1
|
An K, Yang X, Luo M, Yan J, Xu P, Zhang H, Li Y, Wu S, Warshel A, Bai C. Mechanistic study of the transmission pattern of the SARS-CoV-2 omicron variant. Proteins 2024; 92:705-719. [PMID: 38183172 PMCID: PMC11059747 DOI: 10.1002/prot.26663] [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: 10/18/2023] [Revised: 11/25/2023] [Accepted: 12/27/2023] [Indexed: 01/07/2024]
Abstract
The omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) characterized by 30 mutations in its spike protein, has rapidly spread worldwide since November 2021, significantly exacerbating the ongoing COVID-19 pandemic. In order to investigate the relationship between these mutations and the variant's high transmissibility, we conducted a systematic analysis of the mutational effect on spike-angiotensin-converting enzyme-2 (ACE2) interactions and explored the structural/energy correlation of key mutations, utilizing a reliable coarse-grained model. Our study extended beyond the receptor-binding domain (RBD) of spike trimer through comprehensive modeling of the full-length spike trimer rather than just the RBD. Our free-energy calculation revealed that the enhanced binding affinity between the spike protein and the ACE2 receptor is correlated with the increased structural stability of the isolated spike protein, thus explaining the omicron variant's heightened transmissibility. The conclusion was supported by our experimental analyses involving the expression and purification of the full-length spike trimer. Furthermore, the energy decomposition analysis established those electrostatic interactions make major contributions to this effect. We categorized the mutations into four groups and established an analytical framework that can be employed in studying future mutations. Additionally, our calculations rationalized the reduced affinity of the omicron variant towards most available therapeutic neutralizing antibodies, when compared with the wild type. By providing concrete experimental data and offering a solid explanation, this study contributes to a better understanding of the relationship between theories and observations and lays the foundation for future investigations.
Collapse
Affiliation(s)
- Ke An
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
- Chenzhu (MoMeD) Biotechnology Co., Ltd, Hangzhou, Zhejiang, 310005, P.R. China
| | - Xianzhi Yang
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen 518000, China
| | - Mengqi Luo
- College of Management, Shenzhen University, Shenzhen, 518060, China
| | - Junfang Yan
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
| | - Peiyi Xu
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
| | - Honghui Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
| | - Yuqing Li
- Department of Urology, South China Hospital of Shenzhen University, Shenzhen 518116, China
| | - Song Wu
- Department of Urology, South China Hospital of Shenzhen University, Shenzhen 518116, China
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Chen Bai
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
- Chenzhu (MoMeD) Biotechnology Co., Ltd, Hangzhou, Zhejiang, 310005, P.R. China
| |
Collapse
|
2
|
Zhao Z, Bashiri S, Ziora ZM, Toth I, Skwarczynski M. COVID-19 Variants and Vaccine Development. Viruses 2024; 16:757. [PMID: 38793638 PMCID: PMC11125726 DOI: 10.3390/v16050757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), the global pandemic caused by severe acute respiratory syndrome 2 virus (SARS-CoV-2) infection, has caused millions of infections and fatalities worldwide. Extensive SARS-CoV-2 research has been conducted to develop therapeutic drugs and prophylactic vaccines, and even though some drugs have been approved to treat SARS-CoV-2 infection, treatment efficacy remains limited. Therefore, preventive vaccination has been implemented on a global scale and represents the primary approach to combat the COVID-19 pandemic. Approved vaccines vary in composition, although vaccine design has been based on either the key viral structural (spike) protein or viral components carrying this protein. Therefore, mutations of the virus, particularly mutations in the S protein, severely compromise the effectiveness of current vaccines and the ability to control COVID-19 infection. This review begins by describing the SARS-CoV-2 viral composition, the mechanism of infection, the role of angiotensin-converting enzyme 2, the host defence responses against infection and the most common vaccine designs. Next, this review summarizes the common mutations of SARS-CoV-2 and how these mutations change viral properties, confer immune escape and influence vaccine efficacy. Finally, this review discusses global strategies that have been employed to mitigate the decreases in vaccine efficacy encountered against new variants.
Collapse
Affiliation(s)
- Ziyao Zhao
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Sahra Bashiri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| |
Collapse
|
3
|
Glenet M, Lebreil AL, N'Guyen Y, Meyer I, Baud S, Andreoletti L. Structural impact of a new spike Y170W mutation detected in early emerging SARS-CoV-2 Omicron variants in France. Virus Res 2024; 343:199354. [PMID: 38492859 PMCID: PMC10957500 DOI: 10.1016/j.virusres.2024.199354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
To assess the genetic characteristics of the early emerging SARS-CoV-2 Omicron variant strains, we retrospectively analyzed a collection of 150 nasopharyngeal samples taken from a series of outpatient cases tested positive by a referenced qRT-PCR assay during the reported period of Omicron variant emergence in December 2021, in northeastern region of France. Next Generation Sequencing (NGS) analysis of SARS-CoV-2 spike sequences revealed that only 3 (2 %) of these detected strains were Omicron variants, while 147 (98 %) were identified as previously described delta variants. Our phylogenetic analyzes of SARS-CoV-2 RNA genomes showed that these French early emerging Omicron variants may have originated from South Africa or India. In addition, whole viral genome sequences NGS comparison analyzes allowed us to identify an original and uncharacterized Y170W spike mutation that was weakly and transiently detected during the period of SARS-CoV-2 Omicron variant emergence in human populations. Molecular modeling and docking experiments indicated that this original mutated residue Y170W was neither directly involved in binding to the SARS-CoV-2 receptor ACE2 nor in interacting with known neutralizing antibody sites. However, this new mutation may be responsible for preventing the transition from the closed to the open Spike conformation, thus promoting the early emergence of the Omicron variant. Overall, these results underscore the epidemiological utility of a routine whole-genome viral NGS strategy that enables genotypic characterization of emerging or mutant SARS-CoV-2 variants, which could have significant implications for public health policy.
Collapse
Affiliation(s)
- Marie Glenet
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France.
| | - Anne-Laure Lebreil
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France
| | - Yohan N'Guyen
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France; Infectious Diseases and Internal Medicine Department, CHU Reims, Hôpital Robert Debré, Reims, France
| | - Ittah Meyer
- Unilabs BioCT, Private Laboratory Group, Château-Thierry, France
| | - Stéphanie Baud
- Université de Reims Champagne-Ardenne, CNRS, MEDyC UMR 7369, Reims, France
| | - Laurent Andreoletti
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France; Virology Department, CHU Reims, Hôpital Robert Debré, Reims, France
| |
Collapse
|
4
|
Salamango DJ. Finally neutralizing the threat? A novel SARS-CoV-2 vaccine platform that elicits enhanced neutralizing antibody responses. mBio 2024; 15:e0006724. [PMID: 38407097 PMCID: PMC11005347 DOI: 10.1128/mbio.00067-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak took the world by storm due to its rapid global spread and unpredictable disease outcomes. The extraordinary ascension of SARS-CoV-2 to pandemic status motivated a world-wide effort to rapidly develop vaccines that could effectively suppress virus spread and mitigate severe disease. These efforts culminated in the development and deployment of several highly effective vaccines that were heralded as the beginning-of-the-end of the pandemic. However, these successes were short lived due to the unexpected and continuous emergence of more transmissible and immune-evasive SARS-CoV-2 variants. Thus, attention has shifted toward developing novel vaccine platforms that elicit more robust and sustained neutralizing antibody responses. Recent findings by Muñoz-Alía and colleagues address this by combining a live recombinant measles vaccine platform with novel biochemical approaches to generate vaccine candidates that bolster the potency of neutralizing antibody responses against diverse SARS-CoV-2 spike proteins (M. Á. Muñoz-Alía, R. A. Nace, B. Balakrishnan, L. Zhang, et al., mBio 9:e02928-23, 2024, https://doi.org/10.1128/mbio.02928-23).
Collapse
Affiliation(s)
- Daniel J. Salamango
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Science Center, San Antonio, Texas, USA
| |
Collapse
|
5
|
Senevirathne TH, Wekking D, Swain JWR, Solinas C, De Silva P. COVID-19: From emerging variants to vaccination. Cytokine Growth Factor Rev 2024; 76:127-141. [PMID: 38135574 DOI: 10.1016/j.cytogfr.2023.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023]
Abstract
The vigorous spread of SARS-CoV-2 resulted in the rapid infection of millions of people worldwide and devastation of not only public healthcare, but also social, educational, and economic infrastructures. The evolution of SARS-CoV-2 over time is due to the mutations that occurred in the genome during each replication. These mutated forms of SARS-CoV-2, otherwise known as variants, were categorized as variants of interest (VOI) or variants of concern (VOC) based on the increased risk of transmissibility, disease severity, immune escape, decreased effectiveness of current social measures, and available vaccines and therapeutics. The swift development of COVID-19 vaccines has been a great success for biomedical research, and billions of vaccine doses, including boosters, have been administered worldwide. BNT162b2 vaccine (Pfizer-BioNTech), mRNA-1273 (Moderna), ChAdOx1 nCoV-19 (AstraZeneca), and Janssen (Johnson & Johnson) are the four major COVID-19 vaccines that received early regulatory authorization based on their efficacy. However, some SARS-CoV-2 variants resulted in higher resistance to available vaccines or treatments. It has been four years since the first reported infection of SARS-CoV-2, yet the Omicron variant and its subvariants are still infecting people worldwide. Despite this, COVID-19 vaccines are still expected to be effective at preventing severe disease, hospitalization, and death from COVID. In this review, we provide a comprehensive overview of the COVID-19 pandemic focused on evolution of VOC and vaccination strategies against them.
Collapse
Affiliation(s)
- Thilini H Senevirathne
- Faculty of Science, Katholieke Universiteit Leuven, Kasteelpark Arenberg, Leuven, Belgium
| | - Demi Wekking
- Amsterdam UMC, Location Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Cinzia Solinas
- Medical Oncology, AOU Cagliari, P.O. Duilio Casula, Monserrato (CA), Italy.
| | - Pushpamali De Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
6
|
Oktavianthi S, Lages AC, Kusuma R, Kurniasih TS, Trimarsanto H, Andriani F, Rustandi D, Meriyanti T, Yusuf I, Malik SG, Jo J, Suriapranata I. Whole-Genome Sequencing and Mutation Analyses of SARS-CoV-2 Isolates from Indonesia. Pathogens 2024; 13:279. [PMID: 38668234 PMCID: PMC11053823 DOI: 10.3390/pathogens13040279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/12/2024] [Accepted: 03/07/2024] [Indexed: 04/29/2024] Open
Abstract
The SARS-CoV-2 infection that caused the COVID-19 pandemic has become a significant public health concern. New variants with distinct mutations have emerged, potentially impacting its infectivity, immune evasion capacity, and vaccine response. A whole-genome sequencing study of 292 SARS-CoV-2 isolates collected from selected regions of Indonesia between January and October 2021 was performed to identify the distribution of SARS-CoV-2 variants and common mutations in Indonesia. During January-April 2021, Indonesian lineages B.1.466.2 and B.1.470 dominated, but from May 2021, Delta's AY.23 lineage outcompeted them. An analysis of 7515 published sequences from January 2021 to June 2022 revealed a decline in Delta in November 2021, followed by the emergence of Omicron variants in December 2021. We identified C241T (5'UTR), P314L (NSP12b), F106F (NSP3), and D614G (Spike) mutations in all sequences. The other common substitutions included P681R (76.4%) and T478K (60%) in Spike, D377Y in Nucleocapsid (61%), and I82T in Membrane (60%) proteins. Breakthrough infection and prolonged viral shedding cases were associated with Delta variants carrying the Spike T19R, G142D, L452R, T478K, D614G, P681R, D950N, and V1264L mutations. The dynamic of SARS-CoV-2 variants in Indonesia highlights the importance of continuous genomic surveillance in monitoring and identifying potential strains leading to disease outbreaks.
Collapse
Affiliation(s)
- Sukma Oktavianthi
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
| | - Aksar Chair Lages
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Rinaldy Kusuma
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Tri Shinta Kurniasih
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
- Menzies School of Health Research, Charles Darwin University, Darwin 0811, Australia
| | - Febi Andriani
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - David Rustandi
- Siloam Hospital Lippo Village, Tangerang 15810, Indonesia; (D.R.); (T.M.)
| | - Tandry Meriyanti
- Siloam Hospital Lippo Village, Tangerang 15810, Indonesia; (D.R.); (T.M.)
| | - Irawan Yusuf
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Safarina G. Malik
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
| | - Juandy Jo
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Ivet Suriapranata
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| |
Collapse
|
7
|
Wilson C, Thomson EC. Resilience to emerging infectious diseases and the importance of scientific innovation. Future Healthc J 2024; 11:100023. [PMID: 38646044 PMCID: PMC11025050 DOI: 10.1016/j.fhj.2024.100023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
This opinion piece emphasies the critical role of translational research in enhancing the UK's resilience against future pandemics. The COVID-19 pandemic demonstrated the lifesaving potential of scientific innovation, including genomic tracking of SARS-CoV-2, vaccine development, data linkage, modelling, and new treatments. These advances, achieved through collaborations between academic institutions, industry, government, public health bodies, and the NHS, occurred at an unprecedented pace. However, the UK's pandemic preparedness planning, as reflected in the 2016 Exercise Cygnus report, notably lacked provision for scientific innovation. This oversight highlights the necessity of integrating innovation and research into future preparedness strategies, not as a luxury but as a vital component of the healthcare infrastructure. The COVID-19 pandemic has underlined the importance of surge capacity for diagnostic labs, vaccine development and deployment strategies, real-time research embedded within the NHS, efficient data sharing, clear public communication, and the use of genomic tools for outbreak surveillance and monitoring pathogen response. Despite world-leading aspects of some of the UK's research response, the need to build much of the infrastructure in real-time led to avoidable delays. A proactive approach in incorporating research and innovation into the NHS's operational framework will be needed to ensure swift, evidence-based responses to future pandemics.
