151
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Baudrier L, Benamozig O, Langley J, Chopra S, Kalashnikova T, Benaoudia S, Singh G, Mahoney DJ, Wright NAM, Billon P. One-pot DTECT enables rapid and efficient capture of genetic signatures for precision genome editing and clinical diagnostics. CELL REPORTS METHODS 2024; 4:100698. [PMID: 38301655 PMCID: PMC10921016 DOI: 10.1016/j.crmeth.2024.100698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/05/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
The detection of genomic sequences and their alterations is crucial for basic research and clinical diagnostics. However, current methodologies are costly and time-consuming and require outsourcing sample preparation, processing, and analysis to genomic companies. Here, we establish One-pot DTECT, a platform that expedites the detection of genetic signatures, only requiring a short incubation of a PCR product in an optimized one-pot mixture. One-pot DTECT enables qualitative, quantitative, and visual detection of biologically relevant variants, such as cancer mutations, and nucleotide changes introduced by prime editing and base editing into cancer cells and human primary T cells. Notably, One-pot DTECT achieves quantification accuracy for targeted genetic signatures comparable with Sanger and next-generation sequencing. Furthermore, its effectiveness as a diagnostic platform is demonstrated by successfully detecting sickle cell variants in blood and saliva samples. Altogether, One-pot DTECT offers an efficient, versatile, adaptable, and cost-effective alternative to traditional methods for detecting genomic signatures.
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Affiliation(s)
- Lou Baudrier
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Orléna Benamozig
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Jethro Langley
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Sanchit Chopra
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
| | - Tatiana Kalashnikova
- Alberta Children's Hospital Research Institute, Calgary, AB, Canada; The University of Calgary, Cumming School of Medicine, Department of Pediatrics, 28 Oki Drive NW, Calgary, AB T3B 6A8, Canada
| | - Sacha Benaoudia
- Arnie Charbonneau Cancer Institute, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, Calgary, AB, Canada
| | - Gurpreet Singh
- Alberta Children's Hospital Research Institute, Calgary, AB, Canada; The University of Calgary, Cumming School of Medicine, Department of Pediatrics, 28 Oki Drive NW, Calgary, AB T3B 6A8, Canada
| | - Douglas J Mahoney
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, Calgary, AB, Canada; Snyder Institute for Chronic Disease, Calgary, AB, Canada; Department of Microbiology, Immunology and Infectious Disease, Calgary, AB, Canada
| | - Nicola A M Wright
- Alberta Children's Hospital Research Institute, Calgary, AB, Canada; The University of Calgary, Cumming School of Medicine, Department of Pediatrics, 28 Oki Drive NW, Calgary, AB T3B 6A8, Canada
| | - Pierre Billon
- The University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Robson DNA Science Centre, Calgary, AB, Canada; Arnie Charbonneau Cancer Institute, Calgary, AB, Canada.
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152
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Standing JF, Buggiotti L, Guerra-Assuncao JA, Woodall M, Ellis S, Agyeman AA, Miller C, Okechukwu M, Kirkpatrick E, Jacobs AI, Williams CA, Roy S, Martin-Bernal LM, Williams R, Smith CM, Sanderson T, Ashford FB, Emmanuel B, Afzal ZM, Shields A, Richter AG, Dorward J, Gbinigie O, Van Hecke O, Lown M, Francis N, Jani B, Richards DB, Rahman NM, Yu LM, Thomas NPB, Hart ND, Evans P, Andersson M, Hayward G, Hood K, Nguyen-Van-Tam JS, Little P, Hobbs FDR, Khoo S, Butler C, Lowe DM, Breuer J. Randomized controlled trial of molnupiravir SARS-CoV-2 viral and antibody response in at-risk adult outpatients. Nat Commun 2024; 15:1652. [PMID: 38396069 PMCID: PMC10891158 DOI: 10.1038/s41467-024-45641-0] [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: 08/04/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Viral clearance, antibody response and the mutagenic effect of molnupiravir has not been elucidated in at-risk populations. Non-hospitalised participants within 5 days of SARS-CoV-2 symptoms randomised to receive molnupiravir (n = 253) or Usual Care (n = 324) were recruited to study viral and antibody dynamics and the effect of molnupiravir on viral whole genome sequence from 1437 viral genomes. Molnupiravir accelerates viral load decline, but virus is detectable by Day 5 in most cases. At Day 14 (9 days post-treatment), molnupiravir is associated with significantly higher viral persistence and significantly lower anti-SARS-CoV-2 spike antibody titres compared to Usual Care. Serial sequencing reveals increased mutagenesis with molnupiravir treatment. Persistence of detectable viral RNA at Day 14 in the molnupiravir group is associated with higher transition mutations following treatment cessation. Viral viability at Day 14 is similar in both groups with post-molnupiravir treated samples cultured up to 9 days post cessation of treatment. The current 5-day molnupiravir course is too short. Longer courses should be tested to reduce the risk of potentially transmissible molnupiravir-mutated variants being generated. Trial registration: ISRCTN30448031.
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Affiliation(s)
- Joseph F Standing
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Great Ormond Street Hospital for Children NHS Trust, London, UK.
| | - Laura Buggiotti
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Jose Afonso Guerra-Assuncao
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Maximillian Woodall
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Samuel Ellis
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Akosua A Agyeman
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Charles Miller
- Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Mercy Okechukwu
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Emily Kirkpatrick
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Amy I Jacobs
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Charlotte A Williams
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sunando Roy
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Luz M Martin-Bernal
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Rachel Williams
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Claire M Smith
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Fiona B Ashford
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Beena Emmanuel
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Zaheer M Afzal
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Adrian Shields
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Alex G Richter
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Jienchi Dorward
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Oghenekome Gbinigie
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Oliver Van Hecke
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Mark Lown
- Primary Care Research Centre, University of Southampton, Southampton, UK
| | - Nick Francis
- Primary Care Research Centre, University of Southampton, Southampton, UK
| | - Bhautesh Jani
- School of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Duncan B Richards
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Najib M Rahman
- Respiratory Trials Unit and Oxford NIHR Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ly-Mee Yu
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | | | - Nigel D Hart
- School of Medicine, Dentistry and Biomedical Sciences. Queen's University Belfast, Belfast, UK
| | - Philip Evans
- APEx (Exeter Collaboration for Academic Primary Care), University of Exeter Medical School, Exeter, UK
- National Institute of Health and Care Research, Clinical Research Network, University of Leeds, Leeds, UK
| | | | - Gail Hayward
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Kerenza Hood
- Centre for Trials Research, Cardiff University, Wales, UK
| | | | - Paul Little
- Primary Care Research Centre, University of Southampton, Southampton, UK
| | - F D Richard Hobbs
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Saye Khoo
- Department of Pharmacology, University of Liverpool and Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Christopher Butler
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - David M Lowe
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, UK
- Institute of Immunity and Transplantation, University College London, London, UK
| | - Judith Breuer
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
- Great Ormond Street Hospital for Children NHS Trust, London, UK
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153
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Gentile D, Chiummiento L, Santarsiere A, Funicello M, Lupattelli P, Rescifina A, Venuti A, Piperno A, Sciortino MT, Pennisi R. Targeting Viral and Cellular Cysteine Proteases for Treatment of New Variants of SARS-CoV-2. Viruses 2024; 16:338. [PMID: 38543704 PMCID: PMC10976049 DOI: 10.3390/v16030338] [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: 12/19/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 04/21/2024] Open
Abstract
The continuous emergence of SARS-CoV-2 variants caused the persistence of the COVID-19 epidemic and challenged the effectiveness of the existing vaccines. The viral proteases are the most attractive targets for developing antiviral drugs. In this scenario, our study explores the use of HIV-1 protease inhibitors against SARS-CoV-2. An in silico screening of a library of HIV-1 proteases identified four anti-HIV compounds able to interact with the 3CLpro of SARS-CoV-2. Thus, in vitro studies were designed to evaluate their potential antiviral effectiveness against SARS-CoV-2. We employed pseudovirus technology to simulate, in a highly safe manner, the adsorption of the alpha (α-SARS-CoV-2) and omicron (ο-SARS-CoV-2) variants of SARS-CoV-2 and study the inhibitory mechanism of the selected compounds for cell-virus interaction. The results reported a mild activity against the viral proteases 3CLpro and PLpro, but efficient inhibitory effects on the internalization of both variants mediated by cathepsin B/L. Our findings provide insights into the feasibility of using drugs exhibiting antiviral effects for other viruses against the viral and host SARS-CoV-2 proteases required for entry.
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Affiliation(s)
- Davide Gentile
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy
| | - Lucia Chiummiento
- Department of Scienze, University of Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Alessandro Santarsiere
- Department of Scienze, University of Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Maria Funicello
- Department of Scienze, University of Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Paolo Lupattelli
- Department of Chimica, Sapienza University of Roma, p. le Aldo Moro 5, 00185 Roma, Italy
| | - Antonio Rescifina
- Department of Drug and Health Sciences, University of Catania, V. le A. Doria, 95125 Catania, Italy
| | - Assunta Venuti
- International Agency for Research on Cancer (IARC), World Health Organization, 69366 LYON CEDEX 07, France
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Maria Teresa Sciortino
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Rosamaria Pennisi
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
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154
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Ali MA, Caetano-Anollés G. AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Spike Protein Variants. BIOLOGY 2024; 13:134. [PMID: 38534404 DOI: 10.3390/biology13030134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/28/2024]
Abstract
The slow experimental acquisition of high-quality atomic structures of the rapidly changing proteins of the COVID-19 virus challenges vaccine and therapeutic drug development efforts. Fortunately, deep learning tools such as AlphaFold2 can quickly generate reliable models of atomic structure at experimental resolution. Current modeling studies have focused solely on definitions of mutant constellations of Variants of Concern (VOCs), leaving out the impact of haplotypes on protein structure. Here, we conduct a thorough comparative structural analysis of S-proteins belonging to major VOCs and corresponding latitude-delimited haplotypes that affect viral seasonal behavior. Our approach identified molecular regions of importance as well as patterns of structural recruitment. The S1 subunit hosted the majority of structural changes, especially those involving the N-terminal domain (NTD) and the receptor-binding domain (RBD). In particular, structural changes in the NTD were much greater than just translations in three-dimensional space, altering the sub-structures to greater extents. We also revealed a notable pattern of structural recruitment with the early VOCs Alpha and Delta behaving antagonistically by suppressing regions of structural change introduced by their corresponding haplotypes, and the current VOC Omicron behaving synergistically by amplifying or collecting structural change. Remarkably, haplotypes altering the galectin-like structure of the NTD were major contributors to seasonal behavior, supporting its putative environmental-sensing role. Our results provide an extensive view of the evolutionary landscape of the S-protein across the COVID-19 pandemic. This view will help predict important regions of structural change in future variants and haplotypes for more efficient vaccine and drug development.
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Affiliation(s)
- Muhammad Asif Ali
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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155
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Malar DS, Verma K, Prasanth MI, Tencomnao T, Brimson JM. Network analysis-guided drug repurposing strategies targeting LPAR receptor in the interplay of COVID, Alzheimer's, and diabetes. Sci Rep 2024; 14:4328. [PMID: 38383841 PMCID: PMC10882047 DOI: 10.1038/s41598-024-55013-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/19/2024] [Indexed: 02/23/2024] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 virus has greatly affected global health. Emerging evidence suggests a complex interplay between Alzheimer's disease (AD), diabetes (DM), and COVID-19. Given COVID-19's involvement in the increased risk of other diseases, there is an urgent need to identify novel targets and drugs to combat these interconnected health challenges. Lysophosphatidic acid receptors (LPARs), belonging to the G protein-coupled receptor family, have been implicated in various pathological conditions, including inflammation. In this regard, the study aimed to investigate the involvement of LPARs (specifically LPAR1, 3, 6) in the tri-directional relationship between AD, DM, and COVID-19 through network analysis, as well as explore the therapeutic potential of selected anti-AD, anti-DM drugs as LPAR, SPIKE antagonists. We used the Coremine Medical database to identify genes related to DM, AD, and COVID-19. Furthermore, STRING analysis was used to identify the interacting partners of LPAR1, LPAR3, and LPAR6. Additionally, a literature search revealed 78 drugs on the market or in clinical studies that were used for treating either AD or DM. We carried out docking analysis of these drugs against the LPAR1, LPAR3, and LPAR6. Furthermore, we modeled the LPAR1, LPAR3, and LPAR6 in a complex with the COVID-19 spike protein and performed a docking study of selected drugs with the LPAR-Spike complex. The analysis revealed 177 common genes implicated in AD, DM, and COVID-19. Protein-protein docking analysis demonstrated that LPAR (1,3 & 6) efficiently binds with the viral SPIKE protein, suggesting them as targets for viral infection. Furthermore, docking analysis of the anti-AD and anti-DM drugs against LPARs, SPIKE protein, and the LPARs-SPIKE complex revealed promising candidates, including lupron, neflamapimod, and nilotinib, stating the importance of drug repurposing in the drug discovery process. These drugs exhibited the ability to bind and inhibit the LPAR receptor activity and the SPIKE protein and interfere with LPAR-SPIKE protein interaction. Through a combined network and targeted-based therapeutic intervention approach, this study has identified several drugs that could be repurposed for treating COVID-19 due to their expected interference with LPAR(1, 3, and 6) and spike protein complexes. In addition, it can also be hypothesized that the co-administration of these identified drugs during COVID-19 infection may not only help mitigate the impact of the virus but also potentially contribute to the prevention or management of post-COVID complications related to AD and DM.
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Affiliation(s)
- Dicson Sheeja Malar
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, Thailand
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kanika Verma
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, Thailand.
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.
- Department of Molecular Epidemiology, ICMR- National Institute of Malaria Research (NIMR), New Delhi, India.
| | - Mani Iyer Prasanth
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, Thailand
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Tewin Tencomnao
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, Thailand
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - James Michael Brimson
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, Thailand.
- Research Unit for Innovation and International Affairs, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.
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156
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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.
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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
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157
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Altmann DM, Boyton RJ. Arming up against Omicron subvariants. Cell Host Microbe 2024; 32:147-148. [PMID: 38359794 DOI: 10.1016/j.chom.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 02/17/2024]
Abstract
The rapid evolution of COVID-19 Omicron variants is driven by evasion of neutralizing antibodies. Breakthrough infections are common, even in highly vaccinated populations, making it vital to understand immune cross-protective repertoires to variants. Two studies in this issue show that the primed T cell repertoire comprises strong cross-recognition of current variants.
