate this model to the human situation in the future.
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Affiliation(s)
- Sibylle Schirm
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, 04107, Leipzig, Germany.
| | - Geraldine Nouailles
- Department of Infectious Diseases and Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, 04107, Leipzig, Germany
| | - Jakob Trimpert
- Institute of Virology, Freie Universität Berlin, 14163, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
| | - Luiz Gustavo Teixeira Alves
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
- Institute for Biology, Humboldt-Universität zu Berlin, 10099, Berlin, Germany
| | - Peter Ahnert
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, 04107, Leipzig, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases and Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases and Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
- German Center for Lung Research (DZL), Berlin, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, 04107, Leipzig, Germany
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10
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Baig MMFA, Wong LY, Wu H. Development of mRNA nano-vaccines for COVID-19 prevention and its biochemical interactions with various disease conditions and age groups. J Drug Target 2024; 32:21-32. [PMID: 38010097 DOI: 10.1080/1061186x.2023.2288996] [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: 06/24/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
This review has focused on the development of mRNA nano-vaccine and the biochemical interactions of anti-COVID-19 mRNA vaccines with various disease conditions and age groups. It studied five major groups of individuals with different disease conditions and ages, including allergic background, infarction background, adolescent, and adult (youngsters), pregnant women, and elderly. All five groups had been reported to have background-related adverse effects. Allergic background individuals were observed to have higher chances of experiencing allergic reactions and even anaphylaxis. Individuals with an infarction background had a higher risk of vaccine-induced diseases, e.g. pneumonitis and interstitial lung diseases. Pregnant women were seen to suffer from obstetric and gynecological adverse effects after receiving vaccinations. However, interestingly, the elderly individuals (> 65 years old) had experienced milder and less frequent adverse effects compared to the adolescent (<19 and >9 years old) and young adulthood (19-39 years old), or middle adulthood (40-59 years old) age groups, while middle to late adolescent (14-17 years old) was the riskiest age group to vaccine-induced cardiovascular manifestations.
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Affiliation(s)
- Mirza Muhammad Faran Ashraf Baig
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Lok Yin Wong
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongkai Wu
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Hong Kong, China
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11
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Friedrich VD, Pennitz P, Wyler E, Adler JM, Postmus D, Müller K, Teixeira Alves LG, Prigann J, Pott F, Vladimirova D, Hoefler T, Goekeri C, Landthaler M, Goffinet C, Saliba AE, Scholz M, Witzenrath M, Trimpert J, Kirsten H, Nouailles G. Neural network-assisted humanisation of COVID-19 hamster transcriptomic data reveals matching severity states in human disease. EBioMedicine 2024; 108:105312. [PMID: 39317638 DOI: 10.1016/j.ebiom.2024.105312] [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: 04/05/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 09/26/2024] Open
Abstract
BACKGROUND Translating findings from animal models to human disease is essential for dissecting disease mechanisms, developing and testing precise therapeutic strategies. The coronavirus disease 2019 (COVID-19) pandemic has highlighted this need, particularly for models showing disease severity-dependent immune responses. METHODS Single-cell transcriptomics (scRNAseq) is well poised to reveal similarities and differences between species at the molecular and cellular level with unprecedented resolution. However, computational methods enabling detailed matching are still scarce. Here, we provide a structured scRNAseq-based approach that we applied to scRNAseq from blood leukocytes originating from humans and hamsters affected with moderate or severe COVID-19. FINDINGS Integration of data from patients with COVID-19 with two hamster models that develop moderate (Syrian hamster, Mesocricetus auratus) or severe (Roborovski hamster, Phodopus roborovskii) disease revealed that most cellular states are shared across species. A neural network-based analysis using variational autoencoders quantified the overall transcriptomic similarity across species and severity levels, showing highest similarity between neutrophils of Roborovski hamsters and patients with severe COVID-19, while Syrian hamsters better matched patients with moderate disease, particularly in classical monocytes. We further used transcriptome-wide differential expression analysis to identify which disease stages and cell types display strongest transcriptional changes. INTERPRETATION Consistently, hamsters' response to COVID-19 was most similar to humans in monocytes and neutrophils. Disease-linked pathways found in all species specifically related to interferon response or inhibition of viral replication. Analysis of candidate genes and signatures supported the results. Our structured neural network-supported workflow could be applied to other diseases, allowing better identification of suitable animal models with similar pathomechanisms across species. FUNDING This work was supported by German Federal Ministry of Education and Research, (BMBF) grant IDs: 01ZX1304B, 01ZX1604B, 01ZX1906A, 01ZX1906B, 01KI2124, 01IS18026B and German Research Foundation (DFG) grant IDs: 14933180, 431232613.
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Affiliation(s)
- Vincent D Friedrich
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany; Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Leipzig, Germany
| | - Peter Pennitz
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany
| | - Emanuel Wyler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Julia M Adler
- Freie Universität Berlin, Institut für Virologie, Berlin, Germany
| | - Dylan Postmus
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Liverpool School of Tropical Medicine, Department of Tropical Disease Biology, Liverpool, United Kingdom
| | - Kristina Müller
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany
| | - Luiz Gustavo Teixeira Alves
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Julia Prigann
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Gladstone Institutes, San Francisco, USA
| | - Fabian Pott
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Thomas Hoefler
- Freie Universität Berlin, Institut für Virologie, Berlin, Germany
| | - Cengiz Goekeri
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany; Cyprus International University, Faculty of Medicine, Nicosia, Cyprus
| | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany; Humboldt-Universität zu Berlin, Institut fuer Biologie, Berlin, Germany
| | - Christine Goffinet
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Liverpool School of Tropical Medicine, Department of Tropical Disease Biology, Liverpool, United Kingdom
| | - Antoine-Emmanuel Saliba
- Faculty of Medicine, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Markus Scholz
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany; University of Leipzig, Faculty of Mathematics and Computer Science, Leipzig, Germany
| | - Martin Witzenrath
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany; German Center for Lung Research (DZL), Berlin, Germany
| | - Jakob Trimpert
- Freie Universität Berlin, Institut für Virologie, Berlin, Germany
| | - Holger Kirsten
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany.
| | - Geraldine Nouailles
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany.
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12
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Peidli S, Nouailles G, Wyler E, Adler JM, Kunder S, Voß A, Kazmierski J, Pott F, Pennitz P, Postmus D, Teixeira Alves LG, Goffinet C, Gruber AD, Blüthgen N, Witzenrath M, Trimpert J, Landthaler M, Praktiknjo SD. Single-cell-resolved interspecies comparison shows a shared inflammatory axis and a dominant neutrophil-endothelial program in severe COVID-19. Cell Rep 2024; 43:114328. [PMID: 38861386 DOI: 10.1016/j.celrep.2024.114328] [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: 12/15/2023] [Revised: 04/21/2024] [Accepted: 05/22/2024] [Indexed: 06/13/2024] Open
Abstract
A key issue for research on COVID-19 pathogenesis is the lack of biopsies from patients and of samples at the onset of infection. To overcome these hurdles, hamsters were shown to be useful models for studying this disease. Here, we further leverage the model to molecularly survey the disease progression from time-resolved single-cell RNA sequencing data collected from healthy and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected Syrian and Roborovski hamster lungs. We compare our data to human COVID-19 studies, including bronchoalveolar lavage, nasal swab, and postmortem lung tissue, and identify a shared axis of inflammation dominated by macrophages, neutrophils, and endothelial cells, which we show to be transient in Syrian and terminal in Roborovski hamsters. Our data suggest that, following SARS-CoV-2 infection, commitment to a type 1- or type 3-biased immunity determines moderate versus severe COVID-19 outcomes, respectively.
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Affiliation(s)
- Stefan Peidli
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Berlin, Germany; Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Geraldine Nouailles
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Julia M Adler
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Sandra Kunder
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Anne Voß
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Julia Kazmierski
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Fabian Pott
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Pennitz
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany
| | - Dylan Postmus
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Luiz Gustavo Teixeira Alves
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Christine Goffinet
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Achim D Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Nils Blüthgen
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Berlin, Germany; Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Martin Witzenrath
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany; German Center for Lung Research (DZL), Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Markus Landthaler
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany; Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Samantha D Praktiknjo
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
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13
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Yu R, Dong S, Chen B, Si F, Li C. Developing Next-Generation Live Attenuated Vaccines for Porcine Epidemic Diarrhea Using Reverse Genetic Techniques. Vaccines (Basel) 2024; 12:557. [PMID: 38793808 PMCID: PMC11125984 DOI: 10.3390/vaccines12050557] [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: 04/12/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is the etiology of porcine epidemic diarrhea (PED), a highly contagious digestive disease in pigs and especially in neonatal piglets, in which a mortality rate of up to 100% will be induced. Immunizing pregnant sows remains the most promising and effective strategy for protecting their neonatal offspring from PEDV. Although half a century has passed since its first report in Europe and several prophylactic vaccines (inactivated or live attenuated) have been developed, PED still poses a significant economic concern to the swine industry worldwide. Hence, there is an urgent need for novel vaccines in clinical practice, especially live attenuated vaccines (LAVs) that can induce a strong protective lactogenic immune response in pregnant sows. Reverse genetic techniques provide a robust tool for virological research from the function of viral proteins to the generation of rationally designed vaccines. In this review, after systematically summarizing the research progress on virulence-related viral proteins, we reviewed reverse genetics techniques for PEDV and their application in the development of PED LAVs. Then, we probed into the potential methods for generating safe, effective, and genetically stable PED LAV candidates, aiming to provide new ideas for the rational design of PED LAVs.