Collapse
Affiliation(s)
| | - Emma C. Thomson
- NHS Greater Glasgow & Clyde (NHS GG&C), Glasgow, United Kingdom
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- London School of Hygiene and Tropical Medicine (LSHTM), London, United Kingdom
| |
Collapse
|
8
|
Avivi MY, Touitou N, Rohana H, Lerrer B, Shav-Tal Y, Peretz A, Cohen HY. Nucleic acid hybridization-based detection of pathogenic RNA using microscale thermophoresis. J Biol Chem 2024; 300:105676. [PMID: 38278326 PMCID: PMC10881438 DOI: 10.1016/j.jbc.2024.105676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/28/2024] Open
Abstract
Infectious diseases are one of the world's leading causes of morbidity. Their rapid spread emphasizes the need for accurate and fast diagnostic methods for large-scale screening. Here, we describe a robust method for the detection of pathogens based on microscale thermophoresis (MST). The method involves the hybridization of a fluorescently labeled DNA probe to a target RNA and the assessment of thermophoretic migration of the resulting complex in solution within a 2 to 30-time window. We found that the thermophoretic migration of the nucleic acid-based probes is primarily determined by the fluorescent molecule used, rather than the nucleic acid sequence of the probe. Furthermore, a panel of uniformly labeled probes that bind to the same target RNA yields a more responsive detection pattern than a single probe, and moreover, can be used for the detection of specific pathogen variants. In addition, intercalating agents (ICA) can be used to alter migration directionality to improve detection sensitivity and resolving power by several orders of magnitude. We show that this approach can rapidly diagnose viral SARS-CoV2, influenza H1N1, artificial pathogen targets, and bacterial infections. Furthermore, it can be used for anti-microbial resistance testing within 2 h, demonstrating its diagnostic potential for early pathogen detection.
Collapse
Affiliation(s)
- Matan Yosef Avivi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Noga Touitou
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Hanan Rohana
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Tiberias, Israel; Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Batia Lerrer
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Avi Peretz
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Tiberias, Israel; Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Haim Yosef Cohen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
| |
Collapse
|
9
|
Sussman F, Villaverde DS. The Diverse Nature of the Molecular Interactions That Govern the COV-2 Variants' Cell Receptor Affinity Ranking and Its Experimental Variability. Int J Mol Sci 2024; 25:2585. [PMID: 38473831 DOI: 10.3390/ijms25052585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/08/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
A critical determinant of infectivity and virulence of the most infectious and or lethal variants of concern (VOCs): Wild Type, Delta and Omicron is related to the binding interactions between the receptor-binding domain of the spike and its host receptor, the initial step in cell infection. It is of the utmost importance to understand how mutations of a viral strain, especially those that are in the viral spike, affect the resulting infectivity of the emerging VOC, knowledge that could help us understand the variant virulence and inform the therapies applied or the vaccines developed. For this sake, we have applied a battery of computational protocols of increasing complexity to the calculation of the spike binding affinity for three variants of concern to the ACE2 cell receptor. The results clearly illustrate that the attachment of the spikes of the Delta and Omicron variants to the receptor originates through different molecular interaction mechanisms. All our protocols unanimously predict that the Delta variant has the highest receptor-binding affinity, while the Omicron variant displays a substantial variability in the binding affinity of the spike that relates to the structural plasticity of the Omicron spike-receptor complex. We suggest that the latter result could explain (at least in part) the variability of the in vitro binding results for this VOC and has led us to suggest a reason for the lower virulence of the Omicron variant as compared to earlier strains. Several hypotheses have been developed around this subject.
Collapse
Affiliation(s)
- Fredy Sussman
- Department of Organic Chemistry, Faculty of Chemistry, Universidad de Santiago de Compostela, 15784 Santiago de Compostela, Spain
| | - Daniel S Villaverde
- Department of Organic Chemistry, Faculty of Chemistry, Universidad de Santiago de Compostela, 15784 Santiago de Compostela, Spain
| |
Collapse
|
10
|
Korosec CS, Wahl LM, Heffernan JM. Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections? Virus Evol 2024; 10:veae006. [PMID: 38425472 PMCID: PMC10904108 DOI: 10.1093/ve/veae006] [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: 11/15/2023] [Revised: 12/20/2023] [Accepted: 01/12/2024] [Indexed: 03/02/2024] Open
Abstract
Despite a relatively low mutation rate, the large number of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has allowed for substantial genetic change, leading to a multitude of emerging variants. Using a recently determined mutation rate (per site replication), as well as within-host parameter estimates for symptomatic SARS-CoV-2 infection, we apply a stochastic transmission-bottleneck model to describe the survival probability of de novo SARS-CoV-2 mutations as a function of bottleneck size and selection coefficient. For narrow bottlenecks, we find that mutations affecting per-target-cell attachment rate (with phenotypes associated with fusogenicity and ACE2 binding) have similar transmission probabilities to mutations affecting viral load clearance (with phenotypes associated with humoral evasion). We further find that mutations affecting the eclipse rate (with phenotypes associated with reorganization of cellular metabolic processes and synthesis of viral budding precursor material) are highly favoured relative to all other traits examined. We find that mutations leading to reduced removal rates of infected cells (with phenotypes associated with innate immune evasion) have limited transmission advantage relative to mutations leading to humoral evasion. Predicted transmission probabilities, however, for mutations affecting innate immune evasion are more consistent with the range of clinically estimated household transmission probabilities for de novo mutations. This result suggests that although mutations affecting humoral evasion are more easily transmitted when they occur, mutations affecting innate immune evasion may occur more readily. We examine our predictions in the context of a number of previously characterized mutations in circulating strains of SARS-CoV-2. Our work offers both a null model for SARS-CoV-2 mutation rates and predicts which aspects of viral life history are most likely to successfully evolve, despite low mutation rates and repeated transmission bottlenecks.
Collapse
Affiliation(s)
- Chapin S Korosec
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
- Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
| | - Lindi M Wahl
- Applied Mathematics, Western University, 1151 Richmond St, London, ON N6A 5B7, Canada
| | - Jane M Heffernan
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
- Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
| |
Collapse
|
11
|
Yu M, Zhang Y, Zhang L, Wang S, Liu Y, Xu Z, Liu P, Chen Y, Guo R, Meng L, Zhang T, Fan W, Qi X, Gao L, Zhang Y, Cui H, Gao Y. N123I mutation in the ALV-J receptor-binding domain region enhances viral replication ability by increasing the binding affinity with chNHE1. PLoS Pathog 2024; 20:e1011928. [PMID: 38324558 PMCID: PMC10878525 DOI: 10.1371/journal.ppat.1011928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 02/20/2024] [Accepted: 12/28/2023] [Indexed: 02/09/2024] Open
Abstract
The subgroup J avian leukosis virus (ALV-J), a retrovirus, uses its gp85 protein to bind to the receptor, the chicken sodium hydrogen exchanger isoform 1 (chNHE1), facilitating viral invasion. ALV-J is the main epidemic subgroup and shows noteworthy mutations within the receptor-binding domain (RBD) region of gp85, especially in ALV-J layer strains in China. However, the implications of these mutations on viral replication and transmission remain elusive. In this study, the ALV-J layer strain JL08CH3-1 exhibited a more robust replication ability than the prototype strain HPRS103, which is related to variations in the gp85 protein. Notably, the gp85 of JL08CH3-1 demonstrated a heightened binding capacity to chNHE1 compared to HPRS103-gp85 binding. Furthermore, we showed that the specific N123I mutation within gp85 contributed to the enhanced binding capacity of the gp85 protein to chNHE1. Structural analysis indicated that the N123I mutation primarily enhanced the stability of gp85, expanded the interaction interface, and increased the number of hydrogen bonds at the interaction interface to increase the binding capacity between gp85 and chNHE1. We found that the N123I mutation not only improved the viral replication ability of ALV-J but also promoted viral shedding in vivo. These comprehensive data underscore the notion that the N123I mutation increases receptor binding and intensifies viral replication.
Collapse
Affiliation(s)
- Mengmeng Yu
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yao Zhang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Li Zhang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Suyan Wang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yongzhen Liu
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhuangzhuang Xu
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Peng Liu
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuntong Chen
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ru Guo
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lingzhai Meng
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Tao Zhang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wenrui Fan
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiaole Qi
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Li Gao
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yanping Zhang
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hongyu Cui
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yulong Gao
- Avian Immunosuppressive Diseases Division, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, China
- National Poultry Laboratory Animal Resource Center, Harbin, China
| |
Collapse
|
12
|
Zaccaria M, Genovese L, Lawhorn BE, Dawson W, Joyal AS, Hu J, Autissier P, Nakajima T, Johnson WE, Fofana I, Farzan M, Momeni B. Predicting potential SARS-CoV-2 mutations of concern via full quantum mechanical modelling. J R Soc Interface 2024; 21:20230614. [PMID: 38320601 PMCID: PMC10846948 DOI: 10.1098/rsif.2023.0614] [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: 10/20/2023] [Accepted: 01/05/2024] [Indexed: 02/08/2024] Open
Abstract
Ab initio quantum mechanical models can characterize and predict intermolecular binding, but only recently have models including more than a few hundred atoms gained traction. Here, we simulate the electronic structure for approximately 13 000 atoms to predict and characterize binding of SARS-CoV-2 spike variants to the human ACE2 (hACE2) receptor using the quantum mechanics complexity reduction (QM-CR) approach. We compare four spike variants in our analysis: Wuhan, Omicron, and two Omicron-based variants. To assess binding, we mechanistically characterize the energetic contribution of each amino acid involved, and predict the effect of select single amino acid mutations. We validate our computational predictions experimentally by comparing the efficacy of spike variants binding to cells expressing hACE2. At the time we performed our simulations (December 2021), the mutation A484K which our model predicted to be highly beneficial to ACE2 binding had not been identified in epidemiological surveys; only recently (August 2023) has it appeared in variant BA.2.86. We argue that our computational model, QM-CR, can identify mutations critical for intermolecular interactions and inform the engineering of high-specificity interactors.
Collapse
Affiliation(s)
- Marco Zaccaria
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | - Luigi Genovese
- Université Grenoble Alpes, CEA, INAC-MEM, L Sim, Grenoble, France
| | | | | | - Andrew S. Joyal
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | - Jingqing Hu
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | | | | | | | - Ismael Fofana
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | - Michael Farzan
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Center for Integrated Solutions for Infectious Diseases, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Disease, Boston Children's Hospital, Boston, MA, USA
| | - Babak Momeni
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| |
Collapse
|
13
|
Outteridge M, Nunn CM, Devine K, Patel B, McLean GR. Antivirals for Broader Coverage against Human Coronaviruses. Viruses 2024; 16:156. [PMID: 38275966 PMCID: PMC10820748 DOI: 10.3390/v16010156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Coronaviruses (CoVs) are enveloped positive-sense single-stranded RNA viruses with a genome that is 27-31 kbases in length. Critical genes include the spike (S), envelope (E), membrane (M), nucleocapsid (N) and nine accessory open reading frames encoding for non-structural proteins (NSPs) that have multiple roles in the replication cycle and immune evasion (1). There are seven known human CoVs that most likely appeared after zoonotic transfer, the most recent being SARS-CoV-2, responsible for the COVID-19 pandemic. Antivirals that have been approved by the FDA for use against COVID-19 such as Paxlovid can target and successfully inhibit the main protease (MPro) activity of multiple human CoVs; however, alternative proteomes encoded by CoV genomes have a closer genetic similarity to each other, suggesting that antivirals could be developed now that target future CoVs. New zoonotic introductions of CoVs to humans are inevitable and unpredictable. Therefore, new antivirals are required to control not only the next human CoV outbreak but also the four common human CoVs (229E, OC43, NL63, HKU1) that circulate frequently and to contain sporadic outbreaks of the severe human CoVs (SARS-CoV, MERS and SARS-CoV-2). The current study found that emerging antiviral drugs, such as Paxlovid, could target other CoVs, but only SARS-CoV-2 is known to be targeted in vivo. Other drugs which have the potential to target other human CoVs are still within clinical trials and are not yet available for public use. Monoclonal antibody (mAb) treatment and vaccines for SARS-CoV-2 can reduce mortality and hospitalisation rates; however, they target the Spike protein whose sequence mutates frequently and drifts. Spike is also not applicable for targeting other HCoVs as these are not well-conserved sequences among human CoVs. Thus, there is a need for readily available treatments globally that target all seven human CoVs and improve the preparedness for inevitable future outbreaks. Here, we discuss antiviral research, contributing to the control of common and severe CoV replication and transmission, including the current SARS-CoV-2 outbreak. The aim was to identify common features of CoVs for antivirals, biologics and vaccines that could reduce the scientific, political, economic and public health strain caused by CoV outbreaks now and in the future.
Collapse
Affiliation(s)
- Mia Outteridge
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Christine M. Nunn
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Kevin Devine
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Bhaven Patel
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Gary R. McLean
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
- National Heart and Lung Institute, Imperial College London, London W2 1PG, UK
| |
Collapse
|
14
|
Zhang L, Li J. Molecular Dynamics Simulations on Spike Protein Mutants Binding with Human β Defensin Type 2. J Phys Chem B 2024; 128:415-428. [PMID: 38189674 DOI: 10.1021/acs.jpcb.3c05460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Human β defensin type 2 (hBD-2), a cationic cysteine-rich peptide secreted from the human innate immune system, can bind Spike-RBD at the same site as receptor ACE2, thus blocking viral entry into ACE2-expressing cells. In order to find out the impact of CoV-2 mutations on hBD-2's antiviral activity, it is important to investigate the binding and interaction of hBD-2 with RBD mutants. All-atom molecular dynamics simulations were conducted on typical RBD mutants, including N501Y, E484K, P479S, T478I, S477N, N439K, K417N, and N501Y-E484K-K417N, binding with hBD-2. Starting from the stable binding structure of hBD-2 and wt-RBD and ClusPro and HADDOCK docking-predicted initial structures, the RBD variants bound with hBD-2 simulations were set up, and NAMD simulations were conducted. Based on the structure and dynamics analysis, it was found that most RBD variants can still form a similar number of hydrogen bonds with hBD-2, in addition to having a similar-sized buried surface area (BSA) and a similar binding interface to the RBD wildtype. However, the RBD triple mutant formed a less stable binding structure with hBD-2 than other variants. Additionally, the free energy perturbation (FEP) method was applied to calculate the contribution of key mutant residues to the binding and the free energy change caused by the mutations. The result shows that N439K, K417N, and the trimutation increase the binding free energy of RBD with hBD-2; thus, RBD should bind less stably with hBD-2. E484K decreases the binding free energy, thus it should bind more stably with hBD-2, while N501Y, S477N, T478I, and P479S almost do not change the binding free energy with hBD-2. The MM-GBSA method predicted the binding interaction energy which shows that the trimutant should be able to escape the binding with hBD-2 but N501Y should not. The result can provide insight into understanding the functional mechanism of hBD-2 combating SARS-CoV-2 mutants.
