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Özçelik C, Araz CZ, Yılmaz Ö, Gülyüz S, Özdamar P, Salmanlı E, Özkul A, Şeker UÖŞ. Screening Peptide Drug Candidates To Neutralize Whole Viral Agents: A Case Study with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). ACS Pharmacol Transl Sci 2024; 7:1032-1042. [PMID: 38633598 PMCID: PMC11020059 DOI: 10.1021/acsptsci.3c00317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 04/19/2024]
Abstract
The COVID-19 pandemic revealed the need for therapeutic and pharmaceutical molecule development in a short time with different approaches. Although boosting immunological memory by vaccination was the quickest and robust strategy, still medication is required for the immediate treatment of a patient. A popular approach is the mining of new therapeutic molecules. Peptide-based drug candidates are also becoming a popular avenue. To target whole pathogenic viral agents, peptide libraries can be employed. With this motivation, we have used the 12mer M13 phage display library for selecting SARS-CoV-2 targeting peptides as potential neutralizing molecules to prevent viral infections. Panning was applied with four iterative cycles to select SARS-CoV-2 targeting phage particles displaying 12-amino acid-long peptides. Randomly selected peptide sequences were synthesized by a solid-state peptide synthesis method. Later, selected peptides were analyzed by the quartz crystal microbalance method to characterize their molecular interaction with SARS-CoV-2's S protein. Finally, the neutralization activity of the selected peptides was probed with an in-house enzyme-linked immunosorbent assay. The results showed that scpep3, scpep8, and scpep10 peptides have both binding and neutralizing capacity for S1 protein as a candidate for therapeutic molecule. The results of this study have a translational potential with future in vivo and human studies.
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Affiliation(s)
- Cemile
Elif Özçelik
- UNAM—Institute
of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Cemre Zekiye Araz
- Synbiotik
Biotechnology and Biomedical Technology Bilkent Kümeevler, Çankaya, Ankara 06800, Turkey
| | - Özgür Yılmaz
- Material
Technologies, Marmara Research Center, TUBITAK, Gebze, Kocaeli 41470, Turkey
| | - Sevgi Gülyüz
- Material
Technologies, Marmara Research Center, TUBITAK, Gebze, Kocaeli 41470, Turkey
| | - Pınar Özdamar
- Faculty of Veterinary Medicine, Department of Virology, Graduate School of Health
Sciences, Department of Virology, Ankara
University, Ankara 06110, Turkey
| | - Ezgi Salmanlı
- Faculty of Veterinary Medicine, Department of Virology, Graduate School of Health
Sciences, Department of Virology, Ankara
University, Ankara 06110, Turkey
| | - Aykut Özkul
- Faculty of Veterinary Medicine, Department of Virology, Graduate School of Health
Sciences, Department of Virology, Ankara
University, Ankara 06110, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM—Institute
of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
- Interdisciplinary
Program in Neuroscience, Bilkent University, Ankara 06800, Turkey
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Khatri R, Lohiya B, Kaur G, Maithil V, Goswami A, Sarmadhikari D, Asthana S, Samal S. Understanding the role of conserved proline and serine residues in the SARS-CoV-2 spike cleavage sites in the virus entry, fusion, and infectivity. 3 Biotech 2023; 13:323. [PMID: 37663753 PMCID: PMC10469153 DOI: 10.1007/s13205-023-03749-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/27/2023] [Indexed: 09/05/2023] Open
Abstract
The spike (S) glycoprotein of the SARS-CoV-2 virus binds to the host cell receptor and promotes the virus's entry into the target host cell. This interaction is primed by host cell proteases like furin and TMPRSS2, which act at the S1/S2 and S2´ cleavage sites, respectively. Both cleavage sites have serine or proline residues flanking either the single or polybasic region and were found to be conserved in coronaviruses. Unravelling the effects of these conserved residues on the virus entry and infectivity might facilitate the development of novel therapeutics. Here, we have investigated the role of the conserved serine and proline residues in the SARS-CoV-2 spike mediated entry, fusogenicity, and viral infectivity by using the HIV-1/spike-based pseudovirus system. A conserved serine residue mutation to alanine (S2´S-A) at the S2´ cleavage site resulted in the complete loss of spike cleavage. Exogenous treatment with trypsin or overexpression of TMPRSS2 protease could not rescue the loss of spike cleavage and biological activity. The S2´S-A mutant showed no significant responses against E-64d, TMPRSS2 or other relevant inhibitors. Taken together, serine at the S2´ site in the spike protein was indispensable for spike protein cleavage and virus infectivity. Thus, novel interventions targeting the conserved serine at the S2´ cleavage site should be explored to reduce severe disease caused by SARS-CoV-2-and novel emerging variants. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03749-y.