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Affiliation(s)
| | | | | | - Fusheng Si
- Institute of Animal Husbandry and Veterinary Medicine, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai 201106, China; (R.Y.); (S.D.); (B.C.)
| | - Chunhua Li
- Institute of Animal Husbandry and Veterinary Medicine, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai Academy of Agricultural Sciences (SAAS), Shanghai 201106, China; (R.Y.); (S.D.); (B.C.)
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14
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Levy M, Chen JW, Kaiser JA, Park HS, Liu X, Yang L, Santos C, Buchholz UJ, Le Nouën C. Intranasal respiratory syncytial virus vaccine attenuated by codon-pair deoptimization of seven open reading frames is genetically stable and elicits mucosal and systemic immunity and protection against challenge virus replication in hamsters. PLoS Pathog 2024; 20:e1012198. [PMID: 38739647 PMCID: PMC11115275 DOI: 10.1371/journal.ppat.1012198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/23/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Respiratory syncytial virus (RSV) is the most important viral agent of severe pediatric respiratory illness worldwide, but there is no approved pediatric vaccine. Here, we describe the development of the live-attenuated RSV vaccine candidate Min AL as well as engineered derivatives. Min AL was attenuated by codon-pair deoptimization (CPD) of seven of the 11 RSV open reading frames (ORFs) (NS1, NS2, N, P, M, SH and L; 2,073 silent nucleotide substitutions in total). Min AL replicated efficiently in vitro at the permissive temperature of 32°C but was highly temperature sensitive (shut-off temperature of 36°C). When serially passaged at increasing temperatures, Min AL retained greater temperature sensitivity compared to previous candidates with fewer CPD ORFs. However, whole-genome deep-sequencing of passaged Min AL revealed mutations throughout its genome, most commonly missense mutations in the polymerase cofactor P and anti-termination transcription factor M2-1 (the latter was not CPD). Reintroduction of selected mutations into Min AL partially rescued its replication in vitro at temperatures up to 40°C, confirming their compensatory effect. These mutations restored the accumulation of positive-sense RNAs to wild-type (wt) RSV levels, suggesting increased activity by the viral transcriptase, whereas viral protein expression, RNA replication, and virus production were only partly rescued. In hamsters, Min AL and derivatives remained highly restricted in replication in the upper and lower airways, but induced serum IgG and IgA responses to the prefusion form of F (pre F) that were comparable to those induced by wt RSV, as well as robust mucosal and systemic IgG and IgA responses against RSV G. Min AL and derivatives were fully protective against challenge virus replication. The derivatives had increased genetic stability compared to Min AL. Thus, Min AL and derivatives with selected mutations are stable, attenuated, yet highly-immunogenic RSV vaccine candidates that are available for further evaluation.
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Affiliation(s)
- Megan Levy
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Jessica W. Chen
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Jaclyn A. Kaiser
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Hong-Su Park
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Xueqiao Liu
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Lijuan Yang
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Celia Santos
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Ursula J. Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Cyril Le Nouën
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
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15
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Gao R, Feng C, Sheng Z, Li F, Wang D. Research progress in Fc-effector functions against SARS-CoV-2. J Med Virol 2024; 96:e29638. [PMID: 38682662 DOI: 10.1002/jmv.29638] [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: 03/12/2024] [Revised: 03/31/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused more than 676 million cases in the global human population with approximately 7 million deaths and vaccination has been proved as the most effective countermeasure in reducing clinical complications and mortality rate of SARS-CoV-2 infection in people. However, the protective elements and correlation of protection induced by vaccination are still not completely understood. Various antibodies with multiple protective mechanisms can be induced simultaneously by vaccination in vivo, thereby complicating the identification and characterization of individual correlate of protection. Recently, an increasing body of observations suggests that antibody-induced Fc-effector functions play a crucial role in combating SARS-CoV-2 infections, including neutralizing antibodies-escaping variants. Here, we review the recent progress in understanding the impact of Fc-effector functions in broadly disarming SARS-CoV-2 infectivity and discuss various efforts in harnessing this conserved antibody function to develop an effective SARS-CoV-2 vaccine that can protect humans against infections by SARS-CoV-2 virus and its variants of concern.
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Affiliation(s)
- Rongyuan Gao
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - Chenchen Feng
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - Zizhang Sheng
- Zuckerman Mind Brian Behavior Institute, Columbia University, New York, New York, USA
| | - Feng Li
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
| | - Dan Wang
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
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16
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Zhu C, Pang S, Liu J, Duan Q. Current Progress, Challenges and Prospects in the Development of COVID-19 Vaccines. Drugs 2024; 84:403-423. [PMID: 38652356 DOI: 10.1007/s40265-024-02013-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2024] [Indexed: 04/25/2024]
Abstract
The COVID-19 pandemic has resulted in over 772 million confirmed cases, including nearly 7 million deaths, according to the World Health Organization (WHO). Leveraging rapid development, accelerated vaccine approval processes, and large-scale production of various COVID-19 vaccines using different technical platforms, the WHO declared an end to the global health emergency of COVID-19 on May 5, 2023. Current COVID-19 vaccines encompass inactivated, live attenuated, viral vector, protein subunit, nucleic acid (DNA and RNA), and virus-like particle (VLP) vaccines. However, the efficacy of these vaccines is diminishing due to the constant mutation of SARS-CoV-2 and the heightened immune evasion abilities of emerging variants. This review examines the impact of the COVID-19 pandemic, the biological characteristics of the virus, and its diverse variants. Moreover, the review underscores the effectiveness, advantages, and disadvantages of authorized COVID-19 vaccines. Additionally, it analyzes the challenges, strategies, and future prospects of developing a safe, broad-spectrum vaccine that confers sufficient and sustainable immune protection against new variants of SARS-CoV-2. These discussions not only offer insight for the development of next-generation COVID-19 vaccines but also summarize experiences for combating future emerging viruses.
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Affiliation(s)
- Congrui Zhu
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510000, China
| | - Shengmei Pang
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Jiaqi Liu
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Qiangde Duan
- Department of Veterinary Microbiology, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Jiangsu Joint Laboratory for International Cooperation in Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
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17
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Chen Z, Liu Z, Feng Y, Shi A, Wu L, Sang Y, Li C. Global research on RNA vaccines for COVID-19 from 2019 to 2023: a bibliometric analysis. Front Immunol 2024; 15:1259788. [PMID: 38426106 PMCID: PMC10902429 DOI: 10.3389/fimmu.2024.1259788] [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: 07/16/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Background Since the global pandemic of COVID-19 has broken out, thousands of pieces of literature on COVID-19 RNA vaccines have been published in various journals. The overall measurement and analysis of RNA vaccines for COVID-19, with the help of sophisticated mathematical tools, could provide deep insights into global research performance and the collaborative architectural structure within the scientific community of COVID-19 mRNA vaccines. In this bibliometric analysis, we aim to determine the extent of the scientific output related to COVID-19 RNA vaccines between 2019 and 2023. Methods We applied the Bibliometrix R package for comprehensive science mapping analysis of extensive bibliographic metadata retrieved from the Web of Science Core Collection database. On January 11th, 2024, the Web of Science database was searched for COVID-19 RNA vaccine-related publications using predetermined search keywords with specific restrictions. Bradford's law was applied to evaluate the core journals in this field. The data was analyzed with various bibliometric indicators using the Bibliometrix R package. Results The final analysis included 2962 publications published between 2020 and 2023 while there is no related publication in 2019. The most productive year was 2022. The most relevant leading authors in terms of publications were Ugur Sahin and Pei-Yong, Shi, who had the highest total citations in this field. The core journals were Vaccines, Frontiers in Immunology, and Viruses-Basel. The most frequently used author's keywords were COVID-19, SARS-CoV-2, and vaccine. Recent COVID-19 RNA vaccine-related topics included mental health, COVID-19 vaccines in humans, people, and the pandemic. Harvard University was the top-ranked institution. The leading country in terms of publications, citations, corresponding author country, and international collaboration was the United States. The United States had the most robust collaboration with China. Conclusion The research hotspots include COVID-19 vaccines and the pandemic in people. We identified international collaboration and research expenditure strongly associated with COVID-19 vaccine research productivity. Researchers' collaboration among developed countries should be extended to low-income countries to expand COVID-19 vaccine-related research and understanding.
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Affiliation(s)
- Ziyi Chen
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, the First Hospital of Nanchang, Nanchang, China
| | - Zhiliang Liu
- Department of Pathology, Jiangxi Cancer Hospital, Nanchang, China
| | - Yali Feng
- Department of Pathology, Jiangxi Provincial Chest Hospital, Nanchang, China
| | - Aochen Shi
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, the First Hospital of Nanchang, Nanchang, China
| | - Liqing Wu
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, the First Hospital of Nanchang, Nanchang, China
| | - Yi Sang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, the First Hospital of Nanchang, Nanchang, China
| | - Chenxi Li
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, the First Hospital of Nanchang, Nanchang, China
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18
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Adler JM, Martin Vidal R, Langner C, Vladimirova D, Abdelgawad A, Kunecova D, Lin X, Nouailles G, Voss A, Kunder S, Gruber AD, Wu H, Osterrieder N, Kunec D, Trimpert J. An intranasal live-attenuated SARS-CoV-2 vaccine limits virus transmission. Nat Commun 2024; 15:995. [PMID: 38307868 PMCID: PMC10837132 DOI: 10.1038/s41467-024-45348-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/17/2024] [Indexed: 02/04/2024] Open
Abstract
The development of effective SARS-CoV-2 vaccines has been essential to control COVID-19, but significant challenges remain. One problem is intramuscular administration, which does not induce robust mucosal immune responses in the upper airways-the primary site of infection and virus shedding. Here we compare the efficacy of a mucosal, replication-competent yet fully attenuated virus vaccine, sCPD9-ΔFCS, and the monovalent mRNA vaccine BNT162b2 in preventing transmission of SARS-CoV-2 variants B.1 and Omicron BA.5 in two scenarios. Firstly, we assessed the protective efficacy of the vaccines by exposing vaccinated male Syrian hamsters to infected counterparts. Secondly, we evaluated transmission of the challenge virus from vaccinated and subsequently challenged male hamsters to naïve contacts. Our findings demonstrate that the live-attenuated vaccine (LAV) sCPD9-ΔFCS significantly outperformed the mRNA vaccine in preventing virus transmission in both scenarios. Our results provide evidence for the advantages of locally administered LAVs over intramuscularly administered mRNA vaccines in preventing infection and reducing virus transmission.
