1
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Bruch EM, Zhu S, Szymkowicz L, Blake T, Kiss T, James DA, Rak A, Narayan K, Balmer MT, Chicz RM. Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2. Sci Rep 2024; 14:2038. [PMID: 38263191 PMCID: PMC10805794 DOI: 10.1038/s41598-024-52499-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, uses a surface expressed trimeric spike glycoprotein for cell entry. This trimer is the primary target for neutralizing antibodies making it a key candidate for vaccine development. During the global pandemic circulating variants of concern (VOC) caused several waves of infection, severe disease, and death. The reduced efficacy of the ancestral trimer-based vaccines against emerging VOC led to the need for booster vaccines. Here we present a detailed characterization of the Sanofi Beta trimer, utilizing cryo-EM for structural elucidation. We investigate the conformational dynamics and stabilizing features using orthogonal SPR, SEC, nanoDSF, and HDX-MS techniques to better understand how this antigen elicits superior broad neutralizing antibodies as a variant booster vaccine. This structural analysis confirms the Beta trimer preference for canonical quaternary structure with two RBD in the up position and the reversible equilibrium between the canonical spike and open trimer conformations. Moreover, this report provides a better understanding of structural differences between spike antigens contributing to differential vaccine efficacy.
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2
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Xie G, Zhu L, Liu S, Li C, Diao X, Zhang Y, Su X, Song Y, Cao G, Zhong L, Wang P, Liu X, Mok BWY, Zhang S, Jin DY, Zhou J, Chen H, Cai Z. Multi-omics analysis of attenuated variant reveals potential evaluation marker of host damaging for SARS-CoV-2 variants. SCIENCE CHINA. LIFE SCIENCES 2024; 67:83-95. [PMID: 37721637 DOI: 10.1007/s11427-022-2379-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/30/2023] [Indexed: 09/19/2023]
Abstract
SARS-CoV-2 continues to threaten human society by generating novel variants via mutation and recombination. The high number of mutations that appeared in emerging variants not only enhanced their immune-escaping ability but also made it difficult to predict the pathogenicity and virulence based on viral nucleotide sequences. Molecular markers for evaluating the pathogenicity of new variants are therefore needed. By comparing host responses to wild-type and variants with attenuated pathogenicity at proteome and metabolome levels, six key molecules on the polyamine biosynthesis pathway including putrescine, SAM, dc-SAM, ODC1, SAMS, and SAMDC were found to be differentially upregulated and associated with pathogenicity of variants. To validate our discovery, human airway organoids were subsequently used which recapitulates SARS-CoV-2 replication in the airway epithelial cells of COVID-19 patients. Using ODC1 as a proof-of-concept, differential activation of polyamine biosynthesis was found to be modulated by the renin-angiotensin system (RAS) and positively associated with ACE2 activity. Further experiments demonstrated that ODC1 expression could be differentially activated upon a panel of SARS-CoV-2 variants of concern (VOCs) and was found to be correlated with each VOCs' pathogenic properties. Particularly, the presented study revealed the discriminative ability of key molecules on polyamine biosynthesis as a predictive marker for virulence evaluation and assessment of SARS-CoV-2 variants in cell or organoid models. Our work, therefore, presented a practical strategy that could be potentially applied as an evaluation tool for the pathogenicity of current and emerging SARS-CoV-2 variants.
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Affiliation(s)
- Guangshan Xie
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China
| | - Lin Zhu
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China.
- HKBU Shenzhen Institute of Research and Continuing Education, Shenzhen, 518000, China.
| | - Siwen Liu
- State Key Laboratory for Emerging Infectious Diseases, and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Cun Li
- State Key Laboratory for Emerging Infectious Diseases, and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Xin Diao
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yanhao Zhang
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China
| | - Xiuli Su
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yuanyuan Song
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China
| | - Guodong Cao
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China
| | - Li Zhong
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China
| | - Pui Wang
- State Key Laboratory for Emerging Infectious Diseases, and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaojuan Liu
- State Key Laboratory for Emerging Infectious Diseases, and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Bobo Wing-Yee Mok
- State Key Laboratory for Emerging Infectious Diseases, and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shusheng Zhang
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Jie Zhou
- State Key Laboratory for Emerging Infectious Diseases, and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Honglin Chen
- State Key Laboratory for Emerging Infectious Diseases, and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China.
- HKBU Shenzhen Institute of Research and Continuing Education, Shenzhen, 518000, China.
