201
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Wang Y, Chen XY, Yang L, Yao Q, Chen KP. Human SARS-CoV-2 has evolved to increase U content and reduce genome size. Int J Biol Macromol 2022; 204:356-363. [PMID: 35149094 PMCID: PMC8824384 DOI: 10.1016/j.ijbiomac.2022.02.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 12/30/2022]
Abstract
Infections caused by SARS-CoV-2 have brought great harm to human health. After transmission for over two years, SARS-CoV-2 has diverged greatly and formed dozens of different lineages. Understanding the trend of its genome evolution could help foresee difficulties in controlling transmission of the virus. In this study, we conducted an extensive monthly survey and in-depth analysis on variations of nucleotide, amino acid and codon numbers in 311,260 virus samples collected till January 2022. The results demonstrate that the evolution of SARS-CoV-2 is toward increasing U-content and reducing genome-size. C, G and A to U mutations have all contributed to this U-content increase. Mutations of C, G and A at codon position 1, 2 or 3 have no significant difference in most SARS-CoV-2 lineages. Current viruses are more cryptic and more efficient in replication, and are thus less virulent yet more infectious. Delta and Omicron variants have high mutability over other lineages, bringing new threat to human health. This trend of genome evolution may provide a clue for tracing the origin of SARS-CoV-2, because ancestral viruses should have lower U-content and probably bigger genome-size.
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Affiliation(s)
- Yong Wang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China.
| | - Xin-Yu Chen
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Liu Yang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Qin Yao
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China.
| | - Ke-Ping Chen
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China.
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202
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Dejnirattisai W, Huo J, Zhou D, Zahradník J, Supasa P, Liu C, Duyvesteyn HME, Ginn HM, Mentzer AJ, Tuekprakhon A, Nutalai R, Wang B, Dijokaite A, Khan S, Avinoam O, Bahar M, Skelly D, Adele S, Johnson SA, Amini A, Ritter TG, Mason C, Dold C, Pan D, Assadi S, Bellass A, Omo-Dare N, Koeckerling D, Flaxman A, Jenkin D, Aley PK, Voysey M, Costa Clemens SA, Naveca FG, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Baillie V, Serafin N, Kwatra G, Da Silva K, Madhi SA, Nunes MC, Malik T, Openshaw PJM, Baillie JK, Semple MG, Townsend AR, Huang KYA, Tan TK, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Constantinides B, Webster H, Crook D, Pollard AJ, Lambe T, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Schreiber G, Stuart DI, Screaton GR. SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell 2022; 185:467-484.e15. [PMID: 35081335 PMCID: PMC8723827 DOI: 10.1016/j.cell.2021.12.046] [Citation(s) in RCA: 626] [Impact Index Per Article: 313.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/18/2021] [Accepted: 12/29/2021] [Indexed: 12/23/2022]
Abstract
On 24th November 2021, the sequence of a new SARS-CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titers of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic Alpha, Beta, Gamma, or Delta are substantially reduced, or the sera failed to neutralize. Titers against Omicron are boosted by third vaccine doses and are high in both vaccinated individuals and those infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of the large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses and uses mutations that confer tight binding to ACE2 to unleash evolution driven by immune escape. This leads to a large number of mutations in the ACE2 binding site and rebalances receptor affinity to that of earlier pandemic viruses.
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Affiliation(s)
- Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Jiří Zahradník
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aiste Dijokaite
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Suman Khan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mohammad Bahar
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Sandra Adele
- Peter Medawar Building for Pathogen Research, Oxford, UK
| | | | - Ali Amini
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chris Mason
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christina Dold
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Daniel Pan
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK; Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Sara Assadi
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Adam Bellass
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Nicola Omo-Dare
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | | | - Amy Flaxman
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Jenkin
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Parvinder K Aley
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sue Ann Costa Clemens
- Institute of Global Health, University of Siena, Siena, Brazil; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | | | | | - Alex Pauvolid-Correa
- Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | | | - Vicky Baillie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Natali Serafin
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaurav Kwatra
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kelly Da Silva
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology, National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tariq Malik
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | | | - J Kenneth Baillie
- Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Alain R Townsend
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Kuan-Ying A Huang
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital and Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Miles W Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Hermione Webster
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Neil G Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
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203
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Akram F, Haq IU, Aqeel A, Ahmed Z, Shah FI, Nawaz A, Zafar J, Sattar R. Insights into the evolutionary and prophylactic analysis of SARS-CoV-2: A review. J Virol Methods 2022; 300:114375. [PMID: 34838536 PMCID: PMC8610842 DOI: 10.1016/j.jviromet.2021.114375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 10/29/2021] [Accepted: 11/22/2021] [Indexed: 01/04/2023]
Abstract
In late 2019, following the emergence of a β-originated SARS-CoV-2, phylogenetic and evolutionary approaches have been demonstrated to strengthen the diagnostic and prophylactic stratagem of COVID-19 at an unprecedented level. Despite its clinical prominence, the SARS-CoV-2 gene set remains largely irrefutable by impeding the dissection of COVID-19 biology. However, many pieces of molecular and serological evidence have predicted that SARS-CoV-2 related viruses carry their roots from bats and pangolins of South East Asia. Analysis of viral genome predicts that point mutations at a rate of 10-4 nucleotides per base in the receptor-binding domain allow the emergence of new SARS-CoV-2 genomic variants at regular intervals. Research in the evolution of molecular pathways involved in emergence of pandemic is critical for the development of therapeutics and vaccines as well as the prevention of future zoonosis. By determining the phyletic lineages of the SARS-CoV-2 genomic variants and those of the conserved regions in the accessory and spike proteins of all the SARS-related coronaviruses, a universal vaccine against all human coronaviruses could be formulated which would revolutionize the field of medicine. This review highlighted the current development and future prospects of antiviral drugs, inhibitors, mesenchymal stem cells, passive immunization, targeted immune therapy and CRISPR-Cas-based prophylactic and therapeutic strategies against SARS-CoV-2. However, further investigations on Covid-19 pathogenesis is required for the successful fabrication of successful antivirals.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Amna Aqeel
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Zeeshan Ahmed
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Fatima Iftikhar Shah
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ali Nawaz
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Javaria Zafar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Rukhma Sattar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
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204
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Alexandridi M, Mazej J, Palermo E, Hiscott J. The Coronavirus Pandemic – 2022: Viruses, Variants & Vaccines. Cytokine Growth Factor Rev 2022; 63:1-9. [PMID: 35216872 PMCID: PMC8839804 DOI: 10.1016/j.cytogfr.2022.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Since the beginning of the COVID-19 pandemic in 2019–2020, Cytokine & Growth Factor Reviews has published several Special Issues focused on the biology, pathogenesis and therapeutic options in the treatment of COVID-19 infection, including articles on the involvement of the chemokine system in the cytokine storm in COVID-19, intervention in the early stages of COVID-19 pneumonia, the therapeutic value of corticosteroid treatment, early clinical intervention with type 1 interferons, progress in vaccine development, and organ specific complications of COVID-19. By 2022, multiple highly efficacious vaccines are available and are being administered in countries around the world, therapeutic options have been clinically evaluated and approved, and SARS-CoV-2 has arguably become the most thoroughly studied virus in history. But, with progress has also come unanticipated problems – misinformation, anti-vaxxers, opposition to protective masks, and politically motivated interference disguised as knowledge. With this issue of CGFR, we continue to document the global coronavirus pandemic and provide an update on the emergence of viral variants, the global effort to administer vaccines and the impediments to progress posed by misinformation and anti-vaccine sentiment.
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205
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Hsu CK, Chen CY, Chen WC, Lai CC, Hung SH, Lin WT. The effect of sofosbuvir-based treatment on the clinical outcomes of patients with COVID-19: a systematic review and meta-analysis of randomized controlled trials. Int J Antimicrob Agents 2022; 59:106545. [PMID: 35134505 PMCID: PMC8817946 DOI: 10.1016/j.ijantimicag.2022.106545] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/16/2021] [Accepted: 01/27/2022] [Indexed: 11/18/2022]
Abstract
This systematic review and meta-analysis examined the efficacy of sofosbuvir-based antiviral treatment against COVID-19 (coronavirus disease 2019). PubMed, Embase, Cochrane Central Register of Controlled Trials and ClinicalTrials.gov were searched from inception to 15 August 2021. Studies comparing the clinical efficacy and safety of sofosbuvir-based antiviral regimens (study group) with other antivirals or standard of care (control group) in patients with COVID-19 were included. Overall, 687 patients with COVID-19 were included, of which 377 patients received sofosbuvir-based treatment. Mortality was lower in the study group than in the control group [odds ratio (OR) = 0.49, 95% confidence interval (CI) 0.30–0.79; I2 = 0%]. The overall clinical recovery rate was higher in the study group than in the control group (OR = 1.82, 95% CI 1.20–2.76; I2 = 28%). The study group presented a lower requirement for mechanical ventilation (OR = 0.33, 95% CI 0.13–0.89; I2 = 0%) and intensive care unit admission (OR = 0.42, 95% CI 0.25–0.70; I2 = 0%) than the control group. Furthermore, the study group exhibited a shorter hospital length of stay [mean deviation (MD), –1.49, 95% CI –2.62 to –0.37; I2 = 56%] and recovery time (MD, –1.34, 95% CI –2.29 to –0.38; I2 = 46%) than the control group. Sofosbuvir-based treatment may help reduce mortality in patients with COVID-19 and improve associated clinical outcomes. Furthermore, sofosbuvir-based treatment was as safe as the comparator in patients with COVID-19. However, further large-scale studies are warranted to validate these findings.
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206
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Chutipongtanate S, Morrow AL, Newburg DS. Human Milk Oligosaccharides: Potential Applications in COVID-19. Biomedicines 2022; 10:biomedicines10020346. [PMID: 35203555 PMCID: PMC8961778 DOI: 10.3390/biomedicines10020346] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/25/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has become a global health crisis with more than four million deaths worldwide. A substantial number of COVID-19 survivors continue suffering from long-COVID syndrome, a long-term complication exhibiting chronic inflammation and gut dysbiosis. Much effort is being expended to improve therapeutic outcomes. Human milk oligosaccharides (hMOS) are non-digestible carbohydrates known to exert health benefits in breastfed infants by preventing infection, maintaining immune homeostasis and nurturing healthy gut microbiota. These beneficial effects suggest the hypothesis that hMOS might have applications in COVID-19 as receptor decoys, immunomodulators, mucosal signaling agents, and prebiotics. This review summarizes hMOS biogenesis and classification, describes the possible mechanisms of action of hMOS upon different phases of SARS-CoV-2 infection, and discusses the challenges and opportunities of hMOS research for clinical applications in COVID-19.