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Affiliation(s)
- Julia M Adler
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | | | | | | | - Azza Abdelgawad
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Daniela Kunecova
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Xiaoyuan Lin
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Geraldine Nouailles
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anne Voss
- Institut für Tierpathologie, Freie Universität Berlin, Berlin, Germany
| | - Sandra Kunder
- Institut für Tierpathologie, Freie Universität Berlin, Berlin, Germany
| | - Achim D Gruber
- Institut für Tierpathologie, Freie Universität Berlin, Berlin, Germany
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Chongqing, China
| | | | - Dusan Kunec
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany.
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19
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Wei J, Liu C, He X, Abbas B, Chen Q, Li Z, Feng Z. Generation and Characterization of Recombinant Pseudorabies Virus Delivering African Swine Fever Virus CD2v and p54. Int J Mol Sci 2023; 25:335. [PMID: 38203508 PMCID: PMC10779401 DOI: 10.3390/ijms25010335] [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: 11/15/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
African swine fever (ASF) leads to high mortality in domestic pigs and wild boar, and it is caused by the African swine fever virus (ASFV). Currently, no commercially available vaccine exists for its prevention in China. In this study, we engineered a pseudorabies recombinant virus (PRV) expressing ASFV CD2v and p54 proteins (PRV-∆TK-(CD2v)-∆gE-(p54)) using CRISPR/Cas9 and homologous recombination technology. PRV-∆TK-(CD2v)-∆gE-(p54) effectively delivers CD2v and p54, and it exhibits reduced virulence. Immunization with PRV-∆TK-(CD2v)-∆gE-(p54) neither induces pruritus nor causes systemic infection and inflammation. Furthermore, a double knockout of the TK and gE genes eliminates the depletion of T, B, and monocytes/macrophages in the blood caused by wild-type viral infection, decreases the proliferation of granulocytes to eliminate T-cell immunosuppression from granulocytes, and enhances the ability of the immune system against PRV infection. An overexpression of CD2v and p54 proteins does not alter the characteristics of PRV-∆TK/∆gE. Moreover, PRV-∆TK-(CD2v)-∆gE-(p54) successfully induces antibody production via intramuscular (IM) vaccination and confers effective protection for vaccinated mice upon challenge. Thus, PRV-∆TK-(CD2v)-∆gE-(p54) demonstrates good immunogenicity and safety, providing highly effective protection against PRV and ASFV. It potentially represents a suitable candidate for the development of a bivalent vaccine against both PRV and ASFV infections.
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Affiliation(s)
- Jianhui Wei
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou 350117, China; (J.W.); (C.L.); (X.H.); (B.A.); (Q.C.)
| | - Chuancheng Liu
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou 350117, China; (J.W.); (C.L.); (X.H.); (B.A.); (Q.C.)
| | - Xinyan He
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou 350117, China; (J.W.); (C.L.); (X.H.); (B.A.); (Q.C.)
| | - Bilal Abbas
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou 350117, China; (J.W.); (C.L.); (X.H.); (B.A.); (Q.C.)
| | - Qi Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou 350117, China; (J.W.); (C.L.); (X.H.); (B.A.); (Q.C.)
| | - Zhaolong Li
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350117, China
| | - Zhihua Feng
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University Qishan Campus, Fuzhou 350117, China; (J.W.); (C.L.); (X.H.); (B.A.); (Q.C.)
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20
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Lu S, Luo S, Liu C, Li M, An X, Li M, Hou J, Fan H, Mao P, Tong Y, Song L. Induction of significant neutralizing antibodies against SARS-CoV-2 by a highly attenuated pangolin coronavirus variant with a 104nt deletion at the 3'-UTR. Emerg Microbes Infect 2023; 12:2151383. [PMID: 36453209 PMCID: PMC9769135 DOI: 10.1080/22221751.2022.2151383] [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] [Indexed: 12/05/2022]
Abstract
SARS-CoV-2 related coronaviruses (SARS-CoV-2r) from Guangdong and Guangxi pangolins have been implicated in the emergence of SARS-CoV-2 and future pandemics. We previously reported the culture of a SARS-CoV-2r GX_P2V from Guangxi pangolins. Here we report the GX_P2V isolate rapidly adapted to Vero cells by acquiring two genomic mutations: an alanine to valine substitution in the nucleoprotein and a 104-nucleotide deletion in the hypervariable region (HVR) of the 3'-terminus untranslated region (3'-UTR). We further report the characterization of the GX_P2V variant (renamed GX_P2V(short_3UTR)) in in vitro and in vivo infection models. In cultured Vero, BGM and Calu-3 cells, GX_P2V(short_3UTR) had similar robust replication kinetics, and consistently produced minimum cell damage. GX_P2V(short_3UTR) infected golden hamsters and BALB/c mice but was highly attenuated. Golden hamsters infected intranasally had a short duration of productive infection in pulmonary, not extrapulmonary, tissues. These productive infections induced neutralizing antibodies against pseudoviruses of GX_P2V and SARS-CoV-2. Collectively, our data show that the GX_P2V(short_3UTR) is highly attenuated in in vitro and in vivo infection models. Attenuation of the variant is likely partially due to the 104-nt deletion in the HVR in the 3'-UTR. This study furthers our understanding of pangolin coronaviruses pathogenesis and provides novel insights for the design of live attenuated vaccines against SARS-CoV-2.
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Affiliation(s)
- Shanshan Lu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Shengdong Luo
- Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Chang Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Muli Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, People’s Republic of China
| | - Xiaoping An
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Mengzhe Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Jun Hou
- Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Huahao Fan
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China,Huahao Fan Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Panyong Mao
- Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, People’s Republic of China,Panyong Mao Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China,Yigang Tong Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Lihua Song
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China, Lihua Song Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
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21
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Cai HL, Huang YW. Reverse genetics systems for SARS-CoV-2: Development and applications. Virol Sin 2023; 38:837-850. [PMID: 37832720 PMCID: PMC10786661 DOI: 10.1016/j.virs.2023.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused serious harm to human health and struck a blow to global economic development. Research on SARS-CoV-2 has greatly benefited from the use of reverse genetics systems, which have been established to artificially manipulate the viral genome, generating recombinant and reporter infectious viruses or biosafety level 2 (BSL-2)-adapted non-infectious replicons with desired modifications. These tools have been instrumental in studying the molecular biological characteristics of the virus, investigating antiviral therapeutics, and facilitating the development of attenuated vaccine candidates. Here, we review the construction strategies, development, and applications of reverse genetics systems for SARS-CoV-2, which may be applied to other CoVs as well.
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Affiliation(s)
- Hou-Li Cai
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China; State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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22
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Evans JP, Liu SL. Challenges and Prospects in Developing Future SARS-CoV-2 Vaccines: Overcoming Original Antigenic Sin and Inducing Broadly Neutralizing Antibodies. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1459-1467. [PMID: 37931210 DOI: 10.4049/jimmunol.2300315] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/27/2023] [Indexed: 11/08/2023]
Abstract
The impacts of the COVID-19 pandemic led to the development of several effective SARS-CoV-2 vaccines. However, waning vaccine efficacy as well as the antigenic drift of SARS-CoV-2 variants has diminished vaccine efficacy against SARS-CoV-2 infection and may threaten public health. Increasing interest has been given to the development of a next generation of SARS-CoV-2 vaccines with increased breadth and effectiveness against SARS-CoV-2 infection. In this Brief Review, we discuss recent work on the development of these next-generation vaccines and on the nature of the immune response to SARS-CoV-2. We examine recent work to develop pan-coronavirus vaccines as well as to develop mucosal vaccines. We further discuss challenges associated with the development of novel vaccines including the need to overcome "original antigenic sin" and highlight areas requiring further investigation. We place this work in the context of SARS-CoV-2 evolution to inform how the implementation of future vaccine platforms may impact human health.
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Affiliation(s)
- John P Evans
- Center for Retrovirus Research, The Ohio State University, Columbus, OH
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH
- Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH
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23
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Hegelmeyer NK, Parkin LA, Previti ML, Andrade J, Utama R, Sejour RJ, Gardin J, Muller S, Ketchum S, Yurovsky A, Futcher B, Goodwin S, Ueberheide B, Seeliger JC. Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria. mBio 2023; 14:e0084123. [PMID: 37787543 PMCID: PMC10653884 DOI: 10.1128/mbio.00841-23] [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: 04/05/2023] [Accepted: 08/16/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, one of the deadliest infectious diseases worldwide. Previous studies have established that synonymous recoding to introduce rare codon pairings can attenuate viral pathogens. We hypothesized that non-optimal codon pairing could be an effective strategy for attenuating gene expression to create a live vaccine for Mtb. We instead discovered that these synonymous changes enabled the transcription of functional mRNA that initiated in the middle of the open reading frame and from which many smaller protein products were expressed. To our knowledge, this is one of the first reports that synonymous recoding of a gene in any organism can create or induce intragenic transcription start sites.