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3
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Imbiakha B, Ezzatpour S, Buchholz DW, Sahler J, Ye C, Olarte-Castillo XA, Zou A, Kwas C, O’Hare K, Choi A, Adeleke RA, Khomandiak S, Goodman L, Jager MC, Whittaker GR, Martinez-Sobrido L, August A, Aguilar HC. Age-dependent acquisition of pathogenicity by SARS-CoV-2 Omicron BA.5. SCIENCE ADVANCES 2023; 9:eadj1736. [PMID: 37738347 PMCID: PMC10516498 DOI: 10.1126/sciadv.adj1736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/23/2023] [Indexed: 09/24/2023]
Abstract
Pathology studies of SARS-CoV-2 Omicron variants of concern (VOC) are challenged by the lack of pathogenic animal models. While Omicron BA.1 and BA.2 replicate in K18-hACE2 transgenic mice, they cause minimal to negligible morbidity and mortality, and less is known about more recent Omicron VOC. Here, we show that in contrast to Omicron BA.1, BA.5-infected mice exhibited high levels of morbidity and mortality, correlating with higher early viral loads. Neither Omicron BA.1 nor BA.5 replicated in brains, unlike most prior VOC. Only Omicron BA.5-infected mice exhibited substantial weight loss, high pathology scores in lungs, and high levels of inflammatory cells and cytokines in bronchoalveolar lavage fluid, and 5- to 8-month-old mice exhibited 100% fatality. These results identify a rodent model for pathogenesis or antiviral countermeasure studies for circulating SARS-CoV-2 Omicron BA.5. Further, differences in morbidity and mortality between Omicron BA.1 and BA.5 provide a model for understanding viral determinants of pathogenicity.
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Affiliation(s)
- Brian Imbiakha
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Shahrzad Ezzatpour
- Department of Microbiology, Cornell University, College of Agriculture and Life Sciences, Ithaca, NY, 14853, USA
| | - David W. Buchholz
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Julie Sahler
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Ximena A. Olarte-Castillo
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- James A. Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Anna Zou
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Cole Kwas
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Katelyn O’Hare
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Annette Choi
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Richard Ayomide Adeleke
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Solomiia Khomandiak
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Laura Goodman
- James A. Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public & Ecosystem Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Mason C. Jager
- Department of Population Medicine and Diagnostic Sciences, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Gary R. Whittaker
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public & Ecosystem Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | | | - Avery August
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Hector C. Aguilar
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Microbiology, Cornell University, College of Agriculture and Life Sciences, Ithaca, NY, 14853, USA
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4
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Zhou T, Gilliam NJ, Li S, Spandau S, Osborn RM, Connor S, Anderson CS, Mariani TJ, Thakar J, Dewhurst S, Mathews DH, Huang L, Sun Y. Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection. mBio 2023; 14:e0025023. [PMID: 37074178 PMCID: PMC10294654 DOI: 10.1128/mbio.00250-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/28/2023] [Indexed: 04/20/2023] Open
Abstract
Defective viral genomes (DVGs) have been identified in many RNA viruses as a major factor influencing antiviral immune response and viral pathogenesis. However, the generation and function of DVGs in SARS-CoV-2 infection are less known. In this study, we elucidated DVG generation in SARS-CoV-2 and its relationship with host antiviral immune response. We observed DVGs ubiquitously from transcriptome sequencing (RNA-seq) data sets of in vitro infections and autopsy lung tissues of COVID-19 patients. Four genomic hot spots were identified for DVG recombination, and RNA secondary structures were suggested to mediate DVG formation. Functionally, bulk and single-cell RNA-seq analysis indicated the interferon (IFN) stimulation of SARS-CoV-2 DVGs. We further applied our criteria to the next-generation sequencing (NGS) data set from a published cohort study and observed a significantly higher amount and frequency of DVG in symptomatic patients than those in asymptomatic patients. Finally, we observed exceptionally diverse DVG populations in one immunosuppressive patient up to 140 days after the first positive test of COVID-19, suggesting for the first time an association between DVGs and persistent viral infections in SARS-CoV-2. Together, our findings strongly suggest a critical role of DVGs in modulating host IFN responses and symptom development, calling for further inquiry into the mechanisms of DVG generation and into how DVGs modulate host responses and infection outcome during SARS-CoV-2 infection. IMPORTANCE Defective viral genomes (DVGs) are generated ubiquitously in many RNA viruses, including SARS-CoV-2. Their interference activity to full-length viruses and IFN stimulation provide the potential for them to be used in novel antiviral therapies and vaccine development. SARS-CoV-2 DVGs are generated through the recombination of two discontinuous genomic fragments by viral polymerase complex, and this recombination is also one of the major mechanisms for the emergence of new coronaviruses. Focusing on the generation and function of SARS-CoV-2 DVGs, these studies identify new hot spots for nonhomologous recombination and strongly suggest that the secondary structures within viral genomes mediate the recombination. Furthermore, these studies provide the first evidence for IFN stimulation activity of de novo DVGs during natural SARS-CoV-2 infection. These findings set up the foundation for further mechanism studies of SARS-CoV-2 recombination and provide evidence to harness the immunostimulatory potential of DVGs in the development of a vaccine and antivirals for SARS-CoV-2.