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Affiliation(s)
- Daniel M Altmann
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College, London, UK.
| | - Rosemary J Boyton
- Department of Infectious Disease, Faculty of Medicine, Imperial College, London, UK
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158
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Tang J, Xu Q, Zhu C, Xuan K, Li T, Li Q, Pang X, Zha Z, Li J, Qiao L, Xu H, Wu G, Tian Y, Han J, Gao C, Yi J, Qian G, Tian X, Xie L. Immunogenicity of Tetravalent Protein Vaccine SCTV01E-2 against SARS-CoV-2 EG.5 Subvaraint: A Phase 2 Trial. Vaccines (Basel) 2024; 12:175. [PMID: 38400158 PMCID: PMC10893468 DOI: 10.3390/vaccines12020175] [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: 12/12/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
The Omicron EG.5 lineage of SARS-CoV-2 is currently on a trajectory to become the dominant strain. This phase 2 study aims to evaluate the immunogenicity of SCTV01E-2, a tetravalent protein vaccine, with a specific emphasis on its immunogenicity against Omicron EG.5, comparing it with its progenitor vaccine, SCTV01E (NCT05933512). As of 12 September 2023, 429 participants aged ≥18 years were randomized into the groups SCTV01E (N = 215) and SCTV01E-2 (N = 214). Both vaccines showed increases in neutralizing antibody (nAb) against Omicron EG.5, with a 5.7-fold increase and a 9.0-fold increase in the SCTV01E and SCTV01E-2 groups 14 days post-vaccination, respectively. The predetermined statistical endpoints were achieved, showing that the geometric mean titer (GMT) of nAb and the seroresponse rate (SRR) against Omicron EG.5 were significantly higher in the SCTV01E-2 group than in the SCTV01E group. Additionally, SCTV01E and SCTV01E-2 induced a 5.5-fold and a 5.9-fold increase in nAb against XBB.1, respectively. Reactogenicity was generally mild and transient. No vaccine-related serious adverse events (SAEs), adverse events of special interest (AESIs), or deaths were reported. In summary, SCTV01E-2 elicited robust neutralizing responses against Omicron EG.5 and XBB.1 without raising safety concerns, highlighting its potential as a versatile COVID-19 vaccine against SARS-CoV-2 variants.
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Affiliation(s)
- Jihai Tang
- Anhui Provincial Center for Disease Control and Prevention, Public Health Research Institute of Anhui Province, Hefei 230601, China; (J.T.); (Q.X.); (K.X.); (T.L.); (Q.L.); (X.P.); (Z.Z.)
| | - Qinghua Xu
- Anhui Provincial Center for Disease Control and Prevention, Public Health Research Institute of Anhui Province, Hefei 230601, China; (J.T.); (Q.X.); (K.X.); (T.L.); (Q.L.); (X.P.); (Z.Z.)
| | - Chaoyin Zhu
- Funan County Center for Disease Control and Prevention, Fuyang 236399, China; (C.Z.); (L.Q.); (G.W.); (Y.T.)
| | - Kun Xuan
- Anhui Provincial Center for Disease Control and Prevention, Public Health Research Institute of Anhui Province, Hefei 230601, China; (J.T.); (Q.X.); (K.X.); (T.L.); (Q.L.); (X.P.); (Z.Z.)
| | - Tao Li
- Anhui Provincial Center for Disease Control and Prevention, Public Health Research Institute of Anhui Province, Hefei 230601, China; (J.T.); (Q.X.); (K.X.); (T.L.); (Q.L.); (X.P.); (Z.Z.)
| | - Qingru Li
- Anhui Provincial Center for Disease Control and Prevention, Public Health Research Institute of Anhui Province, Hefei 230601, China; (J.T.); (Q.X.); (K.X.); (T.L.); (Q.L.); (X.P.); (Z.Z.)
| | - Xingya Pang
- Anhui Provincial Center for Disease Control and Prevention, Public Health Research Institute of Anhui Province, Hefei 230601, China; (J.T.); (Q.X.); (K.X.); (T.L.); (Q.L.); (X.P.); (Z.Z.)
| | - Zhenqiu Zha
- Anhui Provincial Center for Disease Control and Prevention, Public Health Research Institute of Anhui Province, Hefei 230601, China; (J.T.); (Q.X.); (K.X.); (T.L.); (Q.L.); (X.P.); (Z.Z.)
| | - Jinwei Li
- Fuyang Center for Disease Control and Prevention, Fuyang 236030, China; (J.L.); (H.X.)
| | - Liyang Qiao
- Funan County Center for Disease Control and Prevention, Fuyang 236399, China; (C.Z.); (L.Q.); (G.W.); (Y.T.)
| | - Haiyang Xu
- Fuyang Center for Disease Control and Prevention, Fuyang 236030, China; (J.L.); (H.X.)
| | - Gang Wu
- Funan County Center for Disease Control and Prevention, Fuyang 236399, China; (C.Z.); (L.Q.); (G.W.); (Y.T.)
| | - Yan Tian
- Funan County Center for Disease Control and Prevention, Fuyang 236399, China; (C.Z.); (L.Q.); (G.W.); (Y.T.)
| | - Jun Han
- State Key Laboratory of Infectious, Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China;
| | - Cuige Gao
- Beijing Engineering Research Center of Protein and Antibody, Sinocelltech Ltd., Beijing 100176, China; (C.G.); (J.Y.); (G.Q.); (X.T.)
| | - Jiang Yi
- Beijing Engineering Research Center of Protein and Antibody, Sinocelltech Ltd., Beijing 100176, China; (C.G.); (J.Y.); (G.Q.); (X.T.)
| | - Gui Qian
- Beijing Engineering Research Center of Protein and Antibody, Sinocelltech Ltd., Beijing 100176, China; (C.G.); (J.Y.); (G.Q.); (X.T.)
| | - Xuxin Tian
- Beijing Engineering Research Center of Protein and Antibody, Sinocelltech Ltd., Beijing 100176, China; (C.G.); (J.Y.); (G.Q.); (X.T.)
| | - Liangzhi Xie
- Beijing Engineering Research Center of Protein and Antibody, Sinocelltech Ltd., Beijing 100176, China; (C.G.); (J.Y.); (G.Q.); (X.T.)
- Cell Culture Engineering Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
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159
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Kumar P, Parveen, Raj N, Kumar M, Fakhri KU, Kumar S, Khan AA, Alanazi AM, Solanki R, Harsha, Manzoor N, Kapur MK. Natural products from Streptomyces spp. as potential inhibitors of the major factors (holoRdRp and nsp13) for SARS-CoV-2 replication: an in silico approach. Arch Microbiol 2024; 206:88. [PMID: 38305873 DOI: 10.1007/s00203-023-03820-5] [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: 10/19/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024]
Abstract
The COVID-19 pandemic caused unprecedented damage to humanity, and while vaccines have been developed, they are not fully effective against the SARS-CoV-2 virus. Limited targeted drugs, such as Remdesivir and Paxlovid, are available against the virus. Hence, there is an urgent need to explore and develop new drugs to combat COVID-19. This study focuses on exploring microbial natural products from soil-isolated bacteria Streptomyces sp. strain 196 and RI.24 as a potential source of new targeted drugs against SARS-CoV-2. Molecular docking studies were performed on holoRdRp and nsp13, two key factors responsible for virus replication factor. Our in silico studies, K-252-C aglycone indolocarbazole alkaloid (K252C) and daunorubicin were found to have better binding affinities than the respective control drugs, with K252C exhibiting binding energy of - 9.1 kcal/mol with holoRdRp and - 9.2 kcal/mol with nsp13, and daunorubicin showing binding energy at - 8.1 kcal/mol with holoRdRp and - 9.3 kcal/mol with nsp13. ADMET analysis, MD simulation, and MM/GBSA studies indicated that K252C and daunorubicin have the potential to be developed as targeted drugs against SARS-CoV-2. The study concludes that K252C and daunorubicin are potential lead compounds that might suppress the inhibition of SARS-CoV-2 replication among the tested microbial compounds and could be developed as targeted drugs against COVID-19. In the future, further in vitro studies are required to validate these findings.
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Affiliation(s)
- Prateek Kumar
- Department of Zoology, University of Allahabad, Uttar Pradesh, Prayagraj, 211 002, India.
| | - Parveen
- Medical Mycology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Nafis Raj
- Medical Mycology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Munendra Kumar
- Department of Zoology, Rajiv Gandhi University, Doimukh, 791112, Arunachal Pradesh, India
| | - Khalid Umar Fakhri
- Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Sugandh Kumar
- School of Medicine, University of San Francisco California (UCSF), San Francisco, CA, 95115, USA
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Amer M Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Renu Solanki
- Deen Dayal Upadhyaya College, University of Delhi, New Delhi, 110 078, India
| | - Harsha
- Microbial Technology Lab, Acharya Narendra Dev College, University of Delhi, New Delhi, 110 019, India
| | - Nikhat Manzoor
- Medical Mycology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Monisha Khanna Kapur
- Microbial Technology Lab, Acharya Narendra Dev College, University of Delhi, New Delhi, 110 019, India.
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160
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You C, Jiang S, Ding Y, Ye S, Zou X, Zhang H, Li Z, Chen F, Li Y, Ge X, Guo X. RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages. Virol Sin 2024; 39:156-168. [PMID: 38253258 PMCID: PMC10877444 DOI: 10.1016/j.virs.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for coronavirus disease 2019 (COVID-19), continues to evolve, giving rise to more variants and global reinfections. Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations. In this study, we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples, including human coronaviruses (HCoVs) and SARSr-CoV-2 lineages. Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets, encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages. Through genetic-level species testing, we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2. Subsequently, 75 main and subordinate species-specific barcode segments for SARS-CoV-2, located in ORF1ab, S, E, ORF7a, and N coding sequences, were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores. Post-testing, these segments exhibited high recall rates (nearly 100%), specificity (almost 30% at the nucleotide level), and precision (100%) performance on identification. They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database (http://virusbarcodedatabase.top/). The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis. Moreover, this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.
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Affiliation(s)
- Changqiao You
- College of Biology, Hunan University, Changsha, 410082, China
| | - Shuai Jiang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Yunyun Ding
- College of Biology, Hunan University, Changsha, 410082, China
| | - Shunxing Ye
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Xiaoxiao Zou
- College of Biology, Hunan University, Changsha, 410082, China
| | - Hongming Zhang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Zeqi Li
- College of Biology, Hunan University, Changsha, 410082, China
| | - Fenglin Chen
- College of Biology, Hunan University, Changsha, 410082, China
| | - Yongliang Li
- College of Biology, Hunan University, Changsha, 410082, China.
| | - Xingyi Ge
- College of Biology, Hunan University, Changsha, 410082, China.
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha, 410082, China.
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161
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Melenotte C, Chavarot N, L'Honneur AS, Bodard S, Cheminant M, Flahault A, Nguyen Y, Burgard M, Dannaoui E, Bougnoux ME, Parize P, Rouzaud C, Scemla A, Canouï E, Lafont E, Vimpere D, Zuber J, Charlier C, Suarez F, Anglicheau D, Hermine O, Lanternier F, Mouthon L, Lortholary O. Increased Risk of Invasive Aspergillosis in Immunocompromised Patients With Persistent SARS-CoV-2 Viral Shedding >8 Weeks, Retrospective Case-control Study. Open Forum Infect Dis 2024; 11:ofae012. [PMID: 38390457 PMCID: PMC10883287 DOI: 10.1093/ofid/ofae012] [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: 12/04/2023] [Accepted: 01/07/2024] [Indexed: 02/24/2024] Open
Abstract
Background Immunocompromised patients now represent the population most at risk for severe coronavirus disease 2019. Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral shedding was reported in these patients ranging from several weeks up to 9 months. We conducted a bicentric retrospective case-control study to identify risk and prognostic factors associated with persistent viral shedding in immunocompromised patients. Material and Methods Symptomatic immunocompromised adults with persistent SARS-CoV-2 viral shedding >8 weeks were retrospectively included between 1 March 2020 and 24 April 2022 at 2 university hospitals in Paris, France, and matched with a control group consisting of symptomatic immunocompromised patients without persistent viral shedding. Results Twenty-nine immunocompromised patients with persistent viral shedding were compared with 40 controls. In multivariate analysis, fever and lymphocytopenia (<0.5 G/L) were associated with an increased risk of persistent viral shedding (odds ratio [OR]: 3.3; 95% confidence interval [CI], 1.01-11.09) P = .048 and OR: 4.3; 95% CI, 1.2-14.7; P = .019, respectively). Unvaccinated patients had a 6-fold increased risk of persistent viral shedding (OR, 6.6; 95% CI, 1.7-25.1; P = .006). Patients with persistent viral shedding were at risk of hospitalization (OR: 4.8; 95 CI, 1.5-15.6; P = .008), invasive aspergillosis (OR: 10.17; 95 CI, 1.15-89.8; P = .037) and death (log-rank test <0.01). Conclusions Vaccine coverage was protective against SARS-CoV-2 persistent viral shedding in immunocompromised patients. This new group of immunocompromised patients with SARS-CoV-2 persistent viral shedding is at risk of developing invasive aspergillosis and death and should therefore be systematically screened for this fungal infection for as long as the viral shedding persists.