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Affiliation(s)
- Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- Faculty of Medicine Ramathibodi Hospital, Chakri Naruebodindra Medical Institute, Mahidol University, Samut Prakan 10540, Thailand
- Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
| | - Ardythe L. Morrow
- Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children′s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - David S. Newburg
- Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
- Correspondence: or
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207
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Vargas J, Gómez-Pedrero JA, Quiroga JA, Alonso J. Enhancement of Cryo-EM maps by a multiscale tubular filter. OPTICS EXPRESS 2022; 30:4515-4527. [PMID: 35209686 DOI: 10.1364/oe.444675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
We present an approach to enhance cryo-electron microscopy (cryo-EM) postprocessed maps based on a multiscale tubular filter. The method determines a tubularness measure locally by the analysis of the eigenvalues of the Hessian matrix. This information is used to enhance elongated local structures and to attenuate blob-like and plate-like structures. The approach, thus, introduces a priori information in the reconstructions to improve their interpretability and analysis at high-resolution. The proposed method has been tested with simulated and real cryo-EM maps including recent reconstructions of the SARS-CoV-2. Our results show that our methods can improve obtained reconstructions.
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208
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Mannar D, Saville JW, Zhu X, Srivastava SS, Berezuk AM, Tuttle KS, Marquez AC, Sekirov I, Subramaniam S. SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex. Science 2022; 375:760-764. [PMID: 35050643 DOI: 10.1126/science.abn7760] [Citation(s) in RCA: 393] [Impact Index Per Article: 196.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - James W Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Xing Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Shanti S Srivastava
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Alison M Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Katharine S Tuttle
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Ana Citlali Marquez
- BC Center for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Inna Sekirov
- BC Center for Disease Control Public Health Laboratory, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Gandeeva Therapeutics, Inc., Vancouver, BC, Canada
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209
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Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins G, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A, Williamson C, Hsiao NY, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL. Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.14.476382. [PMID: 35075456 PMCID: PMC8786225 DOI: 10.1101/2022.01.14.476382] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (i) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (ii) interactions of Spike with ACE2 receptors, and (iii) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any genomes within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron over all previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.
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Affiliation(s)
- Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7701, South Africa
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Alexander G Lucaci
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Wolfgang Maier
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany, usegalaxy.eu
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany, usegalaxy.eu
| | - Stephen D Shank
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Oscar A MacLean
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Richard J Orton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gordon Harkins
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jinal N Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Daniel G Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa
| | - Carolyn Williamson
- Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town South Africa
- Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, South Africa
| | - Nei-Yuan Hsiao
- Division of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Arne De Klerk
- Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7701, South Africa
| | - Robert W Shafer
- Division of Infectious Diseases, Department of medicine, Stanford university, Stanford, CA, USA
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Robert J Wilkinson
- Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, South Africa
- Francis Crick Institute, Midland Road, London NW1 1AT, UK
- Department of Infectious Diseases, Imperial College London, W12 0NN, UK
| | - B Trevor Sewell
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Anton Nekrutenko
- Department Of Biochemistry and Molecular Biology, The Pennsylvania State University, usegalaxy.org
| | - Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA3
| | - Tyler N Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science, Stellenbosch University
| | - Ravindra K Gupta
- Africa Health Research Institute, Durban, South Africa
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science, Stellenbosch University
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA
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Jeong BS, Cha JS, Hwang I, Kim U, Adolf-Bryfogle J, Coventry B, Cho HS, Kim KD, Oh BH. Computational design of a neutralizing antibody with picomolar binding affinity for all concerning SARS-CoV-2 variants. MAbs 2022; 14:2021601. [PMID: 35030983 PMCID: PMC8765073 DOI: 10.1080/19420862.2021.2021601] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Coronavirus disease 2019, caused by SARS-CoV-2, remains an on-going pandemic, partly due to the emergence of variant viruses that can “break-through” the protection of the current vaccines and neutralizing antibodies (nAbs), highlighting the needs for broadly nAbs and next-generation vaccines. We report an antibody that exhibits breadth and potency in binding the receptor-binding domain (RBD) of the virus spike glycoprotein across SARS coronaviruses. Initially, a lead antibody was computationally discovered and crystallographically validated that binds to a highly conserved surface of the RBD of wild-type SARS-CoV-2. Subsequently, through experimental affinity enhancement and computational affinity maturation, it was further developed to bind the RBD of all concerning SARS-CoV-2 variants, SARS-CoV-1 and pangolin coronavirus with pico-molar binding affinities, consistently exhibited strong neutralization activity against wild-type SARS-CoV-2 and the Alpha and Delta variants. These results identify a vulnerable target site on coronaviruses for development of pan-sarbecovirus nAbs and vaccines.
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Affiliation(s)
- Bo-Seong Jeong
- Department of Biological Sciences, Kaist Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jeong Seok Cha
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Insu Hwang
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Uijin Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jared Adolf-Bryfogle
- Institute for Protein Innovation, Boston, MA, USA.,Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian Coventry
- Molecular Engineering & Sciences Institute & Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Hyun-Soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Kyun-Do Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Byung-Ha Oh
- Department of Biological Sciences, Kaist Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
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211
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Ngwe Tun MM, Sakura T, Sakurai Y, Kurosaki Y, Inaoka DK, Shioda N, Yasuda J, Kita K, Morita K. Antiviral activity of 5-aminolevulinic acid against variants of severe acute respiratory syndrome coronavirus 2. Trop Med Health 2022; 50:6. [PMID: 34991723 PMCID: PMC8739347 DOI: 10.1186/s41182-021-00397-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/27/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began to emerge in 2020 and have been spreading globally during the coronavirus disease 2019 (COVID-19) pandemic. Despite the presence of different COVID-19 vaccines, the discovery of effective antiviral therapeutics for the treatment of patients infected with SARS-CoV-2 are still urgently needed. A natural amino acid, 5-aminolevulinic acid (5-ALA), has exhibited both antiviral and anti-inflammatory activities. In a previous study, we demonstrated an in vitro antiviral effect of 5-ALA against SARS-CoV-2 infection without significant cytotoxicity. In the present study, we sought to investigate whether 5-ALA with or without sodium ferrous citrate (SFC) can inhibit in vitro both the original SARS-CoV-2 Wuhan strain and its variants, including the Alpha, Beta, Gamma and Delta strains. METHODS The antiviral activity of ALA with or without SFC was determined in Vero-E6 cell. The virus inhibition was quantified by real time RT-PCR. RESULTS Co-administration of 5-ALA and SFC inhibited the Wuhan, Alpha and Delta variants of SARS-CoV-2 with IC50 values of 235, 173 and 397 µM, respectively, and the Beta and Gamma variants with IC50 values of 1311 and 1516 µM. CONCLUSION Our study suggests that 5-ALA with SFC warrants accelerated clinical evaluation as an antiviral drug candidate for treating patients infected with SARS-CoV-2 variants.
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Affiliation(s)
- Mya Myat Ngwe Tun
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
| | - Takaya Sakura
- Shionogi Global Infectious Diseases Division, Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
| | - Yasuteru Sakurai
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
- National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Yohei Kurosaki
- National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Daniel Ken Inaoka
- Shionogi Global Infectious Diseases Division, Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan.
- National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, 852-8523, Japan.
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, 852-8523, Japan.
- Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan.
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
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212
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Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. EPMA J 2022; 13:149-175. [PMID: 35013687 PMCID: PMC8732965 DOI: 10.1007/s13167-021-00267-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/04/2021] [Indexed: 12/12/2022]
Abstract
Aims The rapid spread of new SARS-CoV-2 variants has highlighted the crucial role played in the infection by mutations occurring at the SARS-CoV-2 spike receptor binding domain (RBD) in the interactions with the human ACE2 receptor. In this context, it urgently needs to develop new rapid tools for quickly predicting the affinity of ACE2 for the SARS-CoV-2 spike RBD protein variants to be used with the ongoing SARS-CoV-2 genomic sequencing activities in the clinics, aiming to gain clues about the transmissibility and virulence of new variants, to prevent new outbreaks and to quickly estimate the severity of the disease in the context of the 3PM. Methods In our study, we used a computational pipeline for calculating the interaction energies at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface for a selected group of characterized infectious variants of concern/interest (VoC/VoI). By using our pipeline, we built 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for the VoC B.1.1.7-United Kingdom (carrying the mutations of concern/interest N501Y, S494P, E484K at the RBD), P.1-Japan/Brazil (RBD mutations: K417T, E484K, N501Y), B.1.351-South Africa (RBD mutations: K417N, E484K, N501Y), B.1.427/B.1.429-California (RBD mutations: L452R), the B.1.141 (RBD mutations: N439K), and the recent B.1.617.1-India (RBD mutations: L452R; E484Q) and the B.1.620 (RBD mutations: S477N; E484K). Then, we used the obtained 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for predicting the interaction energies at the protein–protein interface. Results Along SARS-CoV-2 mutation database screening and mutation localization analysis, it was ascertained that the most dangerous mutations at VoC/VoI spike proteins are located mainly at three regions of the SARS-CoV-2 spike “boat-shaped” receptor binding motif, on the RBD domain. Notably, the P.1 Japan/Brazil variant present three mutations, K417T, E484K, N501Y, located along the entire receptor binding motif, which apparently determines the highest interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface, among those calculated. Conversely, it was also observed that the replacement of a single acidic/hydrophilic residue with a basic residue (E484K or N439K) at the “stern” or “bow” regions, of the boat-shaped receptor binding motif on the RBD, appears to determine an interaction energy with ACE2 receptor higher than that observed with single mutations occurring at the “hull” region or with other multiple mutants. In addition, our pipeline allowed searching for ACE2 structurally related proteins, i.e., THOP1 and NLN, which deserve to be investigated for their possible involvement in interactions with the SARS-CoV-2 spike protein, in those tissues showing a low expression of ACE2, or as a novel receptor for future spike variants. A freely available web-tool for the in silico calculation of the interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface, starting from the sequences of the investigated spike and/or ACE2 variants, was made available for the scientific community at: https://www.mitoairm.it/covid19affinities. Conclusion In the context of the PPPM/3PM, the employment of the described pipeline through the provided webservice, together with the ongoing SARS-CoV-2 genomic sequencing, would help to predict the transmissibility of new variants sequenced from future patients, depending on SARS-CoV-2 genomic sequencing activities and on the specific amino acid replacement and/or on its location on the SARS-CoV-2 spike RBD, to put in play all the possible counteractions for preventing the most deleterious scenarios of new outbreaks, taking into consideration that a greater transmissibility has not to be necessarily related to a more severe manifestation of the disease. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-021-00267-w.