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Affiliation(s)
- Terry Zhou
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Nora J. Gilliam
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Medical Scientist Training Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Translational Biomedical Sciences PhD Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Sizhen Li
- School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, Oregon, USA
| | - Simone Spandau
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Raven M. Osborn
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Translational Biomedical Sciences PhD Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Sarah Connor
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Christopher S. Anderson
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Thomas J. Mariani
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Juilee Thakar
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Stephen Dewhurst
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - David H. Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Liang Huang
- School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, Oregon, USA
| | - Yan Sun
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
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5
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Simas MCDC, Costa SM, Gomes PDSFC, Cruz NVGD, Corrêa IA, de Souza MRM, Dornelas-Ribeiro M, Nogueira TLS, Santos CGMD, Hoffmann L, Tanuri A, Moura-Neto RSD, Damaso CR, Costa LJD, Silva R. Evaluation of SARS-CoV-2 ORF7a Deletions from COVID-19-Positive Individuals and Its Impact on Virus Spread in Cell Culture. Viruses 2023; 15:v15030801. [PMID: 36992509 PMCID: PMC10051148 DOI: 10.3390/v15030801] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the COVID-19 outbreak, posed a primary concern of public health worldwide. The most common changes in SARS-CoV-2 are single nucleotide substitutions, also reported insertions and deletions. This work investigates the presence of SARS-CoV-2 ORF7a deletions identified in COVID-19-positive individuals. Sequencing of SARS-CoV-2 complete genomes showed three different ORF7a size deletions (190-nt, 339-nt and 365-nt). Deletions were confirmed through Sanger sequencing. The ORF7a∆190 was detected in a group of five relatives with mild symptoms of COVID-19, and the ORF7a∆339 and ORF7a∆365 in a couple of co-workers. These deletions did not affect subgenomic RNAs (sgRNA) production downstream of ORF7a. Still, fragments associated with sgRNA of genes upstream of ORF7a showed a decrease in size when corresponding to samples with deletions. In silico analysis suggests that the deletions impair protein proper function; however, isolated viruses with partial deletion of ORF7a can replicate in culture cells similarly to wild-type viruses at 24 hpi, but with less infectious particles after 48 hpi. These findings on deleted ORF7a accessory protein gene, contribute to understanding SARS-CoV-2 phenotypes such as replication, immune evasion and evolutionary fitness as well insights into the role of SARS-CoV-2_ORF7a in the mechanism of virus-host interactions.
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Affiliation(s)
- Maria Clara da Costa Simas
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Sara Mesquita Costa
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Priscila da Silva Figueiredo Celestino Gomes
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Physics Department, Auburn University, Auburn, AL 36849, USA
| | | | - Isadora Alonso Corrêa
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | | | - Marcos Dornelas-Ribeiro
- Laboratório de Biodefesa, Instituto de Biologia do Exército, Rio de Janeiro 20911-270, Brazil
| | | | | | - Luísa Hoffmann
- Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Rio de Janeiro 20270-021, Brazil
| | - Amilcar Tanuri
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | | | - Clarissa R Damaso
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Luciana Jesus da Costa
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Rosane Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
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6
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Stauft CB, Sangare K, Wang TT. Differences in New Variant of Concern Replication at Physiological Temperatures In Vitro. J Infect Dis 2023; 227:202-205. [PMID: 35759271 PMCID: PMC9384407 DOI: 10.1093/infdis/jiac264] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/17/2022] [Accepted: 06/24/2022] [Indexed: 01/14/2023] Open
Abstract
Using multiple cell types and isolates of Delta and Omicron variants of SARS-CoV-2, we report differences in virus production, replication, and infectivity in vitro. Ancestral and Delta SARS-CoV-2 variant exhibit reduced virus production and replication at 34°C compared to 37°C while Omicron replication is balanced between temperatures.
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Affiliation(s)
- Charles B Stauft
- Division of Viral Products, Center for Biologics Evaluations and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Kotou Sangare
- Division of Viral Products, Center for Biologics Evaluations and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Tony T Wang
- Division of Viral Products, Center for Biologics Evaluations and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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7
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Wang Y, Yan T, Mei K, Rao D, Wu W, Chen Y, Peng Y, Wang J, Wu S, Zhang Q. Nanomechanical assay for ultrasensitive and rapid detection of SARS-CoV-2 based on peptide nucleic acid. NANO RESEARCH 2023; 16:1183-1195. [PMID: 35610981 PMCID: PMC9118818 DOI: 10.1007/s12274-022-4333-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 05/14/2023]
Abstract
UNLABELLED The massive global spread of the COVID-19 pandemic makes the development of more effective and easily popularized assays critical. Here, we developed an ultrasensitive nanomechanical method based on microcantilever array and peptide nucleic acid (PNA) for the detection of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) RNA. The method has an extremely low detection limit of 0.1 fM (105 copies/mL) for N-gene specific sequence (20 bp). Interestingly, it was further found that the detection limit of N gene (pharyngeal swab sample) was even lower, reaching 50 copies/mL. The large size of the N gene dramatically enhances the sensitivity of the nanomechanical sensor by up to three orders of magnitude. The detection limit of this amplification-free assay method is an order of magnitude lower than RT-PCR (500 copies/mL) that requires amplification. The non-specific signal in the assay is eliminated by the in-situ comparison of the array, reducing the false-positive misdiagnosis rate. The method is amplification-free and label-free, allowing for accurate diagnosis within 1 h. The strong specificity and ultra-sensitivity allow single base mutations in viruses to be distinguished even at very low concentrations. Also, the method remains sensitive to fM magnitude lung cancer marker (miRNA-155). Therefore, this ultrasensitive, amplification-free and inexpensive assay is expected to be used for the early diagnosis of COVID-19 patients and to be extended as a broad detection tool. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material (experimental section, N gene sequences and all nucleic acid sequences used in the study, Figs. S1-S6, and Tables S1-S3) is available in the online version of this article at 10.1007/s12274-022-4333-3.