Collapse
Affiliation(s)
- Liqun Zhang
- Chemical Engineering Department, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Jadeson Li
- Newton North High School, 457 Walnut Street, Newton, Massachusetts 02460, United States
| |
Collapse
|
15
|
Shao H, Lin XQ, Chen Y, Lv L, Ying CQ, Tung TH, Zhu JS. Willingness of college students to receive COVID-19 heterologous vaccination in Taizhou, China. Hum Vaccin Immunother 2023; 19:2158012. [PMID: 36606519 PMCID: PMC9980617 DOI: 10.1080/21645515.2022.2158012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/08/2022] [Accepted: 12/09/2022] [Indexed: 01/07/2023] Open
Abstract
This study aimed to determine the willingness of college students to choose COVID-19 heterologous vaccination and its associated influencing factors in Taizhou, China. A population-based, self-administered online questionnaire was conducted from March 15 to 17, 2022. Of the 2,463 participants who had received the invitation, 1,821 responded to the survey (response rate = 73.9%). Only 14% (86/614) of those willing to receive a booster would chose a heterologous vaccination; the perception of better effectiveness of a COVID-19 heterologous vaccination booster was the significant factor (X2 = 22.671, p < .001). Additionally, female college students'older age (χ2 = 7.523, P = .023), major of medical (χ2 = 6.294, P = .012), and better perceived effectiveness of COVID-19 heterologous vaccination booster (χ2 = 22.659, P < .001), were more willing to receive heterologous booster doses. Chinese college students have a strong willingness to receive booster shots, but the percentage of those willing to receive a heterologous vaccine is only 14.0%, and the lack of understanding of its effectiveness is an important factor in the low proportion of heterologous vaccine selection. Health education, public health awareness, and the disclosure of heterologous vaccine information can help improve the public's understanding of heterologous vaccines and provide them with more choices.
Collapse
Affiliation(s)
- Hui Shao
- Department of Infectious Diseases, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, China
| | - Xiao-Qing Lin
- Department of Infectious Diseases, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, China
| | - Yan Chen
- Department of Infectious Diseases, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, China
| | - Li Lv
- Department of Infectious Diseases, Taizhou Hospital, Zhejiang University, Linhai, Zhejiang, China
| | - Chen-Qian Ying
- Department of Infectious Diseases, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, China
| | - Tao-Hsin Tung
- Evidence-based Medicine Center, Taizhou Hospital of Zhejiang Province, Wenzhou, Medical University, Wenzhou, Linhai, Zhejiang, China
| | - Jian-Sheng Zhu
- Department of Infectious Diseases, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, China
| |
Collapse
|
16
|
Zhang L, Cao H, Medlin K, Pearson J, Aristotelous AC, Chen A, Wessler T, Forest MG. Computational Modeling Insights into Extreme Heterogeneity in COVID-19 Nasal Swab Data. Viruses 2023; 16:69. [PMID: 38257769 PMCID: PMC10820884 DOI: 10.3390/v16010069] [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: 10/05/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/24/2024] Open
Abstract
Throughout the COVID-19 pandemic, an unprecedented level of clinical nasal swab data from around the globe has been collected and shared. Positive tests have consistently revealed viral titers spanning six orders of magnitude! An open question is whether such extreme population heterogeneity is unique to SARS-CoV-2 or possibly generic to viral respiratory infections. To probe this question, we turn to the computational modeling of nasal tract infections. Employing a physiologically faithful, spatially resolved, stochastic model of respiratory tract infection, we explore the statistical distribution of human nasal infections in the immediate 48 h of infection. The spread, or heterogeneity, of the distribution derives from variations in factors within the model that are unique to the infected host, infectious variant, and timing of the test. Hypothetical factors include: (1) reported physiological differences between infected individuals (nasal mucus thickness and clearance velocity); (2) differences in the kinetics of infection, replication, and shedding of viral RNA copies arising from the unique interactions between the host and viral variant; and (3) differences in the time between initial cell infection and the clinical test. Since positive clinical tests are often pre-symptomatic and independent of prior infection or vaccination status, in the model we assume immune evasion throughout the immediate 48 h of infection. Model simulations generate the mean statistical outcomes of total shed viral load and infected cells throughout 48 h for each "virtual individual", which we define as each fixed set of model parameters (1) and (2) above. The "virtual population" and the statistical distribution of outcomes over the population are defined by collecting clinically and experimentally guided ranges for the full set of model parameters (1) and (2). This establishes a model-generated "virtual population database" of nasal viral titers throughout the initial 48 h of infection of every individual, which we then compare with clinical swab test data. Support for model efficacy comes from the sampling of infection dynamics over the virtual population database, which reproduces the six-order-of-magnitude clinical population heterogeneity. However, the goal of this study is to answer a deeper biological and clinical question. What is the impact on the dynamics of early nasal infection due to each individual physiological feature or virus-cell kinetic mechanism? To answer this question, global data analysis methods are applied to the virtual population database that sample across the entire database and de-correlate (i.e., isolate) the dynamic infection outcome sensitivities of each model parameter. These methods predict the dominant, indeed exponential, driver of population heterogeneity in dynamic infection outcomes is the latency time of infected cells (from the moment of infection until onset of viral RNA shedding). The shedding rate of the viral RNA of infected cells in the shedding phase is a strong, but not exponential, driver of infection. Furthermore, the unknown timing of the nasal swab test relative to the onset of infection is an equally dominant contributor to extreme population heterogeneity in clinical test data since infectious viral loads grow from undetectable levels to more than six orders of magnitude within 48 h.
Collapse
Affiliation(s)
- Leyi Zhang
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Han Cao
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen Medlin
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason Pearson
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Simulations Plus, Inc., 6 Davis Dr., Durham, NC 27709, USA
| | | | - Alexander Chen
- Department of Mathematics, California State University, Dominguez Hills, CA 90747, USA
| | - Timothy Wessler
- Department of Applied Mathematics, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - M. Gregory Forest
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Departments of Applied Physical Sciences and Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
17
|
Adams LJ, VanBlargan LA, Liu Z, Gilchuk P, Zhao H, Chen RE, Raju S, Chong Z, Whitener BM, Shrihari S, Jethva PN, Gross ML, Crowe JE, Whelan SPJ, Diamond MS, Fremont DH. A broadly reactive antibody targeting the N-terminal domain of SARS-CoV-2 spike confers Fc-mediated protection. Cell Rep Med 2023; 4:101305. [PMID: 38039973 PMCID: PMC10772349 DOI: 10.1016/j.xcrm.2023.101305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 08/21/2023] [Accepted: 11/06/2023] [Indexed: 12/03/2023]
Abstract
Most neutralizing anti-SARS-CoV-2 monoclonal antibodies (mAbs) target the receptor binding domain (RBD) of the spike (S) protein. Here, we characterize a panel of mAbs targeting the N-terminal domain (NTD) or other non-RBD epitopes of S. A subset of NTD mAbs inhibits SARS-CoV-2 entry at a post-attachment step and avidly binds the surface of infected cells. One neutralizing NTD mAb, SARS2-57, protects K18-hACE2 mice against SARS-CoV-2 infection in an Fc-dependent manner. Structural analysis demonstrates that SARS2-57 engages an antigenic supersite that is remodeled by deletions common to emerging variants. In neutralization escape studies with SARS2-57, this NTD site accumulates mutations, including a similar deletion, but the addition of an anti-RBD mAb prevents such escape. Thus, our study highlights a common strategy of immune evasion by SARS-CoV-2 variants and how targeting spatially distinct epitopes, including those in the NTD, may limit such escape.
Collapse
Affiliation(s)
- Lucas J Adams
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Haiyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rita E Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Saravanan Raju
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zhenlu Chong
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bradley M Whitener
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Swathi Shrihari
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Prashant N Jethva
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
18
|
Zhou J, Uddback I, Kohlmeier JE, Christensen JP, Thomsen AR. Vaccine induced memory CD8 + T cells efficiently prevent viral transmission from the respiratory tract. Front Immunol 2023; 14:1322536. [PMID: 38164135 PMCID: PMC10757911 DOI: 10.3389/fimmu.2023.1322536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction Mucosal immunization eliciting local T-cell memory has been suggested for improved protection against respiratory infections caused by viral variants evading pre-existing antibodies. However, it remains unclear whether T-cell targeted vaccines suffice for prevention of viral transmission and to which extent local immunity is important in this context. Methods To study the impact of T-cell vaccination on the course of viral respiratory infection and in particular the capacity to inhibit viral transmission, we used a mouse model involving natural murine parainfluenza infection with a luciferase encoding virus and an adenovirus based nucleoprotein targeting vaccine. Results and discussion Prior intranasal immunization inducing strong mucosal CD8+ T cell immunity provided an almost immediate shut-down of the incipient infection and completely inhibited contact based viral spreading. If this first line of defense did not operate, as in parentally immunized mice, recirculating T cells participated in accelerated viral control that reduced the intensity of inter-individual transmission. These observations underscore the importance of pursuing the development of mucosal T-cell inducing vaccines for optimal protection of the individual and inhibition of inter-individual transmission (herd immunity), while at the same time explain why induction of a strong systemic T-cell response may still impact viral transmission.
Collapse
Affiliation(s)
- Jinglin Zhou
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Uddback
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jacob E. Kohlmeier
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | | | - Allan Randrup Thomsen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
19
|
Li Y, Ma W, Su W, Yan Z, Jia L, Deng J, Zhu A, Xie Y, Li X, Shao W, Ma Y, Che L, Zhu T, Wang H, Li M, Yu P. Synthesis of cell penetrating peptide sterol coupler and its liposome study on S-mRNA. Eur J Med Chem 2023; 261:115822. [PMID: 37793325 DOI: 10.1016/j.ejmech.2023.115822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023]
Abstract
In order to overcome the current LNP-mRNA delivery system's weakness of poor stability and rapid degradation by nuclease, a novel chol-CGYKK molecule and then the new phospholipid liposome were designed and prepared. A solid phase approach synthesized CGYKK and connected it to cholesterol via a disulfide linker to form the desired chol-CGYKK. Four formulated samples with different proportions of excipients were prepared by freeze-drying cationic liposomes and packaged S-mRNA. The stability test shows that after six months at 4 °C, the encapsulation rate of this novel phospholipid liposome was still approximately 90%, which would significantly improve the storage and transportation requirement. Transmission electron microscopy, atomic force microscopy, and scanning electron microscopy indicated that the liposomes were spherical and uniformly dispersed. On comparing the levels of mRNA protein expression of the four formulated samples, the S protein vaccine expression of formulated sample 1 was the highest. Uptake by vector cells for formulated sample 1 showed that compared to Lipo2000, and the transfection efficiency was 66.7%. Furthermore, the safety evaluation of the CGYKK and mRNA vaccine liposomes revealed no toxic effects. The in vivo study demonstrated that this novel mRNA vaccine had an immune response. However, it was still not as good as the LNP group right now, but its excellent physicochemical properties, stability, in vitro biological activity, and in vivo efficacy against SARS-CoV-2 provided new strategies for developing the next generation of mRNA delivery system.
Collapse
Affiliation(s)
- Yuan Li
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin International Cooperation Research Centre of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Wenlin Ma
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin International Cooperation Research Centre of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Wen Su
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin International Cooperation Research Centre of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zhihong Yan
- CanSino (Shanghai) Biotechnologies Co., Ltd, 1377 Luodong Road, Baoshan District, Shanghai, China; CanSino Biologics (Shanghai) Co., Ltd, 1377 Luodong Road, Baoshan District, Shanghai, China; CanSino (Shanghai) Biological Research Co., Ltd, China (Shanghai) Pilot Free Trade Zone Libing Road 67 Lane 7 No. 7 1-3 floor, China
| | - Lin Jia
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin International Cooperation Research Centre of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Jie Deng
- CanSino (Shanghai) Biotechnologies Co., Ltd, 1377 Luodong Road, Baoshan District, Shanghai, China
| | - Ali Zhu
- CanSino (Shanghai) Biotechnologies Co., Ltd, 1377 Luodong Road, Baoshan District, Shanghai, China
| | - Yanbo Xie
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin International Cooperation Research Centre of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xinyi Li
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin International Cooperation Research Centre of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Wanhui Shao
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin International Cooperation Research Centre of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yuman Ma
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin International Cooperation Research Centre of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Linze Che
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin International Cooperation Research Centre of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Tao Zhu
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin International Cooperation Research Centre of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; CanSino (Shanghai) Biotechnologies Co., Ltd, 1377 Luodong Road, Baoshan District, Shanghai, China; CanSino Biologics (Shanghai) Co., Ltd, 1377 Luodong Road, Baoshan District, Shanghai, China; CanSino (Shanghai) Biological Research Co., Ltd, China (Shanghai) Pilot Free Trade Zone Libing Road 67 Lane 7 No. 7 1-3 floor, China
| | - Haomeng Wang
- CanSino (Shanghai) Biotechnologies Co., Ltd, 1377 Luodong Road, Baoshan District, Shanghai, China; CanSino Biologics (Shanghai) Co., Ltd, 1377 Luodong Road, Baoshan District, Shanghai, China; CanSino (Shanghai) Biological Research Co., Ltd, China (Shanghai) Pilot Free Trade Zone Libing Road 67 Lane 7 No. 7 1-3 floor, China.
| | - Mingyuan Li
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin International Cooperation Research Centre of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.
| | - Peng Yu
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin International Cooperation Research Centre of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.
| |
Collapse
|
20
|
Jawad B, Adhikari P, Podgornik R, Ching WY. Impact of BA.1, BA.2, and BA.4/BA.5 Omicron mutations on therapeutic monoclonal antibodies. Comput Biol Med 2023; 167:107576. [PMID: 37871435 DOI: 10.1016/j.compbiomed.2023.107576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 10/01/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
The emergence of Omicron SARS-CoV-2 subvariants (BA.1, BA.2, BA.4, and BA.5), with an unprecedented number of mutations in their receptor-binding domain (RBD) of the spike-protein, has fueled a resurgence of COVID-19 infections, posing a major challenge to the efficacy of existing vaccines and monoclonal antibody (mAb) therapeutics. We conducted a systematic molecular dynamics (MD) simulation to investigate how the RBD mutations of these subvariants affect the interactions with broad mAbs including AstraZeneca (COV2-2196 and COV2-2130), Brii Biosciences (BRII-196), Celltrion (CT-P59), Eli Lilly (LY-CoV555 and LY-CoV016), Regeneron (REGN10933 and REGN10987), Vir Biotechnology (S309), and S2X259. Our results show a complete loss of binding for COV2-2196, BRII-196, CT-P59, and LY-CoV555 with all Omicron RBDs. Additionally, REGN10987 totally loses its binding with BA.1, but retains a partial binding with BA.2 and BA.4/5. The binding reduction is significant for LY-CoV016 and REGN10933 but moderate for COV2-2130. S309 and S2X259 retain their binding with BA.1 but exhibit decreased binding with other subvariants. We introduce a mutational escape map for each mAb to identify the key RBD sites and the corresponding critical mutations. Overall, our findings suggest that the majority of therapeutic mAbs have diminished or missing activity against Omicron subvariants, indicating the urgent need for a new therapeutic mAb with a better design.