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Niu S, Wang J, Bai B, Wu L, Zheng A, Chen Q, Du P, Han P, Zhang Y, Jia Y, Qiao C, Qi J, Tian W, Wang H, Wang Q, Gao GF. Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. EMBO J 2022; 41:e109962. [PMID: 34981520 PMCID: PMC8724768 DOI: 10.15252/embj.2021109962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022] Open
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214
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Andreata-Santos R, Janini LMR, Durães-Carvalho R. From Alpha to Omicron SARS-CoV-2 variants: What their evolutionary signatures can tell us? J Med Virol 2022; 94:1773-1776. [PMID: 34978091 PMCID: PMC9015558 DOI: 10.1002/jmv.27555] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 01/29/2023]
Affiliation(s)
- Robert Andreata-Santos
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, Sao Paulo, Brazil
| | - Luiz M R Janini
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, Sao Paulo, Brazil
| | - Ricardo Durães-Carvalho
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, Sao Paulo, Brazil
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Hossen ML, Baral P, Sharma T, Gerstman BS, Chapagain P. Significance of the RBD mutations in the SARS-CoV-2 Omicron: from spike opening to antibody escape and cell attachment. Phys Chem Chem Phys 2022; 24:9123-9129. [DOI: 10.1039/d2cp00169a] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We computationally investigated the role of the Omicron RBD mutations on its structure and interactions with surrounding domains in the spike trimer as well as with ACE2. Our results suggest...
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216
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Bassani D, Ragazzi E, Lapolla A, Sartore G, Moro S. Omicron Variant of SARS-CoV-2 Virus: In Silico Evaluation of the Possible Impact on People Affected by Diabetes Mellitus. Front Endocrinol (Lausanne) 2022; 13:847993. [PMID: 35321335 PMCID: PMC8935058 DOI: 10.3389/fendo.2022.847993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
The Omicron variant of SARS-CoV-2 (Spike mutant B.1.1.529) carrying more than 30-point mutations in its structure, of which 15 are localized in the receptor-binding domain (RBD), allows to hypothesize a relevant change in interactivity with ACE2. In previous reports we hypothesized that the worse outcome of the COVID-19 disease in diabetes mellitus condition could be related to the non-enzymatic glycation of ACE2 receptor and an in silico evaluation led to the demonstration that the number of interactions is decreased in comparison to the unmodified model, possibly shifting the virus attack through different, multiple alternative entry routes. Given the evidenced features of this variant, we aimed to investigate with a computational approach the characteristics of Omicron SARS-CoV-2 with respect to its binding to human ACE-2 receptor, in a particular population, namely people affected by diabetes mellitus, at risk for unfavorable outcomes of the COVID-19. The computational analysis, considering the case in which all the lysine residues in the system are subjected to non-enzymatic glycation, confirmed that lysine glycation causes a general loss of interactivity between wild-type (WT)-Spike-RBD and ACE2. In the Omicron variant, Lys417 mutates into an asparagine, preventing the possible non-enzymatic glycation of this residue. Therefore, if non-enzymatic glycation seemed to cause a shift in the way in which the virus enters the cell from the ACE2-mediated mechanism to other pathways, in the case of the Omicron variant the ACE2-mediated approach of the virus seems to remain an important event to take into account. Indeed, interaction profile analysis, together with molecular mechanics-generalized Born surface area (MM-GBSA) calculations, suggests that the Omicron-Spike-RBD maintains a higher affinity for ACE2 subsequently to non-enzymatic glycation with respect to WT-Spike-RBD. The finding of the present computational study may suggest a different clinical relevance of the Omicron variant for the diabetes mellitus field, also in the possible direction of a lower severity of the disease.
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Affiliation(s)
- Davide Bassani
- Department of Pharmaceutical and Pharmacological Sciences (DSF), Molecular Modeling Section (MMS), University of Padova School of Medicine and Surgery, Padua, Italy
| | - Eugenio Ragazzi
- Department of Pharmaceutical and Pharmacological Sciences (DSF), University of Padova School of Medicine and Surgery, Padua, Italy
- *Correspondence: Eugenio Ragazzi,
| | - Annunziata Lapolla
- Department of Medicine (DIMED), University of Padova School of Medicine and Surgery, Padua, Italy
| | - Giovanni Sartore
- Department of Medicine (DIMED), University of Padova School of Medicine and Surgery, Padua, Italy
| | - Stefano Moro
- Department of Pharmaceutical and Pharmacological Sciences (DSF), Molecular Modeling Section (MMS), University of Padova School of Medicine and Surgery, Padua, Italy
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217
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Yin J, Li C, Ye C, Ruan Z, Liang Y, Li Y, Wu J, Luo Z. Advances in the development of therapeutic strategies against COVID-19 and perspectives in the drug design for emerging SARS-CoV-2 variants. Comput Struct Biotechnol J 2022; 20:824-837. [PMID: 35126885 PMCID: PMC8802458 DOI: 10.1016/j.csbj.2022.01.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 12/15/2022] Open
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Bartsch Y, Tong X, Kang J, José Avendaño M, Serrano EF, García-Salum T, Pardo-Roa C, Riquelme A, Medina RA, Alter G. Preserved Omicron Spike specific antibody binding and Fc-recognition across COVID-19 vaccine platforms. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.12.24.21268378. [PMID: 34981072 PMCID: PMC8722615 DOI: 10.1101/2021.12.24.21268378] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Despite the dramatic spread of Omicron globally, even among highly vaccinated populations, death rates have not increased concomitantly. These data argue that alternative immune mechanisms, beyond neutralization, may continue to confer protection against severe disease. Beyond their ability to bind and block infection, antibodies contribute to control and clearance of multiple infections via their ability to direct antiviral immunity via Fc-effector mechanisms. Thus, here we probed the ability of vaccine induced antibodies, across three COVID-19 vaccines, to drive Fc-effector activity against Omicron. Despite the significant loss of IgM, IgA and IgG binding to the Omicron Receptor Binding Domain (RBD) across BNT162b2, mRNA-1273, and CoronaVac vaccines, stable isotype binding was observed across all of these vaccines to the Omicron Spike. Compromised RBD binding IgG was accompanied by a significant loss of cross RBD-specific antibody Fcγ-receptor binding by the CoronaVac vaccine, but preservation of RBD-specific FcγR2a and Fcγ3a binding across the mRNA vaccines. Conversely, Spike-specific antibodies exhibited persistent binding to Fcγ-receptors, across all three vaccines, albeit higher binding was observed with the mRNA vaccines, marked by a selective preservation of FcγR2a and Fcγ3a binding antibodies. Thus, despite the significant to near complete loss of Omicron neutralization across several vaccine platforms against Omicron, vaccine induced Spike-specific antibodies continue to recognize the virus and recruit Fc-receptors pointing to a persistent capacity for extra-neutralizing antibodies to contribute Omicron disease attenuation.
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Affiliation(s)
- Yannic Bartsch
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
| | - Xin Tong
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
| | - Jaweon Kang
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
| | - María José Avendaño
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eileen F Serrano
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tamara García-Salum
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Advanced Interdisciplinary Rehabilitation Register (AIRR) - COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Catalina Pardo-Roa
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Advanced Interdisciplinary Rehabilitation Register (AIRR) - COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Arnoldo Riquelme
- Advanced Interdisciplinary Rehabilitation Register (AIRR) - COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rafael A Medina
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Advanced Interdisciplinary Rehabilitation Register (AIRR) - COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Advanced Interdisciplinary Rehabilitation Register (AIRR) - COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Health Sciences, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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219
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Dejnirattisai W, Huo J, Zhou D, Zahradník J, Supasa P, Liu C, Duyvesteyn HM, Ginn HM, Mentzer AJ, Tuekprakhon A, Nutalai R, Wang B, Dijokaite A, Khan S, Avinoam O, Bahar M, Skelly D, Adele S, Johnson SA, Amini A, Ritter T, Mason C, Dold C, Pan D, Assadi S, Bellass A, Omo-Dare N, Koeckerling D, Flaxman A, Jenkin D, Aley PK, Voysey M, Clemens SAC, Naveca FG, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Baillie V, Serafin N, Ditse Z, Da Silva K, Madhi S, Nunes MC, Malik T, Openshaw PJM, Baillie JK, Semple MG, Townsend AR, Huang KYA, Tan TK, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Constantinides B, Webster H, Crook D, Pollard AJ, Lambe T, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Schreiber G, Stuart DI, Screaton GR. Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.03.471045. [PMID: 34981049 PMCID: PMC8722586 DOI: 10.1101/2021.12.03.471045] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
On the 24 th November 2021 the sequence of a new SARS CoV-2 viral isolate spreading rapidly in Southern Africa was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titres of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic as well as Alpha, Beta, Gamma, Delta are substantially reduced or fail to neutralize. Titres against Omicron are boosted by third vaccine doses and are high in cases both vaccinated and infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of a large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses, combining mutations conferring tight binding to ACE2 to unleash evolution driven by immune escape, leading to a large number of mutations in the ACE2 binding site which rebalance receptor affinity to that of early pandemic viruses.
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Affiliation(s)
- Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Jiří Zahradník
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M.E. Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Helen M. Ginn
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aiste Dijokaite
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Suman Khan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mohammad Bahar
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Sandra Adele
- Peter Medawar Building for Pathogen Research, Oxford, UK
| | | | - Ali Amini
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Thomas Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chris Mason
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christina Dold
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Daniel Pan
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust,
- Department of Respiratory Sciences, University of Leicester
| | - Sara Assadi
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust,
| | - Adam Bellass
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust,
| | - Nikki Omo-Dare
- Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust,
| | | | - Amy Flaxman
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Jenkin
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Parvinder K Aley
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sue Ann Costa Clemens
- Institute of Global Health, University of Siena, Siena, Brazil; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Felipe Gomes Naveca
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Valdinete Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | - Fernanda Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | | | | | - Alex Pauvolid-Correa
- Laboratorio de vírus respiratórios- IOC/FIOCRUZ, Rio de Janeiro, Brazil
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | | | - Vicky Baillie
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Natali Serafin
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zanele Ditse
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kelly Da Silva
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tariq Malik
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | | | - J Kenneth Baillie
- Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Alain R Townsend
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Kuan-Ying A. Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Miles W. Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J. Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, Oxford, UK
- Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand, Department of Medicine, University of Oxford, Oxford, UK
| | | | - Hermione Webster
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | | | | | - Neil G. Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A. Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R. Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E. Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
- corresponding authors: , , , ,
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- corresponding authors: , , , ,
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- corresponding authors: , , , ,
| | - David I. Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK
- corresponding authors: , , , ,
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- corresponding authors: , , , ,
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220
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Li X. Omicron: Call for updated vaccines. J Med Virol 2021; 94:1261-1263. [PMID: 34927258 DOI: 10.1002/jmv.27530] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/09/2022]
Abstract
The Omicron SARS-CoV-2 variant was potentially generated from a chronically infected COVID-19 patient vaccinated with an messenger RNA (mRNA)- or non-mRNA-based vaccine, offering the opportunity for the virus to evolve and mutate to evade the body's immune response. To understand the significance of this SARS-CoV-2 variant and what it means for the global response to the pandemic, vaccinologists should systematically evaluate the role of mRNA- and non-mRNA-based vaccines in the generation of novel SARS-CoV-2 variants, including variants of concerns (VOCs) and interest (VOIs), that occur via breakthrough vaccine-elicited immunity. Although COVID vaccine boosters are likely to offer some protection and mRNA- or non-mRNA-based vaccines can be adapted to new variants, such as Omicron, the requirement of a booster so soon after full vaccination, with further shots potentially required, is of concern given the impacts on human health. Therefore, in the race to protect the global population against novel SARS-CoV-2 VOCs and VOIs, there is an urgent need to create much more effective one-dose vaccines that can protect people over their entire lifetime.