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Affiliation(s)
- Yu Wang
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Tianhao Yan
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Kainan Mei
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Depeng Rao
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Wenjie Wu
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Ye Chen
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Yongpei Peng
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Jianye Wang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, 230022 China
| | - Shangquan Wu
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Qingchuan Zhang
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
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8
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Zhou T, Gilliam NJ, Li S, Spaudau S, Osborn RM, Anderson CS, Mariani TJ, Thakar J, Dewhurst S, Mathews DH, Huang L, Sun Y. Generation and functional analysis of defective viral genomes during SARS-CoV-2 infection.. [PMID: 36172120 PMCID: PMC9516852 DOI: 10.1101/2022.09.22.509123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Defective viral genomes (DVGs) have been identified in many RNA viruses as a major factor influencing antiviral immune response and viral pathogenesis. However, the generation and function of DVGs in SARS-CoV-2 infection are less known. In this study, we elucidated DVG generation in SARS-CoV-2 and its relationship with host antiviral immune response. We observed DVGs ubiquitously from RNA-seq datasets of in vitro infections and autopsy lung tissues of COVID-19 patients. Four genomic hotspots were identified for DVG recombination and RNA secondary structures were suggested to mediate DVG formation. Functionally, bulk and single cell RNA-seq analysis indicated the IFN stimulation of SARS-CoV-2 DVGs. We further applied our criteria to the NGS dataset from a published cohort study and observed significantly higher DVG amount and frequency in symptomatic patients than that in asymptomatic patients. Finally, we observed unusually high DVG frequency in one immunosuppressive patient up to 140 days after admitted to hospital due to COVID-19, first-time suggesting an association between DVGs and persistent viral infections in SARS-CoV-2. Together, our findings strongly suggest a critical role of DVGs in modulating host IFN responses and symptom development, calling for further inquiry into the mechanisms of DVG generation and how DVGs modulate host responses and infection outcome during SARS-CoV-2 infection.
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9
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Tang PCH, Ng WH, King NJC, Mahalingam S. Can live-attenuated SARS-CoV-2 vaccine contribute to stopping the pandemic? PLoS Pathog 2022; 18:e1010821. [PMID: 36129963 PMCID: PMC9491521 DOI: 10.1371/journal.ppat.1010821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Patrick Chun Hean Tang
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Queensland, Australia
| | - Wern Hann Ng
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Queensland, Australia
| | - Nicholas J. C. King
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Queensland, Australia
- The Discipline of Pathology and Bosch Institute, School of Medical Sciences, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Suresh Mahalingam
- Emerging Viruses, Inflammation and Therapeutics Group, Menzies Health Institute Queensland, Griffith University, Queensland, Australia
- * E-mail:
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10
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Magnus CL, Hiergeist A, Schuster P, Rohrhofer A, Medenbach J, Gessner A, Peterhoff D, Schmidt B. Targeted escape of SARS-CoV-2 in vitro from monoclonal antibody S309, the precursor of sotrovimab. Front Immunol 2022; 13:966236. [PMID: 36090991 PMCID: PMC9449809 DOI: 10.3389/fimmu.2022.966236] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/03/2022] [Indexed: 12/01/2022] Open
Abstract
Class 1 and 2 monoclonal antibodies inhibit SARS-CoV-2 entry by blocking the interaction of the viral receptor-binding domain with angiotensin-converting enzyme 2 (ACE2), while class 3 antibodies target a highly conserved epitope outside the ACE2 binding site. We aimed to investigate the plasticity of the spike protein by propagating wild-type SARS-CoV-2 in the presence of class 3 antibody S309. After 12 weeks, we obtained a viral strain that was completely resistant to inhibition by S309, due to successively evolving amino acid exchanges R346S and P337L located in the paratope of S309. The antibody lost affinity to receptor-binding domains carrying P337L or both amino acid exchanges, while ACE2 binding was not affected. The resistant strain replicated efficiently in human CaCo-2 cells and was more susceptible to inhibition of fusion than the original strain. Overall, SARS-CoV-2 escaped inhibition by class 3 antibody S309 through a slow, but targeted evolution enabling immune escape and altering cell entry. This immune-driven enhancement of infectivity and pathogenicity could play an important role in the future evolution of SARS-CoV-2, which is under increasing immunological pressure from vaccination and previous infections.