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Affiliation(s)
- Ritika Khatri
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Bharat Lohiya
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Gurleen Kaur
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Vikas Maithil
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Abhishek Goswami
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Debapriyo Sarmadhikari
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Shailendra Asthana
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Sweety Samal
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
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3
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Clinical and genomic signatures of SARS-CoV-2 Delta breakthrough infections in New York. EBioMedicine 2022; 82:104141. [PMID: 35906172 PMCID: PMC9323230 DOI: 10.1016/j.ebiom.2022.104141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 12/20/2022] Open
Abstract
Background In 2021, Delta became the predominant SARS-CoV-2 variant worldwide. While vaccines have effectively prevented COVID-19 hospitalization and death, vaccine breakthrough infections increasingly occurred. The precise role of clinical and genomic determinants in Delta infections is not known, and whether they contributed to increased rates of breakthrough infections compared to unvaccinated controls. Methods We studied SARS-CoV-2 variant distribution, dynamics, and adaptive selection over time in relation to vaccine status, phylogenetic relatedness of viruses, full genome mutation profiles, and associated clinical and demographic parameters. Findings We show a steep and near-complete replacement of circulating variants with Delta between May and August 2021 in metropolitan New York. We observed an increase of the Delta sublineage AY.25 (14% in vaccinated, 7% in unvaccinated), its spike mutation S112L, and AY.44 (8% in vaccinated, 2% in unvaccinated) with its nsp12 mutation F192V in breakthroughs. Delta infections were associated with younger age and lower hospitalization rates than Alpha. Delta breakthrough infections increased significantly with time since vaccination, and, after adjusting for confounders, they rose at similar rates as in unvaccinated individuals. Interpretation We observed a modest adaptation of Delta genomes in breakthrough infections in New York, suggesting an improved genomic framework to support Delta's epidemic growth in times of waning vaccine protection despite limited impact on vaccine escape. Funding The study was supported by NYU institutional funds. The NYULH Genome Technology Center is partially supported by the Cancer Center Support Grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center.
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4
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Kastenhuber ER, Johnson JL, Yaron TM, Mercadante M, Cantley LC. Evolution of host protease interactions among SARS-CoV-2 variants of concern and related coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.16.496428. [PMID: 35734085 PMCID: PMC9216717 DOI: 10.1101/2022.06.16.496428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Previously, we showed that coagulation factors directly cleave SARS-CoV-2 spike and promote viral entry (Kastenhuber et al., 2022). Here, we show that substitutions in the S1/S2 cleavage site observed in SARS-CoV-2 variants of concern (VOCs) exhibit divergent interactions with host proteases, including factor Xa and furin. Nafamostat remains effective to block coagulation factor-mediated cleavage of variant spike sequences. Furthermore, host protease usage has likely been a selection pressure throughout coronavirus evolution, and we observe convergence of distantly related coronaviruses to attain common host protease interactions, including coagulation factors. Interpretation of genomic surveillance of emerging SARS-CoV-2 variants and future zoonotic spillover is supported by functional characterization of recurrent emerging features.
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Affiliation(s)
- Edward R. Kastenhuber
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jared L. Johnson
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Tomer M. Yaron
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Marisa Mercadante
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Lewis C. Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Dana Farber Cancer Institute, Boston, MA, USA
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5
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Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic demonstrates the threat posed by novel coronaviruses to human health. Coronaviruses share a highly conserved cell entry mechanism mediated by the spike protein, the sole product of the S gene. The structural dynamics by which the spike protein orchestrates infection illuminate how antibodies neutralize virions and how S mutations contribute to viral fitness. Here, we review the process by which spike engages its proteinaceous receptor, angiotensin converting enzyme 2 (ACE2), and how host proteases prime and subsequently enable efficient membrane fusion between virions and target cells. We highlight mutations common among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern and discuss implications for cell entry. Ultimately, we provide a model by which sarbecoviruses are activated for fusion competency and offer a framework for understanding the interplay between humoral immunity and the molecular evolution of the SARS-CoV-2 Spike. In particular, we emphasize the relevance of the Canyon Hypothesis (M. G. Rossmann, J Biol Chem 264:14587-14590, 1989) for understanding evolutionary trajectories of viral entry proteins during sustained intraspecies transmission of a novel viral pathogen.