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Affiliation(s)
- Cléa Melenotte
- Department of Infectious Diseases and Tropical Medicine, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Nathalie Chavarot
- Department of Nephrology and Kidney Transplantation, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
- Paris-Cité University, Paris, France
- Department of Nephrology and Kidney Transplantation, European Hospital Georges Pompidou, Public Assistance of the Hospital of Paris, Paris, France
| | - Anne-Sophie L'Honneur
- Paris-Cité University, Paris, France
- Department of Virology, Cochin University Hospital, Public Assistance of the Hospital of Paris, Paris, France
| | - Sylvain Bodard
- Paris-Cité University, Paris, France
- Department of Imaging, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Morgane Cheminant
- Paris-Cité University, Paris, France
- Department of Hematology, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Adrien Flahault
- Department of Nephrology and Kidney Transplantation, European Hospital Georges Pompidou, Public Assistance of the Hospital of Paris, Paris, France
| | - Yann Nguyen
- Department of Internal Medicine, University Hospital Cochin, Public Assistance of the Hospital of Paris, Paris, France
| | - Marianne Burgard
- Department of Virology, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Eric Dannaoui
- Paris-Cité University, Paris, France
- Department of Mycology and Parasitology, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Marie-Elisabeth Bougnoux
- Paris-Cité University, Paris, France
- Department of Mycology and Parasitology, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Perrine Parize
- Department of Infectious Diseases and Tropical Medicine, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Claire Rouzaud
- Department of Infectious Diseases and Tropical Medicine, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Anne Scemla
- Department of Nephrology and Kidney Transplantation, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Etienne Canouï
- Mobile Team of Infectious Diseases and Tropical Medicine, Cochin University Hospital, Public Assistance of the Hospital of Paris, France
| | - Emmanuel Lafont
- Department of Internal Medicine, European Hospital Georges Pompidou, Public Assistance of the Hospital of Paris, Paris, France
| | - Damien Vimpere
- Department of Intensive Care Unit, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Julien Zuber
- Department of Nephrology and Kidney Transplantation, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
- Paris-Cité University, Paris, France
| | - Caroline Charlier
- Paris-Cité University, Paris, France
- Mobile Team of Infectious Diseases and Tropical Medicine, Cochin University Hospital, Public Assistance of the Hospital of Paris, France
| | - Felipe Suarez
- Paris-Cité University, Paris, France
- Department of Hematology, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Dany Anglicheau
- Department of Nephrology and Kidney Transplantation, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
- Paris-Cité University, Paris, France
| | - Olivier Hermine
- Paris-Cité University, Paris, France
- Department of Hematology, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
| | - Fanny Lanternier
- Department of Infectious Diseases and Tropical Medicine, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
- Paris-Cité University, Paris, France
| | - Luc Mouthon
- Paris-Cité University, Paris, France
- Department of Internal Medicine, University Hospital Cochin, Public Assistance of the Hospital of Paris, Paris, France
| | - Olivier Lortholary
- Department of Infectious Diseases and Tropical Medicine, Hospital Necker-Enfants Malades, Public Assistance of the Hospital of Paris, Paris, France
- Paris-Cité University, Paris, France
- Mycology Department, Institut Pasteur, Université Paris Cité, National Reference Center for Invasives Mycoses and Antifungals, Mycology Translational Research Group, Paris, France
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162
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Huang L, Zhao F, He M, Fang Y, Ma X, Lu S, Li E, Xiao H, Zhu H, Wang X, Tang S, Yu B, Wang J, Zhao D, Wang C, Li H, Gao Y, Peng X, Shen H. An inoculation site-retained mRNA vaccine induces robust immune responses against SARS-CoV-2 variants. J Control Release 2024; 366:479-493. [PMID: 38184234 DOI: 10.1016/j.jconrel.2024.01.002] [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: 07/30/2023] [Revised: 12/20/2023] [Accepted: 01/01/2024] [Indexed: 01/08/2024]
Abstract
mRNA-based vaccines and therapeutic agents hold great promise in prevention and treatment of human diseases, yet high percentage of systemic adverse effect in clinic remains a big safety concern. One major potential cause is a high level of leakage of the locally inoculated mRNA vaccine nanoparticles into circulation. We have screened and optimized a core-shell structured lipopolyplex (LPP) formulation for mRNA with a tissue-retention property. Upon intramuscular inoculation, the mRNA-encapsulated LPP nanoparticles were preferentially taken up by the phagocytic antigen-presentation cells, and potently promoted dendritic cell maturation. We applied the new formulation to prepare a prophylactic vaccine for SARS-CoV-2, and observed potent humoral and cellular immune responses from the vaccine in both murine models and non-human primates. More importantly, the vaccine demonstrated a benign safety profile in non-human primates, with limited side effects after repeated treatment with high dosages of LPP/mRNA. Taken together, the inoculation site-retained vaccine formulation serves as a promising vehicle for mRNA vaccines and therapeutic agents.
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Affiliation(s)
- Lei Huang
- Stemirna Therapeutics, Shanghai 201206, China; Department of Material Science, Fudan University, Shanghai 200433, China
| | - Fanfan Zhao
- Stemirna Therapeutics, Shanghai 201206, China
| | - Muye He
- Stemirna Therapeutics, Shanghai 201206, China
| | - Yi Fang
- Stemirna Therapeutics, Shanghai 201206, China
| | - Xiaoping Ma
- Stemirna Therapeutics, Shanghai 201206, China
| | - Shuaiyao Lu
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming 650118, China
| | - Entao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Hui Xiao
- Stemirna Therapeutics, Shanghai 201206, China
| | - Hanfei Zhu
- Stemirna Therapeutics, Shanghai 201206, China
| | - Xueli Wang
- Stemirna Therapeutics, Shanghai 201206, China
| | - Siyuan Tang
- Stemirna Therapeutics, Shanghai 201206, China
| | - Bo Yu
- Stemirna Therapeutics, Shanghai 201206, China
| | - Jie Wang
- Stemirna Therapeutics, Shanghai 201206, China
| | - Dong Zhao
- Department of Material Science, Fudan University, Shanghai 200433, China
| | - Chao Wang
- Department of Material Science, Fudan University, Shanghai 200433, China
| | - Hangwen Li
- Stemirna Therapeutics, Shanghai 201206, China.
| | - Yuwei Gao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China.
| | - Xiaozhong Peng
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming 650118, China.
| | - Haifa Shen
- Stemirna Therapeutics, Shanghai 201206, China.
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163
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Le Bert N, Samandari T. Silent battles: immune responses in asymptomatic SARS-CoV-2 infection. Cell Mol Immunol 2024; 21:159-170. [PMID: 38221577 PMCID: PMC10805869 DOI: 10.1038/s41423-024-01127-z] [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: 12/17/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/16/2024] Open
Abstract
SARS-CoV-2 infections manifest with a broad spectrum of presentations, ranging from asymptomatic infections to severe pneumonia and fatal outcomes. This review centers on asymptomatic infections, a widely reported phenomenon that has substantially contributed to the rapid spread of the pandemic. In such asymptomatic infections, we focus on the role of innate, humoral, and cellular immunity. Notably, asymptomatic infections are characterized by an early and robust innate immune response, particularly a swift type 1 IFN reaction, alongside a rapid and broad induction of SARS-CoV-2-specific T cells. Often, antibody levels tend to be lower or undetectable after asymptomatic infections, suggesting that the rapid control of viral replication by innate and cellular responses might impede the full triggering of humoral immunity. Even if antibody levels are present in the early convalescent phase, they wane rapidly below serological detection limits, particularly following asymptomatic infection. Consequently, prevalence studies reliant solely on serological assays likely underestimate the extent of community exposure to the virus.
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Affiliation(s)
- Nina Le Bert
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
| | - Taraz Samandari
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
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164
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Hu B, Guo H, Si H, Shi Z. Emergence of SARS and COVID-19 and preparedness for the next emerging disease X. Front Med 2024; 18:1-18. [PMID: 38561562 DOI: 10.1007/s11684-024-1066-6] [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: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 04/04/2024]
Abstract
Severe acute respiratory syndrome (SARS) and Coronavirus disease 2019 (COVID-19) are two human Coronavirus diseases emerging in this century, posing tremendous threats to public health and causing great loss to lives and economy. In this review, we retrospect the studies tracing the molecular evolution of SARS-CoV, and we sort out current research findings about the potential ancestor of SARS-CoV-2. Updated knowledge about SARS-CoV-2-like viruses found in wildlife, the animal susceptibility to SARS-CoV-2, as well as the interspecies transmission risk of SARS-related coronaviruses (SARSr-CoVs) are gathered here. Finally, we discuss the strategies of how to be prepared against future outbreaks of emerging or re-emerging coronaviruses.
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Affiliation(s)
- Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hua Guo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Haorui Si
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhengli Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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165
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Wang X, Lu L, Jiang S. SARS-CoV-2 evolution from the BA.2.86 to JN.1 variants: unexpected consequences. Trends Immunol 2024; 45:81-84. [PMID: 38302341 DOI: 10.1016/j.it.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 02/03/2024]
Abstract
SARS-CoV-2 is continuously evolving. The Omicron subvariant BA.2.86, with >30 mutations in its spike (S) protein compared with its predecessor strain BA.2, was expected to quickly become predominant worldwide, but this has not happened. Instead, its descendant strain, JN.1, with just one additional mutation, has become the predominant SARS-CoV-2 subvariant. Here, we offer a possible explanation for these unexpected consequences.
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Affiliation(s)
- Xinling Wang
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology of MOE/NHC/CAMS, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Lu Lu
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology of MOE/NHC/CAMS, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Shibo Jiang
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology of MOE/NHC/CAMS, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
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166
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Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Cell Mol Immunol 2024; 21:171-183. [PMID: 37985854 PMCID: PMC10805730 DOI: 10.1038/s41423-023-01104-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
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Affiliation(s)
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kata Csiba
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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167
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Al Qurashi YMA, Abdulhakim JA, Alkhalil SS, Alansari M, Almutiri R, Alabbasi R, Fawzy MS. Molecular Epidemiology of Omicron CH.1.1 Lineage: Genomic and Phenotypic Data Perspective. Cureus 2024; 16:e53496. [PMID: 38440013 PMCID: PMC10910519 DOI: 10.7759/cureus.53496] [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] [Accepted: 01/31/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND The Omicron variant (B.1.1.529 lineage) of SARS-CoV-2 represents a substantial global health challenge due to its high transmissibility and potential resistance to immunity from vaccines or previous infections. Among the rapidly evolving Omicron lineages, the BA.2.75 and the emerging CH.1.1 have garnered attention. While BA.2.75 is marked by mutations that may enhance immune evasion, CH.1.1 is distinguished by the S: L452R mutation, linked to increased pathogenicity and transmission. Initially identified in India by the end of 2021, these variants have exhibited global dissemination, signaling an urgent need to track and analyze their progression. METHODS In this study, the genomic and geographical distribution data of CH.1.1 were collected from the Global Initiative on Sharing Avian Influenza Data (GISAID), PANGOLIN, CoV-Spectrum, and NextStrain databases. Due to the unavailability of epidemiological and genomic data of the CH.1.1 lineage, PubMed and ScienceDirect were used as sources of the phenotypic data of the lineage variations. Amino acid variations utilized in the data mining included S: R346T, S: K444T, S: L452R, and S: F486S. RESULTS The current epidemiological data indicate that CH.1.1 is more likely to become one of the dominant spreading lineages in the United Kingdom, New Zealand, Australia, and the United States based on a 32% growth advantage, present CH.1.1 lineage cases number, and the amino acid variation's impact. CONCLUSION A significant increase in the newly detected lineage CH.1.1 is highly anticipated. The rise in the detected sequences number from 13,231 on January 21, 2023, to 23,181 on February 6, 2023, supports the prediction and growth advantage of the lineage detected cases. Increases in viral transmissibility caused by higher affinity to ACE2 receptors and immune evasion are deduced from amino acid variations analyzed in the study.
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Affiliation(s)
| | - Jawaher A Abdulhakim
- Department of Medical Laboratory, College of Applied Medical Sciences, Taibah University, Yanbu, SAU
| | - Samia S Alkhalil
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Alquwayiyah, SAU
| | - Maymuna Alansari
- Department of Medical Laboratory, College of Applied Medical Sciences, Taibah University, Yanbu, SAU
| | - Renad Almutiri
- Department of Medical Laboratory, College of Applied Medical Sciences, Taibah University, Yanbu, SAU
| | - Rageed Alabbasi
- Department of Medical Laboratory, College of Applied Medical Sciences, Taibah University, Yanbu, SAU
| | - Manal S Fawzy
- Department of Biochemistry, Unit of Medical Research and Postgraduate Studies, Faculty of Medicine, Northern Border University, Arar, SAU
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Hasan MM, Saha CK, Hamidullah Mehedi HM, Chakma K, Salauddin A, Hossain MS, Sharmen F, Rafiqul Islam SM, Tanni AA, Yasmin F, Akash A, Hossain ME, Miah M, Biswas SK, Sultana N, Mannan A. Genetic determinants of SARS-CoV-2 and the clinical outcome of COVID-19 in Southern Bangladesh. Immun Inflamm Dis 2024; 12:e1171. [PMID: 38415978 PMCID: PMC10845815 DOI: 10.1002/iid3.1171] [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: 07/10/2023] [Revised: 09/13/2023] [Accepted: 01/21/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic has had a severe impact on population health. The genetic determinants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in southern Bangladesh are not well understood. METHODS This study aimed to determine the genomic variation in SARS-CoV-2 genomes that have evolved over 2 years of the pandemic in southern Bangladesh and their association with disease outcomes and virulence of this virus. We investigated demographic variables, disease outcomes of COVID-19 patients and genomic features of SARS-CoV-2. RESULTS We observed that the disease severity was significantly higher in adults (85.3%) than in children (14.7%), because the expression of angiotensin-converting enzyme-2 (ACE-2) diminishes with ageing that causes differences in innate and adaptive immunity. The clade GK (n = 66) was remarkable between June 2021 and January 2022. Because of the mutation burden, another clade, GRA started a newly separated clustering in December 2021. The burden was significantly higher in GRA (1.5-fold) highlighted in mild symptoms of COVID-19 patients than in other clades (GH, GK, and GR). Mutations were accumulated mainly in S (22.15 mutations per segment) and ORF1ab segments. Missense (67.5%) and synonymous (18.31%) mutations were highly noticed in adult patients with mild cases rather than severe cases, especially in ORF1ab segments. Moreover, we observed many unique mutations in S protein in mild cases compared to severe, and homology modeling revealed that those might cause more folding in the protein's alpha helix and beta sheets. CONCLUSION Our study identifies some risk factors such as age comorbidities (diabetes, hypertension, and renal disease) that are associated with severe COVID-19, providing valuable insight regarding prioritizing vaccination for high-risk individuals and allocating health care and resources. The findings of this work outlined the knowledge and mutational basis of SARS-CoV-2 for the next treatment steps. Further studies are needed to confirm the effects of structural and functional proteins of SARS-CoV-2 in detail for monitoring the emergence of new variants in future.
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Affiliation(s)
- Md. Mahbub Hasan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | | | | | - Kallyan Chakma
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | - Asma Salauddin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
- International Centre for Diarrhoeal Disease ResearchBangladesh (icddr,b)DhakaBangladesh
| | - Md. Shakhawat Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | - Farjana Sharmen
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | - S. M. Rafiqul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | - Afroza Akter Tanni
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | - Farhana Yasmin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | - Al‐Shahriar Akash
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | | | - Mojnu Miah
- International Centre for Diarrhoeal Disease ResearchBangladesh (icddr,b)DhakaBangladesh
| | - Sanjoy Kanti Biswas
- Department of MicrobiologyChattogram Maa‐O‐Shishu HospitalChattogramBangladesh
| | - Nahid Sultana
- Department of MicrobiologyChattogram Maa‐O‐Shishu HospitalChattogramBangladesh
| | - Adnan Mannan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
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169
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Lapuente D, Winkler TH, Tenbusch M. B-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity. Cell Mol Immunol 2024; 21:144-158. [PMID: 37945737 PMCID: PMC10805925 DOI: 10.1038/s41423-023-01095-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 prompted scientific, medical, and biotech communities to investigate infection- and vaccine-induced immune responses in the context of this pathogen. B-cell and antibody responses are at the center of these investigations, as neutralizing antibodies (nAbs) are an important correlate of protection (COP) from infection and the primary target of SARS-CoV-2 vaccine modalities. In addition to absolute levels, nAb longevity, neutralization breadth, immunoglobulin isotype and subtype composition, and presence at mucosal sites have become important topics for scientists and health policy makers. The recent pandemic was and still is a unique setting in which to study de novo and memory B-cell (MBC) and antibody responses in the dynamic interplay of infection- and vaccine-induced immunity. It also provided an opportunity to explore new vaccine platforms, such as mRNA or adenoviral vector vaccines, in unprecedented cohort sizes. Combined with the technological advances of recent years, this situation has provided detailed mechanistic insights into the development of B-cell and antibody responses but also revealed some unexpected findings. In this review, we summarize the key findings of the last 2.5 years regarding infection- and vaccine-induced B-cell immunity, which we believe are of significant value not only in the context of SARS-CoV-2 but also for future vaccination approaches in endemic and pandemic settings.