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Affiliation(s)
- Clara Luzia Magnus
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Philipp Schuster
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Anette Rohrhofer
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Jan Medenbach
- Biochemistry I, Faculty of Biology and Pre-Clinical Medicine, University of Regensburg, Regensburg, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - David Peterhoff
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Barbara Schmidt
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
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11
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Co-existence and co-infection of influenza A viruses and coronaviruses: Public health challenges. Innovation (N Y) 2022; 3:100306. [PMID: 35992368 PMCID: PMC9384331 DOI: 10.1016/j.xinn.2022.100306] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/14/2022] [Indexed: 02/08/2023] Open
Abstract
Since the 20th century, humans have lived through five pandemics caused by influenza A viruses (IAVs) (H1N1/1918, H2N2/1957, H3N2/1968, and H1N1/2009) and the coronavirus (CoV) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). IAVs and CoVs both have broad host ranges and share multiple hosts. Virus co-circulation and even co-infections facilitate genetic reassortment among IAVs and recombination among CoVs, further altering virus evolution dynamics and generating novel variants with increased cross-species transmission risk. Moreover, SARS-CoV-2 may maintain long-term circulation in humans as seasonal IAVs. Co-existence and co-infection of both viruses in humans could alter disease transmission patterns and aggravate disease burden. Herein, we demonstrate how virus-host ecology correlates with the co-existence and co-infection of IAVs and/or CoVs, further affecting virus evolution and disease dynamics and burden, calling for active virus surveillance and countermeasures for future public health challenges.
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12
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Gaiarsa S, Giardina F, Batisti Biffignandi G, Ferrari G, Piazza A, Tallarita M, Novazzi F, Bandi C, Paolucci S, Rovida F, Campanini G, Piralla A, Baldanti F. Comparative analysis of SARS-CoV-2 quasispecies in the upper and lower respiratory tract shows an ongoing evolution in the spike cleavage site. Virus Res 2022; 315:198786. [PMID: 35429618 PMCID: PMC9008095 DOI: 10.1016/j.virusres.2022.198786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/14/2022] [Accepted: 04/12/2022] [Indexed: 02/06/2023]
Abstract
Studies are needed to better understand the genomic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to describe viral quasispecies population of upper and lower respiratory tract by next-generation sequencing in patients admitted to intensive care unit. A deep sequencing of the S gene of SARS-CoV-2 from 109 clinical specimens, sampled from the upper respiratory tract (URT) and lower respiratory tract (LRT) of 77 patients was performed. A higher incidence of non-synonymous mutations and indels was observed in the LRT among minority variants. This might be explained by the ability of the virus to invade cells without interacting with ACE2 (e.g. exploiting macrophage phagocytosis). Minority variants are highly concentrated around the gene portion encoding for the Spike cleavage site, with a higher incidence in the URT; four mutations are highly recurring among samples and were found associated with the URT. Interestingly, 55.8% of minority variants detected in this locus were T>G and G>T transversions. Results from this study evidenced the presence of selective pressure and suggest that an evolutionary process is still ongoing in one of the crucial sites of spike protein associated with the spillover to humans.
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Affiliation(s)
- Stefano Gaiarsa
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy
| | - Federica Giardina
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy
| | | | - Guglielmo Ferrari
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy
| | - Aurora Piazza
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Monica Tallarita
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy
| | - Federica Novazzi
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy
| | - Claudio Bandi
- Department of Biosciences and Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy
| | - Stefania Paolucci
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy
| | - Francesca Rovida
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Giulia Campanini
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy.
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
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13
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Abstract
The dramatic global consequences of the coronavirus disease 2019 (COVID-19) pandemic soon fueled quests for a suitable model that would facilitate the development and testing of therapies and vaccines. In contrast to other rodents, hamsters are naturally susceptible to infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the Syrian hamster (Mesocricetus auratus) rapidly developed into a popular model. It recapitulates many characteristic features as seen in patients with a moderate, self-limiting course of the disease such as specific patterns of respiratory tract inflammation, vascular endothelialitis, and age dependence. Among 4 other hamster species examined, the Roborovski dwarf hamster (Phodopus roborovskii) more closely mimics the disease in highly susceptible patients with frequent lethal outcome, including devastating diffuse alveolar damage and coagulopathy. Thus, different hamster species are available to mimic different courses of the wide spectrum of COVID-19 manifestations in humans. On the other hand, fewer diagnostic tools and information on immune functions and molecular pathways are available than in mice, which limits mechanistic studies and inference to humans in several aspects. Still, under pandemic conditions with high pressure on progress in both basic and clinically oriented research, the Syrian hamster has turned into the leading non-transgenic model at an unprecedented pace, currently used in innumerable studies that all aim to combat the impact of the virus with its new variants of concern. As in other models, its strength rests upon a solid understanding of its similarities to and differences from the human disease, which we review here.