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Affiliation(s)
- Kyle A Wolf
- Department of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Interdiscipinary Ph.D. Program in Structural and Computational Biology and Quantitative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason C Kwan
- Department of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jeremy P Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Shreveport, Shreveport, Louisiana, USA
- Center for Excellence in Emerging Viral Threats, Louisiana State University Health Shreveport, Shreveport, Louisiana, USA
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6
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SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo. Nature 2022; 603:715-720. [PMID: 35104836 DOI: 10.1038/s41586-022-04479-6] [Citation(s) in RCA: 453] [Impact Index Per Article: 226.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 01/27/2022] [Indexed: 11/08/2022]
Abstract
The emergence of SARS-CoV-2 variants of concern with progressively increased transmissibility between humans is a threat to global public health. The Omicron variant of SARS-CoV-2 also evades immunity from natural infection or vaccines1, but it is unclear whether its exceptional transmissibility is due to immune evasion or intrinsic virological properties. Here we compared the replication competence and cellular tropism of the wild-type virus and the D614G, Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2) and Omicron (B.1.1.529) variants in ex vivo explant cultures of human bronchi and lungs. We also evaluated the dependence on TMPRSS2 and cathepsins for infection. We show that Omicron replicates faster than all other SARS-CoV-2 variants studied in the bronchi but less efficiently in the lung parenchyma. All variants of concern have similar cellular tropism compared to the wild type. Omicron is more dependent on cathepsins than the other variants of concern tested, suggesting that the Omicron variant enters cells through a different route compared with the other variants. The lower replication competence of Omicron in the human lungs may explain the reduced severity of Omicron that is now being reported in epidemiological studies, although determinants of severity are multifactorial. These findings provide important biological correlates to previous epidemiological observations.
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7
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Smith DR, Singh C, Green J, Lueder MR, Arnold CE, Voegtly LJ, Long KA, Rice GK, Luquette AE, Miner HL, Glang L, Bennett AJ, Miller RH, Malagon F, Cer RZ, Bishop-Lilly KA. Genomic and Virological Characterization of SARS-CoV-2 Variants in a Subset of Unvaccinated and Vaccinated U.S. Military Personnel. Front Med (Lausanne) 2022; 8:836658. [PMID: 35155489 PMCID: PMC8829001 DOI: 10.3389/fmed.2021.836658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 12/28/2021] [Indexed: 12/19/2022] Open
Abstract
The emergence of SARS-CoV-2 variants complicates efforts to control the COVID-19 pandemic. Increasing genomic surveillance of SARS-CoV-2 is imperative for early detection of emerging variants, to trace the movement of variants, and to monitor effectiveness of countermeasures. Additionally, determining the amount of viable virus present in clinical samples is helpful to better understand the impact these variants have on viral shedding. In this study, we analyzed nasal swab samples collected between March 2020 and early November 2021 from a cohort of United States (U.S.) military personnel and healthcare system beneficiaries stationed worldwide as a part of the Defense Health Agency's (DHA) Global Emerging Infections Surveillance (GEIS) program. SARS-CoV-2 quantitative real time reverse-transcription PCR (qRT-PCR) positive samples were characterized by next-generation sequencing and a subset was analyzed for isolation and quantification of viable virus. Not surprisingly, we found that the Delta variant is the predominant strain circulating among U.S. military personnel beginning in July 2021 and primarily represents cases of vaccine breakthrough infections (VBIs). Among VBIs, we found a 50-fold increase in viable virus in nasal swab samples from Delta variant cases when compared to cases involving other variants. Notably, we found a 40-fold increase in viable virus in nasal swab samples from VBIs involving Delta as compared to unvaccinated personnel infected with other variants prior to the availability of approved vaccines. This study provides important insight about the genomic and virological characterization of SARS-CoV-2 isolates from a unique study population with a global presence.