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Affiliation(s)
- Nuri K. Hegelmeyer
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Lia A. Parkin
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Mary L. Previti
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Joshua Andrade
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
| | - Raditya Utama
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Richard J. Sejour
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Justin Gardin
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Stephanie Muller
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Steven Ketchum
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Alisa Yurovsky
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Bruce Futcher
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - Jessica C. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
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24
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Yuen CK, Wong WM, Mak LF, Lam JY, Cheung LY, Cheung DTY, Ng YY, Lee ACY, Zhong N, Yuen KY, Kok KH. An interferon-integrated mucosal vaccine provides pan-sarbecovirus protection in small animal models. Nat Commun 2023; 14:6762. [PMID: 37875475 PMCID: PMC10598001 DOI: 10.1038/s41467-023-42349-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
A pan-sarbecovirus or pan-betacoronavirus vaccine that can prevent current and potential future beta-coronavirus infections is important for fighting possible future pandemics. Here, we report a mucosal vaccine that cross-protects small animal models from sarbecoviruses including SARS-CoV-1, SARS-CoV-2 and its variants. The vaccine comprises a live-but-defective SARS-CoV-2 virus that is envelope deficient and has the orf8 segment replaced by interferon-beta, hence named Interferon Beta Integrated SARS-CoV-2 (IBIS) vaccine. Nasal vaccination with IBIS protected mice from lethal homotypic SARS-CoV-2 infection and hamsters from co-housing-mediated transmission of homotypic virus. Moreover, IBIS provided complete protection against heterotypic sarbecoviruses, including SARS-CoV-2 Delta and Omicron variants, and SARS-CoV-1 in both mice and hamsters. Besides inducing a strong lung CD8 + T cell response, IBIS specifically heightened the activation of mucosal virus-specific CD4 + T cells compared to the interferon-null vaccine. The direct production of interferon by IBIS also suppressed virus co-infection of SARS-CoV-2 in human cells, reducing the risk of genetic recombination when using as live vaccines. Altogether, IBIS is a next-generation pan-sarbecovirus vaccine and warrants further clinical investigations.
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Affiliation(s)
- Chun-Kit Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Wan-Man Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Long-Fung Mak
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Joy-Yan Lam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Lok-Yi Cheung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Derek Tsz-Yin Cheung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yau-Yee Ng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Andrew Chak-Yiu Lee
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Nanshan Zhong
- Department of Respiratory Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, China State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou, 510120, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China
| | - Kin-Hang Kok
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong SAR, China.
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China.
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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25
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Adler JM, Martin Vidal R, Voß A, Kunder S, Nascimento M, Abdelgawad A, Langner C, Vladimirova D, Osterrieder N, Gruber AD, Kunec D, Trimpert J. A non-transmissible live attenuated SARS-CoV-2 vaccine. Mol Ther 2023; 31:2391-2407. [PMID: 37263272 PMCID: PMC10214529 DOI: 10.1016/j.ymthe.2023.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 03/23/2023] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Abstract
Live attenuated vaccines (LAVs) administered via the mucosal route may offer better control of the COVID-19 pandemic than non-replicating vaccines injected intramuscularly. Conceptionally, LAVs have several advantages, including presentation of the entire antigenic repertoire of the virus, and the induction of strong mucosal immunity. Thus, immunity induced by LAV could offer superior protection against future surges of COVID-19 cases caused by emerging SARS-CoV-2 variants. However, LAVs carry the risk of unintentional transmission. To address this issue, we investigated whether transmission of a SARS-CoV-2 LAV candidate can be blocked by removing the furin cleavage site (FCS) from the spike protein. The level of protection and immunity induced by the attenuated virus with the intact FCS was virtually identical to the one induced by the attenuated virus lacking the FCS. Most importantly, removal of the FCS completely abolished horizontal transmission of vaccine virus between cohoused hamsters. Furthermore, the vaccine was safe in immunosuppressed animals and showed no tendency to recombine in vitro or in vivo with a SARS-CoV-2 field strain. These results indicate that removal of the FCS from SARS-CoV-2 LAV is a promising strategy to increase vaccine safety and prevent vaccine transmission without compromising vaccine efficacy.
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Affiliation(s)
- Julia M Adler
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Anne Voß
- Institut für Tierpathologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Sandra Kunder
- Institut für Tierpathologie, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Azza Abdelgawad
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Christine Langner
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Daria Vladimirova
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Achim D Gruber
- Institut für Tierpathologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Dusan Kunec
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, 14163 Berlin, Germany.
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Zimmermann L, Chlanda P. Cryo-electron tomography of viral infection - from applications to biosafety. Curr Opin Virol 2023; 61:101338. [PMID: 37348443 DOI: 10.1016/j.coviro.2023.101338] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/25/2023] [Accepted: 05/28/2023] [Indexed: 06/24/2023]
Abstract
Cellular cryo-electron tomography (cryo-ET) offers 3D snapshots at molecular resolution capturing pivotal steps during viral infection. However, tomogram quality depends on the vitrification level of the sample and its thickness. In addition, mandatory inactivation protocols to assure biosafety when handling highly pathogenic viruses during cryo-ET can compromise sample preservation. Here, we focus on different strategies applied in cryo-ET and discuss their advantages and limitations with reference to severe acute respiratory syndrome coronavirus 2 studies. We highlight the importance of virus-like particle (VLP) and replicon systems to study virus assembly and replication in a cellular context without inactivation protocols. We discuss the application of chemical fixation and different irradiation methods in cryo-ET sample preparation and acquisition workflows.
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Affiliation(s)
- Liv Zimmermann
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany.
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27
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Ye C, Park JG, Chiem K, Dravid P, Allué-Guardia A, Garcia-Vilanova A, Pino Tamayo P, Shivanna V, Kapoor A, Walter MR, Kobie JJ, Plemper RK, Torrelles JB, Martinez-Sobrido L. Immunization with Recombinant Accessory Protein-Deficient SARS-CoV-2 Protects against Lethal Challenge and Viral Transmission. Microbiol Spectr 2023; 11:e0065323. [PMID: 37191507 PMCID: PMC10269623 DOI: 10.1128/spectrum.00653-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a worldwide coronavirus disease 2019 (COVID-19) pandemic. Despite the high efficacy of the authorized vaccines, there may be uncertain and unknown side effects or disadvantages associated with current vaccination approaches. Live-attenuated vaccines (LAVs) have been shown to elicit robust and long-term protection by the induction of host innate and adaptive immune responses. In this study, we sought to verify an attenuation strategy by generating 3 double open reading frame (ORF)-deficient recombinant SARS-CoV-2s (rSARS-CoV-2s) simultaneously lacking two accessory ORF proteins (ORF3a/ORF6, ORF3a/ORF7a, and ORF3a/ORF7b). We report that these double ORF-deficient rSARS-CoV-2s have slower replication kinetics and reduced fitness in cultured cells compared with their parental wild-type (WT) counterpart. Importantly, these double ORF-deficient rSARS-CoV-2s showed attenuation in both K18 hACE2 transgenic mice and golden Syrian hamsters. A single intranasal dose vaccination induced high levels of neutralizing antibodies against SARS-CoV-2 and some variants of concern and activated viral component-specific T cell responses. Notably, double ORF-deficient rSARS-CoV-2s were able to protect, as determined by the inhibition of viral replication, shedding, and transmission, against challenge with SARS-CoV-2 in both K18 hACE2 mice and golden Syrian hamsters. Collectively, our results demonstrate the feasibility of implementing the double ORF-deficient strategy to develop safe, immunogenic, and protective LAVs to prevent SARS-CoV-2 infection and associated COVID-19. IMPORTANCE Live-attenuated vaccines (LAVs) are able to induce robust immune responses, including both humoral and cellular immunity, representing a very promising option to provide broad and long-term immunity. To develop LAVs for SARS-CoV-2, we engineered attenuated recombinant SARS-CoV-2 (rSARS-CoV-2) that simultaneously lacks the viral open reading frame 3a (ORF3a) in combination with either ORF6, ORF7a, or ORF7b (Δ3a/Δ6, Δ3a/Δ7a, and Δ3a/Δ7b, respectively) proteins. Among them, the rSARS-CoV-2 Δ3a/Δ7b was completely attenuated and able to provide 100% protection against an otherwise lethal challenge in K18 hACE2 transgenic mice. Moreover, the rSARS-CoV-2 Δ3a/Δ7b conferred protection against viral transmission between golden Syrian hamsters.