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14
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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: 1] [Impact Index Per Article: 0.5] [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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15
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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: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [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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16
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Arora P, Sidarovich A, Graichen L, Hörnich B, Hahn A, Hoffmann M, Pöhlmann S. Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. PLoS One 2022; 17:e0265453. [PMID: 35333910 PMCID: PMC8956166 DOI: 10.1371/journal.pone.0265453] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/01/2022] [Indexed: 01/12/2023] Open
Abstract
Several SARS-CoV-2 variants emerged that harbor mutations in the surface unit of the viral spike (S) protein that enhance infectivity and transmissibility. Here, we analyzed whether ten naturally-occurring mutations found within the extended loop harboring the S1/S2 cleavage site of the S protein, a determinant of SARS-CoV-2 cell tropism and pathogenicity, impact S protein processing and function. None of the mutations increased but several decreased S protein cleavage at the S1/S2 site, including S686G and P681H, the latter of which is found in variants of concern B.1.1.7 (Alpha variant) and B.1.1.529 (Omicron variant). None of the mutations reduced ACE2 binding and cell-cell fusion although several modulated the efficiency of host cell entry. The effects of mutation S686G on viral entry were cell-type dependent and could be linked to the availability of cathepsin L for S protein activation. These results show that polymorphisms at the S1/S2 site can modulate S protein processing and host cell entry.
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Affiliation(s)
- Prerna Arora
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Anzhalika Sidarovich
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center, Göttingen, Germany
| | - Bojan Hörnich
- Junior Research Group Herpesviruses - Infection Biology Unit, German Primate Center, Göttingen, Germany
| | - Alexander Hahn
- Junior Research Group Herpesviruses - Infection Biology Unit, German Primate Center, Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
- * E-mail: (MH); (SP)
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
- * E-mail: (MH); (SP)
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17
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A highly immunogenic live-attenuated vaccine candidate prevents SARS-CoV-2 infection and transmission in hamsters. Innovation (N Y) 2022; 3:100221. [PMID: 35252935 PMCID: PMC8888354 DOI: 10.1016/j.xinn.2022.100221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/28/2022] [Indexed: 01/08/2023] Open
Abstract
The highly pathogenic and readily transmissible SARS-CoV-2 has caused a global coronavirus pandemic, urgently requiring effective countermeasures against its rapid expansion. All available vaccine platforms are being used to generate safe and effective COVID-19 vaccines. Here, we generated a live-attenuated candidate vaccine strain by serial passaging of a SARS-CoV-2 clinical isolate in Vero cells. Deep sequencing revealed the dynamic adaptation of SARS-CoV-2 in Vero cells, resulting in a stable clone with a deletion of seven amino acids (N679SPRRAR685) at the S1/S2 junction of the S protein (named VAS5). VAS5 showed significant attenuation of replication in multiple human cell lines, human airway epithelium organoids, and hACE2 mice. Viral fitness competition assays demonstrated that VAS5 showed specific tropism to Vero cells but decreased fitness in human cells compared with the parental virus. More importantly, a single intranasal injection of VAS5 elicited a high level of neutralizing antibodies and prevented SARS-CoV-2 infection in mice as well as close-contact transmission in golden Syrian hamsters. Structural and biochemical analysis revealed a stable and locked prefusion conformation of the S trimer of VAS5, which most resembles SARS-CoV-2-3Q-2P, an advanced vaccine immunogen (NVAX-CoV2373). Further systematic antigenic profiling and immunogenicity validation confirmed that the VAS5 S trimer presents an enhanced antigenic mimic of the wild-type S trimer. Our results not only provide a potent live-attenuated vaccine candidate against COVID-19 but also clarify the molecular and structural basis for the highly attenuated and super immunogenic phenotype of VAS5. Passaging of a protype SARS-CoV-2 in Vero cells generates a live-attenuated VAS5 A 7 amino acids deletion of the S protein contributes to the attenuated phenotype VAS5 immunization prevents SARS-CoV-2 infection and transmission in Syrian hamsters The VAS5 S protein forms a locked prefusion conformation with enhanced immunogenicity
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18
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Penkava J, Muenchhoff M, Badell I, Osterman A, Delbridge C, Niederbuchner F, Soliman S, Rudelius M, Graf A, Krebs S, Blum H, Ulbig M, Baumann C, Zapp D, Maier M, Keppler OT, Lohmann CP, Ledderose S. Detection of SARS-CoV-2-RNA in post-mortem samples of human eyes. Graefes Arch Clin Exp Ophthalmol 2021; 260:1789-1797. [PMID: 34962592 PMCID: PMC8713040 DOI: 10.1007/s00417-021-05529-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/16/2021] [Accepted: 12/16/2021] [Indexed: 01/08/2023] Open
Abstract
Purpose To detect SARS-CoV-2 RNA in post-mortem human eyes. Ocular symptoms are common in patients with COVID-19. In some cases, they can occur before the onset of respiratory and other symptoms. Accordingly, SARS-CoV-2 RNA has been detected in conjunctival samples and tear film of patients suffering from COVID-19. However, the detection and clinical relevance of intravitreal SARS-CoV-2 RNA still remain unclear due to so far contradictory reports in the literature. Methods In our study 20 patients with confirmed diagnosis of COVID-19 were evaluated post-mortem to assess the conjunctival and intraocular presence of SARS-CoV-2 RNA using sterile pulmonary and conjunctival swabs as well as intravitreal biopsies (IVB) via needle puncture. SARS-CoV-2 PCR and whole genome sequencing from the samples of the deceased patients were performed. Medical history and comorbidities of all subjects were recorded and analyzed for correlations with viral data. Results SARS-CoV-2 RNA was detected in 10 conjunctival (50%) and 6 vitreal (30%) samples. SARS-CoV-2 whole genome sequencing showed the distribution of cases largely reflecting the frequency of circulating lineages in the Munich area at the time of examination with no preponderance of specific variants. Especially there was no association between the presence of SARS-CoV-2 RNA in IVBs and infection with the variant of concern (VOC) alpha. Viral load in bronchial samples correlated positively with load in conjunctiva but not the vitreous. Conclusion SARS-CoV-2 RNA can be detected post mortem in conjunctival tissues and IVBs. This is relevant to the planning of ophthalmologic surgical procedures in COVID-19 patients, such as pars plana vitrectomy or corneal transplantation. Furthermore, not only during surgery but also in an outpatient setting it is important to emphasize the need for personal protection in order to avoid infection and spreading of SARS-CoV-2. Prospective studies are needed, especially to determine the clinical relevance of conjunctival and intravitreal SARS-CoV-2 detection concerning intraocular affection in active COVID-19 state and in post-COVID syndrome.