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Affiliation(s)
- Xingguang Li
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
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221
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Quarleri J, Galvan V, Delpino MV. Omicron variant of the SARS-CoV-2: a quest to define the consequences of its high mutational load. GeroScience 2021; 44:53-56. [PMID: 34921354 PMCID: PMC8683309 DOI: 10.1007/s11357-021-00500-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 01/18/2023] Open
Affiliation(s)
- Jorge Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Medicina, Consejo de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Veronica Galvan
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Center for Geroscience and Healthy Brain Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Research Health Scientist, US Department of Veterans Affairs, Oklahoma City VA Health Care System, Oklahoma City, OK, USA
| | - M Victoria Delpino
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Medicina, Consejo de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
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222
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Zahradník J, Dey D, Marciano S, Kolářová L, Charendoff CI, Subtil A, Schreiber G. A Protein-Engineered, Enhanced Yeast Display Platform for Rapid Evolution of Challenging Targets. ACS Synth Biol 2021; 10:3445-3460. [PMID: 34809429 PMCID: PMC8689690 DOI: 10.1021/acssynbio.1c00395] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Indexed: 02/08/2023]
Abstract
Here, we enhanced the popular yeast display method by multiple rounds of DNA and protein engineering. We introduced surface exposure-tailored reporters, eUnaG2 and DnbALFA, creating a new platform of C and N terminal fusion vectors. The optimization of eUnaG2 resulted in five times brighter fluorescence and 10 °C increased thermostability than UnaG. The optimized DnbALFA has 10-fold the level of expression of the starting protein. Following this, different plasmids were developed to create a complex platform allowing a broad range of protein expression organizations and labeling strategies. Our platform showed up to five times better separation between nonexpressing and expressing cells compared with traditional pCTcon2 and c-myc labeling, allowing for fewer rounds of selection and achieving higher binding affinities. Testing 16 different proteins, the enhanced system showed consistently stronger expression signals over c-myc labeling. In addition to gains in simplicity, speed, and cost-effectiveness, new applications were introduced to monitor protein surface exposure and protein retention in the secretion pathway that enabled successful protein engineering of hard-to-express proteins. As an example, we show how we optimized the WD40 domain of the ATG16L1 protein for yeast surface and soluble bacterial expression, starting from a nonexpressing protein. As a second example, we show how using the here-presented enhanced yeast display method we rapidly selected high-affinity binders toward two protein targets, demonstrating the simplicity of generating new protein-protein interactions. While the methodological changes are incremental, it results in a qualitative enhancement in the applicability of yeast display for many applications.
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Affiliation(s)
- Jiří Zahradník
- Weizmann
Institute of Science, Herzl St. 234, Rehovot 7610001, Israel
| | - Debabrata Dey
- Weizmann
Institute of Science, Herzl St. 234, Rehovot 7610001, Israel
| | - Shir Marciano
- Weizmann
Institute of Science, Herzl St. 234, Rehovot 7610001, Israel
| | - Lucie Kolářová
- Institute
of Biotechnology, CAS v.v.i., Prumyslova 595, Vestec 252 50 Prague region, Czech Republic
| | - Chloé I. Charendoff
- Institut
Pasteur, Unité de Biologie cellulaire de l’infection
microbienne, 25 rue du Dr Roux, Paris 75015, France
| | - Agathe Subtil
- Institut
Pasteur, Unité de Biologie cellulaire de l’infection
microbienne, 25 rue du Dr Roux, Paris 75015, France
| | - Gideon Schreiber
- Weizmann
Institute of Science, Herzl St. 234, Rehovot 7610001, Israel
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223
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Lubin JH, Markosian C, Balamurugan D, Pasqualini R, Arap W, Burley SK, Khare SD. Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.12.472313. [PMID: 34931193 PMCID: PMC8687476 DOI: 10.1101/2021.12.12.472313] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There is enormous ongoing interest in characterizing the binding properties of the SARS-CoV-2 Omicron Variant of Concern (VOC) (B.1.1.529), which continues to spread towards potential dominance worldwide. To aid these studies, based on the wealth of available structural information about several SARS-CoV-2 variants in the Protein Data Bank (PDB) and a modeling pipeline we have previously developed for tracking the ongoing global evolution of SARS-CoV-2 proteins, we provide a set of computed structural models (henceforth models) of the Omicron VOC receptor-binding domain (omRBD) bound to its corresponding receptor Angiotensin-Converting Enzyme (ACE2) and a variety of therapeutic entities, including neutralizing and therapeutic antibodies targeting previously-detected viral strains. We generated bound omRBD models using both experimentally-determined structures in the PDB as well as machine learningbased structure predictions as starting points. Examination of ACE2-bound omRBD models reveals an interdigitated multi-residue interaction network formed by omRBD-specific substituted residues (R493, S496, Y501, R498) and ACE2 residues at the interface, which was not present in the original Wuhan-Hu-1 RBD-ACE2 complex. Emergence of this interaction network suggests optimization of a key region of the binding interface, and positive cooperativity among various sites of residue substitutions in omRBD mediating ACE2 binding. Examination of neutralizing antibody complexes for Barnes Class 1 and Class 2 antibodies modeled with omRBD highlights an overall loss of interfacial interactions (with gain of new interactions in rare cases) mediated by substituted residues. Many of these substitutions have previously been found to independently dampen or even ablate antibody binding, and perhaps mediate antibody-mediated neutralization escape ( e.g ., K417N). We observe little compensation of corresponding interaction loss at interfaces when potential escape substitutions occur in combination. A few selected antibodies ( e.g ., Barnes Class 3 S309), however, feature largely unaltered or modestly affected protein-protein interfaces. While we stress that only qualitative insights can be obtained directly from our models at this time, we anticipate that they can provide starting points for more detailed and quantitative computational characterization, and, if needed, redesign of monoclonal antibodies for targeting the Omicron VOC Spike protein. In the broader context, the computational pipeline we developed provides a framework for rapidly and efficiently generating retrospective and prospective models for other novel variants of SARS-CoV-2 bound to entities of virological and therapeutic interest, in the setting of a global pandemic.
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Affiliation(s)
- Joseph H. Lubin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
| | - Christopher Markosian
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - D. Balamurugan
- Office of Advanced Research Computing, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
| | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey, Newark, NJ 07101
- Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103
| | - Stephen K. Burley
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
- RCSB Protein Data Bank, San Diego Supercomputer Center and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92067
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854
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224
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Gunnels TF, Stranford DM, Mitrut RE, Kamat NP, Leonard JN. Elucidating design principles for engineering cell-derived vesicles to inhibit SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.04.471153. [PMID: 34909773 PMCID: PMC8669840 DOI: 10.1101/2021.12.04.471153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The ability of pathogens to develop drug resistance is a global health challenge. The SARS-CoV-2 virus presents an urgent need wherein several variants of concern resist neutralization by monoclonal antibody therapies and vaccine-induced sera. Decoy nanoparticles-cell-mimicking particles that bind and inhibit virions-are an emerging class of therapeutics that may overcome such drug resistance challenges. To date, we lack quantitative understanding as to how design features impact performance of these therapeutics. To address this gap, here we perform a systematic, comparative evaluation of various biologically-derived nanoscale vesicles, which may be particularly well-suited to sustained or repeated administration in the clinic due to low toxicity, and investigate their potential to inhibit multiple classes of model SARS-CoV-2 virions. A key finding is that such particles exhibit potent antiviral efficacy across multiple manufacturing methods, vesicle subclasses, and virus-decoy binding affinities. In addition, these cell-mimicking vesicles effectively inhibit model SARS-CoV-2 variants that evade monoclonal antibodies and recombinant protein-based decoy inhibitors. This study provides a foundation of knowledge that may guide the design of decoy nanoparticle inhibitors for SARS-CoV-2 and other viral infections.
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Affiliation(s)
- Taylor F. Gunnels
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Devin M. Stranford
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Roxana E. Mitrut
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Neha P. Kamat
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Joshua N. Leonard
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
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225
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Miller NL, Clark T, Raman R, Sasisekharan R. Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.06.471499. [PMID: 34909771 PMCID: PMC8669838 DOI: 10.1101/2021.12.06.471499] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The SARS-COV2 Omicron variant has sparked global concern due to the possibility of enhanced transmissibility and escape from vaccines and therapeutics. In this study, we describe the mutational landscape of the Omicron variant using amino acid interaction (AAI) networks. AAI network analysis is particularly well suited for interrogating the impact of constellations of mutations as occur on Omicron that may function in an epistatic manner. Our analyses suggest that as compared to previous variants of concern, the Omicron variant has increased antibody escape breadth due to mutations in class 3 and 4 antibody epitopes as well as increased escape depth due to accumulated mutations in class 1 antibody epitopes. We note certain RBD mutations that might further enhance Omicron's escape, and in particular advise careful surveillance of two subclades bearing R346S/K mutations with relevance for certain therapeutic antibodies. Further, AAI network analysis suggests that the function of certain therapeutic monoclonal antibodies may be disrupted by Omicron mutations as a result of the cumulative indirect perturbations to the epitope surface properties, despite point-mutation analyses suggesting these antibodies are tolerant of the set of Omicron mutations in isolation. Finally, for several Omicron mutations that do not appear to contribute meaningfully to antibody escape, we find evidence for a plausible role in enhanced transmissibility via disruption of RBD-down conformational stability at the RBD-RBD interface.
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Affiliation(s)
- Nathaniel L. Miller
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Thomas Clark
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rahul Raman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ram Sasisekharan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Singapore-MIT Alliance in Research and Technology (SMART), Singapore 138602, Singapore
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226
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Ingraham NE, Ingbar DH. The omicron variant of SARS-CoV-2: Understanding the known and living with unknowns. Clin Transl Med 2021; 11:e685. [PMID: 34911167 PMCID: PMC8673343 DOI: 10.1002/ctm2.685] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022] Open
Abstract
The recently discovered Omicron variant of SARS-CoV-2 has rapidly burst into the public and scientific eye, being detected in more than 26 countries around the world. Given its more than 50 mutations, there is widespread concern about its public health impact, leading the World Health Organization to designate it a variant of concern. This Commentary provides a summary of current knowledge and unknowns about this viral variant as of December 2, 2021 and summarizes the key questions that need to be rapidly answered.