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Affiliation(s)
- Dennis Lapuente
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
| | - Thomas H Winkler
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany.
| | - Matthias Tenbusch
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany
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170
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Ose NJ, Campitelli P, Modi T, Can Kazan I, Kumar S, Banu Ozkan S. Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557827. [PMID: 37745560 PMCID: PMC10515954 DOI: 10.1101/2023.09.14.557827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 Spike (S) protein. With this approach, we first identified Candidate Adaptive Polymorphisms (CAPs) of the SARS-CoV-2 Spike protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.
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Affiliation(s)
- Nicholas J. Ose
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - I. Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - S. Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
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171
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Hendrix N, Sidky H, Sahner DK. Influence of Prior SARS-CoV-2 Infection on COVID-19 Severity: Evidence from the National COVID Cohort Collaborative. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.08.03.23293612. [PMID: 38343824 PMCID: PMC10854322 DOI: 10.1101/2023.08.03.23293612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Background A large share of SARS-CoV-2 infections now occur among previously infected individuals. In this study, we sought to determine whether prior infection modifies disease severity relative to no prior infection. Methods We used data from first and second COVID-19 episodes in the National COVID Cohort Collaborative, a nationwide collection of de-identified electronic health records. We used nested logistic regressions of monthly cohorts weighted on the inverse probability of prior infection to assess risk of hospitalization, death, and increased severity in the first versus second infection cohorts. Results We included a total of 2,058,274 individuals in the analysis, 147,592 of whom had two recorded infections. The impact of prior infection differed meaningfully between months. Prior infection was largely protective prior to March 2022, with odds ratios (ORs) as low as 0.66 (95% confidence interval: 0.51 to 0.86) in November 2021 for hospitalization. and as low as 0.23 (0.06 to 0.86) in June 2021 for death. However, prior infection was associated with an increased risk of hospitalization and death, mostly after March 2022 when the ORs were as high as 1.87 (1.26 to 2.80) and 2.99 (1.65 to 5.41) in April 2022, respectively. The overall OR for more severe disease was 1.06 (1.03 to 1.10) among previously infected individuals. Conclusion In the pandemic's first two years, previously infected patients generally had less severe disease than people without prior infection. During the Omicron era, however, previously infected patients had the same or worse severity of disease as patients without prior infection.
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Affiliation(s)
- Nathaniel Hendrix
- Center for Professionalism and Value in Health Care, American Board of Family Medicine, 1016 16th St NW Ste 800, Washington, DC 20036
| | - Hythem Sidky
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - David K Sahner
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
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172
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Avila-Herrera A, Kimbrel JA, Manuel Martí J, Thissen J, Saada EA, Weisenberger T, Arrildt KT, Segelke BW, Allen JE, Zemla A, Borucki MK. Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies. PLoS One 2024; 19:e0289198. [PMID: 38271318 PMCID: PMC10810540 DOI: 10.1371/journal.pone.0289198] [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: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Viral populations in natural infections can have a high degree of sequence diversity, which can directly impact immune escape. However, antibody potency is often tested in vitro with a relatively clonal viral populations, such as laboratory virus or pseudotyped virus stocks, which may not accurately represent the genetic diversity of circulating viral genotypes. This can affect the validity of viral phenotype assays, such as antibody neutralization assays. To address this issue, we tested whether recombinant virus carrying SARS-CoV-2 spike (VSV-SARS-CoV-2-S) stocks could be made more genetically diverse by passage, and if a stock passaged under selective pressure was more capable of escaping monoclonal antibody (mAb) neutralization than unpassaged stock or than viral stock passaged without selective pressures. We passaged VSV-SARS-CoV-2-S four times concurrently in three cell lines and then six times with or without polyclonal antiserum selection pressure. All three of the monoclonal antibodies tested neutralized the viral population present in the unpassaged stock. The viral inoculum derived from serial passage without antiserum selection pressure was neutralized by two of the three mAbs. However, the viral inoculum derived from serial passage under antiserum selection pressure escaped neutralization by all three mAbs. Deep sequencing revealed the rapid acquisition of multiple mutations associated with antibody escape in the VSV-SARS-CoV-2-S that had been passaged in the presence of antiserum, including key mutations present in currently circulating Omicron subvariants. These data indicate that viral stock that was generated under polyclonal antiserum selection pressure better reflects the natural environment of the circulating virus and may yield more biologically relevant outcomes in phenotypic assays. Thus, mAb assessment assays that utilize a more genetically diverse, biologically relevant, virus stock may yield data that are relevant for prediction of mAb efficacy and for enhancing biosurveillance.
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Affiliation(s)
- Aram Avila-Herrera
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Jeffrey A. Kimbrel
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Jose Manuel Martí
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - James Thissen
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Edwin A. Saada
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Tracy Weisenberger
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Kathryn T. Arrildt
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Brent W. Segelke
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Jonathan E. Allen
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Adam Zemla
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Monica K. Borucki
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
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173
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Zech F, Jung C, Jacob T, Kirchhoff F. Causes and Consequences of Coronavirus Spike Protein Variability. Viruses 2024; 16:177. [PMID: 38399953 PMCID: PMC10892391 DOI: 10.3390/v16020177] [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: 12/28/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Coronaviruses are a large family of enveloped RNA viruses found in numerous animal species. They are well known for their ability to cross species barriers and have been transmitted from bats or intermediate hosts to humans on several occasions. Four of the seven human coronaviruses (hCoVs) are responsible for approximately 20% of common colds (hCoV-229E, -NL63, -OC43, -HKU1). Two others (SARS-CoV-1 and MERS-CoV) cause severe and frequently lethal respiratory syndromes but have only spread to very limited extents in the human population. In contrast the most recent human hCoV, SARS-CoV-2, while exhibiting intermediate pathogenicity, has a profound impact on public health due to its enormous spread. In this review, we discuss which initial features of the SARS-CoV-2 Spike protein and subsequent adaptations to the new human host may have helped this pathogen to cause the COVID-19 pandemic. Our focus is on host forces driving changes in the Spike protein and their consequences for virus infectivity, pathogenicity, immune evasion and resistance to preventive or therapeutic agents. In addition, we briefly address the significance and perspectives of broad-spectrum therapeutics and vaccines.
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Affiliation(s)
- Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Christoph Jung
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; (C.J.); (T.J.)
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; (C.J.); (T.J.)
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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Cianfarini C, Hassler L, Wysocki J, Hassan A, Nicolaescu V, Elli D, Gula H, Ibrahim AM, Randall G, Henkin J, Batlle D. Soluble Angiotensin-Converting Enzyme 2 Protein Improves Survival and Lowers Viral Titers in Lethal Mouse Model of Severe Acute Respiratory Syndrome Coronavirus Type 2 Infection with the Delta Variant. Cells 2024; 13:203. [PMID: 38334597 PMCID: PMC10854654 DOI: 10.3390/cells13030203] [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: 12/22/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 02/10/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) utilizes angiotensin-converting enzyme 2 (ACE2) as its main receptor for cell entry. We bioengineered a soluble ACE2 protein termed ACE2 618-DDC-ABD that has increased binding to SARS-CoV-2 and prolonged duration of action. Here, we investigated the protective effect of this protein when administered intranasally to k18-hACE2 mice infected with the aggressive SARS-CoV-2 Delta variant. k18-hACE2 mice were infected with the SARS-CoV-2 Delta variant by inoculation of a lethal dose (2 × 104 PFU). ACE2 618-DDC-ABD (10 mg/kg) or PBS was administered intranasally six hours prior and 24 and 48 h post-viral inoculation. All animals in the PBS control group succumbed to the disease on day seven post-infection (0% survival), whereas, in contrast, there was only one casualty in the group that received ACE2 618-DDC-ABD (90% survival). Mice in the ACE2 618-DDC-ABD group had minimal disease as assessed using a clinical score and stable weight, and both brain and lung viral titers were markedly reduced. These findings demonstrate the efficacy of a bioengineered soluble ACE2 decoy with an extended duration of action in protecting against the aggressive Delta SARS-CoV-2 variant. Together with previous work, these findings underline the universal protective potential against current and future emerging SARS-CoV-2 variants.
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Affiliation(s)
- Cosimo Cianfarini
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
- Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Luise Hassler
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
| | - Jan Wysocki
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
| | - Abdelsabour Hassan
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
| | - Vlad Nicolaescu
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Derek Elli
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Haley Gula
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Amany M. Ibrahim
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Glenn Randall
- Howard Taylor Ricketts Laboratory, Department of Microbiology, The University of Chicago, Lemont, IL 60637, USA
| | - Jack Henkin
- Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208, USA
| | - Daniel Batlle
- Division of Nephrology/Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, 710 North Fairbanks Court, Chicago, IL 60611, USA
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Sharma T, Mondal T, Khan S, Churqui MP, Nyström K, Thombare K, Baig MH, Dong JJ. Identifying novel inhibitors targeting Exportin-1 for the potential treatment of COVID-19. Arch Microbiol 2024; 206:69. [PMID: 38240823 DOI: 10.1007/s00203-023-03761-z] [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: 10/17/2023] [Revised: 11/09/2023] [Accepted: 11/19/2023] [Indexed: 01/23/2024]
Abstract
The nuclear export protein 1 (XPO1) mediates the nucleocytoplasmic transport of proteins and ribonucleic acids (RNAs) and plays a prominent role in maintaining cellular homeostasis. XPO1 has emerged as a promising therapeutic approach to interfere with the lifecycle of many viruses. In our earlier study, we proved the inhibition of XPO1 as a therapeutic strategy for managing SARS-COV-2 and its variants. In this study, we have utilized pharmacophore-assisted computational methods to identify prominent XPO1 inhibitors. After several layers of screening, a few molecules were shortlisted for further experimental validation on the in vitro SARS-CoV-2 cell infection model. It was observed that these compounds reduced spike positivity, suggesting inhibition of SARS-COV-2 infection. The outcome of this study could be considered further for developing novel antiviral therapeutic strategies against SARS-CoV-2.
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Affiliation(s)
- Tanuj Sharma
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul, 06273, Republic of Korea
| | - Tanmoy Mondal
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Sajid Khan
- Department of Biochemistry, Aligarh Muslim University, Aligarh, India
| | - Marianela Patzi Churqui
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, 41345, Gothenburg, Sweden
| | - Kristina Nyström
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, 41345, Gothenburg, Sweden
| | - Ketan Thombare
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Mohammad Hassan Baig
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul, 06273, Republic of Korea.
| | - Jae-June Dong
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul, 06273, Republic of Korea.
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Aranda Z, Vázquez S, Gopaluni A, Martínez L, Ramírez M, Jiménez A, Bernal D, Rodríguez AL, Chacón S, Vargas B, Fulcher IR, Barnhart DA. Evaluation of the implementation of a community health worker-led COVID-19 contact tracing intervention in Chiapas, Mexico, from March 2020 to December 2021. BMC Health Serv Res 2024; 24:97. [PMID: 38233915 PMCID: PMC10795220 DOI: 10.1186/s12913-024-10590-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 01/10/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Mexico is one of the countries with the greatest excess death due to COVID-19. Chiapas, the poorest state in the country, has been particularly affected. Faced with an exacerbated shortage of health professionals, medical supplies, and infrastructure to respond to the pandemic, the non-governmental organization Compañeros En Salud (CES) implemented a COVID-19 infection prevention and control program to limit the impact of the pandemic in the region. We evaluated CES's implementation of a community health worker (CHW)-led contact tracing intervention in eight rural communities in Chiapas. METHODS Our retrospective observational study used operational data collected during the contract tracing intervention from March 2020 to December 2021. We evaluated three outcomes: contact tracing coverage, defined as the proportion of named contacts that were located by CHWs, successful completion of contact tracing, and incidence of suspected COVID-19 among contacts. We described how these outcomes changed over time as the intervention evolved. In addition, we assessed associations between these three main outcomes and demographic characteristics of contacts and intervention period (pre vs. post March 2021) using univariate and multivariate logistic regression. RESULTS From a roster of 2,177 named contacts, 1,187 (54.5%) received at least one home visit by a CHW and 560 (25.7%) had successful completion of contact tracing according to intervention guidelines. Of 560 contacts with complete contact tracing, 93 (16.6%) became suspected COVID-19 cases. We observed significant associations between sex and coverage (p = 0.006), sex and complete contact tracing (p = 0.049), community of residence and both coverage and complete contact tracing (p < 0.001), and intervention period and both coverage and complete contact tracing (p < 0.001). CONCLUSIONS Our analysis highlights the promises and the challenges of implementing CHW-led COVID-19 contact tracing programs. To optimize implementation, we recommend using digital tools for data collection with a human-centered design, conducting regular data quality assessments, providing CHWs with sufficient technical knowledge of the data collection system, supervising CHWs to ensure contact tracing guidelines are followed, involving communities in the design and implementation of the intervention, and addressing community member needs and concerns surrounding stigmatization arising from lack of privacy.
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Affiliation(s)
- Zeus Aranda
- Partners In Health Mexico (Compañeros En Salud), Compañeros En Salud AC, Calle Primera Pte. Sur 25, Colonia Centro, Ángel Albino Corzo, 30370, Chiapas, México.