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Affiliation(s)
- Josef Penkava
- Department of Ophthalmology, Technical University Munich, Munich, Germany.
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research, Partner Site Munich, Munich, Germany
| | - Irina Badell
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Andreas Osterman
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Claire Delbridge
- Department of Pathology and Neuropathology, TUM School of Medicine, Technical University Munich, Munich, Germany
| | | | - Sarah Soliman
- Department of Pathology, Ludwig-Maximilian University Munich, Munich, Germany
| | - Martina Rudelius
- Department of Pathology, Ludwig-Maximilian University Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University, Munich, Germany
| | - Michael Ulbig
- Department of Ophthalmology, Technical University Munich, Munich, Germany
| | - Carmen Baumann
- Department of Ophthalmology, Technical University Munich, Munich, Germany
| | - Daniel Zapp
- Department of Ophthalmology, Technical University Munich, Munich, Germany
| | - Mathias Maier
- Department of Ophthalmology, Technical University Munich, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research, Partner Site Munich, Munich, Germany
| | - Chris P Lohmann
- Department of Ophthalmology, Technical University Munich, Munich, Germany
| | - Stephan Ledderose
- Department of Pathology, Ludwig-Maximilian University Munich, Munich, Germany
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19
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Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Viruses 2021; 13:v13122511. [PMID: 34960779 PMCID: PMC8705554 DOI: 10.3390/v13122511] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
Genotype screening was implemented in Italy and showed a significant prevalence of new SARS-CoV-2 mutants carrying Q675H mutation, near the furin cleavage site of spike protein. Currently, this mutation, which is expressed on different SARS-CoV-2 lineages circulating worldwide, has not been thoughtfully investigated. Therefore, we performed phylogenetic and biocomputational analysis to better understand SARS-CoV-2 Q675H mutants’ evolutionary relationships with other circulating lineages and Q675H function in its molecular context. Our studies reveal that Q675H spike mutation is the result of parallel evolution because it arose independently in separate evolutionary clades. In silico data show that the Q675H mutation gives rise to a hydrogen-bonds network in the spike polar region. This results in an optimized directionality of arginine residues involved in interaction of spike with the furin binding pocket, thus improving proteolytic exposure of the viral protein. Furin was predicted to have a greater affinity for Q675H than Q675 substrate conformations. As a consequence, Q675H mutation could confer a fitness advantage to SARS-CoV-2 by promoting a more efficient viral entry. Interestingly, here we have shown that Q675H spike mutation is documented in all the VOCs. This finding highlights that VOCs are still evolving to enhance viral fitness and to adapt to the human host. At the same time, it may suggest Q675H spike mutation involvement in SARS-CoV-2 evolution.
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Takeda M. Proteolytic activation of SARS-CoV-2 spike protein. Microbiol Immunol 2021; 66:15-23. [PMID: 34561887 PMCID: PMC8652499 DOI: 10.1111/1348-0421.12945] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/10/2021] [Accepted: 09/18/2021] [Indexed: 11/27/2022]
Abstract
Spike (S) protein cleavage is a crucial step in coronavirus infection. In this review, this process is discussed, with particular focus on the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). Compared with influenza virus and paramyxovirus membrane fusion proteins, the cleavage activation mechanism of coronavirus S protein is much more complex. The S protein has two cleavage sites (S1/S2 and S2′), and the cleavage motif for furin protease at the S1/S2 site that results from a unique four‐amino acid insertion is one of the distinguishing features of SARS‐CoV‐2. The viral particle incorporates the S protein, which has already undergone S1/S2 cleavage by furin, and then undergoes further cleavage at the S2′ site, mediated by the type II transmembrane serine protease transmembrane protease serine 2 (TMPRSS2), after binding to the receptor angiotensin‐converting enzyme 2 (ACE2) to facilitate membrane fusion at the plasma membrane. In addition, SARS‐CoV‐2 can enter the cell by endocytosis and be proteolytically activated by cathepsin L, although this is not a major mode of SARS‐CoV‐2 infection. SARS‐CoV‐2 variants with enhanced infectivity have been emerging throughout the ongoing pandemic, and there is a close relationship between enhanced infectivity and changes in S protein cleavability. All four variants of concern carry the D614G mutation, which indirectly enhances S1/S2 cleavability by furin. The P681R mutation of the delta variant directly increases S1/S2 cleavability, enhancing membrane fusion and SARS‐CoV‐2 virulence. Changes in S protein cleavability can significantly impact viral infectivity, tissue tropism, and virulence. Understanding these mechanisms is critical to counteracting the coronavirus pandemic.