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Affiliation(s)
- Darci R. Smith
- Biological Defense Research Directorate, Department of Microbiology and Immunology, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Christopher Singh
- Biological Defense Research Directorate, Department of Microbiology and Immunology, Naval Medical Research Center, Fort Detrick, MD, United States
- Parsons, Centreville, VA, United States
| | - Jennetta Green
- Biological Defense Research Directorate, Department of Microbiology and Immunology, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Matthew R. Lueder
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Catherine E. Arnold
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Defense Threat Reduction Agency, Fort Belvoir, VA, United States
| | - Logan J. Voegtly
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Kyle A. Long
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Gregory K. Rice
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Andrea E. Luquette
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Haven L. Miner
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Lindsay Glang
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Andrew J. Bennett
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Robin H. Miller
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Francisco Malagon
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Regina Z. Cer
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Kimberly A. Bishop-Lilly
- Biological Defense Research Directorate, Department of Genomics and Bioinformatics, Naval Medical Research Center, Fort Detrick, MD, United States
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Kistler KE, Huddleston J, Bedford T. Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.09.11.459844. [PMID: 34545361 PMCID: PMC8452090 DOI: 10.1101/2021.09.11.459844] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Given the importance of variant SARS-CoV-2 viruses with altered receptor-binding or antigenic phenotypes, we sought to quantify the degree to which adaptive evolution is driving accumulation of mutations in the SARS-CoV-2 genome. Here we assessed adaptive evolution across genes in the SARS-CoV-2 genome by correlating clade growth with mutation accumulation as well as by comparing rates of nonsynonymous to synonymous divergence, clustering of mutations across the SARS-CoV-2 phylogeny and degree of convergent evolution of individual mutations. We find that spike S1 is the focus of adaptive evolution, but also identify positively-selected mutations in other genes that are sculpting the evolutionary trajectory of SARS-CoV-2. Adaptive changes in S1 accumulated rapidly, resulting in a remarkably high ratio of nonsynonymous to synonymous divergence that is 2.5X greater than that observed in HA1 at the beginning of the 2009 H1N1 pandemic.
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Affiliation(s)
- Kathryn E. Kistler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States
- Howard Hughes Medical Institute, Seattle, WA, United States
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9
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SARS-CoV-2 spike engagement of ACE2 primes S2' site cleavage and fusion initiation. Proc Natl Acad Sci U S A 2022; 119:2111199119. [PMID: 34930824 PMCID: PMC8740742 DOI: 10.1073/pnas.2111199119] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 01/10/2023] Open
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in tremendous loss worldwide. Although viral spike (S) protein binding of angiotensin-converting enzyme 2 (ACE2) has been established, the functional consequences of the initial receptor binding and the stepwise fusion process are not clear. By utilizing a cell-cell fusion system, in complement with a pseudoviral infection model, we found that the spike engagement of ACE2 primed the generation of S2' fragments in target cells, a key proteolytic event coupled with spike-mediated membrane fusion. Mutagenesis of an S2' cleavage site at the arginine (R) 815, but not an S2 cleavage site at arginine 685, was sufficient to prevent subsequent syncytia formation and infection in a variety of cell lines and primary cells isolated from human ACE2 knock-in mice. The requirement for S2' cleavage at the R815 site was also broadly shared by other SARS-CoV-2 spike variants, such as the Alpha, Beta, and Delta variants of concern. Thus, our study highlights an essential role for host receptor engagement and the key residue of spike for proteolytic activation, and uncovers a targetable mechanism for host cell infection by SARS-CoV-2.