- Departamento de Salud, El Colegio de La Frontera Sur, San Cristóbal de Las Casas, Chiapas, México.
| | - Sandra Vázquez
- Partners In Health Mexico (Compañeros En Salud), Compañeros En Salud AC, Calle Primera Pte. Sur 25, Colonia Centro, Ángel Albino Corzo, 30370, Chiapas, México
| | - Anuraag Gopaluni
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Mayra Ramírez
- Partners In Health Mexico (Compañeros En Salud), Compañeros En Salud AC, Calle Primera Pte. Sur 25, Colonia Centro, Ángel Albino Corzo, 30370, Chiapas, México
| | - Ariwame Jiménez
- Partners In Health Mexico (Compañeros En Salud), Compañeros En Salud AC, Calle Primera Pte. Sur 25, Colonia Centro, Ángel Albino Corzo, 30370, Chiapas, México
| | - Daniel Bernal
- Escuela de Gobierno y Transformación Pública, Instituto Tecnológico de Monterrey, Ciudad de Mexico, México
| | - Ana L Rodríguez
- Partners In Health Mexico (Compañeros En Salud), Compañeros En Salud AC, Calle Primera Pte. Sur 25, Colonia Centro, Ángel Albino Corzo, 30370, Chiapas, México
- Instituto Nacional de Salud Pública/Escuela de Salud Pública de México, Cuernavaca, Morelos, México
| | - Selene Chacón
- Instituto Nacional de Salud Pública/Escuela de Salud Pública de México, Cuernavaca, Morelos, México
| | - Bruno Vargas
- Partners In Health Mexico (Compañeros En Salud), Compañeros En Salud AC, Calle Primera Pte. Sur 25, Colonia Centro, Ángel Albino Corzo, 30370, Chiapas, México
| | - Isabel R Fulcher
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
- Harvard Data Science Initiative, Boston, MA, USA
| | - Dale A Barnhart
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
- Partners In Health Rwanda (Inshuti Mu Buzima), Kigali, Rwanda
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Negi SS, Sharma K, Bhargava A, Singh P. A comprehensive profile of SARS-CoV-2 variants spreading during the COVID-19 pandemic: a genomic characterization study from Chhattisgarh State, India. Arch Microbiol 2024; 206:68. [PMID: 38238530 DOI: 10.1007/s00203-023-03807-2] [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: 10/31/2023] [Revised: 12/09/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024]
Abstract
SARS-CoV-2 has expressively changed its sequences during the COVID-19 pandemic situation by encompassing persistent evolutionary mutational changes resulting in the emergence of many clades and lineages. Evolution of these SARS-CoV-2 variants have significantly imparted fitness advantage to the virus, enhanced its transmissibility and severity of the disease. These new variants are a potential threat to the vaccine efficacy as well. It is therefore pertinent to monitor the evolution of these variants and their epidemiological and clinical impact, in a geographic setting. This study has thus looked into the geographic distribution and genetic diversity of SARS-CoV-2 variants and the evolutionary circulation of different clades in Chhattisgarh (CG) state from March 2020 to July 2023. A total of 3018 sequences were retrieved from the GISAID database, in which 558 were submitted by us. The demographic data revealed male preponderance of 56.45% versus 43.54% females, with the overall mean age of 36.5 years. SARS-CoV-2 sequences represented many variants viz., Delta (55%), Omicron (22%) and others (15%) with a small proportion of recombinant (5%), Kappa (2%), and Alpha (1%). The viral clades G was found predominant for a year from initial days of pandemic in March, 2020 to January, 2021 which then subsequently evoluted to subclade GK (Delta B.1.617.2) and remained in circulation in CG till November, 2021. From December 2021, the GRA (Omicron B.1.1.529) variant had replaced GK to become the dominant strain and continues to predominate in present time. GRA clade is however continuously encompassing new recombinant strains, having various non-synonymous mutations especially in spike protein. The non-synonymous mutation P314L in ORF1b, S84L in ORF8 and D614G in spike protein were found as the pan mutation carried over from clade G to GRA. The continuous evolution in SARS-CoV2 warrants periodical geographic genomic surveillance monitoring to timely detect any new variants having the potential of causing future outbreak.
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Affiliation(s)
- Sanjay Singh Negi
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - Kuldeep Sharma
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - Anudita Bhargava
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - Pushpendra Singh
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India.
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Ravi V, Shamim U, Khan MA, Swaminathan A, Mishra P, Singh R, Bharali P, Chauhan NS, Pandey R. Unraveling the genetic evolution of SARS-CoV-2 Recombinants using mutational dynamics across the different lineages. Front Med (Lausanne) 2024; 10:1294699. [PMID: 38288302 PMCID: PMC10823376 DOI: 10.3389/fmed.2023.1294699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/18/2023] [Indexed: 01/31/2024] Open
Abstract
Introduction Recombination serves as a common strategy employed by RNA viruses for their genetic evolution. Extensive genomic surveillance during the COVID-19 pandemic has reported SARS-CoV-2 Recombinant strains indicating recombination events during the viral evolution. This study introspects the phenomenon of genome recombination by tracing the footprint of prominent lineages of SARS-CoV-2 at different time points in the context of on-going evolution and emergence of Recombinants. Method Whole genome sequencing was carried out for 2,516 SARS-CoV-2 (discovery cohort) and 1,126 (validation cohort) using nasopharyngeal samples collected between the time period of March 2020 to August 2022, as part of the genomic surveillance program. The sequences were classified according to the different lineages of SARS-CoV-2 prevailing in India at respective time points. Results Mutational diversity and abundance evaluation across the 12 lineages identified 58 Recombinant sequences as harboring the least number of mutations (n = 111), with 14 low-frequency unique mutations with major chunk of mutations coming from the BA.2. The spontaneously/dynamically increasing and decreasing trends of mutations highlight the loss of mutations in the Recombinants that were associated with the SARS-CoV-2 replication efficiency, infectivity, and disease severity, rendering them functionally with low infectivity and pathogenicity. Linkage disequilibrium (LD) analysis revealed that mutations comprising the LD blocks of BA.1, BA.2, and Recombinants were found as minor alleles or as low-frequency alleles in the LD blocks from the previous SARS-CoV-2 variant samples, especially Pre-VOC. Moreover, a dissipation in the size of LD blocks as well as LD decay along with a high negative regression coefficient (R squared) value was demonstrated in the Omicron and BA.1 and BA.2 lineages, which corroborated with the breakpoint analysis. Conclusion Together, the findings help to understand the evolution and emergence of Recombinants after the Omicron lineages, for sustenance and adaptability, to maintain the epidemic spread of SARS-CoV-2 in the host population already high in immunity levels.
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Affiliation(s)
- Varsha Ravi
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Uzma Shamim
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Md Abuzar Khan
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Aparna Swaminathan
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Pallavi Mishra
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Rajender Singh
- CSIR-Central Drug Research Institute, (CSIR-CDRI), Lucknow, Lucknow, India
| | - Pankaj Bharali
- CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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De Luca V, Angeli A, Nocentini A, Gratteri P, Pratesi S, Tanini D, Carginale V, Capperucci A, Supuran CT, Capasso C. Leveraging SARS-CoV-2 Main Protease (M pro) for COVID-19 Mitigation with Selenium-Based Inhibitors. Int J Mol Sci 2024; 25:971. [PMID: 38256046 PMCID: PMC10815619 DOI: 10.3390/ijms25020971] [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: 12/07/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The implementation of innovative approaches is crucial in an ongoing endeavor to mitigate the impact of COVID-19 pandemic. The present study examines the strategic application of the SARS-CoV-2 Main Protease (Mpro) as a prospective instrument in the repertoire to combat the virus. The cloning, expression, and purification of Mpro, which plays a critical role in the viral life cycle, through heterologous expression in Escherichia coli in a completely soluble form produced an active enzyme. The hydrolysis of a specific substrate peptide comprising a six-amino-acid sequence (TSAVLQ) linked to a p-nitroaniline (pNA) fragment together with the use of a fluorogenic substrate allowed us to determine effective inhibitors incorporating selenium moieties, such as benzoselenoates and carbamoselenoates. The new inhibitors revealed their potential to proficiently inhibit Mpro with IC50-s in the low micromolar range. Our study contributes to the development of a new class of protease inhibitors targeting Mpro, ultimately strengthening the antiviral arsenal against COVID-19 and possibly, related coronaviruses.
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Affiliation(s)
- Viviana De Luca
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, 80131 Naples, Italy; (V.D.L.); (V.C.)
| | - Andrea Angeli
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.A.); (A.N.); (P.G.)
| | - Alessio Nocentini
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.A.); (A.N.); (P.G.)
| | - Paola Gratteri
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.A.); (A.N.); (P.G.)
| | - Silvia Pratesi
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy (D.T.); (A.C.)
| | - Damiano Tanini
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy (D.T.); (A.C.)
| | - Vincenzo Carginale
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, 80131 Naples, Italy; (V.D.L.); (V.C.)
| | - Antonella Capperucci
- Department of Chemistry “Ugo Schiff”, University of Florence, Via Della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy (D.T.); (A.C.)
| | - Claudiu T. Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.A.); (A.N.); (P.G.)
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, 80131 Naples, Italy; (V.D.L.); (V.C.)
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Pociūtė A, Kriaučiūnaitė K, Kaušylė A, Zablockienė B, Alčauskas T, Jelinskaitė A, Rudėnaitė A, Jančorienė L, Ročka S, Verkhratsky A, Pivoriūnas A. Plasma of COVID-19 Patients Does Not Alter Electrical Resistance of Human Endothelial Blood-Brain Barrier In Vitro. FUNCTION 2024; 5:zqae002. [PMID: 38486975 PMCID: PMC10935481 DOI: 10.1093/function/zqae002] [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: 11/30/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 03/17/2024] Open
Abstract
The pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 instigated the most serious global health crisis. Clinical presentation of COVID-19 frequently includes severe neurological and neuropsychiatric symptoms. However, it is presently unknown whether and to which extent pathological impairment of blood-brain barrier (BBB) contributes to the development of neuropathology during COVID-19 progression. In the present study, we used human induced pluripotent stem cells-derived brain endothelial cells (iBECs) to study the effects of blood plasma derived from COVID-19 patients on the BBB integrity in vitro. We also performed a comprehensive analysis of the cytokine and chemokine profiles in the plasma of COVID-19 patients, healthy and recovered individuals. We found significantly increased levels of interferon γ-induced protein 10 kDa, hepatocyte growth factor, and interleukin-18 in the plasma of COVID-19 patients. However, blood plasma from COVID-19 patients did not affect transendothelial electrical resistance in iBEC monolayers. Our results demonstrate that COVID-19-associated blood plasma inflammatory factors do not affect BBB paracellular pathway directly and suggest that pathological remodeling (if any) of BBB during COVID-19 may occur through indirect or yet unknown mechanisms.
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Affiliation(s)
- Agnė Pociūtė
- Department of Stem Cell Biology, State Research Institute Centre for Innovative Medicine, LT-01102 Vilnius, Lithuania
| | - Karolina Kriaučiūnaitė
- Department of Stem Cell Biology, State Research Institute Centre for Innovative Medicine, LT-01102 Vilnius, Lithuania
| | - Aida Kaušylė
- Department of Stem Cell Biology, State Research Institute Centre for Innovative Medicine, LT-01102 Vilnius, Lithuania
| | - Birutė Zablockienė
- Faculty of Medicine, Vilnius University, LT-03101 Vilnius, Lithuania
- Centre of Infectious Diseases, Vilnius University Hospital Santaros Klinikos, LT-08406 Vilnius, Lithuania
| | - Tadas Alčauskas
- Faculty of Medicine, Vilnius University, LT-03101 Vilnius, Lithuania
| | - Augustė Jelinskaitė
- Centre of Infectious Diseases, Vilnius University Hospital Santaros Klinikos, LT-08406 Vilnius, Lithuania
| | - Akvilė Rudėnaitė
- Centre of Infectious Diseases, Vilnius University Hospital Santaros Klinikos, LT-08406 Vilnius, Lithuania
| | - Ligita Jančorienė
- Faculty of Medicine, Vilnius University, LT-03101 Vilnius, Lithuania
- Centre of Infectious Diseases, Vilnius University Hospital Santaros Klinikos, LT-08406 Vilnius, Lithuania
| | - Saulius Ročka
- Faculty of Medicine, Vilnius University, LT-03101 Vilnius, Lithuania
- Center of Neurosurgery, Vilnius University Hospital Santaros Klinikos, LT-08661 Vilnius, Lithuania
| | - Alexei Verkhratsky
- Department of Stem Cell Biology, State Research Institute Centre for Innovative Medicine, LT-01102 Vilnius, Lithuania
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
- Achucarro Centre for Neuroscience, IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
- Department of Forensic Analytical Toxicology, School of Forensic Medicine, China Medical University, Shenyang, 110052, China
| | - Augustas Pivoriūnas
- Department of Stem Cell Biology, State Research Institute Centre for Innovative Medicine, LT-01102 Vilnius, Lithuania
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181
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Zahmatkesh A, Salmasi E, Gholizadeh R. Interaction of toll-like receptors and ACE-2 with different variants of SARS-CoV-2: A computational analysis. BIOIMPACTS : BI 2024; 14:30150. [PMID: 39104618 PMCID: PMC11298020 DOI: 10.34172/bi.2024.30150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/03/2023] [Accepted: 12/12/2023] [Indexed: 08/07/2024]
Abstract
Introduction Computational studies were performed to investigate the unknown status of endosomal and cell surface receptors in SARS-CoV-2 infection. The interactions between Toll-like receptors (TLRs)- 4/7/8/9 or ACE2 receptor and different SARS-CoV-2 variants were investigated. Methods The RNA motifs for TLR7, TLR8 and a CpG motif for TLR9 were analyzed in different variants. Molecular docking and molecular dynamics (MD) simulations were performed to investigate receptor-ligand interactions. Results The number of motifs recognized by TLR7/8/9 in the Alpha, Delta and Iranian variants was lower than in the wild type (WT). Docking analysis revealed that the Alpha, Delta and some Iranian spike variants had a higher affinity for ACE2 and TLR4 than the WT, which may account for their higher transmission rate. The MD simulation also showed differences in stability and structure size between the variants and the WT, indicating potential variations in viral load. Conclusion It appears that Alpha and some Iranian isolates are the variants of concern due to their higher transmissibility and rapid spread. The Delta mutant is also a variant of concern, not only because of its closer interaction with ACE2, but also with TLR4. Our results emphasize the importance of ACE2 and TLR4, rather than endosomal TLRs, in mediating the effects of different viral mutations and suggest their potential therapeutic applications.
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Affiliation(s)
- Azadeh Zahmatkesh
- Department of Anaerobic Bacterial Vaccines Research and Production, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Elham Salmasi
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, PR China
| | - Reza Gholizadeh
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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182
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Ko SH, Radecki P, Belinky F, Bhiman JN, Meiring S, Kleynhans J, Amoako D, Guerra Canedo V, Lucas M, Kekana D, Martinson N, Lebina L, Everatt J, Tempia S, Bylund T, Rawi R, Kwong PD, Wolter N, von Gottberg A, Cohen C, Boritz EA. Rapid Emergence and Evolution of SARS-CoV-2 Variants in Advanced HIV Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574420. [PMID: 38313289 PMCID: PMC10836083 DOI: 10.1101/2024.01.05.574420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Previous studies have linked the evolution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic variants to persistent infections in people with immunocompromising conditions1-4, but the evolutionary processes underlying these observations are incompletely understood. Here we used high-throughput, single-genome amplification and sequencing (HT-SGS) to obtain up to ~103 SARS-CoV-2 spike gene sequences in each of 184 respiratory samples from 22 people with HIV (PWH) and 25 people without HIV (PWOH). Twelve of 22 PWH had advanced HIV infection, defined by peripheral blood CD4 T cell counts (i.e., CD4 counts) <200 cells/μL. In PWOH and PWH with CD4 counts ≥200 cells/μL, most single-genome spike sequences in each person matched one haplotype that predominated throughout the infection. By contrast, people with advanced HIV showed elevated intra-host spike diversity with a median of 46 haplotypes per person (IQR 14-114). Higher intra-host spike diversity immediately after COVID-19 symptom onset predicted longer SARS-CoV-2 RNA shedding among PWH, and intra-host spike diversity at this timepoint was significantly higher in people with advanced HIV than in PWOH. Composition of spike sequence populations in people with advanced HIV fluctuated rapidly over time, with founder sequences often replaced by groups of new haplotypes. These population-level changes were associated with a high total burden of intra-host mutations and positive selection at functionally important residues. In several cases, delayed emergence of detectable serum binding to spike was associated with positive selection for presumptive antibody-escape mutations. Taken together, our findings show remarkable intra-host genetic diversity of SARS-CoV-2 in advanced HIV infection and suggest that adaptive intra-host SARS-CoV-2 evolution in this setting may contribute to the emergence of new variants of concern (VOCs).