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Affiliation(s)
- Chengjin Ye
- Disease Intervention and Prevention, and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Jun-Gyu Park
- Disease Intervention and Prevention, and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Kevin Chiem
- Disease Intervention and Prevention, and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Piyush Dravid
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Anna Allué-Guardia
- Disease Intervention and Prevention, and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Andreu Garcia-Vilanova
- Disease Intervention and Prevention, and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Paula Pino Tamayo
- Disease Intervention and Prevention, and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Vinay Shivanna
- Disease Intervention and Prevention, and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Amit Kapoor
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Mark R. Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - James J. Kobie
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Richard K. Plemper
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
| | - Jordi B. Torrelles
- Disease Intervention and Prevention, and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Luis Martinez-Sobrido
- Disease Intervention and Prevention, and Population Health Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA
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28
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Nouailles G, Adler JM, Pennitz P, Peidli S, Teixeira Alves LG, Baumgardt M, Bushe J, Voss A, Langenhagen A, Langner C, Martin Vidal R, Pott F, Kazmierski J, Ebenig A, Lange MV, Mühlebach MD, Goekeri C, Simmons S, Xing N, Abdelgawad A, Herwig S, Cichon G, Niemeyer D, Drosten C, Goffinet C, Landthaler M, Blüthgen N, Wu H, Witzenrath M, Gruber AD, Praktiknjo SD, Osterrieder N, Wyler E, Kunec D, Trimpert J. Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters. Nat Microbiol 2023; 8:860-874. [PMID: 37012419 PMCID: PMC10159847 DOI: 10.1038/s41564-023-01352-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 03/01/2023] [Indexed: 04/05/2023]
Abstract
Vaccines play a critical role in combating the COVID-19 pandemic. Future control of the pandemic requires improved vaccines with high efficacy against newly emerging SARS-CoV-2 variants and the ability to reduce virus transmission. Here we compare immune responses and preclinical efficacy of the mRNA vaccine BNT162b2, the adenovirus-vectored spike vaccine Ad2-spike and the live-attenuated virus vaccine candidate sCPD9 in Syrian hamsters, using both homogeneous and heterologous vaccination regimens. Comparative vaccine efficacy was assessed by employing readouts from virus titrations to single-cell RNA sequencing. Our results show that sCPD9 vaccination elicited the most robust immunity, including rapid viral clearance, reduced tissue damage, fast differentiation of pre-plasmablasts, strong systemic and mucosal humoral responses, and rapid recall of memory T cells from lung tissue after challenge with heterologous SARS-CoV-2. Overall, our results demonstrate that live-attenuated vaccines offer advantages over currently available COVID-19 vaccines.
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Affiliation(s)
- Geraldine Nouailles
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julia M Adler
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Peter Pennitz
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Peidli
- Institute of Pathology Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Institute for Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Luiz Gustavo Teixeira Alves
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Morris Baumgardt
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Judith Bushe
- Institut für Tierpathologie, Freie Universität Berlin, Berlin, Germany
| | - Anne Voss
- Institut für Tierpathologie, Freie Universität Berlin, Berlin, Germany
| | - Alina Langenhagen
- Institut für Tierpathologie, Freie Universität Berlin, Berlin, Germany
| | | | | | - Fabian Pott
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Julia Kazmierski
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Aileen Ebenig
- Product Testing of IVMPs, Division of Veterinary Medicines, Paul-Ehrlich-Institut, Langen, Germany
| | - Mona V Lange
- Product Testing of IVMPs, Division of Veterinary Medicines, Paul-Ehrlich-Institut, Langen, Germany
| | - Michael D Mühlebach
- Product Testing of IVMPs, Division of Veterinary Medicines, Paul-Ehrlich-Institut, Langen, Germany
- German Center for Infection Research (DZIF), partner site Gießen-Marburg-Langen, Giessen, Germany
| | - Cengiz Goekeri
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Faculty of Medicine, Cyprus International University, Nicosia, Cyprus
| | - Szandor Simmons
- Institute of Physiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Na Xing
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Azza Abdelgawad
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Susanne Herwig
- Department of Gynecology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Günter Cichon
- Department of Gynecology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Daniela Niemeyer
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), partner site Charité, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), partner site Charité, Berlin, Germany
| | - Christine Goffinet
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology (BIMSB) Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), and Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nils Blüthgen
- Institute of Pathology Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Institute for Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Martin Witzenrath
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Achim D Gruber
- Institut für Tierpathologie, Freie Universität Berlin, Berlin, Germany
| | | | - Nikolaus Osterrieder
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Dusan Kunec
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany.
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Cristina Diaconu C, Madalina Pitica I, Chivu-Economescu M, Georgiana Necula L, Botezatu A, Virginia Iancu I, Iulia Neagu A, L. Radu E, Matei L, Maria Ruta S, Bleotu C. SARS-CoV-2 Variant Surveillance in Genomic Medicine Era. Infect Dis (Lond) 2023. [DOI: 10.5772/intechopen.107137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/26/2024] Open
Abstract
In the genomic medicine era, the emergence of SARS-CoV-2 was immediately followed by viral genome sequencing and world-wide sequences sharing. Almost in real-time, based on these sequences, resources were developed and applied around the world, such as molecular diagnostic tests, informed public health decisions, and vaccines. Molecular SARS-CoV-2 variant surveillance was a normal approach in this context yet, considering that the viral genome modification occurs commonly in viral replication process, the challenge is to identify the modifications that significantly affect virulence, transmissibility, reduced effectiveness of vaccines and therapeutics or failure of diagnostic tests. However, assessing the importance of the emergence of new mutations and linking them to epidemiological trend, is still a laborious process and faster phenotypic evaluation approaches, in conjunction with genomic data, are required in order to release timely and efficient control measures.
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30
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Hegelmeyer NK, Previti ML, Andrade J, Utama R, Sejour RJ, Gardin J, Muller S, Ketchum S, Yurovsky A, Futcher B, Goodwin S, Ueberheide B, Seeliger JC. Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.532606. [PMID: 36993691 PMCID: PMC10055193 DOI: 10.1101/2023.03.17.532606] [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: 06/19/2023]
Abstract
Each genome encodes some codons more frequently than their synonyms (codon usage bias), but codons are also arranged more frequently into specific pairs (codon pair bias). Recoding viral genomes and yeast or bacterial genes with non-optimal codon pairs has been shown to decrease gene expression. Gene expression is thus importantly regulated not only by the use of particular codons but by their proper juxtaposition. We therefore hypothesized that non-optimal codon pairing could likewise attenuate Mtb genes. We explored the role of codon pair bias by recoding Mtb genes ( rpoB, mmpL3, ndh ) and assessing their expression in the closely related and tractable model organism M. smegmatis . To our surprise, recoding caused the expression of multiple smaller protein isoforms from all three genes. We confirmed that these smaller proteins were not due to protein degradation, but instead issued from new transcription initiation sites positioned within the open reading frame. New transcripts gave rise to intragenic translation initiation sites, which in turn led to the expression of smaller proteins. We next identified the nucleotide changes associated with these new sites of transcription and translation. Our results demonstrated that apparently benign, synonymous changes can drastically alter gene expression in mycobacteria. More generally, our work expands our understanding of the codon-level parameters that control translation and transcription initiation. IMPORTANCE Mycobacterium tuberculosis ( Mtb ) is the causative agent of tuberculosis, one of the deadliest infectious diseases worldwide. Previous studies have established that synonymous recoding to introduce rare codon pairings can attenuate viral pathogens. We hypothesized that non-optimal codon pairing could be an effective strategy for attenuating gene expression to create a live vaccine for Mtb . We instead discovered that these synonymous changes enabled the transcription of functional mRNA that initiated in the middle of the open reading frame and from which many smaller protein products were expressed. To our knowledge, this is the first report that synonymous recoding of a gene in any organism can create or induce intragenic transcription start sites.
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Affiliation(s)
- Nuri K. Hegelmeyer
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Mary L. Previti
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Joshua Andrade
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
| | - Raditya Utama
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Richard J. Sejour
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Justin Gardin
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Stephanie Muller
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Steven Ketchum
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Alisa Yurovsky
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Bruce Futcher
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, New York University Grossman School of Medicine, New York, New York, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - Jessica C. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, USA
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31
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Pacheco-García U, Serafín-López J. Indirect Dispersion of SARS-CoV-2 Live-Attenuated Vaccine and Its Contribution to Herd Immunity. Vaccines (Basel) 2023; 11:655. [PMID: 36992239 PMCID: PMC10055900 DOI: 10.3390/vaccines11030655] [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: 12/29/2022] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
It has been 34 months since the beginning of the SARS-CoV-2 coronavirus pandemic, which causes the COVID-19 disease. In several countries, immunization has reached a proportion near what is required to reach herd immunity. Nevertheless, infections and re-infections have been observed even in vaccinated persons. That is because protection conferred by vaccines is not entirely effective against new virus variants. It is unknown how often booster vaccines will be necessary to maintain a good level of protective immunity. Furthermore, many individuals refuse vaccination, and in developing countries, a large proportion of the population has not yet been vaccinated. Some live-attenuated vaccines against SARS-CoV-2 are being developed. Here, we analyze the indirect dispersion of a live-attenuated virus from vaccinated individuals to their contacts and the contribution that this phenomenon could have to reaching Herd Immunity.
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Affiliation(s)
- Ursino Pacheco-García
- Department of Cardio-Renal Pathophysiology, Instituto Nacional de Cardiología “Ignacio Chávez”, Mexico City 14080, Mexico
| | - Jeanet Serafín-López
- Department of Immunology, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico
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32
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Miao G, Chen Z, Cao H, Wu W, Chu X, Liu H, Zhang L, Zhu H, Cai H, Lu X, Shi J, Liu Y, Feng T. From Immunogen to COVID-19 vaccines: Prospects for the post-pandemic era. Biomed Pharmacother 2023; 158:114208. [PMID: 36800265 PMCID: PMC9805901 DOI: 10.1016/j.biopha.2022.114208] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/30/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023] Open
Abstract
The COVID-19 pandemic has affected millions of people and posed an unprecedented burden on healthcare systems and economies worldwide since the outbreak of the COVID-19. A considerable number of nations have investigated COVID-19 and proposed a series of prevention and treatment strategies thus far. The pandemic prevention strategies implemented in China have suggested that the spread of COVID-19 can be effectively reduced by restricting large-scale gathering, developing community-scale nucleic acid testing, and conducting epidemiological investigations, whereas sporadic cases have always been identified in numerous places. Currently, there is still no decisive therapy for COVID-19 or related complications. The development of COVID-19 vaccines has raised the hope for mitigating this pandemic based on the intercross immunity induced by COVID-19. Thus far, several types of COVID-19 vaccines have been developed and released to into financial markets. From the perspective of vaccine use in globe, COVID-19 vaccines are beneficial to mitigate the pandemic, whereas the relative adverse events have been reported progressively. This is a review about the development, challenges and prospects of COVID-19 vaccines, and it can provide more insights into all aspects of the vaccines.