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Affiliation(s)
- Nicholas E. Ingraham
- PulmonaryAllergyCritical Care, and Sleep Medicine DivisionDepartment of MedicineUniversity of Minnesota Twin CitiesMinneapolisMinnesotaUSA
| | - David H. Ingbar
- PulmonaryAllergyCritical Care, and Sleep Medicine DivisionDepartment of MedicineUniversity of Minnesota Twin CitiesMinneapolisMinnesotaUSA
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227
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Chaouat AE, Achdout H, Kol I, Berhani O, Roi G, Vitner EB, Melamed S, Politi B, Zahavy E, Brizic I, Lenac Rovis T, Alfi O, Wolf D, Jonjic S, Israely T, Mandelboim O. SARS-CoV-2 receptor binding domain fusion protein efficiently neutralizes virus infection. PLoS Pathog 2021; 17:e1010175. [PMID: 34929007 PMCID: PMC8722722 DOI: 10.1371/journal.ppat.1010175] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 01/03/2022] [Accepted: 12/03/2021] [Indexed: 01/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic. Currently, as dangerous mutations emerge, there is an increased demand for specific treatments for SARS-CoV-2 infected patients. The spike glycoprotein on the virus envelope binds to the angiotensin converting enzyme 2 (ACE2) on host cells through its receptor binding domain (RBD) to mediate virus entry. Thus, blocking this interaction may inhibit viral entry and consequently stop infection. Here, we generated fusion proteins composed of the extracellular portions of ACE2 and RBD fused to the Fc portion of human IgG1 (ACE2-Ig and RBD-Ig, respectively). We demonstrate that ACE2-Ig is enzymatically active and that it can be recognized by the SARS-CoV-2 RBD, independently of its enzymatic activity. We further show that RBD-Ig efficiently inhibits in-vivo SARS-CoV-2 infection better than ACE2-Ig. Mechanistically, we show that anti-spike antibody generation, ACE2 enzymatic activity, and ACE2 surface expression were not affected by RBD-Ig. Finally, we show that RBD-Ig is more efficient than ACE2-Ig at neutralizing high virus titers. We thus propose that RBD-Ig physically blocks virus infection by binding to ACE2 and that RBD-Ig should be used for the treatment of SARS-CoV-2-infected patients.
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Affiliation(s)
- Abigael Eva Chaouat
- The Concern Foundation Laboratories at the Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research Israel Canada (IMRIC), The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Hagit Achdout
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Inbal Kol
- The Concern Foundation Laboratories at the Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research Israel Canada (IMRIC), The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Orit Berhani
- The Concern Foundation Laboratories at the Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research Israel Canada (IMRIC), The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Gil Roi
- The Concern Foundation Laboratories at the Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research Israel Canada (IMRIC), The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Einat B. Vitner
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Sharon Melamed
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Boaz Politi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Eran Zahavy
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ilija Brizic
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Tihana Lenac Rovis
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Or Alfi
- Lautenberg Center for General and Tumor Immunology, The Hebrew University Faculty of Medicine, Jerusalem, Israel
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Dana Wolf
- Lautenberg Center for General and Tumor Immunology, The Hebrew University Faculty of Medicine, Jerusalem, Israel
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Stipan Jonjic
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofer Mandelboim
- The Concern Foundation Laboratories at the Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research Israel Canada (IMRIC), The Hebrew University Hadassah Medical School, Jerusalem, Israel
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228
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Kimura I, Kosugi Y, Wu J, Zahradnik J, Yamasoba D, Butlertanaka EP, Tanaka YL, Uriu K, Liu Y, Morizako N, Shirakawa K, Kazuma Y, Nomura R, Horisawa Y, Tokunaga K, Ueno T, Takaori-Kondo A, Schreiber G, Arase H, Motozono C, Saito A, Nakagawa S, Sato K. The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Cell Rep 2021; 38:110218. [PMID: 34968415 PMCID: PMC8683271 DOI: 10.1016/j.celrep.2021.110218] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/24/2021] [Accepted: 12/14/2021] [Indexed: 12/20/2022] Open
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229
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Vöhringer HS, Sanderson T, Sinnott M, De Maio N, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani CV, Gonçalves S, Jackson DK, Johnston I, Jung AW, Saint C, Sillitoe J, Suciu M, Goldman N, Panovska-Griffiths J, Birney E, Volz E, Funk S, Kwiatkowski D, Chand M, Martincorena I, Barrett JC, Gerstung M. Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature 2021; 600:506-511. [PMID: 34649268 PMCID: PMC8674138 DOI: 10.1038/s41586-021-04069-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/29/2021] [Indexed: 11/09/2022]
Abstract
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.
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Affiliation(s)
- Harald S Vöhringer
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK
| | - Theo Sanderson
- Wellcome Sanger Institute, Hinxton, UK
- The Francis Crick Institute, London, UK
| | | | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK
| | | | | | - Frank Schwach
- Wellcome Sanger Institute, Hinxton, UK
- Public Health England, London, UK
| | | | - Joel Hellewell
- London School of Hygiene & Tropical Medicine, London, UK
| | | | | | | | | | - Alexander W Jung
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK
| | | | | | | | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK
| | | | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK
| | - Erik Volz
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Sebastian Funk
- London School of Hygiene & Tropical Medicine, London, UK
| | | | - Meera Chand
- Public Health England, London, UK
- Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | | | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK.
- Division for AI in Oncology, German Cancer Research Centre DKFZ, Heidelberg, Germany.
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230
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Schepens B, van Schie L, Nerinckx W, Roose K, Van Breedam W, Fijalkowska D, Devos S, Weyts W, De Cae S, Vanmarcke S, Lonigro C, Eeckhaut H, Van Herpe D, Borloo J, Oliveira AF, Catani JPP, Creytens S, De Vlieger D, Michielsen G, Marchan JCZ, Moschonas GD, Rossey I, Sedeyn K, Van Hecke A, Zhang X, Langendries L, Jacobs S, Ter Horst S, Seldeslachts L, Liesenborghs L, Boudewijns R, Thibaut HJ, Dallmeier K, Velde GV, Weynand B, Beer J, Schnepf D, Ohnemus A, Remory I, Foo CS, Abdelnabi R, Maes P, Kaptein SJF, Rocha-Pereira J, Jochmans D, Delang L, Peelman F, Staeheli P, Schwemmle M, Devoogdt N, Tersago D, Germani M, Heads J, Henry A, Popplewell A, Ellis M, Brady K, Turner A, Dombrecht B, Stortelers C, Neyts J, Callewaert N, Saelens X. An affinity-enhanced, broadly neutralizing heavy chain-only antibody protects against SARS-CoV-2 infection in animal models. Sci Transl Med 2021; 13:eabi7826. [PMID: 34609205 PMCID: PMC9924070 DOI: 10.1126/scitranslmed.abi7826] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Broadly neutralizing antibodies are an important treatment for individuals with coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Antibody-based therapeutics are also essential for pandemic preparedness against future Sarbecovirus outbreaks. Camelid-derived single domain antibodies (VHHs) exhibit potent antimicrobial activity and are being developed as SARS-CoV-2–neutralizing antibody-like therapeutics. Here, we identified VHHs that neutralize both SARS-CoV-1 and SARS-CoV-2, including now circulating variants. We observed that the VHHs bound to a highly conserved epitope in the receptor binding domain of the viral spike protein that is difficult to access for human antibodies. Structure-guided molecular modeling, combined with rapid yeast-based prototyping, resulted in an affinity enhanced VHH-human immunoglobulin G1 Fc fusion molecule with subnanomolar neutralizing activity. This VHH-Fc fusion protein, produced in and purified from cultured Chinese hamster ovary cells, controlled SARS-CoV-2 replication in prophylactic and therapeutic settings in mice expressing human angiotensin converting enzyme 2 and in hamsters infected with SARS-CoV-2. These data led to affinity-enhanced selection of the VHH, XVR011, a stable anti–COVID-19 biologic that is now being evaluated in the clinic.
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Affiliation(s)
- Bert Schepens
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Loes van Schie
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Wim Nerinckx
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Kenny Roose
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Wander Van Breedam
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Daria Fijalkowska
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Simon Devos
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Wannes Weyts
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Sieglinde De Cae
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Sandrine Vanmarcke
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Chiara Lonigro
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Hannah Eeckhaut
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Dries Van Herpe
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Jimmy Borloo
- VIB Discovery Sciences, Technologiepark-Zwijnaarde 104B, 9052 Ghent, Belgium
| | - Ana Filipa Oliveira
- VIB Discovery Sciences, Technologiepark-Zwijnaarde 104B, 9052 Ghent, Belgium
| | - João Paulo Portela Catani
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Sarah Creytens
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Dorien De Vlieger
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Gitte Michielsen
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Jackeline Cecilia Zavala Marchan
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - George D Moschonas
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Iebe Rossey
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Koen Sedeyn
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Annelies Van Hecke
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Xin Zhang
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium.,GVN, Global Virus Network, Baltimore, MD 21201, USA
| | - Lana Langendries
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium.,GVN, Global Virus Network, Baltimore, MD 21201, USA
| | - Sofie Jacobs
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium.,GVN, Global Virus Network, Baltimore, MD 21201, USA
| | - Sebastiaan Ter Horst
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium.,GVN, Global Virus Network, Baltimore, MD 21201, USA
| | - Laura Seldeslachts
- KU Leuven Department of Imaging and Pathology, Biomedical MRI and MoSAIC, 3000 Leuven, Belgium
| | - Laurens Liesenborghs
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium.,GVN, Global Virus Network, Baltimore, MD 21201, USA
| | - Robbert Boudewijns
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium.,GVN, Global Virus Network, Baltimore, MD 21201, USA.,KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery Group, 3000 Leuven, Belgium
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium.,KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery Group, 3000 Leuven, Belgium.,KU Leuven Department of Microbiology, Immunology and Transplantation, Translational Platform Virology and Chemotherapy (TPVC), Rega Institute, 3000 Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium.,GVN, Global Virus Network, Baltimore, MD 21201, USA.,KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery Group, 3000 Leuven, Belgium
| | - Greetje Vande Velde
- KU Leuven Department of Imaging and Pathology, Biomedical MRI and MoSAIC, 3000 Leuven, Belgium
| | - Birgit Weynand
- KU Leuven Department of Imaging and Pathology, Division of Translational Cell and Tissue Research, Translational Cell and Tissue Research, 3000 Leuven, Belgium
| | - Julius Beer
- Institute of Virology, Medical Center University Freiburg, 79104 Freiburg, Germany
| | - Daniel Schnepf
- Institute of Virology, Medical Center University Freiburg, 79104 Freiburg, Germany
| | - Annette Ohnemus
- Institute of Virology, Medical Center University Freiburg, 79104 Freiburg, Germany
| | - Isabel Remory
- Department of Medical Imaging, In vivo Cellular and Molecular Imaging Laboratory, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Caroline S Foo
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium
| | - Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium.,GVN, Global Virus Network, Baltimore, MD 21201, USA
| | - Piet Maes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, 3000 Leuven, Belgium
| | - Suzanne J F Kaptein
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium.,GVN, Global Virus Network, Baltimore, MD 21201, USA
| | - Joana Rocha-Pereira
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium.,GVN, Global Virus Network, Baltimore, MD 21201, USA
| | - Dirk Jochmans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium.,GVN, Global Virus Network, Baltimore, MD 21201, USA
| | - Leen Delang
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium.,GVN, Global Virus Network, Baltimore, MD 21201, USA
| | - Frank Peelman
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Peter Staeheli
- Institute of Virology, Medical Center University Freiburg, 79104 Freiburg, Germany.,Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Martin Schwemmle
- Institute of Virology, Medical Center University Freiburg, 79104 Freiburg, Germany.,Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Nick Devoogdt
- Department of Medical Imaging, In vivo Cellular and Molecular Imaging Laboratory, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | | | | | | | | | | | | | | | | | - Bruno Dombrecht
- VIB Discovery Sciences, Technologiepark-Zwijnaarde 104B, 9052 Ghent, Belgium
| | | | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium.,GVN, Global Virus Network, Baltimore, MD 21201, USA.,KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery Group, 3000 Leuven, Belgium
| | - Nico Callewaert
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
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Marques AD, Sherrill-Mix S, Everett J, Reddy S, Hokama P, Roche AM, Hwang Y, Glascock A, Whiteside SA, Graham-Wooten J, Khatib LA, Fitzgerald AS, Moustafa AM, Bianco C, Rajagopal S, Helton J, Deming R, Denu L, Ahmed A, Kitt E, Coffin SE, Newbern C, Mell JC, Planet PJ, Badjatia N, Richards B, Wang ZX, Cannuscio CC, Strelau KM, Jaskowiak-Barr A, Cressman L, Loughrey S, Ganguly A, Feldman MD, Collman RG, Rodino KG, Kelly BJ, Bushman FD. SARS-CoV-2 variants associated with vaccine breakthrough in the Delaware Valley through summer 2021. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.10.18.21264623. [PMID: 34704098 PMCID: PMC8547530 DOI: 10.1101/2021.10.18.21264623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The severe acute respiratory coronavirus-2 (SARS-CoV-2) is the cause of the global outbreak of COVID-19. Evidence suggests that the virus is evolving to allow efficient spread through the human population, including vaccinated individuals. Here we report a study of viral variants from surveillance of the Delaware Valley, including the city of Philadelphia, and variants infecting vaccinated subjects. We sequenced and analyzed complete viral genomes from 2621 surveillance samples from March 2020 to September 2021 and compared them to genome sequences from 159 vaccine breakthroughs. In the early spring of 2020, all detected variants were of the B.1 and closely related lineages. A mixture of lineages followed, notably including B.1.243 followed by B.1.1.7 (alpha), with other lineages present at lower levels. Later isolations were dominated by B.1.617.2 (delta) and other delta lineages; delta was the exclusive variant present by the last time sampled. To investigate whether any variants appeared preferentially in vaccine breakthroughs, we devised a model based on Bayesian autoregressive moving average logistic multinomial regression to allow rigorous comparison. This revealed that B.1.617.2 (delta) showed three-fold enrichment in vaccine breakthrough cases (odds ratio of 3; 95% credible interval 0.89-11). Viral point substitutions could also be associated with vaccine breakthroughs, notably the N501Y substitution found in the alpha, beta and gamma variants (odds ratio 2.04; 95% credible interval of 1.25-3.18). This study thus provides a detailed picture of viral evolution in the Delaware Valley and a geographically matched analysis of vaccine breakthroughs; it also introduces a rigorous statistical approach to interrogating enrichment of viral variants.