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Affiliation(s)
- Sung Hee Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pierce Radecki
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frida Belinky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinal N. Bhiman
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- SAMRC Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan Meiring
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jackie Kleynhans
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Daniel Amoako
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Integrative Biology and Bioinformatics, College of Biological Sciences, University of Guelph, Ontario, Canada
| | - Vanessa Guerra Canedo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Margaret Lucas
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dikeledi Kekana
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Neil Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University, Center for TB Research, Baltimore, MD 21218, USA
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stefano Tempia
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Wolter
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Kulemzin SV, Guselnikov SV, Nekrasov BG, Molodykh SV, Kuvshinova IN, Murasheva SV, Belovezhets TN, Gorchakov AA, Chikaev AN, Chikaev NA, Volkova OY, Yurina AA, Najakshin AM, Taranin AV. Hybrid Immunity from Gam-COVID-Vac Vaccination and Natural SARS-CoV-2 Infection Confers Broader Neutralizing Activity against Omicron Lineage VOCs Than Revaccination or Reinfection. Vaccines (Basel) 2024; 12:55. [PMID: 38250868 PMCID: PMC10818410 DOI: 10.3390/vaccines12010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/13/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
SARS-CoV-2 has a relatively high mutation rate, with the frequent emergence of new variants of concern (VOCs). Each subsequent variant is more difficult to neutralize by the sera of vaccinated individuals and convalescents. Some decrease in neutralizing activity against new SARS-CoV-2 variants has also been observed in patients vaccinated with Gam-COVID-Vac. In the present study, we analyzed the interplay between the history of a patient's repeated exposure to SARS-CoV-2 antigens and the breadth of neutralization activity. Our study includes four cohorts of patients: Gam-COVID-Vac booster vaccinated individuals (revaccinated, RV), twice-infected unvaccinated individuals (reinfected, RI), breakthrough infected (BI), and vaccinated convalescents (VC). We assessed S-protein-specific antibody levels and the ability of sera to neutralize lentiviral particles pseudotyped with Spike protein from the original Wuhan variant, as well as the Omicron variants BA.1 and BA.4/5. Individuals with hybrid immunity (BI and VC cohorts) exhibited significantly higher levels of virus-binding IgG and enhanced breadth of virus-neutralizing activity compared to individuals from either the revaccination or reinfection (RV and RI) cohorts. These findings suggest that a combination of infection and vaccination, regardless of the sequence, results in significantly higher levels of S-protein-specific IgG antibodies and the enhanced neutralization of SARS-CoV-2 variants, thereby underscoring the importance of hybrid immunity in the context of emerging viral variants.
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Affiliation(s)
- Sergey V. Kulemzin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Sergey V. Guselnikov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | | | | | | | - Svetlana V. Murasheva
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Tatyana N. Belovezhets
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Andrey A. Gorchakov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Anton N. Chikaev
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Nikolai A. Chikaev
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Olga Y. Volkova
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Anna A. Yurina
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Alexander M. Najakshin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
| | - Alexander V. Taranin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia; (S.V.K.); (S.V.G.)
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184
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Khalil AM, Martinez-Sobrido L, Mostafa A. Zoonosis and zooanthroponosis of emerging respiratory viruses. Front Cell Infect Microbiol 2024; 13:1232772. [PMID: 38249300 PMCID: PMC10796657 DOI: 10.3389/fcimb.2023.1232772] [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: 06/01/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Lung infections in Influenza-Like Illness (ILI) are triggered by a variety of respiratory viruses. All human pandemics have been caused by the members of two major virus families, namely Orthomyxoviridae (influenza A viruses (IAVs); subtypes H1N1, H2N2, and H3N2) and Coronaviridae (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2). These viruses acquired some adaptive changes in a known intermediate host including domestic birds (IAVs) or unknown intermediate host (SARS-CoV-2) following transmission from their natural reservoirs (e.g. migratory birds or bats, respectively). Verily, these acquired adaptive substitutions facilitated crossing species barriers by these viruses to infect humans in a phenomenon that is known as zoonosis. Besides, these adaptive substitutions aided the variant strain to transmit horizontally to other contact non-human animal species including pets and wild animals (zooanthroponosis). Herein we discuss the main zoonotic and reverse-zoonosis events that occurred during the last two pandemics of influenza A/H1N1 and SARS-CoV-2. We also highlight the impact of interspecies transmission of these pandemic viruses on virus evolution and possible prophylactic and therapeutic interventions. Based on information available and presented in this review article, it is important to close monitoring viral zoonosis and viral reverse zoonosis of pandemic strains within a One-Health and One-World approach to mitigate their unforeseen risks, such as virus evolution and resistance to limited prophylactic and therapeutic interventions.
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Affiliation(s)
- Ahmed Magdy Khalil
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Luis Martinez-Sobrido
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ahmed Mostafa
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Center of Scientific Excellence for Influenza Viruses, Water Pollution Research Department, Environment and Climate Change Research Institute, National Research Centre, Giza, Egypt
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185
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Feng Y, Yi J, Yang L, Wang Y, Wen J, Zhao W, Kim P, Zhou X. COV2Var, a function annotation database of SARS-CoV-2 genetic variation. Nucleic Acids Res 2024; 52:D701-D713. [PMID: 37897356 PMCID: PMC10767816 DOI: 10.1093/nar/gkad958] [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: 08/15/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has resulted in the loss of millions of lives and severe global economic consequences. Every time SARS-CoV-2 replicates, the viruses acquire new mutations in their genomes. Mutations in SARS-CoV-2 genomes led to increased transmissibility, severe disease outcomes, evasion of the immune response, changes in clinical manifestations and reducing the efficacy of vaccines or treatments. To date, the multiple resources provide lists of detected mutations without key functional annotations. There is a lack of research examining the relationship between mutations and various factors such as disease severity, pathogenicity, patient age, patient gender, cross-species transmission, viral immune escape, immune response level, viral transmission capability, viral evolution, host adaptability, viral protein structure, viral protein function, viral protein stability and concurrent mutations. Deep understanding the relationship between mutation sites and these factors is crucial for advancing our knowledge of SARS-CoV-2 and for developing effective responses. To fill this gap, we built COV2Var, a function annotation database of SARS-CoV-2 genetic variation, available at http://biomedbdc.wchscu.cn/COV2Var/. COV2Var aims to identify common mutations in SARS-CoV-2 variants and assess their effects, providing a valuable resource for intensive functional annotations of common mutations among SARS-CoV-2 variants.
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Affiliation(s)
- Yuzhou Feng
- Department of Laboratory Medicine and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
| | - Jiahao Yi
- School of Big Health, Guizhou Medical University, Guiyang 550025, China
| | - Lin Yang
- Department of Cardiology and Laboratory of Gene Therapy for Heart Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yanfei Wang
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jianguo Wen
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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186
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McGaughran A, Dhami MK, Parvizi E, Vaughan AL, Gleeson DM, Hodgins KA, Rollins LA, Tepolt CK, Turner KG, Atsawawaranunt K, Battlay P, Congrains C, Crottini A, Dennis TPW, Lange C, Liu XP, Matheson P, North HL, Popovic I, Rius M, Santure AW, Stuart KC, Tan HZ, Wang C, Wilson J. Genomic Tools in Biological Invasions: Current State and Future Frontiers. Genome Biol Evol 2024; 16:evad230. [PMID: 38109935 PMCID: PMC10776249 DOI: 10.1093/gbe/evad230] [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: 09/15/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023] Open
Abstract
Human activities are accelerating rates of biological invasions and climate-driven range expansions globally, yet we understand little of how genomic processes facilitate the invasion process. Although most of the literature has focused on underlying phenotypic correlates of invasiveness, advances in genomic technologies are showing a strong link between genomic variation and invasion success. Here, we consider the ability of genomic tools and technologies to (i) inform mechanistic understanding of biological invasions and (ii) solve real-world issues in predicting and managing biological invasions. For both, we examine the current state of the field and discuss how genomics can be leveraged in the future. In addition, we make recommendations pertinent to broader research issues, such as data sovereignty, metadata standards, collaboration, and science communication best practices that will require concerted efforts from the global invasion genomics community.
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Affiliation(s)
- Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Manpreet K Dhami
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Elahe Parvizi
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Amy L Vaughan
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Dianne M Gleeson
- Centre for Conservation Ecology and Genomics, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Carolyn K Tepolt
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Kathryn G Turner
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
| | - Kamolphat Atsawawaranunt
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Carlos Congrains
- Entomology Section, Department of Plant and Environmental Protection Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
- US Department of Agriculture-Agricultural Research Service, Daniel K. Inouye US Pacific Basin Agricultural Research Center, Hilo, HI 96720, USA
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169–007, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Tristan P W Dennis
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Claudia Lange
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Xiaoyue P Liu
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Paige Matheson
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Henry L North
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Iva Popovic
- School of the Environment, University of Queensland, Brisbane, QLD, Australia
| | - Marc Rius
- Centre for Advanced Studies of Blanes (CEAB, CSIC), Accés a la Cala Sant Francesc, Blanes, Spain
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg 2006, South Africa
| | - Anna W Santure
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Katarina C Stuart
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Hui Zhen Tan
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Cui Wang
- The Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Jonathan Wilson
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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187
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Biskupek I, Gieldon A. Two-Stage Recognition Mechanism of the SARS-CoV-2 Receptor-Binding Domain to Angiotensin-Converting Enzyme-2 (ACE2). Int J Mol Sci 2024; 25:679. [PMID: 38203850 PMCID: PMC10779479 DOI: 10.3390/ijms25010679] [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: 11/02/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
The SARS-CoV-2 virus, commonly known as COVID-19, occurred in 2019. It is a highly contagious illness with effects ranging from mild symptoms to severe illness. It is also one of the best-known pathogens since more than 200,000 scientific papers occurred in the last few years. With the publication of the SARS-CoV-2 (SARS-CoV-2-CTD) spike (S) protein in a complex with human ACE2 (hACE2) (PDB (6LZG)), the molecular analysis of one of the most crucial steps on the infection pathway was possible. The aim of this manuscript is to simulate the most widely spread mutants of SARS-CoV-2, namely Alpha, Beta, Gamma, Delta, Omicron, and the first recognized variant (natural wild type). With the wide search of the hypersurface of the potential energy performed using the UNRES force field, the intermediate state of the ACE2-RBD complex was found. R403, K/N/T417, L455, F486, Y489, F495, Y501, and Y505 played a crucial role in the protein recognition mechanism. The intermediate state cannot be very stable since it will prevent the infection cascade.
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Affiliation(s)
| | - Artur Gieldon
- Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63, 80-308 Gdansk, Poland;
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188
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Zhou Z, Zheng H, Xiao G, Xie X, Rang J, Peng D. Effectiveness and safety of azvudine in older adults with mild and moderate COVID-19: a retrospective observational study. BMC Infect Dis 2024; 24:47. [PMID: 38177982 PMCID: PMC10765789 DOI: 10.1186/s12879-023-08944-z] [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: 07/12/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Azvudine has clinical benefits and acceptable safety against COVID-19, including in patients with comorbidities, but there is a lack of available data for its use in older adult patients. This study explored the effectiveness and safety of azvudine in older adults with mild or moderate COVID-19. METHODS This retrospective cohort study included patients aged ≥80 diagnosed with COVID-19 at the Central Hospital of Shaoyang between October and November 2022. According to the therapies they received, the eligible patients were divided into the azvudine, nirmatrelvir/ritonavir, and standard-of-care (SOC) groups. The outcomes were the proportion of patients progressing to severe COVID-19, time to nucleic acid negative conversion (NANC), and the 5-, 7-, 10-, and 14-day NANC rates from admission. RESULTS The study included 55 patients treated with azvudine (n = 14), nirmatrelvir/ritonavir (n = 18), and SOC (n = 23). The median time from symptom onset to NANC of the azvudine, nirmatrelvir/ritonavir, and SOC groups was 14 (range, 6-25), 15 (range, 11-24), and 19 (range, 18-23) days, respectively. The median time from treatment initiation to NANC of the azvudine and nirmatrelvir/ritonavir groups was 8 (range, 4-20) and 9 (range, 5-16) days, respectively. The median length of hospital stay in the three groups was 10.5 (range, 5-23), 13.5 (range, 10-21), and 17 (range, 10-23) days, respectively. No treatment-related adverse events or serious adverse events were reported. CONCLUSION Azvudine showed satisfactory effectiveness and acceptable safety in older adults with mild or moderate COVID-19. Therefore, azvudine could be a treatment option for this special patient population.
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Affiliation(s)
- Zhiguo Zhou
- Department of Respiratory and Critical Care Medicine, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University, The First Hospital of Changsha, Changsha, Hunan, China
| | - He Zheng
- Department of Infectious Disease, The Central Hospital of Shaoyang, Shaoyang, Hunan, China
| | - Gui'e Xiao
- Department of Infectious Disease, The Central Hospital of Shaoyang, Shaoyang, Hunan, China
| | - Xiangping Xie
- Department of Infectious Disease, The Central Hospital of Shaoyang, Shaoyang, Hunan, China
| | - Jiaxi Rang
- Department of Nursing, The First Hospital of Changsha, Changsha, Hunan, China.
| | - Danhong Peng
- Department of Infectious Disease, The Central Hospital of Shaoyang, Shaoyang, Hunan, China.
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189
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Zaidi AK, Singh RB. SARS-CoV-2 variant biology and immune evasion. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 202:45-66. [PMID: 38237990 DOI: 10.1016/bs.pmbts.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
This chapter discusses the SARS-CoV-2 variants and their immune evasion strategies, shedding light on the dynamic nature of the COVID-19 pandemic. The ecological dynamics and viral evolution of SARS-CoV-2 are explored, considering carriers of infection, individual immunity profiles, and human movement as key factors in the emergence and dissemination of variants. The chapter discusses SARS-CoV-2 mutation, including mutation rate, substitution rate, and recombination, influencing genetic diversity and evolution. Transmission bottlenecks are highlighted as determinants of dominant variants during viral spread. The evolution phases of the pandemic are outlined, from limited early evolution to the emergence of notable changes like the D614G substitution and variants with heavy mutations. Variants of Concern (VOCs), including Alpha, Beta, Gamma, and the recent Omicron variant, are examined, with insights into inter-lineage and intra-lineage dynamics. The origin of VOCs and the Omicron variant is explored, alongside the role of the furin cleavage site (FCS) in variant emergence. The impact of structural and non-structural proteins on viral infectivity is assessed, as well as innate immunity evasion strategies employed by SARS-CoV-2 variants. The chapter concludes by considering future possibilities, including ongoing virus evolution, the need for surveillance, vaccine development, and public health measures.
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Affiliation(s)
| | - Rohan Bir Singh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States; Department of Population, Policy and Practice, Greater Ormond Street Institute of Child Health, University College London, United Kingdom; Discipline of Ophthalmology and Visual Sciences, Adelaide Medical School, University of Adelaide, Australia.