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Affiliation(s)
- Ganggang Miao
- Department of General Surgery, The People’s Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, China,Department of General Surgery, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing, China
| | - Zhiqiang Chen
- Department of Nuclear Medicine, The First Affiliated Hospital of Suzhou University, Suzhou, China
| | - Hengsong Cao
- Department of General Surgery, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing, China
| | - Wenhao Wu
- Department of Clinical Medicine, Nanjing Medical University The First School of Clinical Medicine, Nanjing, China
| | - Xi Chu
- Department of Radiology, Nanjing Medical University The Fourth School of Clinical Medicine, Nanjing, China
| | - Hanyuan Liu
- Department of General Surgery, The Affiliated Nanjing Hospital of Nanjing Medical University, Nanjing, China
| | - Leyao Zhang
- Department of Clinical Medicine, Nanjing Medical University The First School of Clinical Medicine, Nanjing, China
| | - Hongfei Zhu
- Department of Clinical Medicine, Nanjing Medical University The First School of Clinical Medicine, Nanjing, China
| | - Hongzhou Cai
- Department of Urology, Jiangsu Cancer Hospital &The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Nanjing, China.
| | - Xiaolan Lu
- Department of Clinical laboratory, Canglang Hospital of Suzhou, Suzhou, China.
| | - Junfeng Shi
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China; Department of Molecular and Celluar Biochemistry, Markey Cancer Center, University of Kentucky, Lexington, KY, USA.
| | - Yuan Liu
- Department of Infectious Disease,The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Tingting Feng
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Soochow University, Suzhou, China.
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33
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Zhang J, Xia Y, Liu X, Liu G. Advanced Vaccine Design Strategies against SARS-CoV-2 and Emerging Variants. Bioengineering (Basel) 2023; 10:148. [PMID: 36829642 PMCID: PMC9951973 DOI: 10.3390/bioengineering10020148] [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: 12/12/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Vaccination is the most cost-effective means in the fight against infectious diseases. Various kinds of vaccines have been developed since the outbreak of COVID-19, some of which have been approved for clinical application. Though vaccines available achieved partial success in protecting vaccinated subjects from infection or hospitalization, numerous efforts are still needed to end the global pandemic, especially in the case of emerging new variants. Safe and efficient vaccines are the key elements to stop the pandemic from attacking the world now; novel and evolving vaccine technologies are urged in the course of fighting (re)-emerging infectious diseases. Advances in biotechnology offered the progress of vaccinology in the past few years, and lots of innovative approaches have been applied to the vaccine design during the ongoing pandemic. In this review, we summarize the state-of-the-art vaccine strategies involved in controlling the transmission of SARS-CoV-2 and its variants. In addition, challenges and future directions for rational vaccine design are discussed.
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Affiliation(s)
- Jianzhong Zhang
- Center for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Yutian Xia
- Center for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Xuan Liu
- Center for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Gang Liu
- Center for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
- Innovation Center for Cell Biology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
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34
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He DC, He CQ. Discovery of vaccine-like recombinant SARS-CoV-2 circulating in human. Virol J 2022; 19:209. [PMID: 36482293 PMCID: PMC9733243 DOI: 10.1186/s12985-022-01945-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022] Open
Abstract
For viral diseases, vaccination with live attenuated vaccine (LAV) is one of the most effective means for fighting the diseases. However, LAV occasionally overflows from vaccinated individuals circulate in the population with unforeseen consequences. Currently, SARS-CoV-2 LAVs are undergoing clinical trials. In this study, we found that the viruses isolated from Indian SARS CoV-2 infected persons may be candidate LAV-derived strains, indicating the risk of SARS-CoV-2 LAV spillover from vaccinated persons, increasing the complexity of SARS-CoV-2 detection. In addition, the property of frequent recombination of SARS-CoV-2 increases the chance of LAV virulence reversion. Therefore, how to distinguish the LAV viruses from the wild strain and how to avoid the recombination of the circulating vaccine strain and the wild strain are the challenges currently faced by SARS CoV-2 LAV development.
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Affiliation(s)
- Daniel Chang He
- grid.410585.d0000 0001 0495 1805International Department, High School Attached to Shandong Normal University, Jinan, 250014 China
| | - Cheng-Qiang He
- grid.410585.d0000 0001 0495 1805Dongying Institute, Shandong Normal University, Dongying, 257000 China ,grid.410585.d0000 0001 0495 1805Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Science, Shandong Normal University, Jinan, 250014 Shandong Province China
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35
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Sungsuwan S, Kadkanklai S, Mhuantong W, Jongkaewwattana A, Jaru-Ampornpan P. Zinc-finger antiviral protein-mediated inhibition of porcine epidemic diarrhea virus growth is antagonized by the coronaviral nucleocapsid protein. Front Microbiol 2022; 13:975632. [PMID: 36160209 PMCID: PMC9493364 DOI: 10.3389/fmicb.2022.975632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Coronaviruses have long posed a major threat not only to human health but also to agriculture. Outbreaks of an animal coronavirus such as porcine epidemic diarrhea virus (PEDV) can cause up-to-100% mortality in suckling piglets, resulting in devastating effects on the livestock industry. Understanding how the virus evades its host's defense can help us better manage the infection. Zinc-finger antiviral protein (ZAP) is an important class of host antiviral factors against a variety of viruses, including the human coronavirus. In this study, we have shown that a representative porcine coronavirus, PEDV, can be suppressed by endogenous or porcine-cell-derived ZAP in VeroE6 cells. An uneven distribution pattern of CpG dinucleotides in the viral genome is one of the factors contributing to suppression, as an increase in CpG content in the nucleocapsid (N) gene renders the virus more susceptible to ZAP. Our study revealed that the virus uses its own nucleocapsid protein (pCoV-N) to interact with ZAP and counteract the activity of ZAP. The insights into coronavirus-host interactions shown in this work could be used in the design and development of modern vaccines and antiviral agents for the next pandemic.
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Affiliation(s)
- Suttipun Sungsuwan
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Pathum Thani, Thailand
| | - Supasek Kadkanklai
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Pathum Thani, Thailand
| | - Wuttichai Mhuantong
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Pathum Thani, Thailand
| | - Anan Jongkaewwattana
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Pathum Thani, Thailand
| | - Peera Jaru-Ampornpan
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Pathum Thani, Thailand
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36
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Synthetically recoded virus sCPD9 - A tool to accelerate SARS-CoV-2 research under biosafety level 2 conditions. Comput Struct Biotechnol J 2022; 20:4376-4380. [PMID: 35992535 PMCID: PMC9375251 DOI: 10.1016/j.csbj.2022.08.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/20/2022] Open
Abstract
Research with infectious SARS-CoV-2 is complicated because it must be conducted under biosafety level 3 (BSL-3) conditions. Recently, we constructed a live attenuated SARS-CoV-2 virus by rational design through partial recoding of the SARS-CoV-2 genome and showed that the attenuated virus, designated sCPD9, was highly attenuated in preclinical animal models. The recoded sequence was designed by codon pair deoptimization and is located at the distal end of gene ORF1ab. Codon pair deoptimization involves recoding of the viral sequence with underrepresented codon pairs but without altering the amino acid sequence of the encoded proteins. Thus, parental and attenuated viruses produce exactly the same proteins. In Germany, the live attenuated SARS-CoV-2 mutant sCPD9 was recently classified as a BSL-2 pathogen based on its genetic stability and strong attenuation in preclinical animal models. Despite its high attenuation in vivo, sCPD9 grows to high titers in common cell lines, making it suitable as substitute for virulent SARS-CoV-2 in many experimental setups. Consequently, sCPD9 can ease and accelerate SARS-CoV-2 research under BSL-2 conditions, particularly in experiments requiring replicating virus, such as diagnostics and development of antiviral drugs.
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37
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Reverse genetics in virology: A double edged sword. BIOSAFETY AND HEALTH 2022. [DOI: 10.1016/j.bsheal.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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38
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Andreotti S, Altmüller J, Quedenau C, Borodina T, Nouailles G, Teixeira Alves LG, Landthaler M, Bieniara M, Trimpert J, Wyler E. De Novo Whole Genome Assembly of the Roborovski Dwarf Hamster (Phodopus roborovskii) Genome, an Animal Model for Severe/Critical COVID-19. Genome Biol Evol 2022; 14:6626084. [PMID: 35778793 PMCID: PMC9254642 DOI: 10.1093/gbe/evac100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2022] [Indexed: 11/14/2022] Open
Abstract
The Roborovski dwarf hamster Phodopus roborovskii belongs to the Phodopus genus, one of seven within Cricetinae subfamily. Like other rodents such as mice, rats or ferrets, hamsters can be important animal models for a range of diseases. Whereas the Syrian hamster from the genus Mesocricetus is now widely used as a model for mild to moderate COVID-19, Roborovski dwarf hamster show a severe to lethal course of disease upon infection with the novel human coronavirus SARS-CoV-2.
