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Sharifi E, Yousefiasl S, Trovato M, Sartorius R, Esmaeili Y, Goodarzi H, Ghomi M, Bigham A, Moghaddam FD, Heidarifard M, Pourmotabed S, Nazarzadeh Zare E, Paiva-Santos AC, Rabiee N, Wang X, Tay FR. Nanostructures for prevention, diagnosis, and treatment of viral respiratory infections: from influenza virus to SARS-CoV-2 variants. J Nanobiotechnology 2023; 21:199. [PMID: 37344894 PMCID: PMC10283343 DOI: 10.1186/s12951-023-01938-8] [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: 12/21/2022] [Accepted: 05/24/2023] [Indexed: 06/23/2023] Open
Abstract
Viruses are a major cause of mortality and socio-economic downfall despite the plethora of biopharmaceuticals designed for their eradication. Conventional antiviral therapies are often ineffective. Live-attenuated vaccines can pose a safety risk due to the possibility of pathogen reversion, whereas inactivated viral vaccines and subunit vaccines do not generate robust and sustained immune responses. Recent studies have demonstrated the potential of strategies that combine nanotechnology concepts with the diagnosis, prevention, and treatment of viral infectious diseases. The present review provides a comprehensive introduction to the different strains of viruses involved in respiratory diseases and presents an overview of recent advances in the diagnosis and treatment of viral infections based on nanotechnology concepts and applications. Discussions in diagnostic/therapeutic nanotechnology-based approaches will be focused on H1N1 influenza, respiratory syncytial virus, human parainfluenza virus type 3 infections, as well as COVID-19 infections caused by the SARS-CoV-2 virus Delta variant and new emerging Omicron variant.
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Affiliation(s)
- Esmaeel Sharifi
- Department of Tissue Engineering and Biomaterials, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, Hamadan, 6517838736, Iran.
| | - Satar Yousefiasl
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Maria Trovato
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), 80131, Naples, Italy
| | - Rossella Sartorius
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), 80131, Naples, Italy
| | - Yasaman Esmaeili
- School of Advanced Technologies in Medicine, Biosensor Research Center, Isfahan University of Medical Sciences, Isfahan, 8174673461, Iran
| | - Hamid Goodarzi
- Centre de recherche, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
- Départment d'Ophtalmologie, Université de Montréal, Montreal, QC, Canada
| | - Matineh Ghomi
- School of Chemistry, Damghan University, Damghan, 36716-45667, Iran
| | - Ashkan Bigham
- Department of Tissue Engineering and Biomaterials, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, Hamadan, 6517838736, Iran
| | - Farnaz Dabbagh Moghaddam
- Institute for Photonics and Nanotechnologies, National Research Council, Via Fosso del Cavaliere, 100, 00133, Rome, Italy
| | - Maryam Heidarifard
- Centre de recherche, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
- Départment d'Ophtalmologie, Université de Montréal, Montreal, QC, Canada
| | - Samiramis Pourmotabed
- Department of Emergency Medicine, School of Medicine, Hamadan University of Medical Sciences, Hamadan, 6517838736, Iran
| | | | - Ana Cláudia Paiva-Santos
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548, Coimbra, Portugal
- Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548, Coimbra, Portugal
| | - Navid Rabiee
- School of Engineering, Macquarie University, Sydney, NSW, 2109, Australia
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Xiangdong Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Franklin R Tay
- The Graduate School, Augusta University, Augusta, GA, 30912, USA.
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2
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Wang SC, Zhang F, Zhu H, Yang H, Liu Y, Wang P, Parpura V, Wang YF. Potential of Endogenous Oxytocin in Endocrine Treatment and Prevention of COVID-19. Front Endocrinol (Lausanne) 2022; 13:799521. [PMID: 35592777 PMCID: PMC9110836 DOI: 10.3389/fendo.2022.799521] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/14/2022] [Indexed: 01/09/2023] Open
Abstract
Coronavirus disease 2019 or COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a significant threat to the health of human beings. While wearing mask, maintaining social distance and performing self-quarantine can reduce virus spreading passively, vaccination actively enhances immune defense against COVID-19. However, mutations of SARS-CoV-2 and presence of asymptomatic carriers frustrate the effort of completely conquering COVID-19. A strategy that can reduce the susceptibility and thus prevent COVID-19 while blocking viral invasion and pathogenesis independent of viral antigen stability is highly desirable. In the pathogenesis of COVID-19, endocrine disorders have been implicated. Correspondingly, many hormones have been identified to possess therapeutic potential of treating COVID-19, such as estrogen, melatonin, corticosteroids, thyroid hormone and oxytocin. Among them, oxytocin has the potential of both treatment and prevention of COVID-19. This is based on oxytocin promotion of immune-metabolic homeostasis, suppression of inflammation and pre-existing comorbidities, acceleration of damage repair, and reduction of individuals' susceptibility to pathogen infection. Oxytocin may specifically inactivate SARS-COV-2 spike protein and block viral entry into cells via angiotensin-converting enzyme 2 by suppressing serine protease and increasing interferon levels and number of T-lymphocytes. In addition, oxytocin can promote parasympathetic outflow and the secretion of body fluids that could dilute and even inactivate SARS-CoV-2 on the surface of cornea, oral cavity and gastrointestinal tract. What we need to do now is clinical trials. Such trials should fully balance the advantages and disadvantages of oxytocin application, consider the time- and dose-dependency of oxytocin effects, optimize the dosage form and administration approach, combine oxytocin with inhibitors of SARS-CoV-2 replication, apply specific passive immunization, and timely utilize efficient vaccines. Meanwhile, blocking COVID-19 transmission chain and developing other efficient anti-SARS-CoV-2 drugs are also important. In addition, relative to the complex issues with drug applications over a long term, oxytocin can be mobilized through many physiological stimuli, and thus used as a general prevention measure. In this review, we explore the potential of oxytocin for treatment and prevention of COVID-19 and perhaps other similar pathogens.