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190
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Kopel H, Bogdanov A, Winer-Jones JP, Adams C, Winer IH, Bonafede M, Nguyen VH, Mansi JA. Comparison of COVID-19 and Influenza-Related Outcomes in the United States during Fall-Winter 2022-2023: A Cross-Sectional Retrospective Study. Diseases 2024; 12:16. [PMID: 38248367 PMCID: PMC10814040 DOI: 10.3390/diseases12010016] [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: 11/20/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
Influenza and COVID-19 contribute significantly to the infectious disease burden during the respiratory season, but their relative burden remains unknown. This study characterizes the frequency and severity of medically attended COVID-19 and influenza during the peak of the 2022-2023 influenza season in the pediatric, adult, and older adult populations and characterizes the prevalence of underlying conditions among patients hospitalized with COVID-19. This cross-sectional analysis included individuals in the Veradigm EHR Database linked to Komodo claims data with a medical encounter between 1 October 2022 and 31 March 2023 (study period). Patients with medical encounters were identified with a diagnosis of COVID-19 or influenza during the study period and stratified based on the highest level of care received with that diagnosis. Among 23,526,196 individuals, there were more COVID-19-related medical encounters than influenza-related encounters, overall and by outcome. Hospitalizations with COVID-19 were more common than hospitalizations with influenza overall (incidence ratio = 4.6) and in all age groups. Nearly all adults hospitalized with COVID-19 had at least one underlying medical condition, but 37.1% of 0-5-year-olds and 25.0% of 6-17-year-olds had no underlying medical conditions. COVID-19 was associated greater burden than influenza during the peak of the 2022-2023 influenza season.
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191
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Kodsi IA, Rayes DE, Koweyes J, Khoury CA, Rahy K, Thoumi S, Chamoun M, Haddad H, Mokhbat J, Tokajian S. Tracking SARS-CoV-2 variants during the 2023 flu season and beyond in Lebanon. Virus Res 2024; 339:199289. [PMID: 38036064 PMCID: PMC10704499 DOI: 10.1016/j.virusres.2023.199289] [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: 10/18/2023] [Revised: 11/12/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Early SARS-CoV-2 variant detection relies on testing and genomic surveillance. The Omicron variant (B.1.1.529) has quickly become the dominant type among the previous circulating variants worldwide. Several subvariants have emerged exhibiting greater infectivity and immune evasion. In this study we aimed at studying the prevalence of the Omicron subvariants during the flu season and beyond in Lebanon through genomic screening and at determining the overall standing and trajectory of the pandemic in the country. METHODS A total of 155 SARS-CoV-2 RNA samples were sequenced, using Nanopore sequencing technology. RESULTS Nanopore sequencing of 155 genomes revealed their distribution over 39 Omicron variants. XBB.1.5 (23.29 %) was the most common, followed by XBB.1.9.1 (10.96 %) and XBB.1.42 (7.5 %). The first batch collected between September and November 2022, included the BA.2.75.2, BA.5.2, BA.5.2.20, BA.5.2.25 and BQ.1.1.5 lineages. Between December 2022 and January 2023, those lineages were replaced by BA.2.75.5, BN.1, BN.1.4, BQ.1, BQ.1.1, BQ.1.1.23, CH.1.1, CM.4 and XBK. Starting February 2023, we observed a gradual emergence and dominance of the recombinant XBB and its sub-lineages (XBB.1, XBB.1.5, XBB.1.5.2, XBB.1.5.3, XBB.1.9, XBB.1.9.1, XBB.1.9.2, XBB.1.16, XBB.1.22 and XBB.1.42). CONCLUSIONS The timely detection and characterization of SARS-CoV-2 variants is important to reduce transmission through established disease control measures and to avoid introductions into animal populations that could lead to serious public health implications.
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Affiliation(s)
- Ibrahim Al Kodsi
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Douaa El Rayes
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Charbel Al Khoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Kelven Rahy
- School of Medicine, Lebanese American University, Lebanon
| | - Sergio Thoumi
- Department of Computer Science and Mathematics, School of Arts and Sciences, Lebanese American University, Lebanon
| | | | - Hoda Haddad
- Clinical Microbiology laboratory, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Jacques Mokhbat
- Clinical Microbiology laboratory, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon.
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192
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Pontiroli AE, Scovenna F, Carlini V, Tagliabue E, Martin-Delgado J, Sala LL, Tanzi E, Zanoni I. Vaccination against influenza viruses reduces infection, not hospitalization or death, from respiratory COVID-19: A systematic review and meta-analysis. J Med Virol 2024; 96:e29343. [PMID: 38163281 PMCID: PMC10924223 DOI: 10.1002/jmv.29343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/01/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 and has brought a huge burden in terms of human lives. Strict social distance and influenza vaccination have been recommended to avoid co-infections between influenza viruses and SARS-CoV-2. Scattered reports suggested a protective effect of influenza vaccine on COVID-19 development and severity. We analyzed 51 studies on the capacity of influenza vaccination to affect infection with SARS-CoV-2, hospitalization, admission to Intensive Care Units (ICU), and mortality. All subjects taken into consideration did not receive any anti-SARS-CoV-2 vaccine, although their status with respect to previous infections with SARS-CoV-2 is not known. Comparison between vaccinated and not-vaccinated subjects for each of the four endpoints was expressed as odds ratio (OR), with 95% confidence intervals (CIs); all analyses were performed by DerSimonian and Laird model, and Hartung-Knapp model when studies were less than 10. In a total of 61 029 936 subjects from 33 studies, influenza vaccination reduced frequency of SARS-CoV-2 infection [OR plus 95% CI = 0.70 (0.65-0.77)]. The effect was significant in all studies together, in health care workers and in the general population; distance from influenza vaccination and the type of vaccine were also of importance. In 98 174 subjects from 11 studies, frequency of ICU admission was reduced with influenza vaccination [OR (95% CI) = 0.71 (0.54-0.94)]; the effect was significant in all studies together, in pregnant women and in hospitalized subjects. In contrast, in 4 737 328 subjects from 14 studies hospitalization was not modified [OR (95% CI) = 1.05 (0.82-1.35)], and in 4 139 660 subjects from 19 studies, mortality was not modified [OR (95% CI) = 0.76 (0.26-2.20)]. Our study emphasizes the importance of influenza vaccination in the protection against SARS-CoV-2 infection.
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Affiliation(s)
- Antonio E. Pontiroli
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, 20142 Milan, Italy
| | - Francesco Scovenna
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, 20142 Milan, Italy
| | - Valentina Carlini
- IRCCS MultiMedica, Laboratory of Cardiovascular and Dysmetabolic Disease, 20138 Milan, Italy
| | - Elena Tagliabue
- IRCCS MultiMedica, Value-Based Healthcare Unit, 20099 Milan, Italy
| | - Jimmy Martin-Delgado
- Hospital Luis Vernaza, Junta de Beneficiencia de Guayaquil 090603, Ecuador
- Instituto de Investigacion e Innovacion en Salud Integral, Universidad Catolica de Santiago de Guayaquil, Guayaquil 090603, Ecuador
| | - Lucia La Sala
- IRCCS MultiMedica, Laboratory of Cardiovascular and Dysmetabolic Disease, 20138 Milan, Italy
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Milan, Italy
| | - Elisabetta Tanzi
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, 20142 Milan, Italy
| | - Ivan Zanoni
- Harvard Medical School, Boston Children’s Hospital, Division of Immunology and Division of Gastroenterology, Boston, MA 02115, USA
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Favresse J, Gillot C, Closset M, Cabo J, Wauthier L, David C, Elsen M, Dogné JM, Douxfils J. Durability of humoral and cellular immunity six months after the BNT162b2 bivalent booster. J Med Virol 2024; 96:e29365. [PMID: 38185981 DOI: 10.1002/jmv.29365] [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: 09/26/2023] [Revised: 11/22/2023] [Accepted: 12/20/2023] [Indexed: 01/09/2024]
Abstract
Studies about the duration of the humoral and cellular response following the bivalent booster administration are still scarce. We aimed at assessing the humoral and cellular response in a cohort of healthcare workers that received this booster. Blood samples were collected before the administration of the bivalent booster from Pfizer-BioNTech and after 14, 28, 90, and 180 days. Neutralizing antibodies against either the D614G strain, the delta variant, the BA.5 variant, or the XBB.1.5 subvariant were measured. The cellular response was assessed by measurement of the release of interferon gamma from T cells in response to an in vitro SARS-CoV-2 stimulation. A substantial waning of neutralizing antibodies was observed after 6 months (23.1-fold decrease), especially considering the XBB.1.5 subvariant. The estimated T1/2 of neutralizing antibodies was 16.1 days (95% CI = 10.2-38.4 days). Although most participants still present a robust cellular response after 6 months (i.e., 95%), a significant decrease was also observed compared to the peak response (0.95 vs. 0.41 UI/L, p = 0.0083). A significant waning of the humoral and cellular response was observed after 6 months. These data can also help competent national authorities in their recommendation regarding the administration of an additional booster.
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Affiliation(s)
- Julien Favresse
- Research Unit in Clinical Pharmacology and Toxicology, Namur Research Institute for Life Sciences, Namur Thrombosis and Hemostasis Center, University of Namur, Namur, Belgium
- Department of Laboratory Medicine, Clinique St-Luc Bouge, Namur, Belgium
| | - Constant Gillot
- Research Unit in Clinical Pharmacology and Toxicology, Namur Research Institute for Life Sciences, Namur Thrombosis and Hemostasis Center, University of Namur, Namur, Belgium
| | - Mélanie Closset
- Department of Laboratory Medicine, Université catholique de Louvain, CHU UCL Namur, Namur, Belgium
| | - Julien Cabo
- Department of Laboratory Medicine, Clinique St-Luc Bouge, Namur, Belgium
| | - Loris Wauthier
- Department of Laboratory Medicine, Clinique St-Luc Bouge, Namur, Belgium
| | - Clara David
- Qualiblood s.a., Research and Development Department, Namur, Belgium
| | - Marc Elsen
- Department of Laboratory Medicine, Clinique St-Luc Bouge, Namur, Belgium
| | - Jean-Michel Dogné
- Research Unit in Clinical Pharmacology and Toxicology, Namur Research Institute for Life Sciences, Namur Thrombosis and Hemostasis Center, University of Namur, Namur, Belgium
| | - Jonathan Douxfils
- Research Unit in Clinical Pharmacology and Toxicology, Namur Research Institute for Life Sciences, Namur Thrombosis and Hemostasis Center, University of Namur, Namur, Belgium
- Qualiblood s.a., Research and Development Department, Namur, Belgium
- Department of Biological Hematology, Centre Hospitalier Universitaire Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France
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194
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Gabdoulkhakova AG, Mingaleeva RN, Romozanova AM, Sagdeeva AR, Filina YV, Rizvanov AA, Miftakhova RR. Immunology of SARS-CoV-2 Infection. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:65-83. [PMID: 38467546 DOI: 10.1134/s0006297924010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 03/13/2024]
Abstract
According to the data from the World Health Organization, about 800 million of the world population had contracted coronavirus infection caused by SARS-CoV-2 by mid-2023. Properties of this virus have allowed it to circulate in the human population for a long time, evolving defense mechanisms against the host immune system. Severity of the disease depends largely on the degree of activation of the systemic immune response, including overstimulation of macrophages and monocytes, cytokine production, and triggering of adaptive T- and B-cell responses, while SARS-CoV-2 evades the immune system actions. In this review, we discuss immune responses triggered in response to the SARS-CoV-2 virus entry into the cell and malfunctions of the immune system that lead to the development of severe disease.
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Affiliation(s)
- Aida G Gabdoulkhakova
- Kazan Federal University, Kazan, 420008, Russia.
- Kazan State Medical Academy - Branch Campus of the Federal State Budgetary Educational Institution of Further Professional Education "Russian Medical Academy of Continuous Professional Education" of the Ministry of Health of the Russian Federation, Kazan, 420012, Russia
| | | | | | | | | | - Albert A Rizvanov
- Kazan Federal University, Kazan, 420008, Russia
- Division of Medical and Biological Sciences, Tatarstan Academy of Sciences, Kazan, 420111, Russia
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Wondeu ALD, Abakar MF, Frasca F, Nodjikouambaye AZ, Abdelrazakh F, Naibei N, Dzomo GRT, Djimtoibaye D, Mad‐Toingue J, Scagnolari C, Antonelli G, Linardos G, Russo C, Perno CF, Yandai FH, Atturo S, Hiscott J, Colizzi V, Cappelli G, Ngueadoum N, Haroun A, Choua O, Moussa AM. Presence of neutralizing SARS-CoV-2 antibodies in asymptomatic population of N'Djamena, Chad. Immun Inflamm Dis 2024; 12:e1154. [PMID: 38270301 PMCID: PMC10790679 DOI: 10.1002/iid3.1154] [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: 06/12/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024] Open
Abstract
INTRODUCTION Neutralizing antibodies (NAbs) are an important specific defence against viral infections, as these antibodies bind to specific receptor(s) and block the viral entry. NAbs assessments are therefore useful in determining individual or herd immunity to SARS-CoV-2. This study aims to deepen the investigation by assessing the positivity rate of neutralizing anti-spike antibodies to understand the real protection of the studied population against SARS-CoV-2. METHODS This study involved 260 plasma samples from a larger cohort of 2,700 asymptomatic volunteer donors, enrolled between August and October 2021 in health facilities of N'Djamena. In this study four different kits and techniques including the pseudotype assay have been used and compared with detect the SARS-CoV-2 antibodies. Pseudotyped vesicular stomatitis virus (VSV), was used both the identify and measure the NAbs that to evaluate the performance of two cheaper and easy to use commercial kits, specific for the detection of receptor-binding domain antibodies (anti-RBD) against the SARS-CoV-2 spike protein. RESULTS The VSV spike neutralization assay showed that 59.0% (n = 59) samples were positive for NAbs with titers ranging from 1:10 to 1:4800. While 23 out the 41 negative NAbs samples were detected positive using anti-RBD (Abbott) test. Furthermore, a direct and significant strong correlation was found between NAbs and anti-RBD, specifically with Abbott kit. Taken together, the Roche and Abbott methods indicated agreement at the high concentrations of antibodies with the VSV-pseudovirus method. Abbott and Roche indicated a good sensitivity, but the Abbott system test appeared to have better specificity than the Roche test. CONCLUSION Our findings indicated a high presence of NAbs against SARS-CoV-2 spike protein among asymptomatic individuals in N'Djamena. This could be one of the reasons for the low severity of Covid-19 observed in this area, given the key role of NAbs in blocking SARS-CoV-2 infection.