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Affiliation(s)
- Sandro Andreotti
- Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne. Present address: Scientific Genomics Platforms, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Claudia Quedenau
- Scientific Genomics Platforms, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Tatiana Borodina
- Scientific Genomics Platforms, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Geraldine Nouailles
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Division of Pulmonary Inflammation, Berlin, Germany
| | - Luiz Gustavo Teixeira Alves
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany.,Institut für Biologie, Humboldt Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
| | - Maximilian Bieniara
- Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
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Peng Q, Zhang X, Li J, He W, Fan B, Ni Y, Liu M, Li B. Comprehensive analysis of codon usage pattern of porcine deltacoronavirus and its host adaptability. Transbound Emerg Dis 2022; 69:e2443-e2455. [PMID: 35526257 DOI: 10.1111/tbed.14588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Qi Peng
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- Jiangsu Key Laboratory for Food Quality and Safety‐State Key Laboratory Cultivation Base Ministry of Science and Technology Nanjing 210014 China
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory of Zoonoses Yangzhou University Yangzhou 225009 China
| | - Xue Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- Jiangsu Key Laboratory for Food Quality and Safety‐State Key Laboratory Cultivation Base Ministry of Science and Technology Nanjing 210014 China
- Key Laboratory of Animal Disease Diagnosis and Immunology, College of Veterinary Medicine Nanjing Agricultural University Nanjing 210095 China
| | - Jizong Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- Jiangsu Key Laboratory for Food Quality and Safety‐State Key Laboratory Cultivation Base Ministry of Science and Technology Nanjing 210014 China
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory of Zoonoses Yangzhou University Yangzhou 225009 China
| | - Wenlong He
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- College of Veterinary Medicine Hebei Agricultural University Baoding 071001 China
| | - Baochao Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- Jiangsu Key Laboratory for Food Quality and Safety‐State Key Laboratory Cultivation Base Ministry of Science and Technology Nanjing 210014 China
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory of Zoonoses Yangzhou University Yangzhou 225009 China
| | - Yanxiu Ni
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- Jiangsu Key Laboratory for Food Quality and Safety‐State Key Laboratory Cultivation Base Ministry of Science and Technology Nanjing 210014 China
| | - Maojun Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- Jiangsu Key Laboratory for Food Quality and Safety‐State Key Laboratory Cultivation Base Ministry of Science and Technology Nanjing 210014 China
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture Nanjing 210014 China
- Jiangsu Key Laboratory for Food Quality and Safety‐State Key Laboratory Cultivation Base Ministry of Science and Technology Nanjing 210014 China
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Laboratory of Zoonoses Yangzhou University Yangzhou 225009 China
- Key Laboratory of Animal Disease Diagnosis and Immunology, College of Veterinary Medicine Nanjing Agricultural University Nanjing 210095 China
- College of Veterinary Medicine Hebei Agricultural University Baoding 071001 China
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Goławski M, Lewandowski P, Jabłońska I, Delijewski M. The Reassessed Potential of SARS-CoV-2 Attenuation for COVID-19 Vaccine Development—A Systematic Review. Viruses 2022; 14:v14050991. [PMID: 35632736 PMCID: PMC9146402 DOI: 10.3390/v14050991] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
Live-attenuated SARS-CoV-2 vaccines received relatively little attention during the COVID-19 pandemic. Despite this, several methods of obtaining attenuated coronaviruses are known. In this systematic review, the strategies of coronavirus attenuation, which may potentially be applied to SARS-CoV-2, were identified. PubMed, Scopus, Web of Science and Embase databases were searched to identify relevant articles describing attenuating mutations tested in vivo. In case of coronaviruses other than SARS-CoV-2, sequence alignment was used to exclude attenuating mutations that cannot be applied to SARS-CoV-2. Potential immunogenicity, safety and efficacy of the attenuated SARS-CoV-2 vaccine were discussed based on animal studies data. A total of 27 attenuation strategies, used to create 101 different coronaviruses, have been described in 56 eligible articles. The disruption of the furin cleavage site in the SARS-CoV-2 spike protein was identified as the most promising strategy. The replacement of core sequences of transcriptional regulatory signals, which prevents recombination with wild-type viruses, also appears particularly advantageous. Other important attenuating mutations encompassed mostly the prevention of evasion of innate immunity. Sufficiently attenuated coronaviruses typically caused no meaningful disease in susceptible animals and protected them from challenges with virulent virus. This indicates that attenuated COVID-19 vaccines may be considered as a potential strategy to fight the threat posed by SARS-CoV-2.
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Affiliation(s)
- Marcin Goławski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
- Correspondence:
| | - Piotr Lewandowski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
| | - Iwona Jabłońska
- Department of Biophysics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland;
| | - Marcin Delijewski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Katowice, Poland; (P.L.); (M.D.)
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Li M, Wang H, Tian L, Pang Z, Yang Q, Huang T, Fan J, Song L, Tong Y, Fan H. COVID-19 vaccine development: milestones, lessons and prospects. Signal Transduct Target Ther 2022; 7:146. [PMID: 35504917 PMCID: PMC9062866 DOI: 10.1038/s41392-022-00996-y] [Citation(s) in RCA: 237] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 12/15/2022] Open
Abstract
With the constantly mutating of SARS-CoV-2 and the emergence of Variants of Concern (VOC), the implementation of vaccination is critically important. Existing SARS-CoV-2 vaccines mainly include inactivated, live attenuated, viral vector, protein subunit, RNA, DNA, and virus-like particle (VLP) vaccines. Viral vector vaccines, protein subunit vaccines, and mRNA vaccines may induce additional cellular or humoral immune regulations, including Th cell responses and germinal center responses, and form relevant memory cells, greatly improving their efficiency. However, some viral vector or mRNA vaccines may be associated with complications like thrombocytopenia and myocarditis, raising concerns about the safety of these COVID-19 vaccines. Here, we systemically assess the safety and efficacy of COVID-19 vaccines, including the possible complications and different effects on pregnant women, the elderly, people with immune diseases and acquired immunodeficiency syndrome (AIDS), transplant recipients, and cancer patients. Based on the current analysis, governments and relevant agencies are recommended to continue to advance the vaccine immunization process. Simultaneously, special attention should be paid to the health status of the vaccines, timely treatment of complications, vaccine development, and ensuring the lives and health of patients. In addition, available measures such as mix-and-match vaccination, developing new vaccines like nanoparticle vaccines, and optimizing immune adjuvant to improve vaccine safety and efficacy could be considered.
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Affiliation(s)
- Maochen Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Han Wang
- Laboratory for Clinical Immunology, Harbin Children's Hospital, Harbin, China
| | - Lili Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zehan Pang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Qingkun Yang
- College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Tianqi Huang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Junfen Fan
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China. .,Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China.
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
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42
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K.C N, Noatia L, Priyadarshini S, M P, Gali JM, Ali MA, Behera S, Sharma B, Roychoudhury P, Kumar A, Behera P. Recoding anaerobic regulator fnr of Salmonella Typhimurium attenuates it's pathogenicity. Microb Pathog 2022; 168:105591. [DOI: 10.1016/j.micpath.2022.105591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/28/2022]
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43
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Ye ZW, Ong CP, Tang K, Fan Y, Luo C, Zhou R, Luo P, Cheng Y, Gray VS, Wang P, Chu H, Chan JFW, To KKW, Chen H, Chen Z, Yuen KY, Ling GS, Yuan S, Jin DY. Intranasal administration of a single dose of a candidate live attenuated vaccine derived from an NSP16-deficient SARS-CoV-2 strain confers sterilizing immunity in animals. Cell Mol Immunol 2022; 19:588-601. [PMID: 35352010 PMCID: PMC8961489 DOI: 10.1038/s41423-022-00855-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/01/2022] [Indexed: 12/17/2022] Open
Abstract
Live attenuated vaccines might elicit mucosal and sterilizing immunity against SARS-CoV-2 that the existing mRNA, adenoviral vector and inactivated vaccines fail to induce. Here, we describe a candidate live attenuated vaccine strain of SARS-CoV-2 in which the NSP16 gene, which encodes 2'-O-methyltransferase, is catalytically disrupted by a point mutation. This virus, designated d16, was severely attenuated in hamsters and transgenic mice, causing only asymptomatic and nonpathogenic infection. A single dose of d16 administered intranasally resulted in sterilizing immunity in both the upper and lower respiratory tracts of hamsters, thus preventing viral spread in a contact-based transmission model. It also robustly stimulated humoral and cell-mediated immune responses, thus conferring full protection against lethal challenge with SARS-CoV-2 in a transgenic mouse model. The neutralizing antibodies elicited by d16 effectively cross-reacted with several SARS-CoV-2 variants. Secretory immunoglobulin A was detected in the blood and nasal wash of vaccinated mice. Our work provides proof-of-principle evidence for harnessing NSP16-deficient SARS-CoV-2 for the development of live attenuated vaccines and paves the way for further preclinical studies of d16 as a prototypic vaccine strain, to which new features might be introduced to improve safety, transmissibility, immunogenicity and efficacy.
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Affiliation(s)
- Zi-Wei Ye
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Chon Phin Ong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - Kaiming Tang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Yilan Fan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - Cuiting Luo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Runhong Zhou
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Peng Luo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Yun Cheng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - Victor Sebastien Gray
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - Pui Wang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Hin Chu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Kelvin Kai-Wang To
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Honglin Chen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Zhiwei Chen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Guang Sheng Ling
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China.
| | - Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China.
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China.
| | - Dong-Yan Jin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China.