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Affiliation(s)
- Stephani C. Wang
- Division of Cardiology, Department of Medicine, University of California-Irvine, Irvine, CA, United States
| | - Fengmin Zhang
- Department of Microbiology, School of Basic Medical Sciences, Harbin Medical University, Harbin, China
| | - Hui Zhu
- Department of Physiology, School of Basic Medical Sciences, Harbin Medical University, Harbin, China
| | - Haipeng Yang
- Neonatal Division of the Department of Pediatrics, Harbin Medical University The Fourth Affiliated Hospital, Harbin, China
| | - Yang Liu
- Department of Physiology, School of Basic Medical Sciences, Harbin Medical University, Harbin, China
| | - Ping Wang
- Department of Genetics, School of Basic Medical Sciences, Harbin Medical University, Harbin, China
| | - Vladimir Parpura
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Yu-Feng Wang
- Department of Physiology, School of Basic Medical Sciences, Harbin Medical University, Harbin, China
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3
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Wang Y, Liu C, Zhang C, Wang Y, Hong Q, Xu S, Li Z, Yang Y, Huang Z, Cong Y. Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Nat Commun 2022; 13:871. [PMID: 35169135 PMCID: PMC8847413 DOI: 10.1038/s41467-022-28528-w] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/28/2022] [Indexed: 12/11/2022] Open
Abstract
The SARS-CoV-2 Delta variant is currently the dominant circulating strain in the world. Uncovering the structural basis of the enhanced transmission and altered immune sensitivity of Delta is particularly important. Here we present cryo-EM structures revealing two conformational states of Delta spike and S/ACE2 complex in four states. Our cryo-EM analysis suggests that RBD destabilizations lead to population shift towards the more RBD-up and S1 destabilized fusion-prone state, beneficial for engagement with ACE2 and shedding of S1. Noteworthy, we find the Delta T478K substitution plays a vital role in stabilizing and reshaping the RBM loop473-490, enhancing interaction with ACE2. Collectively, increased propensity for more RBD-up states and the affinity-enhancing T478K substitution together contribute to increased ACE2 binding, providing structural basis of rapid spread of Delta. Moreover, we identify a previously generated MAb 8D3 as a cross-variant broadly neutralizing antibody and reveal that 8D3 binding induces a large K478 side-chain orientation change, suggesting 8D3 may use an “induced-fit” mechanism to tolerate Delta T478K mutation. We also find that all five RBD-targeting MAbs tested remain effective on Delta, suggesting that Delta well preserves the neutralizing antigenic landscape in RBD. Our findings shed new lights on the pathogenicity and antibody neutralization of Delta. Here the authors reveal conformational dynamics of SARS-CoV-2 Delta spike and its complex with ACE2 receptor or broadly neutralizing Mab 8D3 by cryo-EM, shedding new insights into mechanisms of receptor recognition and antibody neutralization for the Delta variant.
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Affiliation(s)
- Yifan Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Caixuan Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chao Zhang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yanxing Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Qin Hong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shiqi Xu
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Zuyang Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yong Yang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Zhong Huang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
| | - Yao Cong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China. .,University of Chinese Academy of Sciences, Beijing, China.