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10
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Abstract
The unprecedented public health and economic impact of the COVID-19 pandemic caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been met with an equally unprecedented scientific response. Much of this response has focused, appropriately, on the mechanisms of SARS-CoV-2 entry into host cells, and in particular the binding of the spike (S) protein to its receptor, angiotensin-converting enzyme 2 (ACE2), and subsequent membrane fusion. This Review provides the structural and cellular foundations for understanding the multistep SARS-CoV-2 entry process, including S protein synthesis, S protein structure, conformational transitions necessary for association of the S protein with ACE2, engagement of the receptor-binding domain of the S protein with ACE2, proteolytic activation of the S protein, endocytosis and membrane fusion. We define the roles of furin-like proteases, transmembrane protease, serine 2 (TMPRSS2) and cathepsin L in these processes, and delineate the features of ACE2 orthologues in reservoir animal species and S protein adaptations that facilitate efficient human transmission. We also examine the utility of vaccines, antibodies and other potential therapeutics targeting SARS-CoV-2 entry mechanisms. Finally, we present key outstanding questions associated with this critical process.
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Affiliation(s)
- Cody B Jackson
- Department of Immunology and Microbiology, Scripps Research, Jupiter, FL, USA
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, Scripps Research, Jupiter, FL, USA
| | - Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Hyeryun Choe
- Department of Immunology and Microbiology, Scripps Research, Jupiter, FL, USA.
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11
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Fan S, Xiao K, Li D, Zhao H, Zhang J, Yu L, Chang P, Zhu S, Xu X, Liao Y, Ji T, Jiang G, Yan D, Zeng F, Duan S, Xia B, Wang L, Yang F, He Z, Song Y, Cui P, Li X, Zhang Y, Zheng B, Zhang Y, Xu W, Li Q. Preclinical immunological evaluation of an intradermal heterologous vaccine against SARS-CoV-2 variants. Emerg Microbes Infect 2021; 11:212-226. [PMID: 34931939 PMCID: PMC8745378 DOI: 10.1080/22221751.2021.2021807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The recent emergence of COVID-19 variants has necessitated the development of new vaccines that stimulate the formation of high levels of neutralizing antibodies against S antigen variants. A new strategy involves the intradermal administration of heterologous vaccines composed of one or two doses of inactivated vaccine and a booster dose with the mutated S1 protein (K-S). Such vaccines improve the immune efficacy by increasing the neutralizing antibody titers and promoting specific T cell responses against five variants of the RBD protein. A viral challenge test with the B.1.617.2 (Delta) variant confirmed that both administration schedules (i.e. “1 + 1” and “2 + 1”) ensured protection against this strain. These results suggest that the aforementioned strategy is effective for protecting against new variants and enhances the anamnestic immune response in the immunized population.
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Affiliation(s)
- Shengtao Fan
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Kang Xiao
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Dandan Li
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Heng Zhao
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Jingjing Zhang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Li Yu
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Penglan Chang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Shuangli Zhu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Xingli Xu
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Yun Liao
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Tianjiao Ji
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Guorun Jiang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Dongmei Yan
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Fengyuan Zeng
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Suqin Duan
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Baicheng Xia
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Lichun Wang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Fengmei Yang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Zhanlong He
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Yang Song
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Pingfang Cui
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Xiaolei Li
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Yaxing Zhang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Bangyi Zheng
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Ying Zhang
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
| | - Wenbo Xu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China
| | - Qihan Li
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development for Severe Infectious Diseases, Kunming, 650118, China
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Duerr R, Dimartino D, Marier C, Zappile P, Levine S, François F, Iturrate E, Wang G, Dittmann M, Lighter J, Elbel B, Troxel AB, Goldfeld KS, Heguy A. Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.12.07.21267431. [PMID: 34909779 PMCID: PMC8669846 DOI: 10.1101/2021.12.07.21267431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In 2021, Delta has become the predominant SARS-CoV-2 variant worldwide. While vaccines effectively prevent COVID-19 hospitalization and death, vaccine breakthrough infections increasingly occur. The precise role of clinical and genomic determinants in Delta infections is not known, and whether they contribute to increased rates of breakthrough infections compared to unvaccinated controls. Here, we show a steep and near complete replacement of circulating variants with Delta between May and August 2021 in metropolitan New York. We observed an increase of the Delta sublineage AY.25, its spike mutation S112L, and nsp12 mutation F192V in breakthroughs. Delta infections were associated with younger age and lower hospitalization rates than Alpha. Delta breakthroughs increased significantly with time since vaccination, and, after adjusting for confounders, they rose at similar rates as in unvaccinated individuals. Our data indicate a limited impact of vaccine escape in favor of Delta's increased epidemic growth in times of waning vaccine protection.