Collapse
Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, 64110, United States; Department of Applied Sciences, University of Technology, Baghdad, 10066, Iraq.
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, 64110, United States
| | - Rudolf Podgornik
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing, 100049, China; CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100090, China; Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000, Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, 64110, United States
| |
Collapse
|
21
|
Lythgoe KA, Golubchik T, Hall M, House T, Cahuantzi R, MacIntyre-Cockett G, Fryer H, Thomson L, Nurtay A, Ghafani M, Buck D, Green A, Trebes A, Piazza P, Lonie LJ, Studley R, Rourke E, Smith D, Bashton M, Nelson A, Crown M, McCann C, Young GR, Andre Nunes dos Santos R, Richards Z, Tariq A, Fraser C, Diamond I, Barrett J, Walker AS, Bonsall D. Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey. Proc Biol Sci 2023; 290:20231284. [PMID: 37848057 PMCID: PMC10581763 DOI: 10.1098/rspb.2023.1284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/08/2023] [Indexed: 10/19/2023] Open
Abstract
The Office for National Statistics Coronavirus (COVID-19) Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors, although this was also accompanied by a gradual fall in average viral burdens from June 2021 to March 2023. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non-SGTF over time. Evolution was characterized by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens.
Collapse
Affiliation(s)
- Katrina A. Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Sydney Infectious Diseases Institute (Sydney ID), School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester M13 9PL, UK
| | - Roberto Cahuantzi
- Department of Mathematics, University of Manchester, Manchester M13 9PL, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Helen Fryer
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Laura Thomson
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Anel Nurtay
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Mahan Ghafani
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - David Buck
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Angie Green
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Amy Trebes
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Paolo Piazza
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Lorne J. Lonie
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | | | | | - Darren Smith
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Nothumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Nothumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Andrew Nelson
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Nothumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Matthew Crown
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Nothumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Clare McCann
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Gregory R. Young
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Nothumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Rui Andre Nunes dos Santos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Zack Richards
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Adnan Tariq
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | | | | | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | | | - Jeff Barrett
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Ann Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- MRC Clinical Trials Unit at UCL, UCL, London, UK
| | - David Bonsall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
| |
Collapse
|
22
|
Albright C, Van Egeren D, Thakur A, Chakravarty A, White LF, Stoddard M. Antibody escape, the risk of serotype formation, and rapid immune waning: Modeling the implications of SARS-CoV-2 immune evasion. PLoS One 2023; 18:e0292099. [PMID: 37851632 PMCID: PMC10584102 DOI: 10.1371/journal.pone.0292099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/12/2023] [Indexed: 10/20/2023] Open
Abstract
As the COVID-19 pandemic progresses, widespread community transmission of SARS-CoV-2 has ushered in a volatile era of viral immune evasion rather than the much-heralded stability of "endemicity" or "herd immunity." At this point, an array of viral strains has rendered essentially all monoclonal antibody therapeutics obsolete and strongly undermined the impact of vaccinal immunity on SARS-CoV-2 transmission. In this work, we demonstrate that antibody escape resulting in evasion of pre-existing immunity is highly evolutionarily favored and likely to cause waves of short-term transmission. In the long-term, invading strains that induce weak cross-immunity against pre-existing strains may co-circulate with those pre-existing strains. This would result in the formation of serotypes that increase disease burden, complicate SARS-CoV-2 control, and raise the potential for increases in viral virulence. Less durable immunity does not drive positive selection as a trait, but such strains may transmit at high levels if they establish. Overall, our results draw attention to the importance of inter-strain cross-immunity as a driver of transmission trends and the importance of early immune evasion data to predict the trajectory of the pandemic.
Collapse
Affiliation(s)
| | - Debra Van Egeren
- Stanford University School of Medicine, Stanford, CA, United States of America
| | - Aditya Thakur
- Boston University, Boston, MA, United States of America
| | | | - Laura F. White
- Boston University School of Public Health, Boston, MA, United States of America
| | | |
Collapse
|
23
|
Rucker G, Qin H, Zhang L. Structure, dynamics and free energy studies on the effect of point mutations on SARS-CoV-2 spike protein binding with ACE2 receptor. PLoS One 2023; 18:e0289432. [PMID: 37796794 PMCID: PMC10553274 DOI: 10.1371/journal.pone.0289432] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023] Open
Abstract
The ongoing COVID-19 pandemic continues to infect people worldwide, and the virus continues to evolve in significant ways which can pose challenges to the efficiency of available vaccines and therapeutic drugs and cause future pandemic. Therefore, it is important to investigate the binding and interaction of ACE2 with different RBD variants. A comparative study using all-atom MD simulations was conducted on ACE2 binding with 8 different RBD variants, including N501Y, E484K, P479S, T478I, S477N, N439K, K417N and N501Y-E484K-K417N on RBD. Based on the RMSD, RMSF, and DSSP results, overall the binding of RBD variants with ACE2 is stable, and the secondary structure of RBD and ACE2 are consistent after the point mutation. Besides that, a similar buried surface area, a consistent binding interface and a similar amount of hydrogen bonds formed between RBD and ACE2 although the exact residue pairs on the binding interface were modified. The change of binding free energy from point mutation was predicted using the free energy perturbation (FEP) method. It is found that N501Y, N439K, and K417N can strengthen the binding of RBD with ACE2, while E484K and P479S weaken the binding, and S477N and T478I have negligible effect on the binding. Point mutations modified the dynamic correlation of residues in RBD based on the dihedral angle covariance matrix calculation. Doing dynamic network analysis, a common intrinsic network community extending from the tail of RBD to central, then to the binding interface region was found, which could communicate the dynamics in the binding interface region to the tail thus to the other sections of S protein. The result can supply unique methodology and molecular insight on studying the molecular structure and dynamics of possible future pandemics and design novel drugs.
Collapse
Affiliation(s)
- George Rucker
- Chemical Engineering Department, Tennessee Technological University, Cookeville, TN, United States of America
| | - Hong Qin
- Computer Science Department, University of Tennessee Chattanooga, Chattanooga, TN, United States of America
| | - Liqun Zhang
- Chemical Engineering Department, University of Rhode Island, Kingston, RI, United States of America
| |
Collapse
|
24
|
Onigbinde S, Reyes CDG, Fowowe M, Daramola O, Atashi M, Bennett AI, Mechref Y. Variations in O-Glycosylation Patterns Influence Viral Pathogenicity, Infectivity, and Transmissibility in SARS-CoV-2 Variants. Biomolecules 2023; 13:1467. [PMID: 37892149 PMCID: PMC10604390 DOI: 10.3390/biom13101467] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023] Open
Abstract
The highly glycosylated S protein plays a vital role in host cell invasion, making it the principal target for vaccine development. Differences in mutations observed on the spike (S) protein of SARS-CoV-2 variants may result in distinct glycosylation patterns, thus influencing immunological evasion, infectivity, and transmissibility. The glycans can mask key epitopes on the S1 protein and alter its structural conformation, allowing the virus to escape the immune system. Therefore, we comprehensively characterize O-glycosylation in eleven variants of SARS-CoV-2 S1 subunits to understand the differences observed in the biology of the variants. In-depth characterization was performed with a double digestion strategy and an efficient LC-MS/MS approach. We observed that O-glycosylation is highly conserved across all variants in the region between the NTD and RBD, whereas other domains and regions exhibit variation in O-glycosylation. Notably, omicron has the highest number of O-glycosylation sites on the S1 subunit. Also, omicron has the highest level of sialylation in the RBD and RBM functional motifs. Our findings may shed light on how differences in O-glycosylation impact viral pathogenicity in variants of SARS-CoV-2 and facilitate the development of a robust vaccine with high protective efficacy against the variants of concern.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (S.O.); (C.D.G.R.); (M.F.); (O.D.); (M.A.); (A.I.B.)
| |
Collapse
|
25
|
Sun Z, Wang L, Li L, Sun Y, Zhang D, Zhou S, Li Y, Li X, Qiao H, Cui Q, Lan Z, Meng X, Xu J, Geng Y, Dai Y. Structure basis of two nanobodies neutralizing SARS-CoV-2 Omicron variant by targeting ultra-conservative epitopes. J Struct Biol 2023; 215:107996. [PMID: 37419228 DOI: 10.1016/j.jsb.2023.107996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/25/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
The evolving SARS-CoV-2 Omicron strain has repeatedly caused widespread disease epidemics, and effective antibody drugs continue to be in short supply. Here, we identified a batch of nanobodies with high affinity for receptor binding domain (RBD) of SARS-CoV-2 spike protein, separated them into three classes using high performance liquid chromatography (HPLC), and then resolved the crystal structure of the ternary complexes of two non-competing nanobodies (NB1C6 and NB1B5) with RBD using X-ray crystallography. The structures showed that NB1B5 and NB1C6 bind to the left and right flank of the RBD, respectively, and that the binding epitopes are highly conserved cryptic sites in all SARS-CoV-2 mutant strains, as well as that NB1B5 can effectively block the ACE2. These two nanobodies were covalently linked into multivalent and bi-paratopic formats, and have a high affinity and neutralization potency for omicron, potentially inhibiting viral escape. The binding sites of these two nanobodies are relatively conserved, which help guide the structural design of antibodies targeting future variants of SARS-CoV-2 to combat COVID-19 epidemics and pandemics.
Collapse
Affiliation(s)
- Zengchao Sun
- Department of Biopharmaceutics, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lu Wang
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lingyun Li
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yili Sun
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
| | - Daizhou Zhang
- Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China
| | - Siyu Zhou
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuying Li
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiyang Li
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Huarui Qiao
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qianqian Cui
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhongyun Lan
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiangjing Meng
- Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China.
| | - Jianfeng Xu
- Department of Biopharmaceutics, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
| | - Yong Geng
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yuanyuan Dai
- Department of Pharmacy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital of Chinese Academy of Medical Sciences Langfang Campus, Langfang, 065001, China.
| |
Collapse
|
26
|
Lu M, Yao W, Li Y, Ma D, Zhang Z, Wang H, Tang X, Wang Y, Li C, Cheng D, Lin H, Yin Y, Zhao J, Zhong G. Broadly Effective ACE2 Decoy Proteins Protect Mice from Lethal SARS-CoV-2 Infection. Microbiol Spectr 2023; 11:e0110023. [PMID: 37395664 PMCID: PMC10434153 DOI: 10.1128/spectrum.01100-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/06/2023] [Indexed: 07/04/2023] Open
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have been causing increasingly serious drug resistance problem, development of broadly effective and hard-to-escape anti-SARS-CoV-2 agents is an urgent need. Here, we describe further development and characterization of two SARS-CoV-2 receptor decoy proteins, ACE2-Ig-95 and ACE2-Ig-105/106. We found that both proteins had potent and robust in vitro neutralization activities against diverse SARS-CoV-2 variants, including BQ.1 and XBB.1, that are resistant to most clinically used monoclonal antibodies. In a stringent lethal SARS-CoV-2 infection mouse model, both proteins lowered the lung viral load by up to ~1,000-fold, prevented the emergence of clinical signs in >75% animals, and increased the animal survival rate from 0% (untreated) to >87.5% (treated). These results demonstrate that both proteins are good drug candidates for protecting animals from severe COVID-19. In a head-to-head comparison of these two proteins with five previously described ACE2-Ig constructs, we found that two constructs, each carrying five surface mutations in the ACE2 region, had partial loss of neutralization potency against three SARS-CoV-2 variants. These data suggest that extensively mutating ACE2 residues near the receptor binding domain (RBD)-binding interface should be avoided or performed with extra caution. Furthermore, we found that both ACE2-Ig-95 and ACE2-Ig-105/106 could be produced to the level of grams per liter, demonstrating the developability of them as biologic drug candidates. Stress condition stability testing of them further suggests that more studies are required in the future to improve the stability of these proteins. These studies provide useful insight into critical factors for engineering and preclinical development of ACE2 decoys as broadly effective therapeutics against diverse ACE2-utilizing coronaviruses. IMPORTANCE Engineering soluble ACE2 proteins that function as a receptor decoy to block SARS-CoV-2 infection is a very attractive approach to creating broadly effective and hard-to-escape anti-SARS-CoV-2 agents. This article describes development of two antibody-like soluble ACE2 proteins that broadly block diverse SARS-CoV-2 variants, including Omicron. In a stringent COVID-19 mouse model, both proteins successfully protected >87.5% animals from lethal SARS-CoV-2 infection. In addition, a head-to-head comparison of the two constructs developed in this study with five previously described ACE2 decoy constructs was performed here. Two previously described constructs with relatively more ACE2 surface mutations were found with less robust neutralization activities against diverse SARS-CoV-2 variants. Furthermore, the developability of the two proteins as biologic drug candidates was also assessed here. This study provides two broad anti-SARS-CoV-2 drug candidates and useful insight into critical factors for engineering and preclinical development of ACE2 decoys as broadly effective therapeutics against diverse ACE2-utilizing coronaviruses.