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44
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Fang E, Liu X, Li M, Zhang Z, Song L, Zhu B, Wu X, Liu J, Zhao D, Li Y. Advances in COVID-19 mRNA vaccine development. Signal Transduct Target Ther 2022; 7:94. [PMID: 35322018 PMCID: PMC8940982 DOI: 10.1038/s41392-022-00950-y] [Citation(s) in RCA: 289] [Impact Index Per Article: 96.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/10/2022] [Accepted: 03/03/2022] [Indexed: 12/15/2022] Open
Abstract
To date, the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has determined 399,600,607 cases and 5,757,562 deaths worldwide. COVID-19 is a serious threat to human health globally. The World Health Organization (WHO) has declared COVID-19 pandemic a major public health emergency. Vaccination is the most effective and economical intervention for controlling the spread of epidemics, and consequently saving lives and protecting the health of the population. Various techniques have been employed in the development of COVID-19 vaccines. Among these, the COVID-19 messenger RNA (mRNA) vaccine has been drawing increasing attention owing to its great application prospects and advantages, which include short development cycle, easy industrialization, simple production process, flexibility to respond to new variants, and the capacity to induce better immune response. This review summarizes current knowledge on the structural characteristics, antigen design strategies, delivery systems, industrialization potential, quality control, latest clinical trials and real-world data of COVID-19 mRNA vaccines as well as mRNA technology. Current challenges and future directions in the development of preventive mRNA vaccines for major infectious diseases are also discussed.
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Affiliation(s)
- Enyue Fang
- National Institute for Food and Drug Control, Beijing, 102629, China
- Wuhan Institute of Biological Products, Co., Ltd., Wuhan, 430207, China
| | - Xiaohui Liu
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Miao Li
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Zelun Zhang
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Lifang Song
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Baiyu Zhu
- Texas A&M University, College Station, TX, 77843, USA
| | - Xiaohong Wu
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Jingjing Liu
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Danhua Zhao
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Yuhua Li
- National Institute for Food and Drug Control, Beijing, 102629, China.
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Ye C, Park JG, Chiem K, Dravid P, Allué-Guardia A, Garcia-Vilanova A, Kapoor A, Walter MR, Kobie JJ, Plemper RK, Torrelles JB, Martinez-Sobrido L. Immunization with recombinant accessory protein-deficient SARS-CoV-2 protects against lethal challenge and viral transmission. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.03.13.484172. [PMID: 35313573 PMCID: PMC8936109 DOI: 10.1101/2022.03.13.484172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to a worldwide Coronavirus Disease 2019 (COVID-19) pandemic. Despite high efficacy of the authorized vaccines, protection against the surging variants of concern (VoC) was less robust. Live-attenuated vaccines (LAV) have been shown to elicit robust and long-term protection by induction of host innate and adaptive immune responses. We sought to develop a COVID-19 LAV by generating 3 double open reading frame (ORF)-deficient recombinant (r)SARS-CoV-2 simultaneously lacking two accessory open reading frame (ORF) proteins (ORF3a/ORF6, ORF3a/ORF7a, and ORF3a/ORF7b). Here, we report that these double ORF-deficient rSARS-CoV-2 have slower replication kinetics and reduced fitness in cultured cells as compared to their parental wild-type (WT) counterpart. Importantly, these double ORF-deficient rSARS-CoV-2 showed attenuation in both K18 hACE2 transgenic mice and golden Syrian hamsters. A single intranasal dose vaccination induced high levels of neutralizing antibodies against different SARS-CoV-2 VoC, and also activated viral component-specific T-cell responses. Notably, the double ORF-deficient rSARS-CoV-2 were able to protect, as determined by inhibition of viral replication, shedding, and transmission, against challenge with SARS-CoV-2. Collectively, our results demonstrate the feasibility to implement these double ORF-deficient rSARS-CoV-2 as safe, stable, immunogenic and protective LAV for the prevention of SARS-CoV-2 infection and associated COVID-19 disease.
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46
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Le T, Sun C, Chang J, Zhang G, Yin X. mRNA Vaccine Development for Emerging Animal and Zoonotic Diseases. Viruses 2022; 14:401. [PMID: 35215994 PMCID: PMC8877136 DOI: 10.3390/v14020401] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
In the prevention and treatment of infectious diseases, mRNA vaccines hold great promise because of their low risk of insertional mutagenesis, high potency, accelerated development cycles, and potential for low-cost manufacture. In past years, several mRNA vaccines have entered clinical trials and have shown promise for offering solutions to combat emerging and re-emerging infectious diseases such as rabies, Zika, and influenza. Recently, the successful application of mRNA vaccines against COVID-19 has further validated the platform and opened the floodgates to mRNA vaccine's potential in infectious disease prevention, especially in the veterinary field. In this review, we describe our current understanding of the mRNA vaccines and the technologies used for mRNA vaccine development. We also provide an overview of mRNA vaccines developed for animal infectious diseases and discuss directions and challenges for the future applications of this promising vaccine platform in the veterinary field.
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Affiliation(s)
- Ting Le
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (T.L.); (C.S.)
| | - Chao Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (T.L.); (C.S.)
| | - Jitao Chang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (T.L.); (C.S.)
| | - Guijie Zhang
- Departments of Animal Science, School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Xin Yin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China; (T.L.); (C.S.)
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47
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Trimpert J, Adler JM, Eschke K, Abdelgawad A, Firsching TC, Ebert N, Thao TTN, Gruber AD, Thiel V, Osterrieder N, Kunec D. Live attenuated virus vaccine protects against SARS-CoV-2 variants of concern B.1.1.7 (Alpha) and B.1.351 (Beta). SCIENCE ADVANCES 2021; 7:eabk0172. [PMID: 34851677 PMCID: PMC8635430 DOI: 10.1126/sciadv.abk0172] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Vaccines are instrumental and indispensable in the fight against the COVID-19 pandemic. Several recent SARS-CoV-2 variants are more transmissible and evade infection- or vaccine-induced protection. We constructed live attenuated vaccine candidates by large-scale recoding of the SARS-CoV-2 genome and showed that the lead candidate, designated sCPD9, protects Syrian hamsters from a challenge with ancestral virus. Here, we assessed immunogenicity and protective efficacy of sCPD9 in the Roborovski dwarf hamster, a nontransgenic rodent species that is highly susceptible to SARS-CoV-2 and severe COVID-19–like disease. We show that a single intranasal vaccination with sCPD9 elicited strong cross-neutralizing antibody responses against four current SARS-CoV-2 variants of concern, B.1.1.7 (Alpha), B.1.351 (Beta), B.1.1.28.1 (Gamma), and B.1.617.2 (Delta). The sCPD9 vaccine offered complete protection from COVID-19–like disease caused by the ancestral SARS-CoV-2 variant B.1 and the two variants of concern B.1.1.7 and B.1.351.
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Affiliation(s)
- Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Julia M. Adler
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Kathrin Eschke
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Azza Abdelgawad
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | | | - Nadine Ebert
- Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tran Thi Nhu Thao
- Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Achim D. Gruber
- Institut für Tierpathologie, Freie Universität Berlin, Berlin, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nikolaus Osterrieder
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Dusan Kunec
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
- Corresponding author.
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48
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Vaccines against COVID-19: Priority to mRNA-Based Formulations. Cells 2021; 10:cells10102716. [PMID: 34685696 PMCID: PMC8534873 DOI: 10.3390/cells10102716] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/23/2022] Open
Abstract
As of September 2021, twenty-one anti-COVID-19 vaccines have been approved in the world. Their utilization will expedite an end to the current pandemic. Besides the usual vaccine formats that include inactivated viruses (eight approved vaccines) and protein-based vaccines (four approved vaccines), three new formats have been validated: recombinant adenovirus (six approved vaccines), DNA (one approved vaccine), and messenger RNA (mRNA, two approved vaccines). The latter was the fastest (authorized in 2020 in the EU, the USA, and Switzerland). Most Western countries have reserved or use the protein vaccines, the adenovirus vaccines, and mRNA vaccines. I describe here the different vaccine formats in the context of COVID-19, detail the three formats that are chiefly reserved or used in Europe, Canada, and the USA, and discuss why the mRNA vaccines appear to be the superior format.
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49
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Meekins DA, Gaudreault NN, Richt JA. Natural and Experimental SARS-CoV-2 Infection in Domestic and Wild Animals. Viruses 2021; 13:1993. [PMID: 34696423 PMCID: PMC8540328 DOI: 10.3390/v13101993] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 is the etiological agent responsible for the ongoing COVID-19 pandemic, which continues to spread with devastating effects on global health and socioeconomics. The susceptibility of domestic and wild animal species to infection is a critical facet of SARS-CoV-2 ecology, since reverse zoonotic spillover events resulting in SARS-CoV-2 outbreaks in animal populations could result in the establishment of new virus reservoirs. Adaptive mutations in the virus to new animal species could also complicate ongoing mitigation strategies to combat SARS-CoV-2. In addition, animal species susceptible to SARS-CoV-2 infection are essential as standardized preclinical models for the development and efficacy testing of vaccines and therapeutics. In this review, we summarize the current findings regarding the susceptibility of different domestic and wild animal species to experimental SARS-CoV-2 infection and provide detailed descriptions of the clinical disease and transmissibility in these animals. In addition, we outline the documented natural infections in animals that have occurred at the human-animal interface. A comprehensive understanding of animal susceptibility to SARS-CoV-2 is crucial to inform public health, veterinary, and agricultural systems, and to guide environmental policies.
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Affiliation(s)
- David A. Meekins
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (D.A.M.); (N.N.G.)
- Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (D.A.M.); (N.N.G.)
- Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (D.A.M.); (N.N.G.)
- Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502, USA
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