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Affiliation(s)
- Ralf Duerr
- Department of Microbiology, NYU Grossman School of Medicine
| | - Dacia Dimartino
- Genome Technology Center, Office of Science and Research, NYU Langone Health
| | - Christian Marier
- Genome Technology Center, Office of Science and Research, NYU Langone Health
| | - Paul Zappile
- Genome Technology Center, Office of Science and Research, NYU Langone Health
| | | | | | | | - Guiqing Wang
- Department of Pathology, NYU Grossman School of Medicine
| | - Meike Dittmann
- Department of Microbiology, NYU Grossman School of Medicine
| | - Jennifer Lighter
- Department of Pediatric Infectious Diseases, NYU Grossman School of Medicine
| | - Brian Elbel
- Department of Population Health, NYU Grossman School of Medicine
- NYU Wagner Graduate School of Public Service
| | - Andrea B. Troxel
- Department of Population Health, NYU Grossman School of Medicine
| | | | - Adriana Heguy
- Genome Technology Center, Office of Science and Research, NYU Langone Health
- Department of Pathology, NYU Grossman School of Medicine
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13
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Lubinski B, Fernandes MHV, Frazier L, Tang T, Daniel S, Diel DG, Jaimes JA, Whittaker GR. Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.06.438731. [PMID: 33851153 PMCID: PMC8043443 DOI: 10.1101/2021.04.06.438731] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent causing the COVID-19 pandemic. SARS-CoV-2 B.1.1.7 (Alpha), a WHO variant of concern (VOC) first identified in the UK in late 2020, contains several mutations including P681H in the spike S1/S2 cleavage site, which is predicted to increase cleavage by furin, potentially impacting the viral cell entry. Here, we studied the role of the P681H mutation in B.1.1.7 cell entry. We performed assays using fluorogenic peptides mimicking the Wuhan-Hu-1 and B.1.1.7 S1/S2 sequence and observed no significant difference in furin cleavage. Functional assays using pseudoparticles harboring SARS-CoV-2 spikes and cell-to-cell fusion assays demonstrated no differences between Wuhan-Hu-1, B.1.1.7 or a P681H point mutant. Likewise, we observed no differences in viral growth between USA-WA1/2020 and a B.1.1.7 isolate in cell culture. Our findings suggest that while the B.1.1.7 P681H mutation may slightly increase S1/S2 cleavage this does not significantly impact viral entry or cell-cell spread.
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Affiliation(s)
- Bailey Lubinski
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Maureen H. V. Fernandes
- Department of Population Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Laura Frazier
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Diego G. Diel
- Department of Population Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Javier A. Jaimes
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gary R. Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Master of Public Health Program, Cornell University, Ithaca, NY, 14853, USA
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14
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Despres HW, Mills MG, Shirley DJ, Schmidt MM, Huang ML, Jerome KR, Greninger AL, Bruce EA. Quantitative measurement of infectious virus in SARS-CoV-2 Alpha, Delta and Epsilon variants reveals higher infectivity (viral titer:RNA ratio) in clinical samples containing the Delta and Epsilon variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.09.07.21263229. [PMID: 34580674 PMCID: PMC8475961 DOI: 10.1101/2021.09.07.21263229] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Novel SARS-CoV-2 Variants of Concern (VoC) pose a challenge to controlling the COVID-19 pandemic. Previous studies indicate that clinical samples collected from individuals infected with the Delta variant may contain higher levels of RNA than previous variants, but the relationship between viral RNA and infectious virus for individual variants is unknown. METHODS We measured infectious viral titer (using a micro-focus forming assay) as well as total and subgenomic viral RNA levels (using RT-PCR) in a set of 165 clinical samples containing SARS-CoV-2 Alpha, Delta and Epsilon variants that were processed within two days of collection from the patient. RESULTS We observed a high degree of variation in the relationship between viral titers and RNA levels. Despite the variability we observed for individual samples the overall infectivity differed among the three variants. Both Delta and Epsilon had significantly higher infectivity than Alpha, as measured by the number of infectious units per quantity of viral E gene RNA (6 and 4 times as much, p=0.0002 and 0.009 respectively) or subgenomic E RNA (11 and 7 times as much, p<0.0001 and 0.006 respectively). CONCLUSION In addition to higher viral RNA levels reported for the Delta variant, the infectivity (amount of replication competent virus per viral genome copy) may also be increased compared to Alpha. Measuring the relationship between live virus and viral RNA is an important step in assessing the infectivity of novel SARS-CoV-2 variants. An increase in the infectivity of the Delta variant may further explain increased spread and suggests a need for increased measures to prevent viral transmission. SIGNIFICANCE STATEMENT Current and future SARS-CoV-2 variants threaten our ability to control the COVID-19 pandemic. Variants with increased transmission, higher viral loads, or greater immune evasion are of particular concern. Viral loads are currently measured by the amount of viral RNA in a clinical sample rather than the amount of infectious virus. We measured both RNA and infectious virus levels directly in a set of 165 clinical specimens from Alpha, Epsilon or Delta variants. Our data shows that Delta is more infectious compared to Alpha, with ∼ six times as much infectious virus for the same amount of RNA. This increase in infectivity suggests increased measures (vaccination, masking, distancing, ventilation) are needed to control Delta compared to Alpha.