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Affiliation(s)
- Andrillene Laure Deutou Wondeu
- Laboratoire des Grandes Epidémies Tropicales (LAGET)Complexe Hospitalo‐Universitaire le Bon SamaritainN'DjamenaChad
- Department of Biology and Interdepartmental Centre for Comparative MedicineUniversity of Rome Tor VergataRomeItaly
- Laboratory of Molecular Biology and ImmunopathologyEvangelical University of CameroonMbouo‐BandjounCameroon
| | | | - Federica Frasca
- Laboratory of Virology, Department of Molecular MedicineSapienza University of RomeItaly
| | - Aleyo Zita Nodjikouambaye
- Laboratoire des Grandes Epidémies Tropicales (LAGET)Complexe Hospitalo‐Universitaire le Bon SamaritainN'DjamenaChad
| | - Fatima Abdelrazakh
- Institut de Recherche en Elevage pour le Développement (IRED)N'DjamenaChad
| | - Nathan Naibei
- Communauté des Amis de l'Informatique pour le Développement (CAID‐Tchad)N'DjamenaChad
| | - Guy Rodrigue Takoudjou Dzomo
- Laboratoire des Grandes Epidémies Tropicales (LAGET)Complexe Hospitalo‐Universitaire le Bon SamaritainN'DjamenaChad
| | - Djallaye Djimtoibaye
- Laboratoire des Grandes Epidémies Tropicales (LAGET)Complexe Hospitalo‐Universitaire le Bon SamaritainN'DjamenaChad
| | - Joseph Mad‐Toingue
- Centre Hospitalier Universitaire de Référence Nationale (CHU‐RN)N'DjamenaChad
- Coordination nationale de riposte sanitaire contre la Covid‐19, Ministère de la Santé PubliqueN'DjamenaChad
| | - Carolina Scagnolari
- Laboratory of Virology, Department of Molecular MedicineSapienza University of RomeItaly
| | - Guido Antonelli
- Laboratory of Virology, Department of Molecular MedicineSapienza University of RomeItaly
| | - Giulia Linardos
- Virology and Mycobacteriology Unit, “Bambino Gesù” Children Hospital—Healthcare and Research Institute—RomeRomeItaly
| | - Cristina Russo
- Virology and Mycobacteriology Unit, “Bambino Gesù” Children Hospital—Healthcare and Research Institute—RomeRomeItaly
| | - Carlo Federico Perno
- Virology and Mycobacteriology Unit, “Bambino Gesù” Children Hospital—Healthcare and Research Institute—RomeRomeItaly
| | - Fissou Henry Yandai
- Centre Hospitalier Universitaire de Référence Nationale (CHU‐RN)N'DjamenaChad
| | - Sabrina Atturo
- Laboratoire des Grandes Epidémies Tropicales (LAGET)Complexe Hospitalo‐Universitaire le Bon SamaritainN'DjamenaChad
| | - John Hiscott
- Institute Pasteur Cenci‐Bolognetti FoundationRomeItaly
| | - Vittorio Colizzi
- Laboratoire des Grandes Epidémies Tropicales (LAGET)Complexe Hospitalo‐Universitaire le Bon SamaritainN'DjamenaChad
- Department of Biology and Interdepartmental Centre for Comparative MedicineUniversity of Rome Tor VergataRomeItaly
- Laboratory of Molecular Biology and ImmunopathologyEvangelical University of CameroonMbouo‐BandjounCameroon
| | - Giulia Cappelli
- Institute for Biological SystemsNational Research CouncilRomeItaly
| | - Nambatibe Ngueadoum
- Direction Générale des Laboratoires, Pharmacie & Médicaments, Ministère de la Santé PubliqueN'DjamenaChad
| | - Alsadick Haroun
- Coordination nationale de riposte sanitaire contre la Covid‐19, Ministère de la Santé PubliqueN'DjamenaChad
- Direction Générale des Laboratoires, Pharmacie & Médicaments, Ministère de la Santé PubliqueN'DjamenaChad
| | - Ouchemi Choua
- Centre Hospitalier Universitaire de Référence Nationale (CHU‐RN)N'DjamenaChad
- Coordination nationale de riposte sanitaire contre la Covid‐19, Ministère de la Santé PubliqueN'DjamenaChad
| | - Ali Mahamat Moussa
- Laboratoire des Grandes Epidémies Tropicales (LAGET)Complexe Hospitalo‐Universitaire le Bon SamaritainN'DjamenaChad
- Centre Hospitalier Universitaire de Référence Nationale (CHU‐RN)N'DjamenaChad
- Coordination nationale de riposte sanitaire contre la Covid‐19, Ministère de la Santé PubliqueN'DjamenaChad
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Wang E, Yang QJ, Xu XX, Zou QC, Long Y, Ma G, Deng ZH, Zhao JB, Li MH, Zeng J. Differential pathogenic and molecular features in neurological infection of SARS-CoV-2 Omicron BA.5.2 and BA.2.75 and Delta. J Med Virol 2024; 96:e29357. [PMID: 38235532 DOI: 10.1002/jmv.29357] [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: 07/31/2023] [Revised: 11/07/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024]
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a global threat, exacerbated by the emergence of viral variants. Two variants of SARS-CoV-2, Omicron BA.2.75 and BA.5, led to global infection peaks between May 2022 and May 2023, yet their precise characteristics in pathogenesis are not well understood. In this study, we compared these two Omicron sublineages with the previously dominant Delta variant using a human angiotensin-converting enzyme 2 knock-in mouse model. As expected, Delta exhibited higher viral replication in the lung and brain than both Omicron sublineages which induced less severe lung damage and immune activation. In contrast, the Omicron variants especially BA.5.2 showed a propensity for cellular proliferation and developmental pathways. Both Delta and BA.5.2 variants, but not BA.2.75, led to decreased pulmonary lymphocytes, indicating differential adaptive immune response. Neuroinvasiveness was shared with all strains, accompanied by vascular abnormalities, synaptic injury, and loss of astrocytes. However, Immunostaining assays and transcriptomic analysis showed that BA.5.2 displayed stronger immune suppression and neurodegeneration, while BA.2.75 exhibited more similar characteristics to Delta in the cortex. Such differentially infectious features could be partially attributed to the weakened interaction between Omicron Spike protein and host proteomes decoded via co-immunoprecipitation followed by mass spectrometry in neuronal cells. Our present study supports attenuated replication and pathogenicity of Omicron variants but also highlights their newly infectious characteristics in the lung and brain, especially with BA.5.2 demonstrating enhanced immune evasion and neural damage that could exacerbate neurological sequelae.
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Affiliation(s)
- Erlin Wang
- Songjiang Research Institute, Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qiao-Jiang Yang
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiang-Xiong Xu
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qing-Cui Zou
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yanghaopeng Long
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Guanqin Ma
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhong-Hua Deng
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jie-Bin Zhao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ming-Hua Li
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jianxiong Zeng
- Songjiang Research Institute, Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, China
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197
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Levi R, Zerhouni EG, Altuvia S. Predicting the spread of SARS-CoV-2 variants: An artificial intelligence enabled early detection. PNAS NEXUS 2024; 3:pgad424. [PMID: 38170049 PMCID: PMC10759796 DOI: 10.1093/pnasnexus/pgad424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
During more than 3 years since its emergence, SARS-CoV-2 has shown great ability to mutate rapidly into diverse variants, some of which turned out to be very infectious and have spread throughout the world causing waves of infections. At this point, many countries have already experienced up to six waves of infections. Extensive academic work has focused on the development of models to predict the pandemic trajectory based on epidemiological data, but none has focused on predicting variant-specific spread. Moreover, important scientific literature analyzes the genetic evolution of SARS-CoV-2 variants and how it might functionally affect their infectivity. However, genetic attributes have not yet been incorporated into existing epidemiological modeling that aims to capture infection trajectory. Thus, this study leverages variant-specific genetic characteristics together with epidemiological information to systematically predict the future spread trajectory of newly detected variants. The study describes the analysis of 9.0 million SARS-CoV-2 genetic sequences in 30 countries and identifies temporal characteristic patterns of SARS-CoV-2 variants that caused significant infection waves. Using this descriptive analysis, a machine-learning-enabled risk assessment model has been developed to predict, as early as 1 week after their first detection, which variants are likely to constitute the new wave of infections in the following 3 months. The model's out-of-sample area under the curve (AUC) is 86.3% for predictions after 1 week and 90.8% for predictions after 2 weeks. The methodology described in this paper could contribute more broadly to the development of improved predictive models for variants of other infectious viruses.
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Affiliation(s)
- Retsef Levi
- Sloan School of Management, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - El Ghali Zerhouni
- Operations Research Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shoshy Altuvia
- Department of Microbiology and Molecular Genetics, The Hebrew University-Hadassah Medical School, Jerusalem, 9112102, Israel
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198
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Lamb KD, Luka MM, Saathoff M, Orton RJ, Phan MVT, Cotten M, Yuan K, Robertson DL. Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. PLoS Comput Biol 2024; 20:e1011795. [PMID: 38271457 PMCID: PMC10868779 DOI: 10.1371/journal.pcbi.1011795] [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: 07/12/2023] [Revised: 02/15/2024] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
The COVID-19 pandemic has been characterised by sequential variant-specific waves shaped by viral, individual human and population factors. SARS-CoV-2 variants are defined by their unique combinations of mutations and there has been a clear adaptation to more efficient human infection since the emergence of this new human coronavirus in late 2019. Here, we use machine learning models to identify shared signatures, i.e., common underlying mutational processes and link these to the subset of mutations that define the variants of concern (VOCs). First, we examined the global SARS-CoV-2 genomes and associated metadata to determine how viral properties and public health measures have influenced the magnitude of waves, as measured by the number of infection cases, in different geographic locations using regression models. This analysis showed that, as expected, both public health measures and virus properties were associated with the waves of regional SARS-CoV-2 reported infection numbers and this impact varies geographically. We attribute this to intrinsic differences such as vaccine coverage, testing and sequencing capacity and the effectiveness of government stringency. To assess underlying evolutionary change, we used non-negative matrix factorisation and observed three distinct mutational signatures, unique in their substitution patterns and exposures from the SARS-CoV-2 genomes. Signatures 1, 2 and 3 were biased to C→T, T→C/A→G and G→T point mutations. We hypothesise assignments of these mutational signatures to the host antiviral molecules APOBEC, ADAR and ROS respectively. We observe a shift amidst the pandemic in relative mutational signature activity from predominantly Signature 1 changes to an increasingly high proportion of changes consistent with Signature 2. This could represent changes in how the virus and the host immune response interact and indicates how SARS-CoV-2 may continue to generate variation in the future. Linkage of the detected mutational signatures to the VOC-defining amino acids substitutions indicates the majority of SARS-CoV-2's evolutionary capacity is likely to be associated with the action of host antiviral molecules rather than virus replication errors.
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Affiliation(s)
- Kieran D. Lamb
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
- School of Computing Science, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Martha M. Luka
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
- School of Computing Science, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Megan Saathoff
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
| | - Richard J. Orton
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
| | - My V. T. Phan
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- College of Health Solutions, Arizona State University, Phoenix, Arizona, United States of America
| | - Matthew Cotten
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- College of Health Solutions, Arizona State University, Phoenix, Arizona, United States of America
- Complex Adaptive Systems Initiative, Arizona State University, Scottsdale, Arizona, United States of America
| | - Ke Yuan
- School of Computing Science, University of Glasgow, Glasgow, Scotland, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- Cancer Research UK Scotland Institute, Glasgow, Scotland, United Kingdom
| | - David L. Robertson
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
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Zhao J, Kang M, Wu H, Sun B, Baele G, He WT, Lu M, Suchard MA, Ji X, He N, Su S, Veit M. Risk assessment of SARS-CoV-2 replicating and evolving in animals. Trends Microbiol 2024; 32:79-92. [PMID: 37541811 DOI: 10.1016/j.tim.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
The retransmissions of SARS-CoV-2 from several mammals - primarily mink and white-tailed deer - to humans have raised concerns for the emergence of a new animal-derived SARS-CoV-2 variant to worsen the pandemic. Here, we discuss animal species that are susceptible to natural or experimental infection with SARS-CoV-2 and can transmit the virus to mates or humans. We describe cutting-edge techniques to assess the impact of a mutation in the viral spike (S) protein on its receptor and on antibody binding. Our review of spike sequences of animal-derived viruses identified nine unique amino acid exchanges in the receptor-binding domain (RBD) that are not present in any variant of concern (VOC). These mutations are present in SARS-CoV-2 found in companion animals such as dogs and cats, and they exhibit a higher frequency in SARS-CoV-2 found in mink and white-tailed deer, suggesting that sustained transmissions may contribute to maintaining novel mutations. Four of these exchanges, such as Leu452Met, could undermine acquired immune protection in humans while maintaining high affinity for the human angiotensin-converting enzyme 2 (ACE2) receptor. Finally, we discuss important avenues of future research into animal-derived viruses with public health risks.
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Affiliation(s)
- Jin Zhao
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Mei Kang
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China; Clinical Research Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongyan Wu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Bowen Sun
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Guy Baele
- Department of Microbiology, Immunology, and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Wan-Ting He
- School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Meng Lu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA; Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Na He
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Shuo Su
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China.
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin, Germany.
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Holdenrieder S, Dos Santos Ferreira CE, Izopet J, Theel ES, Wieser A. Clinical and laboratory considerations: determining an antibody-based composite correlate of risk for reinfection with SARS-CoV-2 or severe COVID-19. Front Public Health 2023; 11:1290402. [PMID: 38222091 PMCID: PMC10788057 DOI: 10.3389/fpubh.2023.1290402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/30/2023] [Indexed: 01/16/2024] Open
Abstract
Much of the global population now has some level of adaptive immunity to SARS-CoV-2 induced by exposure to the virus (natural infection), vaccination, or a combination of both (hybrid immunity). Key questions that subsequently arise relate to the duration and the level of protection an individual might expect based on their infection and vaccination history. A multi-component composite correlate of risk (CoR) could inform individuals and stakeholders about protection and aid decision making. This perspective evaluates the various elements that need to be accommodated in the development of an antibody-based composite CoR for reinfection with SARS-CoV-2 or development of severe COVID-19, including variation in exposure dose, transmission route, viral genetic variation, patient factors, and vaccination status. We provide an overview of antibody dynamics to aid exploration of the specifics of SARS-CoV-2 antibody testing. We further discuss anti-SARS-CoV-2 immunoassays, sample matrices, testing formats, frequency of sampling and the optimal time point for such sampling. While the development of a composite CoR is challenging, we provide our recommendations for each of these key areas and highlight areas that require further work to be undertaken.
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Affiliation(s)
- Stefan Holdenrieder
- Institute of Laboratory Medicine, German Heart Centre Munich, Technical University Munich, Munich, Germany
| | | | - Jacques Izopet
- Laboratory of Virology, Toulouse University Hospital and INFINITY Toulouse Institute for Infections and Inflammatory Diseases, INSERM UMR 1291 CNRS UMR 5051, University Toulouse III, Toulouse, France
| | - Elitza S. Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
- German Centre for Infection Research (DZIF), Munich, Germany
- Faculty of Medicine, Max Von Pettenkofer Institute, LMU Munich, Munich, Germany
- Immunology, Infection and Pandemic Research, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Munich, Germany
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