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4
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Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Nat Commun 2022; 13:742. [PMID: 35136050 PMCID: PMC8826856 DOI: 10.1038/s41467-022-28324-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/19/2022] [Indexed: 12/23/2022] Open
Abstract
The Delta and Kappa variants of SARS-CoV-2 co-emerged in India in late 2020, with the Delta variant underlying the resurgence of COVID-19, even in countries with high vaccination rates. In this study, we assess structural and biochemical aspects of viral fitness for these two variants using cryo-electron microscopy (cryo-EM), ACE2-binding and antibody neutralization analyses. Both variants demonstrate escape of antibodies targeting the N-terminal domain, an important immune hotspot for neutralizing epitopes. Compared to wild-type and Kappa lineages, Delta variant spike proteins show modest increase in ACE2 affinity, likely due to enhanced electrostatic complementarity at the RBD-ACE2 interface, which we characterize by cryo-EM. Unexpectedly, Kappa variant spike trimers form a structural head-to-head dimer-of-trimers assembly, which we demonstrate is a result of the E484Q mutation and with unknown biological implications. The combination of increased antibody escape and enhanced ACE2 binding provides an explanation, in part, for the rapid global dominance of the Delta variant. Saville, Mannar et al. provide a structural basis for enhanced antibody evasion and ACE2 binding by the Delta SARS-CoV-2 spike protein. They further identify a head-to-head dimer-of-trimers cryoEM reconstruction unique to the Kappa variant spike.
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5
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Seeker LA, Williams A. Oligodendroglia heterogeneity in the human central nervous system. Acta Neuropathol 2022; 143:143-157. [PMID: 34860266 PMCID: PMC8742806 DOI: 10.1007/s00401-021-02390-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/30/2021] [Accepted: 11/28/2021] [Indexed: 12/13/2022]
Abstract
It is the centenary of the discovery of oligodendrocytes and we are increasingly aware of their importance in the functioning of the brain in development, adult learning, normal ageing and in disease across the life course, even in those diseases classically thought of as neuronal. This has sparked more interest in oligodendroglia for potential therapeutics for many neurodegenerative/neurodevelopmental diseases due to their more tractable nature as a renewable cell in the central nervous system. However, oligodendroglia are not all the same. Even from the first description, differences in morphology were described between the cells. With advancing techniques to describe these differences in human tissue, the complexity of oligodendroglia is being discovered, indicating apparent functional differences which may be of critical importance in determining vulnerability and response to disease, and targeting of potential therapeutics. It is timely to review the progress we have made in discovering and understanding oligodendroglial heterogeneity in health and neuropathology.
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Affiliation(s)
- Luise A Seeker
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Anna Williams
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK.
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6
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Madewell ZJ, Yang Y, Longini IM, Halloran ME, Dean NE. Household secondary attack rates of SARS-CoV-2 by variant and vaccination status: an updated systematic review and meta-analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.01.09.22268984. [PMID: 35043125 PMCID: PMC8764734 DOI: 10.1101/2022.01.09.22268984] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We previously reported a household secondary attack rate (SAR) for SARS-CoV-2 of 18.9% through June 17, 2021. To examine how emerging variants and increased vaccination have affected transmission rates, we searched PubMed from June 18, 2021, through January 7, 2022. Meta-analyses used generalized linear mixed models to obtain SAR estimates and 95%CI, disaggregated by several covariates. SARs were used to estimate vaccine effectiveness based on the transmission probability for susceptibility ( VE S,p ), infectiousness ( VE I,p ), and total vaccine effectiveness ( VE T,p ). Household SAR for 27 studies with midpoints in 2021 was 35.8% (95%CI, 30.6%-41.3%), compared to 15.7% (95%CI, 13.3%-18.4%) for 62 studies with midpoints through April 2020. Household SARs were 38.0% (95%CI, 36.0%-40.0%), 30.8% (95%CI, 23.5%-39.3%), and 22.5% (95%CI, 18.6%-26.8%) for Alpha, Delta, and Beta, respectively. VE I,p , VE S,p , and VE T,p were 56.6% (95%CI, 28.7%-73.6%), 70.3% (95%CI, 59.3%-78.4%), and 86.8% (95%CI, 76.7%-92.5%) for full vaccination, and 27.5% (95%CI, -6.4%-50.7%), 43.9% (95%CI, 21.8%-59.7%), and 59.9% (95%CI, 34.4%-75.5%) for partial vaccination, respectively. Household contacts exposed to Alpha or Delta are at increased risk of infection compared to the original wild-type strain. Vaccination reduced susceptibility to infection and transmission to others. SUMMARY Household secondary attack rates (SARs) were higher for Alpha and Delta variants than previous estimates. SARs were higher to unvaccinated contacts than to partially or fully vaccinated contacts and were higher from unvaccinated index cases than from fully vaccinated index cases.