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Affiliation(s)
- Hannah W. Despres
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Margaret G. Mills
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
| | - David J. Shirley
- Faraday, Inc. Data Science Department. Burlington VT, 05405, USA
| | - Madaline M. Schmidt
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Meei-Li Huang
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
| | - Keith R. Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Alexander L. Greninger
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Emily A. Bruce
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
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16
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Duerr R, Dimartino D, Marier C, Zappile P, Wang G, Lighter J, Elbel B, Troxel AB, Heguy A. Dominance of alpha and Iota variants in SARS-CoV-2 vaccine breakthrough infections in New York City. J Clin Invest 2021; 131:e152702. [PMID: 34375308 DOI: 10.1172/jci152702] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/05/2021] [Indexed: 11/17/2022] Open
Abstract
The efficacy of COVID-19 mRNA vaccines is high, but breakthrough infections still occur. We compared the SARS-CoV-2 genomes of 76 breakthrough cases after full vaccination with BNT162b2 (Pfizer/BioNTech), mRNA-1273 (Moderna), or JNJ-78436735 (Janssen) to unvaccinated controls (February-April 2021) in metropolitan New York, including their phylogenetic relationship, distribution of variants, and full spike mutation profiles. Their median age was 48 years; seven required hospitalization and one died. Most breakthrough infections (57/76) occurred with B.1.1.7 (Alpha) or B.1.526 (Iota). Among the 7 hospitalized cases, 4 were infected with B.1.1.7, including 1 death. Both unmatched and matched statistical analyses considering age, sex, vaccine type, and study month as covariates supported the null hypothesis of equal variant distributions between vaccinated and unvaccinated in chi-squared and McNemar tests (p>0.1) highlighting a high vaccine efficacy against B.1.1.7 and B.1.526. There was no clear association among breakthroughs between type of vaccine received and variant. In the vaccinated group, spike mutations in the N-terminal domain and receptor-binding domain that have been associated with immune evasion were overrepresented. The evolving dynamic of SARS-CoV-2 variants requires broad genomic analyses of breakthrough infections to provide real-life information on immune escape mediated by circulating variants and their spike mutations.
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Affiliation(s)
- Ralf Duerr
- Department of Microbiology, NYU Langone Health, New York, United States of America
| | - Dacia Dimartino
- Office for Science and Research, NYU Langone Health, New York, United States of America
| | - Christian Marier
- Office for Science and Research, NYU Langone Health, New York, United States of America
| | - Paul Zappile
- Office for Science and Research, NYU Langone Health, New York, United States of America
| | - Guiqing Wang
- Department of Pathology, NYU Langone Health, New York, United States of America
| | - Jennifer Lighter
- Department of Pediatric Infectious Diseases, NYU Langone Health, New York, United States of America
| | - Brian Elbel
- Department of Population Health, NYU Langone Health, New York, United States of America
| | - Andrea B Troxel
- Department of Population Health, NYU Langone Health, New York, United States of America
| | - Adriana Heguy
- NYU Langone Health, New York, United States of America
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