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Affiliation(s)
- Andrew D. Marques
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - John Everett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Shantan Reddy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Pascha Hokama
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Aoife M. Roche
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Young Hwang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Abigail Glascock
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Samantha A. Whiteside
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
| | - Jevon Graham-Wooten
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
| | - Layla A. Khatib
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
| | - Ayannah S. Fitzgerald
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
| | - Ahmed M. Moustafa
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA
- Division of Gastroenterology, Hepatology & Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Colleen Bianco
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Swetha Rajagopal
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Jenna Helton
- Division of COVID-19 Containment, Philadelphia Department of Public Health, Philadelphia, PA
| | - Regan Deming
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Lidiya Denu
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Azad Ahmed
- Department of Microbiology & Immunology, Center for Genomic Sciences, Drexel University College of Medicine. Philadelphia, PA
| | - Eimear Kitt
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Susan E. Coffin
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Claire Newbern
- Division of COVID-19 Containment, Philadelphia Department of Public Health, Philadelphia, PA
| | - Josh Chang Mell
- Department of Microbiology & Immunology, Center for Genomic Sciences, Drexel University College of Medicine. Philadelphia, PA
| | - Paul J. Planet
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY
| | - Nitika Badjatia
- Molecular & Genomic Pathology Laboratory, Thomas Jefferson University Hospital, Philadelphia, PA
| | - Bonnie Richards
- Jefferson Occupational Health Network for Employees and Students (JOHN), Thomas Jefferson University, Philadelphia, PA
| | - Zi-Xuan Wang
- Molecular & Genomic Pathology Laboratory, Thomas Jefferson University Hospital, Philadelphia, PA
- Department of Anatomy, Pathology, and Cell Biology, Thomas Jefferson University Hospital, Philadelphia, PA
| | - Carolyn C. Cannuscio
- Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia, PA
- Department of Family Medicine and Community Health, University of Pennsylvania, Philadelphia, PA
| | - Katherine M. Strelau
- Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia, PA
- Department of Family Medicine and Community Health, University of Pennsylvania, Philadelphia, PA
| | - Anne Jaskowiak-Barr
- Division of Infectious Diseases; Department of Medicine & Department of Biostatistics, Epidemiology, and Informatics; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Leigh Cressman
- Division of Infectious Diseases; Department of Medicine & Department of Biostatistics, Epidemiology, and Informatics; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Sean Loughrey
- Division of Infectious Diseases; Department of Medicine & Department of Biostatistics, Epidemiology, and Informatics; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Arupa Ganguly
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Michael D. Feldman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ronald G. Collman
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA
| | - Kyle G. Rodino
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Brendan J. Kelly
- Division of Infectious Diseases; Department of Medicine & Department of Biostatistics, Epidemiology, and Informatics; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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232
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Zhang Y, Ye T, Xi H, Juhas M, Li J. Deep Learning Driven Drug Discovery: Tackling Severe Acute Respiratory Syndrome Coronavirus 2. Front Microbiol 2021; 12:739684. [PMID: 34777286 PMCID: PMC8581544 DOI: 10.3389/fmicb.2021.739684] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
Deep learning significantly accelerates the drug discovery process, and contributes to global efforts to stop the spread of infectious diseases. Besides enhancing the efficiency of screening of antimicrobial compounds against a broad spectrum of pathogens, deep learning has also the potential to efficiently and reliably identify drug candidates against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Consequently, deep learning has been successfully used for the identification of a number of potential drugs against SARS-CoV-2, including Atazanavir, Remdesivir, Kaletra, Enalaprilat, Venetoclax, Posaconazole, Daclatasvir, Ombitasvir, Toremifene, Niclosamide, Dexamethasone, Indomethacin, Pralatrexate, Azithromycin, Palmatine, and Sauchinone. This mini-review discusses recent advances and future perspectives of deep learning-based SARS-CoV-2 drug discovery.
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Affiliation(s)
- Yang Zhang
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, China
| | - Taoyu Ye
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, China
| | - Hui Xi
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, China
| | - Mario Juhas
- Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Junyi Li
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, China
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233
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Puligedda RD, Al-Saleem FH, Wirblich C, Kattala CD, Jović M, Geiszler L, Devabhaktuni H, Feuerstein GZ, Schnell MJ, Sack M, Livornese LL, Dessain SK. A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. Diagnostics (Basel) 2021; 11:2092. [PMID: 34829439 PMCID: PMC8625484 DOI: 10.3390/diagnostics11112092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/18/2022] Open
Abstract
Efforts to control SARS-CoV-2 have been challenged by the emergence of variant strains that have important implications for clinical and epidemiological decision making. Four variants of concern (VOCs) have been designated by the Centers for Disease Control and Prevention (CDC), namely, B.1.617.2 (delta), B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma), although the last three have been downgraded to variants being monitored (VBMs). VOCs and VBMs have shown increased transmissibility and/or disease severity, resistance to convalescent SARS-CoV-2 immunity and antibody therapeutics, and the potential to evade diagnostic detection. Methods are needed for point-of-care (POC) testing to rapidly identify these variants, protect vulnerable populations, and improve surveillance. Antigen-detection rapid diagnostic tests (Ag-RDTs) are ideal for POC use, but Ag-RDTs that recognize specific variants have not yet been implemented. Here, we describe a mAb (2E8) that is specific for the SARS-CoV-2 spike protein N501 residue. The 2E8 mAb can distinguish the delta VOC from variants with the N501Y meta-signature, which is characterized by convergent mutations that contribute to increased virulence and evasion of host immunity. Among the N501Y-containing mutants formerly designated as VOCs (alpha, beta, and gamma), a previously described mAb, CB6, can distinguish beta from alpha and gamma. When used in a sandwich ELISA, these mAbs sort these important SARS-CoV-2 variants into three diagnostic categories, namely, (1) delta, (2) alpha or gamma, and (3) beta. As delta is currently the predominant variant globally, they will be useful for POC testing to identify N501Y meta-signature variants, protect individuals in high-risk settings, and help detect epidemiological shifts among SARS-CoV-2 variants.
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Affiliation(s)
- Rama Devudu Puligedda
- Center for Human Antibody Technology, Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA; (R.D.P.); (F.H.A.-S.); (C.D.K.); (H.D.)
| | - Fetweh H. Al-Saleem
- Center for Human Antibody Technology, Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA; (R.D.P.); (F.H.A.-S.); (C.D.K.); (H.D.)
| | - Cristoph Wirblich
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (C.W.); (M.J.S.)
| | - Chandana Devi Kattala
- Center for Human Antibody Technology, Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA; (R.D.P.); (F.H.A.-S.); (C.D.K.); (H.D.)
| | - Marko Jović
- Nicoya Lifesciences, Kitchener, ON N2G 2K4, Canada;
| | - Laura Geiszler
- Department of Internal Medicine, Lankenau Medical Center, Wynnewood, PA 19096, USA; (L.G.); (L.L.L.J.)
| | - Himani Devabhaktuni
- Center for Human Antibody Technology, Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA; (R.D.P.); (F.H.A.-S.); (C.D.K.); (H.D.)
| | | | - Matthias J. Schnell
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (C.W.); (M.J.S.)
| | | | - Lawrence L. Livornese
- Department of Internal Medicine, Lankenau Medical Center, Wynnewood, PA 19096, USA; (L.G.); (L.L.L.J.)
| | - Scott K. Dessain
- Center for Human Antibody Technology, Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA; (R.D.P.); (F.H.A.-S.); (C.D.K.); (H.D.)
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (C.W.); (M.J.S.)