Collapse
Affiliation(s)
- Mengjia Lu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Weitong Yao
- Hubei JiangXia Laboratory, Wuhan, Hubei, China
| | - Yujun Li
- Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Danting Ma
- Tianjin Medical University Chu Hsien-I Memorial Hospital, Tianjin, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Haimin Wang
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Xiaojuan Tang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Chao Li
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Dechun Cheng
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Hua Lin
- Biomedical Research Center of South China, Fujian Normal University, Fuzhou, Fujian, China
| | - Yandong Yin
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Guocai Zhong
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| |
Collapse
|
27
|
Zhang I, Rufa DA, Pulido I, Henry MM, Rosen LE, Hauser K, Singh S, Chodera JD. Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex. J Chem Theory Comput 2023; 19:4863-4882. [PMID: 37450482 DOI: 10.1021/acs.jctc.3c00333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Relative alchemical binding free energy calculations are routinely used in drug discovery projects to optimize the affinity of small molecules for their drug targets. Alchemical methods can also be used to estimate the impact of amino acid mutations on protein:protein binding affinities, but these calculations can involve sampling challenges due to the complex networks of protein and water interactions frequently present in protein:protein interfaces. We investigate these challenges by extending a graphics processing unit (GPU)-accelerated open-source relative free energy calculation package (Perses) to predict the impact of amino acid mutations on protein:protein binding. Using the well-characterized model system barnase:barstar, we describe analyses for identifying and characterizing sampling problems in protein:protein relative free energy calculations. We find that mutations with sampling problems often involve charge-changes, and inadequate sampling can be attributed to slow degrees of freedom that are mutation-specific. We also explore the accuracy and efficiency of current state-of-the-art approaches─alchemical replica exchange and alchemical replica exchange with solute tempering─for overcoming relevant sampling problems. By employing sufficiently long simulations, we achieve accurate predictions (RMSE 1.61, 95% CI: [1.12, 2.11] kcal/mol), with 86% of estimates within 1 kcal/mol of the experimentally determined relative binding free energies and 100% of predictions correctly classifying the sign of the changes in binding free energies. Ultimately, we provide a model workflow for applying protein mutation free energy calculations to protein:protein complexes, and importantly, catalog the sampling challenges associated with these types of alchemical transformations. Our free open-source package (Perses) is based on OpenMM and is available at https://github.com/choderalab/perses.
Collapse
Affiliation(s)
- Ivy Zhang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, Cornell University, New York, New York 10065, United States
| | - Dominic A Rufa
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medical College, Cornell University, New York, New York 10065, United States
| | - Iván Pulido
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Michael M Henry
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Laura E Rosen
- Vir Biotechnology, San Francisco, California 94158, United States
| | - Kevin Hauser
- Vir Biotechnology, San Francisco, California 94158, United States
| | - Sukrit Singh
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| |
Collapse
|
28
|
Plikusiene I, Maciulis V, Juciute S, Ramanavicius A, Ramanaviciene A. Study of SARS-CoV-2 Spike Protein Wild-Type and the Variants of Concern Real-Time Interactions with Monoclonal Antibodies and Convalescent Human Serum. BIOSENSORS 2023; 13:784. [PMID: 37622870 PMCID: PMC10452135 DOI: 10.3390/bios13080784] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023]
Abstract
The spike (S) protein and its receptor-binding domain (RBD) of the coronavirus SARS-CoV-2 have been continually evolving, yielding the majority of significant missense mutations and new variants of concern. In this study, we examined how monoclonal antibodies against RBD (mAbs-SCoV2-RBD) and polyclonal antibodies present in convalescent human serum specifically interact with the S protein of wild-type and SARS-CoV-2 variants of concern (VOCs) in real time and how this can be reflected through surface mass density. Moreover, we combined two distinct, label-free measurement techniques: one based on changes in surface electromagnetic waves after reflection from the surface, and the other on changes in acoustic waves. The results demonstrated that dry surface mass density (ΓSE) of mAbs-SCoV2-RBD attached to the RBD of the S protein decreases three-fold, from 148 ng/cm2 to 46 ng/cm2, due to the B.1.351 or so-called beta mutation of coronavirus and its S protein (SCoV2-β). Consequently, the obtained wet mass ΓQCM-D resulted in values two times lower, from 319 ng/cm2 to 158 ng/cm2, and the hydration of mAbs-SCoV2-RBD/SCoV2-β immune complex was 70.88%. Conversely, when polyclonal antibodies present in convalescent human serum form immune complexes with the S protein of SARS-CoV-2 variants of concern, the ΓSE decreased from 279 ng/cm2 to 249 ng/cm2, and ΓQCM-D from 1545 ng/cm2 to 1366 ng/cm2. These results can give insights into the differences between the interaction of monoclonal and polyclonal antibodies with SARS-CoV-2 VOCs.
Collapse
Affiliation(s)
- Ieva Plikusiene
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, LT-03225 Vilnius, Lithuania
- State Research Institute Center for Physical and Technological Sciences, Sauletekio ave. 3, LT-10257 Vilnius, Lithuania
| | - Vincentas Maciulis
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, LT-03225 Vilnius, Lithuania
- State Research Institute Center for Physical and Technological Sciences, Sauletekio ave. 3, LT-10257 Vilnius, Lithuania
| | - Silvija Juciute
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, LT-03225 Vilnius, Lithuania
| | - Arunas Ramanavicius
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, LT-03225 Vilnius, Lithuania
| | - Almira Ramanaviciene
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, LT-03225 Vilnius, Lithuania
| |
Collapse
|
29
|
Wang G, Liu X, Wang K, Gao Y, Li G, Baptista-Hon DT, Yang XH, Xue K, Tai WH, Jiang Z, Cheng L, Fok M, Lau JYN, Yang S, Lu L, Zhang P, Zhang K. Deep-learning-enabled protein-protein interaction analysis for prediction of SARS-CoV-2 infectivity and variant evolution. Nat Med 2023; 29:2007-2018. [PMID: 37524952 DOI: 10.1038/s41591-023-02483-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 06/28/2023] [Indexed: 08/02/2023]
Abstract
Host-pathogen interactions and pathogen evolution are underpinned by protein-protein interactions between viral and host proteins. An understanding of how viral variants affect protein-protein binding is important for predicting viral-host interactions, such as the emergence of new pathogenic SARS-CoV-2 variants. Here we propose an artificial intelligence-based framework called UniBind, in which proteins are represented as a graph at the residue and atom levels. UniBind integrates protein three-dimensional structure and binding affinity and is capable of multi-task learning for heterogeneous biological data integration. In systematic tests on benchmark datasets and further experimental validation, UniBind effectively and scalably predicted the effects of SARS-CoV-2 spike protein variants on their binding affinities to the human ACE2 receptor, as well as to SARS-CoV-2 neutralizing monoclonal antibodies. Furthermore, in a cross-species analysis, UniBind could be applied to predict host susceptibility to SARS-CoV-2 variants and to predict future viral variant evolutionary trends. This in silico approach has the potential to serve as an early warning system for problematic emerging SARS-CoV-2 variants, as well as to facilitate research on protein-protein interactions in general.
Collapse
Affiliation(s)
- Guangyu Wang
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, China.
| | - Xiaohong Liu
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China
- UCL Cancer Institute, University College London, London, UK
| | - Kai Wang
- Department of Big Data and Biomedical Artificial Intelligence, National Biomedical Imaging Center, College of Future Technology, Peking University and Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Yuanxu Gao
- Guangzhou National Laboratory, Guangzhou, China
| | - Gen Li
- Guangzhou National Laboratory, Guangzhou, China
- Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Daniel T Baptista-Hon
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China
- Zhuhai International Eye Center and Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital and the First Affiliated Hospital of Faculty of Medicine, Macau University of Science and Technology, Guangdong, China
| | - Xiaohong Helena Yang
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Kanmin Xue
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Wa Hou Tai
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Zeyu Jiang
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, China
| | - Linling Cheng
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China
- Zhuhai International Eye Center and Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital and the First Affiliated Hospital of Faculty of Medicine, Macau University of Science and Technology, Guangdong, China
| | - Manson Fok
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Johnson Yiu-Nam Lau
- Departments of Biology and Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Shengyong Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ligong Lu
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China
- Zhuhai International Eye Center and Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital and the First Affiliated Hospital of Faculty of Medicine, Macau University of Science and Technology, Guangdong, China
| | - Ping Zhang
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, China
| | - Kang Zhang
- Instutite for Artificial Intelligence in Medicine and Faculty of Medicine, Macau University of Science and Technology, Macau, China.
- Department of Big Data and Biomedical Artificial Intelligence, National Biomedical Imaging Center, College of Future Technology, Peking University and Peking-Tsinghua Center for Life Sciences, Beijing, China.
- Guangzhou National Laboratory, Guangzhou, China.
- Zhuhai International Eye Center and Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital and the First Affiliated Hospital of Faculty of Medicine, Macau University of Science and Technology, Guangdong, China.
| |
Collapse
|
30
|
Sansoè G, Aragno M. New Viral Diseases and New Possible Remedies by Means of the Pharmacology of the Renin-Angiotensin System. J Renin Angiotensin Aldosterone Syst 2023; 2023:3362391. [PMID: 37476705 PMCID: PMC10356449 DOI: 10.1155/2023/3362391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/01/2023] [Accepted: 06/21/2023] [Indexed: 07/22/2023] Open
Abstract
All strains of SARS-CoV-2, as well as previously described SARS-CoV and MERS-CoV, bind to ACE2, the cell membrane receptor of β-coronaviruses. Monocarboxypeptidase ACE2 activity stops upon viral entry into cells, leading to inadequate tissue production of angiotensin 1-7 (Ang1-7). Acute lung injury due to the human respiratory syncytial virus (hRSV) or avian influenza A H7N9 and H5N1 viruses is also characterized by significant downregulation of lung ACE2 and increased systemic levels of angiotensin II (Ang II). Restoration of Ang1-7 anti-inflammatory, antifibrotic, vasodilating, and natriuretic properties was attempted at least in some COVID-19 patients through i.v. infusion of recombinant human ACE2 or intranasal administration of the modified ACE2 protein, with inconsistent clinical results. Conversely, use of ACE inhibitors (ACEis), which increase ACE2 cell expression, seemed to improve the prognosis of hypertensive patients with COVID-19. To restore Ang1-7 tissue levels in all these viral diseases and avoid the untoward effects frequently seen with ACE2 systemic administration, a different strategy may be hypothesized. Experimentally, when metallopeptidase inhibitors block ACE2, neprilysin (NEP), highly expressed in higher and lower airways, starts cleaving angiotensin I (Ang I) into Ang1-7. We suggest a discerning use of ACEis in normohypertensive patients with β-coronavirus disease as well as in atypical pneumonia caused by avian influenza viruses or hRSV to block the main ACE-dependent effects: Ang II synthesis and Ang1-7 degradation into angiotensin 1-5. At the same time, i.v.-infused Ang I, which is not hypertensive provided ACE is inhibited, may become the primary substrate for local Ang1-7 synthesis via ubiquitous NEP; i.e., NEP could replace inadequate ACE2 function if Ang I was freely available. Moreover, inhibitors of chymase, a serine endopeptidase responsible for 80% of Ang II-forming activity in tissues and vessel walls, could protect patients with atypical pneumonia from Ang II-mediated microvascular damage without reducing arterial blood pressure.
Collapse
Affiliation(s)
- Giovanni Sansoè
- Gastroenterology Unit, Humanitas Institute, Gradenigo Hospital, Corso Regina Margherita 10, 10153 Torino, Italy
| | - Manuela Aragno
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| |
Collapse
|
31
|
Hamdy ME, El Deeb AH, Hagag NM, Shahein MA, Alaidi O, Hussein HA. Interspecies transmission of SARS CoV-2 with special emphasis on viral mutations and ACE-2 receptor homology roles. Int J Vet Sci Med 2023; 11:55-86. [PMID: 37441062 PMCID: PMC10334861 DOI: 10.1080/23144599.2023.2222981] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 05/11/2023] [Accepted: 05/19/2023] [Indexed: 07/15/2023] Open
Abstract
COVID-19 outbreak was first reported in 2019, Wuhan, China. The spillover of the disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), to a wide range of pet, zoo, wild, and farm animals has emphasized potential zoonotic and reverse zoonotic viral transmission. Furthermore, it has evoked inquiries about susceptibility of different animal species to SARS-CoV-2 infection and role of these animals as viral reservoirs. Therefore, studying susceptible and non-susceptible hosts for SARS-CoV-2 infection could give a better understanding for the virus and will help in preventing further outbreaks. Here, we review structural aspects of SARS-CoV-2 spike protein, the effect of the different mutations observed in the spike protein, and the impact of ACE2 receptor variations in different animal hosts on inter-species transmission. Moreover, the SARS-CoV-2 spillover chain was reviewed. Combination of SARS-CoV-2 high mutation rate and homology of cellular ACE2 receptors enable the virus to transcend species barriers and facilitate its transmission between humans and animals.
Collapse
Affiliation(s)
- Mervat E. Hamdy
- Genome Research Unit, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Ayman H. El Deeb
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
- Department of Virology, Faculty of Veterinary Medicine, King Salman International University, South Sinai, Egypt
| | - Naglaa M. Hagag
- Genome Research Unit, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Momtaz A. Shahein
- Department of Virology, Animal Health Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Osama Alaidi
- Biocomplexity for Research and Consulting Co., Cairo, Egypt
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Hussein A. Hussein
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| |
Collapse
|
32
|
Gupta P, Gupta V, Singh CM, Singhal L. Emergence of COVID-19 Variants: An Update. Cureus 2023; 15:e41295. [PMID: 37539393 PMCID: PMC10394493 DOI: 10.7759/cureus.41295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2023] [Indexed: 08/05/2023] Open
Abstract
Severe acute respiratory disease virus-2 (SARS CoV-2) is one of the deadliest global threats faced by mankind to date. Despite the colossal efforts, the viral pandemic swept across all boundaries. Besides the virulence and susceptible population, the low proofreading capacity and error-prone mechanism of RNA-dependent RNA polymerase (RdRp) have contributed to new variants and reinfections. The World Health Organization has officially categorized these variants as variants of concern or variants of interest. This nomenclature is not merely to suffice the surveillance but also to have effective treatment and vaccine options in place. Coronavirus disease 2019 (COVID-19) variants have the propensity to render the available treatment strategies futile owing to the mutations they acquire. The futility of treatment strategies can be attributed either to the ineffectiveness or the shortage of supply given the skyrocketing increase in the number of cases. Presently, the Omicron variant is the most widespread one and is known to escape the protection, be it immune-derived, vaccination-derived, or hybrid. WHO has recommended modification in vaccine development policies and few companies have introduced Omicron-adapted vaccine jabs. Keeping in view the unending tale of COVID-19 variants and the huge data available on the same, this review focuses on providing insight into the emergence and ongoing dynamics of these new COVID-19 variants.