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Affiliation(s)
| | - Yang Yang
- Department of Biostatistics, University of Florida, Gainesville, FL
| | - Ira M. Longini
- Department of Biostatistics, University of Florida, Gainesville, FL
| | - M. Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Natalie E. Dean
- Department of Biostatistics, University of Florida, Gainesville, FL
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7
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McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, Ji X, Raghwani J, Jackson B, Colquhoun R, O'Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R, Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, Kraemer MUG. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.12.14.21267606. [PMID: 34981069 PMCID: PMC8722612 DOI: 10.1101/2021.12.14.21267606] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Delta variant of concern of SARS-CoV-2 has spread globally causing large outbreaks and resurgences of COVID-19 cases 1-3 . The emergence of Delta in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions 4,5 . Here we analyse 52,992 Delta genomes from England in combination with 93,649 global genomes to reconstruct the emergence of Delta, and quantify its introduction to and regional dissemination across England, in the context of changing travel and social restrictions. Through analysis of human movement, contact tracing, and virus genomic data, we find that the focus of geographic expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced >1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers from India reduced onward transmission from importations; however the transmission chains that later dominated the Delta wave in England had been already seeded before restrictions were introduced. In England, increasing inter-regional travel drove Delta's nationwide dissemination, with some cities receiving >2,000 observable lineage introductions from other regions. Subsequently, increased levels of local population mixing, not the number of importations, was associated with faster relative growth of Delta. Among US states, we find that regions that previously experienced large waves also had faster Delta growth rates, and a model including interactions between immunity and human behaviour could accurately predict the rise of Delta there. Delta's invasion dynamics depended on fine scale spatial heterogeneity in immunity and contact patterns and our findings will inform optimal spatial interventions to reduce transmission of current and future VOCs such as Omicron.
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Affiliation(s)
- John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- contributed equally as first authors
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- contributed equally as first authors
| | - Sumali Bajaj
- Department of Zoology, University of Oxford, Oxford, UK
- contributed equally as first authors
| | - Rosario Evans Pena
- Department of Zoology, University of Oxford, Oxford, UK
- contributed equally as first authors
| | - Ben C Lambert
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Rhys Inward
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Erik Volz
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | | | - Neo Wu
- Google, Mountain View, CA, USA
| | | | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA, USA
| | | | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- UK Health Security Agency, London, UK
| | | | | | | | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | - Isaac I Bogoch
- Divisions of Internal Medicine & Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, ON, Canada
| | - Kamran Khan
- BlueDot, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, ON, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | | | | | - David M Aanensen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Thomas Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK
- Quadram Institute, Norwich, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Marc A Suchard
- Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
- jointly supervised this work
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- jointly supervised this work
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK
- jointly supervised this work
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8
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Duerr R, Dimartino D, Marier C, Zappile P, Levine S, François F, Iturrate E, Wang G, Dittmann M, Lighter J, Elbel B, Troxel AB, Goldfeld KS, Heguy A. Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.12.07.21267431. [PMID: 34909779 PMCID: PMC8669846 DOI: 10.1101/2021.12.07.21267431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In 2021, Delta has become the predominant SARS-CoV-2 variant worldwide. While vaccines effectively prevent COVID-19 hospitalization and death, vaccine breakthrough infections increasingly occur. The precise role of clinical and genomic determinants in Delta infections is not known, and whether they contribute to increased rates of breakthrough infections compared to unvaccinated controls. Here, we show a steep and near complete replacement of circulating variants with Delta between May and August 2021 in metropolitan New York. We observed an increase of the Delta sublineage AY.25, its spike mutation S112L, and nsp12 mutation F192V in breakthroughs. Delta infections were associated with younger age and lower hospitalization rates than Alpha. Delta breakthroughs increased significantly with time since vaccination, and, after adjusting for confounders, they rose at similar rates as in unvaccinated individuals. Our data indicate a limited impact of vaccine escape in favor of Delta's increased epidemic growth in times of waning vaccine protection.
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Affiliation(s)
- Ralf Duerr
- Department of Microbiology, NYU Grossman School of Medicine
| | - Dacia Dimartino
- Genome Technology Center, Office of Science and Research, NYU Langone Health
| | - Christian Marier
- Genome Technology Center, Office of Science and Research, NYU Langone Health
| | - Paul Zappile
- Genome Technology Center, Office of Science and Research, NYU Langone Health
| | | | | | | | - Guiqing Wang
- Department of Pathology, NYU Grossman School of Medicine
| | - Meike Dittmann
- Department of Microbiology, NYU Grossman School of Medicine
| | - Jennifer Lighter
- Department of Pediatric Infectious Diseases, NYU Grossman School of Medicine
| | - Brian Elbel
- Department of Population Health, NYU Grossman School of Medicine
- NYU Wagner Graduate School of Public Service
| | - Andrea B. Troxel
- Department of Population Health, NYU Grossman School of Medicine
| | | | - Adriana Heguy
- Genome Technology Center, Office of Science and Research, NYU Langone Health
- Department of Pathology, NYU Grossman School of Medicine
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9
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