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234
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Dong Y, Dai T, Wang B, Zhang L, Zeng LH, Huang J, Yan H, Zhang L, Zhou F. The way of SARS-CoV-2 vaccine development: success and challenges. Signal Transduct Target Ther 2021; 6:387. [PMID: 34753918 PMCID: PMC8575680 DOI: 10.1038/s41392-021-00796-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/10/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). To halt the pandemic, multiple SARS-CoV-2 vaccines have been developed and several have been allowed for emergency use and rollout worldwide. With novel SARS-CoV-2 variants emerging and circulating widely, whether the original vaccines that were designed based on the wild-type SARS-CoV-2 were effective against these variants has been a contentious discussion. Moreover, some studies revealed the long-term changes of immune responses post SARS-CoV-2 infection or vaccination and the factors that might impact the vaccine-induced immunity. Thus, in this review, we have summarized the influence of mutational hotspots on the vaccine efficacy and characteristics of variants of interest and concern. We have also discussed the reasons that might result in discrepancies in the efficacy of different vaccines estimated in different trials. Furthermore, we provided an overview of the duration of immune responses after natural infection or vaccination and shed light on the factors that may affect the immunity induced by the vaccines, such as special disease conditions, sex, and pre-existing immunity, with the aim of aiding in combating COVID-19 and distributing SARS-CoV-2 vaccines under the prevalence of diverse SARS-CoV-2 variants.
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Affiliation(s)
- Yetian Dong
- School of Medicine, Zhejiang University City College, Hangzhou, 310015, Zhejiang, China
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Orthopaedic Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Rui'an, China
| | - Tong Dai
- Institutes of Biology and Medical Science, Soochow University, Suzhou 215123, China
| | - Bin Wang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lei Zhang
- Department of Orthopaedic Surgery, The Third Affiliated Hospital of Wenzhou Medical University, Rui'an, China
| | - Ling-Hui Zeng
- School of Medicine, Zhejiang University City College, Hangzhou, 310015, Zhejiang, China
| | - Jun Huang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Haiyan Yan
- School of Medicine, Zhejiang University City College, Hangzhou, 310015, Zhejiang, China
| | - Long Zhang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou 215123, China.
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235
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Ahmad L. Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. Front Immunol 2021; 12:742167. [PMID: 34804022 PMCID: PMC8596465 DOI: 10.3389/fimmu.2021.742167] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/14/2021] [Indexed: 11/20/2022] Open
Abstract
COVID-19 pandemic remains an on-going global health and economic threat that has amassed millions of deaths. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of this disease and is constantly under evolutionary pressures that drive the modification of its genome which may represent a threat to the efficacy of current COVID-19 vaccines available. This article highlights the pressures that facilitate the rise of new SARS-CoV-2 variants and the key mutations of the viral spike protein - L452R, E484K, N501Y and D614G- that promote immune escape mechanism and warrant a cautionary point for clinical and public health responses in terms of re-infection, vaccine breakthrough infection and therapeutic values.
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Affiliation(s)
- Liyana Ahmad
- Pengiran Anak Puteri Rashidah Sa'adatul Bolkiah (PAPRSB) Institute of Health Sciences, Universiti Brunei Darussalam, Bandar Seri Begawan, Brunei
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236
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Conquer by cryo-EM without physically dividing. Biochem Soc Trans 2021; 49:2287-2298. [PMID: 34709401 DOI: 10.1042/bst20210360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 12/15/2022]
Abstract
This mini-review provides an update regarding the substantial progress that has been made in using single-particle cryo-EM to obtain high-resolution structures for proteins and other macromolecules whose particle sizes are smaller than 100 kDa. We point out that establishing the limits of what can be accomplished, both in terms of particle size and attainable resolution, serves as a guide for what might be expected when attempting to improve the resolution of small flexible portions of a larger structure using focused refinement approaches. These approaches, which involve computationally ignoring all but a specific, targeted region of interest on the macromolecules, is known as 'masking and refining,' and it thus is the computational equivalent of the 'divide and conquer' approach that has been used so successfully in X-ray crystallography. The benefit of masked refinement, however, is that one is able to determine structures in their native architectural context, without physically separating them from the biological connections that they require for their function. This mini-review also compares where experimental achievements currently stand relative to various theoretical estimates for the smallest particle size that can be successfully reconstructed to high resolution. Since it is clear that a substantial gap still remains between the two, we briefly recap the areas in which further improvement seems possible, both in equipment and in methods.
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237
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Bayarri-Olmos R, Jarlhelt I, Johnsen LB, Hansen CB, Helgstrand C, Rose Bjelke J, Matthiesen F, Nielsen SD, Iversen KK, Ostrowski SR, Bundgaard H, Frikke-Schmidt R, Garred P, Skjoedt MO. Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Front Immunol 2021; 12:757197. [PMID: 34691078 PMCID: PMC8529273 DOI: 10.3389/fimmu.2021.757197] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
The recent identification and rise to dominance of the P.1 and B.1.351 SARS-CoV-2 variants have brought international concern because they may confer fitness advantages. The same three positions in the receptor-binding domain (RBD) are affected in both variants, but where the 417 substitution differs, the E484K/N501Y have co-evolved by convergent evolution. Here we characterize the functional and immune evasive consequences of the P.1 and B.1.351 RBD mutations. E484K and N501Y result in gain-of-function with two different outcomes: The N501Y confers a ten-fold affinity increase towards ACE-2, but a modest antibody evasion potential of plasma from convalescent or vaccinated individuals, whereas the E484K displays a significant antibody evasion capacity without a major impact on affinity. On the other hand, the two different 417 substitutions severely impair the RBD/ACE-2 affinity, but in the combined P.1 and B.1.351 RBD variants, this effect is partly counterbalanced by the effect of the E484K and N501Y. Our results suggest that the combination of these three mutations is a two-step forward and one step back in terms of viral fitness.
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Affiliation(s)
- Rafael Bayarri-Olmos
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ida Jarlhelt
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Cecilie Bo Hansen
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | | | - Susanne Dam Nielsen
- Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kasper Karmark Iversen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Emergency Medicine, Herlev and Gentofte Hospital, Copenhagen, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Blood Bank, Department of Clinical Immunology, Section 2034, Rigshospitalet, Copenhagen, Denmark
| | - Henning Bundgaard
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, Rigshospitalet, Copenhagen, Denmark
| | - Ruth Frikke-Schmidt
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen, Denmark
| | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel-Ole Skjoedt
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Section 7631, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Institute of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
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238
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Rajah MM, Hubert M, Bishop E, Saunders N, Robinot R, Grzelak L, Planas D, Dufloo J, Gellenoncourt S, Bongers A, Zivaljic M, Planchais C, Guivel-Benhassine F, Porrot F, Mouquet H, Chakrabarti LA, Buchrieser J, Schwartz O. SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. EMBO J 2021; 40:e108944. [PMID: 34601723 PMCID: PMC8646911 DOI: 10.15252/embj.2021108944] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/23/2022] Open
Abstract
Severe COVID‐19 is characterized by lung abnormalities, including the presence of syncytial pneumocytes. Syncytia form when SARS‐CoV‐2 spike protein expressed on the surface of infected cells interacts with the ACE2 receptor on neighboring cells. The syncytia forming potential of spike variant proteins remain poorly characterized. Here, we first assessed Alpha (B.1.1.7) and Beta (B.1.351) spread and fusion in cell cultures, compared with the ancestral D614G strain. Alpha and Beta replicated similarly to D614G strain in Vero, Caco‐2, Calu‐3, and primary airway cells. However, Alpha and Beta formed larger and more numerous syncytia. Variant spike proteins displayed higher ACE2 affinity compared with D614G. Alpha, Beta, and D614G fusion was similarly inhibited by interferon‐induced transmembrane proteins (IFITMs). Individual mutations present in Alpha and Beta spikes modified fusogenicity, binding to ACE2 or recognition by monoclonal antibodies. We further show that Delta spike also triggers faster fusion relative to D614G. Thus, SARS‐CoV‐2 emerging variants display enhanced syncytia formation.
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Affiliation(s)
- Maaran Michael Rajah
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Mathieu Hubert
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Creteil, France
| | - Elodie Bishop
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Sorbonne Université, Paris, France
| | - Nell Saunders
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Remy Robinot
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Ludivine Grzelak
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Delphine Planas
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Creteil, France
| | - Jérémy Dufloo
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Stacy Gellenoncourt
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Alice Bongers
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Marija Zivaljic
- Integrative Neurobiology of Cholinergic Systems, Department of Neuroscience, Institut Pasteur, CNRS UMR 3571, Paris, France.,Sorbonne Université, ED3C "Brain, Cognition, Behavior", Paris, France
| | - Cyril Planchais
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, INSERM U1222, Paris, France
| | | | - Françoise Porrot
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Hugo Mouquet
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, INSERM U1222, Paris, France
| | - Lisa A Chakrabarti
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Julian Buchrieser
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
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Rajah MM, Bernier A, Buchrieser J, Schwartz O. The Mechanism and Consequences of SARS-CoV-2 Spike-Mediated Fusion and Syncytia Formation. J Mol Biol 2021; 434:167280. [PMID: 34606831 PMCID: PMC8485708 DOI: 10.1016/j.jmb.2021.167280] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 12/12/2022]
Abstract
Syncytia are formed when individual cells fuse. SARS-CoV-2 induces syncytia when the viral spike (S) protein on the surface of an infected cell interacts with receptors on neighboring cells. Syncytia may potentially contribute to pathology by facilitating viral dissemination, cytopathicity, immune evasion, and inflammatory response. SARS-CoV-2 variants of concern possess several mutations within the S protein that enhance receptor interaction, fusogenicity and antibody binding. In this review, we discuss the molecular determinants of S mediated fusion and the antiviral innate immunity components that counteract syncytia formation. Several interferon-stimulated genes, including IFITMs and LY6E act as barriers to S protein-mediated fusion by altering the composition or biophysical properties of the target membrane. We also summarize the effect that the mutations associated with the variants of concern have on S protein fusogenicity. Altogether, this review contextualizes the current understanding of Spike fusogenicity and the role of syncytia during SARS-CoV-2 infection and pathology.
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Affiliation(s)
- Maaran Michael Rajah
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France; Université de Paris, Sorbonne Paris Cité, Paris, France. https://twitter.com/MaaranRajah
| | - Annie Bernier
- Institut Curie, INSERM U932, Paris, France. https://twitter.com/nini_bernier
| | - Julian Buchrieser
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France. https://twitter.com/JBuchrieser
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France; Université de Paris, Sorbonne Paris Cité, Paris, France; Vaccine Research Institute, Creteil, France.
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240
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Plavec Z, Pöhner I, Poso A, Butcher SJ. Virus structure and structure-based antivirals. Curr Opin Virol 2021; 51:16-24. [PMID: 34564030 PMCID: PMC8460353 DOI: 10.1016/j.coviro.2021.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/13/2021] [Accepted: 09/12/2021] [Indexed: 01/18/2023]
Abstract
Structure-based antiviral developments in the past two years have been dominated by the structure determination and inhibition of SARS-CoV-2 proteins and new lead molecules for picornaviruses. The SARS-CoV-2 spike protein has been targeted successfully with antibodies, nanobodies, and receptor protein mimics effectively blocking receptor binding or fusion. The two most promising non-structural proteins sharing strong structural and functional conservation across virus families are the main protease and the RNA-dependent RNA polymerase, for which design and reuse of broad range inhibitors already approved for use has been an attractive avenue. For picornaviruses, the increasing recognition of the transient expansion of the capsid as a critical transition towards RNA release has been targeted through a newly identified, apparently widely conserved, druggable, interprotomer pocket preventing viral entry. We summarize some of the key papers in these areas and ponder the practical uses and contributions of molecular modeling alongside empirical structure determination.