Collapse
Affiliation(s)
- Parakriti Gupta
- Microbiology, Government Medical College and Hospital, Chandigarh, Chandigarh, IND
| | - Varsha Gupta
- Microbiology, Government Medical College and Hospital, Chandigarh, Chandigarh, IND
| | - Chander Mohan Singh
- Microbiology, Government Medical College and Hospital, Chandigarh, Chandigarh, IND
| | - Lipika Singhal
- Microbiology, Government Medical College and Hospital, Chandigarh, Chandigarh, IND
| |
Collapse
|
33
|
Addetia A, Park YJ, Starr T, Greaney AJ, Sprouse KR, Bowen JE, Tiles SW, Van Voorhis WC, Bloom JD, Corti D, Walls AC, Veesler D. Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Cell Rep 2023; 42:112621. [PMID: 37300832 PMCID: PMC10213294 DOI: 10.1016/j.celrep.2023.112621] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/18/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is eroding antibody responses elicited by prior vaccination and infection. The SARS-CoV-2 receptor-binding domain (RBD) E406W mutation abrogates neutralization mediated by the REGEN-COV therapeutic monoclonal antibody (mAb) COVID-19 cocktail and the AZD1061 (COV2-2130) mAb. Here, we show that this mutation remodels the receptor-binding site allosterically, thereby altering the epitopes recognized by these three mAbs and vaccine-elicited neutralizing antibodies while remaining functional. Our results demonstrate the spectacular structural and functional plasticity of the SARS-CoV-2 RBD, which is continuously evolving in emerging SARS-CoV-2 variants, including currently circulating strains that are accumulating mutations in the antigenic sites remodeled by the E406W substitution.
Collapse
Affiliation(s)
- Amin Addetia
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA; Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Tyler Starr
- Howard Hughes Medical Institute, Seattle, WA 98195, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Sasha W Tiles
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Wesley C Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jesse D Bloom
- Howard Hughes Medical Institute, Seattle, WA 98195, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
| |
Collapse
|
34
|
Arabi M, Al-Najjar Y, Sharma O, Kamal I, Javed A, Gohil HS, Paul P, Al-Khalifa AM, Laws S, Zakaria D. Role of previous infection with SARS-CoV-2 in protecting against omicron reinfections and severe complications of COVID-19 compared to pre-omicron variants: a systematic review. BMC Infect Dis 2023; 23:432. [PMID: 37365490 DOI: 10.1186/s12879-023-08328-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/13/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 virus elicited a major public concern worldwide since December 2019 due to the high number of infections and deaths caused by COVID-19. The Omicron variant was detected in October 2021 which evolved from the wild-type SARS-CoV-2 and was found to possess many mutations. Omicron exhibited high transmissibility and immune evasion as well as reduced severity when compared to the earlier variants. Although vaccinated individuals were largely protected against infections in previous waves, the high prevalence of both reinfections and breakthrough infections with Omicron was observed. The aim of this review is to understand the effectiveness of previous infection on subsequent reinfection, given its significance in driving public health policy, including vaccination prioritization and lockdown requirements. METHODS A comprehensive literature search was conducted using several databases to target studies reporting data related to the effectiveness of the previous infection with SARS-CoV-2 in protecting against the Omicron variant. Screening of the studies, quality assessment and data extraction were conducted by two reviewers for each study. RESULTS Only 27 studies met our inclusion criteria. It was observed that previous infection was less effective in preventing reinfections with the Omicron variant compared to the Delta variant irrespective of vaccination status. Furthermore, being fully vaccinated with a booster dose provided additional protection from the Omicron variant. Additionally, most infections caused by Omicron were asymptomatic or mild and rarely resulted in hospitalizations or death in comparison to the Delta wave. CONCLUSION A majority of the studies reached a consensus that although previous infection provides some degree of immunity against Omicron reinfection, it is much lower in comparison to Delta. Full vaccination with two doses was more protective against Delta than Omicron. Receiving a booster dose provided additional protection against Omicron. It is therefore clear that neither vaccination nor previous infection alone provide optimal protection; hybrid immunity has shown the best results in terms of protecting against either Omicron or Delta variants. However, additional research is needed to quantify how long immunity from vaccination versus previous infection lasts and whether individuals will benefit from variant-specific vaccinations to enhance protection from infection.
Collapse
Affiliation(s)
- Maryam Arabi
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Yousef Al-Najjar
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Omna Sharma
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Ibtihal Kamal
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Aimen Javed
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Harsh S Gohil
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Pradipta Paul
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Aljazi M Al-Khalifa
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Sa'ad Laws
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar
| | - Dalia Zakaria
- Weill Cornell Medicine Qatar, Qatar Foundation, Education City, Al Luqta St. Ar-Rayyan, P.O. Box 24144, Doha, Qatar.
| |
Collapse
|
35
|
Senthilazhagan K, Sakthimani S, Kallanja D, Venkataraman S. SARS-CoV-2: analysis of the effects of mutations in non-structural proteins. Arch Virol 2023; 168:186. [PMID: 37344726 DOI: 10.1007/s00705-023-05818-2] [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: 03/06/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023]
Abstract
A worldwide pandemic that started in China in late 2019 was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a single-stranded RNA virus belonging to the family Coronaviridae. Due to its structural variability and mutability, this virus continues to evolve and pose a major health threat around the world. Its characteristics, such as transmissibility, antigenicity, and resistance to drugs and vaccines, are continually altered through mutations. Examining mutational hotspots and their structural repercussions can thus aid in the development of more-effective vaccinations and treatment plans. In this study, we used full genome sequences of SARS-CoV-2 variants to predict structural changes in viral proteins. These sequences were obtained from the Global Initiative on Sharing Avian Influenza Data (GISAID), and a set of significant mutations were identified in each of the non-structural proteins (NSP1-16) and structural proteins, including the envelope, nucleocapsid, membrane, and spike proteins. The mutations were characterized as stabilizing or destabilizing based on their effect on protein dynamics and stability, and their impact on structure and function was evaluated. Among all of the proteins, NSP6 stands out as especially variable. The results of this study augment our understanding of how mutational events influence virus pathogenicity and evolution.
Collapse
Affiliation(s)
- Kavya Senthilazhagan
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Seshagiri Sakthimani
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Deepthi Kallanja
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India
| | - Sangita Venkataraman
- Department of Biotechnology, Anna University, 600025, Guindy, Chennai, Tamil Nādu, India.
| |
Collapse
|
36
|
Soriano JB, Peláez A, Busquets X, Rodrigo-García M, Pérez-Urría EÁ, Alonso T, Girón R, Valenzuela C, Marcos C, García-Castillo E, Ancochea J. ABO blood group as a determinant of COVID-19 and Long COVID: An observational, longitudinal, large study. PLoS One 2023; 18:e0286769. [PMID: 37267401 DOI: 10.1371/journal.pone.0286769] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/23/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND An association of ABO blood group and COVID-19 remains controversial. METHODS Following STROBE guidance for observational research, we explored the distribution of ABO blood group in patients hospitalized for acute COVID-19 and in those with Long COVID. Contingency tables were made and risk factors were explored using crude and adjusted Mantle-Haentzel odds ratios (OR and 95% CI). RESULTS Up to September 2022, there were a total of 5,832 acute COVID-19 hospitalizations in our hospital, corresponding to 5,503 individual patients, of whom blood group determination was available for 1,513 (27.5%). Their distribution by ABO was: 653 (43.2%) group 0, 690 (45.6%) A, 113 (7.5%) B, and 57 (3.8%) AB, which corresponds to the expected frequencies in the general population. In parallel, of 676 patients with Long COVID, blood group determination was available for 135 (20.0%). Their distribution was: 60 (44.4%) from group 0, 61 (45.2%) A, 9 (6.7%) B, and 5 (3.7%) AB. The distribution of the ABO system of Long COVID patients did not show significant differences with respect to that of the total group (p ≥ 0.843). In a multivariate analysis adjusting for age, sex, ethnicity, and severity of acute COVID-19 infection, subgroups A, AB, and B were not significantly associated with developing Long COVID with an OR of 1.015 [0.669-1.541], 1.327 [0.490-3.594] and 0.965 [0.453-2.058], respectively. The effect of the Rh+ factor was also not significant 1,423 [0.772-2,622] regarding Long COVID. CONCLUSIONS No association of any ABO blood subgroup with COVID-19 or developing Long COVID was identified.
Collapse
Affiliation(s)
- Joan B Soriano
- Servicio de Neumología, Hospital Universitario de la Princesa, Madrid, Spain
- Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Adrián Peláez
- Servicio de Neumología, Hospital Universitario de la Princesa, Madrid, Spain
- Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Xavier Busquets
- Laboratory of Molecular Cell Biomedicine, University of the Balearic Islands, Palma, Spain
| | | | - Elena Ávalos Pérez-Urría
- Servicio de Neumología, Hospital Universitario de la Princesa, Madrid, Spain
- Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Tamara Alonso
- Servicio de Neumología, Hospital Universitario de la Princesa, Madrid, Spain
- Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Rosa Girón
- Servicio de Neumología, Hospital Universitario de la Princesa, Madrid, Spain
- Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Claudia Valenzuela
- Servicio de Neumología, Hospital Universitario de la Princesa, Madrid, Spain
- Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Celeste Marcos
- Servicio de Neumología, Hospital Universitario de la Princesa, Madrid, Spain
- Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Elena García-Castillo
- Servicio de Neumología, Hospital Universitario de la Princesa, Madrid, Spain
- Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Julio Ancochea
- Servicio de Neumología, Hospital Universitario de la Princesa, Madrid, Spain
- Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
37
|
Pearson J, Wessler T, Chen A, Boucher RC, Freeman R, Lai SK, Pickles R, Forest MG. Modeling identifies variability in SARS-CoV-2 uptake and eclipse phase by infected cells as principal drivers of extreme variability in nasal viral load in the 48 h post infection. J Theor Biol 2023; 565:111470. [PMID: 36965846 PMCID: PMC10033495 DOI: 10.1016/j.jtbi.2023.111470] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/25/2023]
Abstract
The SARS-CoV-2 coronavirus continues to evolve with scores of mutations of the spike, membrane, envelope, and nucleocapsid structural proteins that impact pathogenesis. Infection data from nasal swabs, nasal PCR assays, upper respiratory samples, ex vivo cell cultures and nasal epithelial organoids reveal extreme variabilities in SARS-CoV-2 RNA titers within and between the variants. Some variabilities are naturally prone to clinical testing protocols and experimental controls. Here we focus on nasal viral load sensitivity arising from the timing of sample collection relative to onset of infection and from heterogeneity in the kinetics of cellular infection, uptake, replication, and shedding of viral RNA copies. The sources of between-variant variability are likely due to SARS-CoV-2 structural protein mutations, whereas within-variant population variability is likely due to heterogeneity in cellular response to that particular variant. With the physiologically faithful, agent-based mechanistic model of inhaled exposure and infection from (Chen et al., 2022), we perform statistical sensitivity analyses of the progression of nasal viral titers in the first 0-48 h post infection, focusing on three kinetic mechanisms. Model simulations reveal shorter latency times of infected cells (including cellular uptake, viral RNA replication, until the onset of viral RNA shedding) exponentially accelerate nasal viral load. Further, the rate of infectious RNA copies shed per day has a proportional influence on nasal viral load. Finally, there is a very weak, negative correlation of viral load with the probability of infection per virus-cell encounter, the model proxy for spike-receptor binding affinity.
Collapse
Affiliation(s)
- Jason Pearson
- Department of Mathematics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy Wessler
- Department of Mathematics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alex Chen
- Department of Mathematics, California State University-Dominguez Hills, Carson, CA 90747, USA
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samuel K Lai
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; UNC/NCSU Joint Department of Biomedical Engineering, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA and North Carolina State University, Raleigh, NC 27606, USA; Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Raymond Pickles
- Marsico Lung Institute, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA
| | - M Gregory Forest
- Department of Mathematics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; Department of Applied Physical Sciences, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA; UNC/NCSU Joint Department of Biomedical Engineering, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA and North Carolina State University, Raleigh, NC 27606, USA.
| |
Collapse
|
38
|
Sipala F, Cavallaro G, Forte G, Satriano C, Giuffrida A, Fraix A, Spadaro A, Petralia S, Bonaccorso C, Fortuna CG, Ronsisvalle S. Different In Silico Approaches Using Heterocyclic Derivatives against the Binding between Different Lineages of SARS-CoV-2 and ACE2. Molecules 2023; 28:molecules28093908. [PMID: 37175318 PMCID: PMC10180195 DOI: 10.3390/molecules28093908] [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: 03/22/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Over the last few years, the study of the SARS-CoV-2 spike protein and its mutations has become essential in understanding how it interacts with human host receptors. Since the crystallized structure of the spike protein bound to the angiotensin-converting enzyme 2 (ACE2) receptor was released (PDB code 6M0J), in silico studies have been performed to understand the interactions between these two proteins. Specifically, in this study, heterocyclic compounds with different chemical characteristics were examined to highlight the possibility of interaction with the spike protein and the disruption of the interaction between ACE2 and the spike protein. Our results showed that these compounds interacted with the spike protein and interposed in the interaction zone with ACE2. Although further studies are needed, this work points to these heterocyclic push-pull compounds as possible agents capable of interacting with the spike protein, with the potential for the inhibition of spike protein-ACE2 binding.
Collapse
Affiliation(s)
- Federica Sipala
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Gianfranco Cavallaro
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Giuseppe Forte
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Cristina Satriano
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Alessandro Giuffrida
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Aurore Fraix
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Angelo Spadaro
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Salvatore Petralia
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Carmela Bonaccorso
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Cosimo Gianluca Fortuna
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Simone Ronsisvalle
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| |
Collapse
|
39
|
Modeling the spread dynamics of multiple-variant coronavirus disease under public health interventions: A general framework. Inf Sci (N Y) 2023; 628:469-487. [PMID: 36777698 PMCID: PMC9901228 DOI: 10.1016/j.ins.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/11/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023]
Abstract
The COVID-19 pandemic was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is a single-stranded positive-stranded RNA virus with a high multi-directional mutation rate. Many new variants even have an immune-evading property, which means that some individuals with antibodies against one variant can be reinfected by other variants. As a result, the realistic is still suffering from new waves of COVID-19 by its new variants. How to control the transmission or even eradicate the COVID-19 pandemic remains a critical issue for the whole world. This work presents an epidemiological framework for mimicking the multi-directional mutation process of SARS-CoV-2 and the epidemic spread of COVID-19 under realistic scenarios considering multiple variants. The proposed framework is used to evaluate single and combined public health interventions, which include non-pharmaceutical interventions, pharmaceutical interventions, and vaccine interventions under the existence of multi-directional mutations of SARS-CoV-2. The results suggest that several combined intervention strategies give optimal results and are feasible, requiring only moderate levels of individual interventions. Furthermore, the results indicate that even if the mutation rate of SARS-CoV-2 decreased 100 times, the pandemic would still not be eradicated without appropriate public health interventions.