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Affiliation(s)
- Makoto Takeda
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
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Shou S, Liu M, Yang Y, Kang N, Song Y, Tan D, Liu N, Wang F, Liu J, Xie Y. Animal Models for COVID-19: Hamsters, Mouse, Ferret, Mink, Tree Shrew, and Non-human Primates. Front Microbiol 2021; 12:626553. [PMID: 34531831 PMCID: PMC8438334 DOI: 10.3389/fmicb.2021.626553] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus causing acute respiratory tract infection in humans. The virus has the characteristics of rapid transmission, long incubation period and strong pathogenicity, and has spread all over the world. Therefore, it is of great significance to select appropriate animal models for antiviral drug development and therapeutic effect evaluation. Here, we review and compare the current animal models of SARS-CoV-2.
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Affiliation(s)
- Shuyu Shou
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Menghui Liu
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yang Yang
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ning Kang
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yingying Song
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Dan Tan
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Nannan Liu
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Feifei Wang
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jing Liu
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Youhua Xie
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Children’s Hospital, Fudan University, Shanghai, China
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Zou W, Xiong M, Hao S, Zhang EY, Baumlin N, Kim MD, Salathe M, Yan Z, Qiu J. The SARS-CoV-2 Transcriptome and the Dynamics of the S Gene Furin Cleavage Site in Primary Human Airway Epithelia. mBio 2021; 12:e01006-21. [PMID: 33975939 PMCID: PMC8262919 DOI: 10.1128/mbio.01006-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 02/01/2023] Open
Abstract
The spike (S) polypeptide of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) consists of the S1 and S2 subunits and is processed by cellular proteases at the S1/S2 boundary that contains a furin cleavage site (FCS), 682RRAR↓S686 Various deletions surrounding the FCS have been identified in patients. When SARS-CoV-2 propagated in Vero cells, it acquired deletions surrounding the FCS. We studied the viral transcriptome in Vero cell-derived SARS-CoV-2-infected primary human airway epithelia (HAE) cultured at an air-liquid interface (ALI) with an emphasis on the viral genome stability of the FCS. While we found overall the viral transcriptome is similar to that generated from infected Vero cells, we identified a high percentage of mutated viral genome and transcripts in HAE-ALI. Two highly frequent deletions were found at the FCS region: a 12 amino acid deletion (678TNSPRRAR↓SVAS689) that contains the underlined FCS and a 5 amino acid deletion (675QTQTN679) that is two amino acids upstream of the FCS. Further studies on the dynamics of the FCS deletions in apically released virions from 11 infected HAE-ALI cultures of both healthy and lung disease donors revealed that the selective pressure for the FCS maintains the FCS stably in 9 HAE-ALI cultures but with 2 exceptions, in which the FCS deletions are retained at a high rate of >40% after infection of ≥13 days. Our study presents evidence for the role of unique properties of human airway epithelia in the dynamics of the FCS region during infection of human airways, which is likely donor dependent.IMPORTANCE Polarized human airway epithelia at an air-liquid interface (HAE-ALI) are an in vitro model that supports efficient infection of SARS-CoV-2. The spike (S) protein of SARS-CoV-2 contains a furin cleavage site (FCS) at the boundary of the S1 and S2 domains which distinguishes it from SARS-CoV. However, FCS deletion mutants have been identified in patients and in vitro cell cultures, and how the airway epithelial cells maintain the unique FCS remains unknown. We found that HAE-ALI cultures were capable of suppressing two prevalent FCS deletion mutants (Δ678TNSPRRAR↓SVAS689 and Δ675QTQTN679) that were selected during propagation in Vero cells. While such suppression was observed in 9 out of 11 of the tested HAE-ALI cultures derived from independent donors, 2 exceptions that retained a high rate of FCS deletions were also found. Our results present evidence of the donor-dependent properties of human airway epithelia in the evolution of the FCS during infection.
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Affiliation(s)
- Wei Zou
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Min Xiong
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Siyuan Hao
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | | | - Nathalie Baumlin
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Michael D Kim
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Matthias Salathe
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Ziying Yan
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, USA
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
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