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Affiliation(s)
- Zlatka Plavec
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Ina Pöhner
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland; University Hospital Tübingen, Department of Internal Medicine VII, Tübingen, Germany
| | - Sarah J Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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241
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Niu S, Wang J, Bai B, Wu L, Zheng A, Chen Q, Du P, Han P, Zhang Y, Jia Y, Qiao C, Qi J, Tian W, Wang H, Wang Q, Gao GF. Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. EMBO J 2021; 40:e107786. [PMID: 34018203 PMCID: PMC8209949 DOI: 10.15252/embj.2021107786] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/08/2021] [Accepted: 05/14/2021] [Indexed: 12/02/2022] Open
Abstract
Pangolins have been suggested as potential reservoir of zoonotic viruses, including SARS-CoV-2 causing the global COVID-19 outbreak. Here, we study the binding of two SARS-CoV-2-like viruses isolated from pangolins, GX/P2V/2017 and GD/1/2019, to human angiotensin-converting enzyme 2 (hACE2), the receptor of SARS-CoV-2. We find that the spike protein receptor-binding domain (RBD) of pangolin CoVs binds to hACE2 as efficiently as the SARS-CoV-2 RBD in vitro. Furthermore, incorporation of pangolin CoV RBDs allows entry of pseudotyped VSV particles into hACE2-expressing cells. A screen for binding of pangolin CoV RBDs to ACE2 orthologs from various species suggests a broader host range than that of SARS-CoV-2. Additionally, cryo-EM structures of GX/P2V/2017 and GD/1/2019 RBDs in complex with hACE2 show their molecular binding in modes similar to SARS-CoV-2 RBD. Introducing the Q498H substitution found in pangolin CoVs into the SARS-CoV-2 RBD expands its binding capacity to ACE2 homologs of mouse, rat, and European hedgehog. These findings suggest that these two pangolin CoVs may infect humans, highlighting the necessity of further surveillance of pangolin CoVs.
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Affiliation(s)
- Sheng Niu
- College of Veterinary MedicineShanxi Agricultural UniversityJinzhongChina
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Jia Wang
- Ministry of Education Key Laboratory of Protein SciencesTsinghua‐Peking Joint Center for Life SciencesBeijing Advanced Innovation Center for Structural BiologyBeijing Frontier Research Center of Biological StructuresSchool of Life SciencesTsinghua UniversityBeijingChina
| | - Bin Bai
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Lili Wu
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Anqi Zheng
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Qian Chen
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Institute of Physical Science and InformationAnhui UniversityHefeiChina
| | - Pei Du
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Pengcheng Han
- Department of biomedical engineeringEmory UniversityAtlantaGAUSA
| | - Yanfang Zhang
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Laboratory of Protein Engineering and VaccinesTianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
| | - Yunfei Jia
- College of Veterinary MedicineShanxi Agricultural UniversityJinzhongChina
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Chengpeng Qiao
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Wen‐xia Tian
- College of Veterinary MedicineShanxi Agricultural UniversityJinzhongChina
| | - Hong‐Wei Wang
- Ministry of Education Key Laboratory of Protein SciencesTsinghua‐Peking Joint Center for Life SciencesBeijing Advanced Innovation Center for Structural BiologyBeijing Frontier Research Center of Biological StructuresSchool of Life SciencesTsinghua UniversityBeijingChina
| | - Qihui Wang
- College of Veterinary MedicineShanxi Agricultural UniversityJinzhongChina
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Institute of Physical Science and InformationAnhui UniversityHefeiChina
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - George Fu Gao
- College of Veterinary MedicineShanxi Agricultural UniversityJinzhongChina
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
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242
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Marques AD, Sherrill-Mix S, Everett JK, Reddy S, Hokama P, Roche AM, Hwang Y, Glascock A, Whiteside SA, Graham-Wooten J, Khatib LA, Fitzgerald AS, Moustafa AM, Bianco C, Rajagopal S, Helton J, Deming R, Denu L, Ahmed A, Kitt E, Coffin SE, Newbern C, Mell JC, Planet PJ, Badjatia N, Richards B, Wang ZX, Cannuscio CC, Strelau KM, Jaskowiak-Barr A, Cressman L, Loughrey S, Ganguly A, Feldman MD, Collman RG, Rodino KG, Kelly BJ, Bushman FD. SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. mBio 2021; 13:e0378821. [PMID: 35130727 PMCID: PMC8942461 DOI: 10.1128/mbio.03788-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/12/2022] [Indexed: 12/29/2022] Open
Abstract
The severe acute respiratory coronavirus-2 (SARS-CoV-2) is the cause of the global outbreak of COVID-19. Evidence suggests that the virus is evolving to allow efficient spread through the human population, including vaccinated individuals. Here, we report a study of viral variants from surveillance of the Delaware Valley, including the city of Philadelphia, and variants infecting vaccinated subjects. We sequenced and analyzed complete viral genomes from 2621 surveillance samples from March 2020 to September 2021 and compared them to genome sequences from 159 vaccine breakthroughs. In the early spring of 2020, all detected variants were of the B.1 and closely related lineages. A mixture of lineages followed, notably including B.1.243 followed by B.1.1.7 (alpha), with other lineages present at lower levels. Later isolations were dominated by B.1.617.2 (delta) and other delta lineages; delta was the exclusive variant present by the last time sampled. To investigate whether any variants appeared preferentially in vaccine breakthroughs, we devised a model based on Bayesian autoregressive moving average logistic multinomial regression to allow rigorous comparison. This revealed that B.1.617.2 (delta) showed 3-fold enrichment in vaccine breakthrough cases (odds ratio of 3; 95% credible interval 0.89-11). Viral point substitutions could also be associated with vaccine breakthroughs, notably the N501Y substitution found in the alpha, beta and gamma variants (odds ratio 2.04; 95% credible interval of1.25-3.18). This study thus overviews viral evolution and vaccine breakthroughs in the Delaware Valley and introduces a rigorous statistical approach to interrogating enrichment of breakthrough variants against a changing background. IMPORTANCE SARS-CoV-2 vaccination is highly effective at reducing viral infection, hospitalization and death. However, vaccine breakthrough infections have been widely observed, raising the question of whether particular viral variants or viral mutations are associated with breakthrough. Here, we report analysis of 2621 surveillance isolates from people diagnosed with COVID-19 in the Delaware Valley in southeastern Pennsylvania, allowing rigorous comparison to 159 vaccine breakthrough case specimens. Our best estimate is a 3-fold enrichment for some lineages of delta among breakthroughs, and enrichment of a notable spike substitution, N501Y. We introduce statistical methods that should be widely useful for evaluating vaccine breakthroughs and other viral phenotypes.
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Affiliation(s)
- Andrew D. Marques
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John K. Everett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shantan Reddy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pascha Hokama
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aoife M. Roche
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Young Hwang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Abigail Glascock
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Samantha A. Whiteside
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jevon Graham-Wooten
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Layla A. Khatib
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ayannah S. Fitzgerald
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ahmed M. Moustafa
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Gastroenterology, Hepatology & Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Colleen Bianco
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Swetha Rajagopal
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jenna Helton
- Division of COVID-19 Containment, Philadelphia Department of Public Health, Philadelphia, Pennsylvania, USA
| | - Regan Deming
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lidiya Denu
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Azad Ahmed
- Department of Microbiology & Immunology, Center for Genomic Sciences, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Eimear Kitt
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Susan E. Coffin
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Claire Newbern
- Division of COVID-19 Containment, Philadelphia Department of Public Health, Philadelphia, Pennsylvania, USA
| | - Josh Chang Mell
- Department of Microbiology & Immunology, Center for Genomic Sciences, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Paul J. Planet
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Nitika Badjatia
- Molecular & Genomic Pathology Laboratory, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, USA
| | - Bonnie Richards
- Jefferson Occupational Health Network for Employees and Students (JOHN), Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Zi-Xuan Wang
- Molecular & Genomic Pathology Laboratory, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, USA
- Department of Anatomy, Pathology, and Cell Biology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, USA
| | - Carolyn C. Cannuscio
- Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Family Medicine and Community Health, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katherine M. Strelau
- Leonard Davis Institute of Health Economics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Family Medicine and Community Health, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anne Jaskowiak-Barr
- Division of Infectious Diseases, Department of Medicine & Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Leigh Cressman
- Division of Infectious Diseases, Department of Medicine & Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sean Loughrey
- Division of Infectious Diseases, Department of Medicine & Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arupa Ganguly
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael D. Feldman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kyle G. Rodino
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brendan J. Kelly
- Division of Infectious Diseases, Department of Medicine & Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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243
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Park G, Hwang BH. SARS-CoV-2 Variants: Mutations and Effective Changes. BIOTECHNOL BIOPROC E 2021; 26:859-870. [PMID: 34975266 PMCID: PMC8713537 DOI: 10.1007/s12257-021-0327-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/14/2021] [Accepted: 11/14/2021] [Indexed: 11/26/2022]
Abstract
One of the primary threats to the goal of controlling and eventually defeating SARS-CoV-2 is that of mutation. Recognizing this, a great amount of effort and dedicated study is being given to the matter. Due to the novel coronavirus's general prevalence and rate of mutation, this is an extremely dynamic area with constant new developments. Therefore, understanding the virus's pathogenesis and how mutations affect it is crucial. This review attempts to aid in understanding the currently most important strains and what primary changes they entail in connection to more specific mutations, and how they each affect infectivity, antigen resistance, and other properties. In an attempt to maintain relevance to the time at which this paper will be published, priority has been given to variants classified by the WHO and the CDC as of Sep. 23, 2021, as "Variants of Concern". Of particular interest in B.1.1.7, B.1.351, B.1.617.2, P.1 are the mutations affecting the Spike protein and Receptor Binding Domain, as they directly affect infectivity and susceptibility to neutralization. Certain mutations (D614G, E484K, N501Y, K417N, L452R and P681R) have appeared across several different strains, often accompanied by others that may be complementary working together to confer increased infectivity, fitness, or resistance to neutralization. We anticipate that the understanding of such COVID-19 mutations will, in the near future, prove important for diagnosis, treatment development, and vaccine development.
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Affiliation(s)
- Gene Park
- Whitmore School, Morgantown, WV 26505 USA
| | - Byeong Hee Hwang
- Division of Bioengineering, Incheon National University, Incheon, 22012 Korea
- Department of Bio·nanobioengineering, Incheon National University, Incheon, 22012 Korea
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