Collapse
|
40
|
Pascall DJ, Vink E, Blacow R, Bulteel N, Campbell A, Campbell R, Clifford S, Davis C, da Silva Filipe A, El Sakka N, Fjodorova L, Forrest R, Goldstein E, Gunson R, Haughney J, Holden MTG, Honour P, Hughes J, James E, Lewis T, Lycett S, MacLean O, McHugh M, Mollett G, Onishi Y, Parcell B, Ray S, Robertson DL, Shabaan S, Shepherd JG, Smollett K, Templeton K, Wastnedge E, Wilkie C, Williams T, Thomson EC. The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis. PLoS One 2023; 18:e0284187. [PMID: 37053201 PMCID: PMC10101505 DOI: 10.1371/journal.pone.0284187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/24/2023] [Indexed: 04/14/2023] Open
Abstract
OBJECTIVES The SARS-CoV-2 Alpha variant was associated with increased transmission relative to other variants present at the time of its emergence and several studies have shown an association between Alpha variant infection and increased hospitalisation and 28-day mortality. However, none have addressed the impact on maximum severity of illness in the general population classified by the level of respiratory support required, or death. We aimed to do this. METHODS In this retrospective multi-centre clinical cohort sub-study of the COG-UK consortium, 1475 samples from Scottish hospitalised and community cases collected between 1st November 2020 and 30th January 2021 were sequenced. We matched sequence data to clinical outcomes as the Alpha variant became dominant in Scotland and modelled the association between Alpha variant infection and severe disease using a 4-point scale of maximum severity by 28 days: 1. no respiratory support, 2. supplemental oxygen, 3. ventilation and 4. death. RESULTS Our cumulative generalised linear mixed model analyses found evidence (cumulative odds ratio: 1.40, 95% CI: 1.02, 1.93) of a positive association between increased clinical severity and lineage (Alpha variant versus pre-Alpha variants). CONCLUSIONS The Alpha variant was associated with more severe clinical disease in the Scottish population than co-circulating lineages.
Collapse
Affiliation(s)
- David J. Pascall
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
- Joint Universities Pandemic and Epidemiological Research (JUNIPER) Consortium, United Kingdom
| | - Elen Vink
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- NHS Lothian, Edinburgh, United Kingdom
| | - Rachel Blacow
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | | | | | | | | | - Chris Davis
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | | | | | | | - Rory Gunson
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - John Haughney
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Matthew T. G. Holden
- Public Health Scotland, Edinburgh, United Kingdom
- School of Medicine, University of St Andrews, St Andrews, Fife, United Kingdom
| | | | - Joseph Hughes
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Edward James
- NHS Borders, Melrose, Scottish Borders, United Kingdom
| | - Tim Lewis
- NHS Lothian, Edinburgh, United Kingdom
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Oscar MacLean
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | - Guy Mollett
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | | | - Ben Parcell
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Surajit Ray
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - David L. Robertson
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | - James G. Shepherd
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Katherine Smollett
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | | | - Craig Wilkie
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Thomas Williams
- NHS Lothian, Edinburgh, United Kingdom
- Royal Hospital for Children and Young People, University of Edinburgh, Edinburgh, United Kingdom
| | - Emma C. Thomson
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | |
Collapse
|
41
|
Payen SH, Gorzalski A, Siao DD, Pandori M, Verma SC, Rossetto CC. Analysis of SARS-CoV-2 variants from patient specimens in Nevada from October 2020 to August 2021. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 111:105434. [PMID: 37059256 PMCID: PMC10098042 DOI: 10.1016/j.meegid.2023.105434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023]
Abstract
In early 2020, the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the human population quickly developed into a global pandemic. SARS-CoV-2 is the etiological agent of coronavirus disease 2019 (COVID-19) which has a broad range of respiratory illnesses. As the virus circulates, it acquires nucleotide changes. These mutations are potentially due to the inherent differences in the selection pressures within the human population compared to the original zoonotic reservoir of SARS-CoV-2 and formerly naïve humans. The acquired mutations will most likely be neutral, but some may have implications for viral transmission, disease severity and resistance to therapies or vaccines. This is a follow-up study from our early report (Hartley et al. J Genet Genomics. 01202021;48(1):40-51) which detected a rare variant (nsp12, RdRp P323F) circulating within Nevada in mid 2020 at high frequency. The primary goals of the current study were to determine the phylogenetic relationship of the SARS-CoV-2 genomes within Nevada and to determine if there are any unusual variants within Nevada compared to the current database of SARS-CoV-2 sequences. Whole genome sequencing and analysis of SARS-CoV-2 from 425 positively identified nasopharyngeal/nasal swab specimens were performed from October 2020 to August 2021 to determine any variants that could result in potential escape from current therapeutics. Our analysis focused on nucleotide mutations that generated amino acid variations in the viral Spike (S) protein, Receptor binding domain (RBD) and the RNA-dependent RNA-polymerase (RdRp) complex. The data indicate that SARS-CoV-2 sequences from Nevada did not contain any unusual variants that had not been previously reported. Additionally, we did not detect the previously identified the RdRp P323F variant in any of the samples. This suggests that the rare variant we detected before was only able to circulate because of the stay-at-home orders and semi-isolation experience during the early months of the pandemic. IMPORTANCE: SARS-COV-2 continues to circulate in the human population. In this study, SARS-CoV-2 positive nasopharyngeal/nasal swab samples were used for whole genome sequencing to determine the phylogenetic relationship of SARS-CoV-2 sequences within Nevada from October 2020 to August 2021. The resulting data is being added to a continually growing database of SARS-CoV-2 sequences that will be important for understanding the transmission and evolution of the virus as it spreads around the globe.
Collapse
Affiliation(s)
- Shannon Harger Payen
- Department of Microbiology & Immunology; School of Medicine, University of Nevada, Reno
| | | | | | - Mark Pandori
- School of Medicine, University of Nevada, Reno; Nevada State Public Health Lab
| | - Subhash C Verma
- Department of Microbiology & Immunology; School of Medicine, University of Nevada, Reno
| | - Cyprian C Rossetto
- Department of Microbiology & Immunology; School of Medicine, University of Nevada, Reno.
| |
Collapse
|
42
|
Borghi M, Gallinaro A, Pirillo MF, Canitano A, Michelini Z, De Angelis ML, Cecchetti S, Tinari A, Falce C, Mariotti S, Capocefalo A, Chiantore MV, Iacobino A, Di Virgilio A, van Gils MJ, Sanders RW, Lo Presti A, Nisini R, Negri D, Cara A. Different configurations of SARS-CoV-2 spike protein delivered by integrase-defective lentiviral vectors induce persistent functional immune responses, characterized by distinct immunogenicity profiles. Front Immunol 2023; 14:1147953. [PMID: 37090707 PMCID: PMC10113491 DOI: 10.3389/fimmu.2023.1147953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/13/2023] [Indexed: 04/08/2023] Open
Abstract
Several COVID-19 vaccine strategies utilizing new formulations for the induction of neutralizing antibodies (nAbs) and T cell immunity are still under evaluation in preclinical and clinical studies. Here we used Simian Immunodeficiency Virus (SIV)-based integrase defective lentiviral vector (IDLV) delivering different conformations of membrane-tethered Spike protein in the mouse immunogenicity model, with the aim of inducing persistent nAbs against multiple SARS-CoV-2 variants of concern (VoC). Spike modifications included prefusion-stabilizing double proline (2P) substitutions, mutations at the furin cleavage site (FCS), D614G mutation and truncation of the cytoplasmic tail (delta21) of ancestral and Beta (B.1.351) Spike, the latter mutation to markedly improve IDLV membrane-tethering. BALB/c mice were injected once with IDLV delivering the different forms of Spike or the recombinant trimeric Spike protein with 2P substitutions and FCS mutations in association with a squalene-based adjuvant. Anti-receptor binding domain (RBD) binding Abs, nAbs and T cell responses were detected up to six months from a single immunization with escalating doses of vaccines in all mice, but with different levels and kinetics. Results indicated that IDLV delivering the Spike protein with all the combined modifications, outperformed the other candidates in terms of T cell immunity and level of both binding Abs and nAbs soon after the single immunization and persistence over time, showing the best capacity to neutralize all formerly circulating VoC Alpha, Beta, Gamma and Delta. Although present, the lowest response was detected against Omicron variants (BA.1, BA.2 and BA.4/5), suggesting that the magnitude of immune evasion may be related to the higher genetic distance of Omicron as indicated by increased number of amino acid substitutions in Spike acquired during virus evolution.
Collapse
Affiliation(s)
- Martina Borghi
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | | | - Andrea Canitano
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Zuleika Michelini
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Laura De Angelis
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Serena Cecchetti
- Confocal Microscopy Unit, Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Antonella Tinari
- Center for Gender Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Chiara Falce
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Sabrina Mariotti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Antonio Capocefalo
- Department of Veterinary Public Health & Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | | | - Angelo Iacobino
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Antonio Di Virgilio
- Center for Animal Research and Welfare, Istituto Superiore di Sanità, Rome, Italy
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | | | - Roberto Nisini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Donatella Negri
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Donatella Negri, ; Andrea Cara,
| | - Andrea Cara
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Donatella Negri, ; Andrea Cara,
| |
Collapse
|
43
|
Ahmadi S, Bazargan M, Elahi R, Esmaeilzadeh A. Immune evasion of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2); molecular approaches. Mol Immunol 2023; 156:10-19. [PMID: 36857806 PMCID: PMC9684099 DOI: 10.1016/j.molimm.2022.11.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 11/04/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
In December 2019, a new betacoronavirus, known as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), caused an outbreak at the Wuhan seafood market in China. The disease was further named coronavirus disease 2019 (COVID-19). In March 2020, the World Health Organization (WHO) announced the disease to be a pandemic, as more cases were reported globally. SARS-CoV-2, like many other viruses, employs diverse strategies to elude the host immune response and/or counter immune responses. The infection outcome mainly depends on interactions between the virus and the host immune system. Inhibiting IFN production, blocking IFN signaling, enhancing IFN resistance, and hijacking the host's translation machinery to expedite the production of viral proteins are among the main immune evasion mechanisms of SARS-CoV-2. SARS-CoV-2 also downregulates the expression of MHC-I on infected cells, which is an additional immune-evasion mechanism of this virus. Moreover, antigenic modifications to the spike (S) protein, such as deletions, insertions, and also substitutions are essential for resistance to SARS-CoV-2 neutralizing antibodies. This review assesses the interaction between SARS-CoV-2 and host immune response and cellular and molecular approaches used by SARS-CoV-2 for immune evasion. Understanding the mechanisms of SARS-CoV-2 immune evasion is essential since it can improve the development of novel antiviral treatment options as well as vaccination methods.
Collapse
Affiliation(s)
- Shahrzad Ahmadi
- Virology Research Center, The National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Allergy and Immunology Subspecialty Lab, Tehran, Iran
| | - Mahsa Bazargan
- Virology Research Center, The National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Allergy and Immunology Subspecialty Lab, Tehran, Iran,Department of Immunology, School of Medicine, Sahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Elahi
- M.D., School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Abdolreza Esmaeilzadeh
- Department of Immunology, Zanjan University of Medical Sciences, Zanjan, Iran; Cancer Gene Therapy Research Center (CGRC), Zanjan University of Medical Sciences, Zanjan, Iran.
| |
Collapse
|
44
|
Zhang H, Jin H, Yan F, Song Y, Dai J, Jiao C, Bai Y, Sun J, Liu D, Wang S, Zhang M, Lu J, Huang J, Huang P, Li Y, Xia X, Wang H. An inactivated recombinant rabies virus chimerically expressed RBD induces humoral and cellular immunity against SARS-CoV-2 and RABV. Virol Sin 2023; 38:244-256. [PMID: 36587795 PMCID: PMC9797420 DOI: 10.1016/j.virs.2022.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022] Open
Abstract
Many studies suggest that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect various animals and transmit among animals, and even to humans, posing a threat to humans and animals. There is an urgent need to develop inexpensive and efficient animal vaccines to prevent and control coronavirus disease 2019 (COVID-19) in animals. Rabies virus (RABV) is another important zoonotic pathogen that infects almost all warm-blooded animals and poses a great public health threat. The present study constructed two recombinant chimeric viruses expressing the S1 and RBD proteins of the SARS-CoV-2 Wuhan01 strain based on a reverse genetic system of the RABV SRV9 strain and evaluated their immunogenicity in mice, cats and dogs. The results showed that both inactivated recombinant viruses induced durable neutralizing antibodies against SARS-CoV-2 and RABV and a strong cellular immune response in mice. Notably, inactivated SRV-nCoV-RBD induced earlier antibody production than SRV-nCoV-S1, which was maintained at high levels for longer periods. Inactivated SRV-nCoV-RBD induced neutralizing antibodies against both SARS-CoV-2 and RABV in cats and dogs, with a relatively broad-spectrum cross-neutralization capability against the SARS-CoV-2 pseudoviruses including Alpha, Beta, Gamma, Delta, and Omicron, showing potential to be used as a safe bivalent vaccine candidate against COVID-19 and rabies in animals.
Collapse
Affiliation(s)
- Haili Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Hongli Jin
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China; Changchun Sino Biotechnology Co., Ltd., Changchun, 130012, China
| | - Feihu Yan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
| | - Yumeng Song
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Jiaxin Dai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Cuicui Jiao
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yujie Bai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Jingxuan Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Di Liu
- Changchun Sino Biotechnology Co., Ltd., Changchun, 130012, China
| | - Shen Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
| | - Mengyao Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Jilong Lu
- Changchun Sino Biotechnology Co., Ltd., Changchun, 130012, China
| | - Jingbo Huang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Pei Huang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yuanyuan Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Xianzhu Xia
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
| | - Hualei Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| |
Collapse
|
45
|
Wang L, Møhlenberg M, Wang P, Zhou H. Immune evasion of neutralizing antibodies by SARS-CoV-2 Omicron. Cytokine Growth Factor Rev 2023; 70:13-25. [PMID: 36948931 PMCID: PMC9985919 DOI: 10.1016/j.cytogfr.2023.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/13/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
Since its emergence at the end of 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the infection of more than 600 million people worldwide and has significant damage to global medical, economic, and political structures. Currently, a highly mutated variant of concern, SARS-CoV-2 Omicron, has evolved into many different subvariants mainly including BA.1, BA.2, BA.3, BA.4/5, and the recently emerging BA.2.75.2, BA.2.76, BA.4.6, BA.4.7, BA.5.9, BF.7, BQ.1, BQ.1.1, XBB, XBB.1, etc. Mutations in the N-terminal domain (NTD) of the spike protein, such as A67V, G142D, and N212I, alter the antigenic structure of Omicron, while mutations in the spike receptor binding domain (RBD), such as R346K, Q493R, and N501Y, increase the affinity for angiotensin-converting enzyme 2 (ACE2). Both types of mutations greatly increase the capacity of Omicron to evade immunity from neutralizing antibodies, produced by natural infection and/or vaccination. In this review, we systematically assess the immune evasion capacity of SARS-CoV-2, with an emphasis on the neutralizing antibodies generated by different vaccination regimes. Understanding the host antibody response and the evasion strategies employed by SARS-CoV-2 variants will improve our capacity to combat newly emerging Omicron variants.
Collapse
Affiliation(s)
- Lidong Wang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | | | - Pengfei Wang
- State Key Laboratory of Genetic Engineering, Shanghai Institute of Infectious Disease and Biosecurity, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hao Zhou
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| |
Collapse
|
46
|
Kumar R, Srivastava Y, Muthuramalingam P, Singh SK, Verma G, Tiwari S, Tandel N, Beura SK, Panigrahi AR, Maji S, Sharma P, Rai PK, Prajapati DK, Shin H, Tyagi RK. Understanding Mutations in Human SARS-CoV-2 Spike Glycoprotein: A Systematic Review & Meta-Analysis. Viruses 2023; 15:856. [PMID: 37112836 PMCID: PMC10142771 DOI: 10.3390/v15040856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Genetic variant(s) of concern (VoC) of SARS-CoV-2 have been emerging worldwide due to mutations in the gene encoding spike glycoprotein. We performed comprehensive analyses of spike protein mutations in the significant variant clade of SARS-CoV-2, using the data available on the Nextstrain server. We selected various mutations, namely, A222V, N439K, N501Y, L452R, Y453F, E484K, K417N, T478K, L981F, L212I, N856K, T547K, G496S, and Y369C for this study. These mutations were chosen based on their global entropic score, emergence, spread, transmission, and their location in the spike receptor binding domain (RBD). The relative abundance of these mutations was mapped with global mutation D614G as a reference. Our analyses suggest the rapid emergence of newer global mutations alongside D614G, as reported during the recent waves of COVID-19 in various parts of the world. These mutations could be instrumentally imperative for the transmission, infectivity, virulence, and host immune system's evasion of SARS-CoV-2. The probable impact of these mutations on vaccine effectiveness, antigenic diversity, antibody interactions, protein stability, RBD flexibility, and accessibility to human cell receptor ACE2 was studied in silico. Overall, the present study can help researchers to design the next generation of vaccines and biotherapeutics to combat COVID-19 infection.
Collapse
Affiliation(s)
- Reetesh Kumar
- Faculty of Agricultural Sciences, Institute of Applied Sciences & Humanities, GLA University, Mathura 281406, India
- Department of Biotherapeutics, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Yogesh Srivastava
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pandiyan Muthuramalingam
- Division of Horticultural Science, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Sunil Kumar Singh
- Department of Zoology, School of Biological Sciences, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Geetika Verma
- Department of Biotherapeutics, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Savitri Tiwari
- Division of Life Sciences, Department of Biosciences, School of Basic and Applied Sciences, Galgotias University, Gautam Buddha Nagar, Greater Noida 201310, India
| | - Nikunj Tandel
- Institute of Science, Nirma University, SG Highway, Gujarat 382481, India
| | - Samir Kumar Beura
- Department of Zoology, School of Biological Sciences, Central University of Punjab, Ghudda, Bathinda 151401, India
| | | | - Somnath Maji
- Department of Radiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Prakriti Sharma
- Biomedical Parasitology and Translational-Immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| | - Pankaj Kumar Rai
- Department of Biotechnology, IIET, Invertis University, Bareilly 243001, India
| | | | - Hyunsuk Shin
- Division of Horticultural Science, Gyeongsang National University, Jinju 52725, Republic of Korea
| | - Rajeev K. Tyagi
- Biomedical Parasitology and Translational-Immunology Lab, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160036, India
| |
Collapse
|
47
|
Bianchini F, Crivelli V, Abernathy ME, Guerra C, Palus M, Muri J, Marcotte H, Piralla A, Pedotti M, De Gasparo R, Simonelli L, Matkovic M, Toscano C, Biggiogero M, Calvaruso V, Svoboda P, Cervantes Rincón T, Fava T, Podešvová L, Shanbhag AA, Celoria A, Sgrignani J, Stefanik M, Hönig V, Pranclova V, Michalcikova T, Prochazka J, Guerrini G, Mehn D, Ciabattini A, Abolhassani H, Jarrossay D, Uguccioni M, Medaglini D, Pan-Hammarström Q, Calzolai L, Fernandez D, Baldanti F, Franzetti-Pellanda A, Garzoni C, Sedlacek R, Ruzek D, Varani L, Cavalli A, Barnes CO, Robbiani DF. Human neutralizing antibodies to cold linear epitopes and subdomain 1 of the SARS-CoV-2 spike glycoprotein. Sci Immunol 2023; 8:eade0958. [PMID: 36701425 PMCID: PMC9972897 DOI: 10.1126/sciimmunol.ade0958] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
Emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike glycoprotein that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four genera, including the nine human coronaviruses, through recognition of a conserved motif that includes the S2' site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization, and, similar to fp.006 and hr2.016, protects mice expressing human angiotensin-converting enzyme 2 against infection when present as a bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with Orthocoronavirinae, including SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Filippo Bianchini
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Virginia Crivelli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | | | - Concetta Guerra
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Martin Palus
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
| | - Jonathan Muri
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Harold Marcotte
- Department of Biosciences and Nutrition, Karolinska Institutet; Huddinge, Sweden
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo; Pavia, Italy
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Raoul De Gasparo
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Milos Matkovic
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Chiara Toscano
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Maira Biggiogero
- Clinical Research Unit, Clinica Luganese Moncucco; Lugano, Switzerland
| | | | - Pavel Svoboda
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University; Brno, Czech Republic
- Department of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, University of Veterinary Sciences; Brno, Czech Republic
| | - Tomás Cervantes Rincón
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Tommaso Fava
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Lucie Podešvová
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Akanksha A. Shanbhag
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Andrea Celoria
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Michal Stefanik
- Veterinary Research Institute; Brno, Czech Republic
- Department of Chemistry and Biochemistry, Mendel University in Brno; Brno, Czech Republic
| | - Vaclav Hönig
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
| | - Veronika Pranclova
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia; Ceske Budejovice, Czech Republic
| | - Tereza Michalcikova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences; Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences; Vestec, Czech Republic
| | | | - Dora Mehn
- European Commission, Joint Research Centre (JRC); Ispra, Italy
| | - Annalisa Ciabattini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies; University of Siena, Siena, Italy
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institutet; Huddinge, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences; Tehran, Iran
| | - David Jarrossay
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies; University of Siena, Siena, Italy
| | | | - Luigi Calzolai
- European Commission, Joint Research Centre (JRC); Ispra, Italy
| | - Daniel Fernandez
- Sarafan ChEM-H Macromolecular Structure Knowledge Center, Stanford University; Stanford, USA
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo; Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia; Pavia, Italy
| | | | - Christian Garzoni
- Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco; Lugano, Switzerland
| | - Radislav Sedlacek
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences; Vestec, Czech Republic
| | - Daniel Ruzek
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University; Brno, Czech Republic
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
- Swiss Institute of Bioinformatics; Lausanne, Switzerland
| | - Christopher O. Barnes
- Department of Biology, Stanford University; Stanford, USA
- Chan Zuckerberg Biohub; San Francisco, USA
| | - Davide F. Robbiani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| |
Collapse
|
48
|
Zhang I, Rufa DA, Pulido I, Henry MM, Rosen LE, Hauser K, Singh S, Chodera JD. Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.530278. [PMID: 36945557 PMCID: PMC10028896 DOI: 10.1101/2023.03.07.530278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Relative alchemical binding free energy calculations are routinely used in drug discovery projects to optimize the affinity of small molecules for their drug targets. Alchemical methods can also be used to estimate the impact of amino acid mutations on protein:protein binding affinities, but these calculations can involve sampling challenges due to the complex networks of protein and water interactions frequently present in protein:protein interfaces. We investigate these challenges by extending a GPU-accelerated opensource relative free energy calculation package (Perses) to predict the impact of amino acid mutations on protein:protein binding. Using the well-characterized model system barnase:barstar, we describe analyses for identifying and characterizing sampling problems in protein:protein relative free energy calculations. We find that mutations with sampling problems often involve charge-changes, and inadequate sampling can be attributed to slow degrees of freedom that are mutation-specific. We also explore the accuracy and efficiency of current state-of-the-art approaches-alchemical replica exchange and alchemical replica exchange with solute tempering-for overcoming relevant sampling problems. By employing sufficiently long simulations, we achieve accurate predictions (RMSE 1.61, 95% CI: [1.12, 2.11] kcal/mol), with 86% of estimates within 1 kcal/mol of the experimentally-determined relative binding free energies and 100% of predictions correctly classifying the sign of the changes in binding free energies. Ultimately, we provide a model workflow for applying protein mutation free energy calculations to protein:protein complexes, and importantly, catalog the sampling challenges associated with these types of alchemical transformations. Our free open-source package (Perses) is based on OpenMM and available at https://github.com/choderalab/perses .
Collapse
|
49
|
Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes J, Peacock SJ, Barclay WS, de Silva TI, Towers GJ, Robertson DL. SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat Rev Microbiol 2023; 21:162-177. [PMID: 36653446 PMCID: PMC9847462 DOI: 10.1038/s41579-022-00841-7] [Citation(s) in RCA: 180] [Impact Index Per Article: 180.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 01/19/2023]
Abstract
In late 2020, after circulating for almost a year in the human population, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited a major step change in its adaptation to humans. These highly mutated forms of SARS-CoV-2 had enhanced rates of transmission relative to previous variants and were termed 'variants of concern' (VOCs). Designated Alpha, Beta, Gamma, Delta and Omicron, the VOCs emerged independently from one another, and in turn each rapidly became dominant, regionally or globally, outcompeting previous variants. The success of each VOC relative to the previously dominant variant was enabled by altered intrinsic functional properties of the virus and, to various degrees, changes to virus antigenicity conferring the ability to evade a primed immune response. The increased virus fitness associated with VOCs is the result of a complex interplay of virus biology in the context of changing human immunity due to both vaccination and prior infection. In this Review, we summarize the literature on the relative transmissibility and antigenicity of SARS-CoV-2 variants, the role of mutations at the furin spike cleavage site and of non-spike proteins, the potential importance of recombination to virus success, and SARS-CoV-2 evolution in the context of T cells, innate immunity and population immunity. SARS-CoV-2 shows a complicated relationship among virus antigenicity, transmission and virulence, which has unpredictable implications for the future trajectory and disease burden of COVID-19.
Collapse
Affiliation(s)
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Wendy S Barclay
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
| |
Collapse
|
50
|
Minimal Antigenic Evolution after a Decade of Norovirus GII.4 Sydney_2012 Circulation in Humans. J Virol 2023; 97:e0171622. [PMID: 36688654 PMCID: PMC9973034 DOI: 10.1128/jvi.01716-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Norovirus is a major human pathogen that can cause severe gastroenteritis in vulnerable populations. The extensive viral diversity presented by human noroviruses constitutes a major roadblock for the development of effective vaccines. In addition to the large number of genotypes, antigenically distinct variants of GII.4 noroviruses have chronologically emerged over the last 3 decades. The last variant to emerge, Sydney_2012, has been circulating at high incidence worldwide for over a decade. We analyzed 1449 capsid sequences from GII.4 Sydney_2012 viruses to determine genetic changes indicative of antigenic diversification. Phylogenetic analyses show that Sydney_2012 viruses scattered within the tree topology with no single cluster dominating during a given year or geographical location. Fourteen residues presented high variability, 7 of which mapped to 4 antigenic sites. Notably, ~52% of viruses presented mutations at 2 or more antigenic sites. Mutational patterns showed that residues 297 and 372, which map to antigenic site A, changed over time. Virus-like particles (VLPs) developed from wild-type Sydney_2012 viruses and engineered to display all mutations detected at antigenic sites were tested against polyclonal sera and monoclonal antibodies raised against Sydney_2012 and Farmington_Hills_2002 VLPs. Minimal changes in reactivity were detected with polyclonal sera and only 4 MAbs lost binding, with all mapping to antigenic site A. Notably, reversion of residues from Sydney_2012 reconstituted epitopes from ancestral GII.4 variants. Overall, this study demonstrates that, despite circulating for over a decade, Sydney_2012 viruses present minimal antigenic diversification and provides novel insights on the diversification of GII.4 noroviruses that could inform vaccine design. IMPORTANCE GII.4 noroviruses are the major cause of acute gastroenteritis in all age groups. This predominance has been attributed to the continued emergence of phylogenetically discrete variants that escape immune responses to previous infections. The last GII.4 variant to emerge, Sydney_2012, has been circulating at high incidence for over a decade, raising the question of whether this variant is undergoing antigenic diversification without presenting a major distinction at the phylogenetic level. Sequence analyses that include >1400 capsid sequences from GII.4 Sydney_2012 showed changes in 4 out of the 6 major antigenic sites. Notably, while changes were detected in one of the most immunodominant sites over time, these resulted in minimal changes in the antigenic profile of these viruses. This study provides new insights on the mechanism governing the antigenic diversification of GII.4 norovirus that could help in the development of cross-protective vaccines to human noroviruses.
Collapse
|