1
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Xu J, Zhu Q, Li W, Yin X, Li J. Structural basis for the inhibition of the HCoV-NL63 main protease M pro by X77. Biochem Biophys Res Commun 2024; 724:150231. [PMID: 38852502 DOI: 10.1016/j.bbrc.2024.150231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
Human coronaviruses are a group of pathogens that primarily cause respiratory and intestinal diseases. Infection can easily cause respiratory symptoms, as well as a variety of serious complications. There are several types of human coronaviruses, such as SARS-CoV, MERS-CoV, HCoV-229E, HCoV-OC43, HCoV-NL63, HCoV-HKU1, and SARS-CoV-2. The prevalence of COVID-19 has led to a growing focus on drug research against human coronaviruses. The main protease (Mpro) from human coronaviruses is a relatively conserved that controls viral replication. X77 was discovered to have extremely high inhibitory activity against SARS-CoV-2 Mpro through the use of computer-simulated docking. In this paper, we have resolved the crystal structure of the HCoV-NL63 Mpro complexed with X77 and analyzed their interaction in detail. This data provides essential information for solving their binding modes and their structural determinants. Then, we compared the binding modes of X77 with SARS-CoV-2 Mpro and HCoV-NL63 Mpro in detail. This study illustrates the structural basis of HCoV-NL63 Mpro binding to the inhibitor X77. The structural insights derived from this study will inform the development of new drugs with broad-spectrum resistance to human coronaviruses.
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Affiliation(s)
- Jie Xu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Qinyao Zhu
- Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang, 110142, China
| | - Wenwen Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China
| | - Xiushan Yin
- Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang, 110142, China
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China.
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2
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Liao JM, Hong ST, Wang YT, Cheng YA, Ho KW, Toh SI, Shih O, Jeng US, Lyu PC, Hu IC, Huang MY, Chang CY, Cheng TL. Integrating molecular dynamics simulation with small- and wide-angle X-ray scattering to unravel the flexibility, antigen-blocking, and protease-restoring functions in a hindrance-based pro-antibody. Protein Sci 2024; 33:e5124. [PMID: 39145427 PMCID: PMC11325194 DOI: 10.1002/pro.5124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 06/11/2024] [Accepted: 07/11/2024] [Indexed: 08/16/2024]
Abstract
Spatial hindrance-based pro-antibodies (pro-Abs) are engineered antibodies to reduce monoclonal antibodies' (mAbs) on-target toxicity using universal designed blocking segments that mask mAb antigen-binding sites through spatial hindrance. By linking through protease substrates and linkers, these blocking segments can be removed site-specifically. Although many types of blocking segments have been developed, such as coiled-coil and hinge-based Ab locks, the molecular structure of the pro-Ab, particularly the region showing how the blocking fragment blocks the mAb, has not been elucidated by X-ray crystallography or cryo-EM. To achieve maximal effect, a pro-Ab must have high antigen-blocking and protease-restoring efficiencies, but the unclear structure limits its further optimization. Here, we utilized molecular dynamics (MD) simulations to study the dynamic structures of a hinge-based Ab lock pro-Ab, pro-Nivolumab, and validated the simulated structures with small- and wide-angle X-ray scattering (SWAXS). The MD results were closely consistent with SWAXS data (χ2 best-fit = 1.845, χ2 allMD = 3.080). The further analysis shows a pronounced flexibility of the Ab lock (root-mean-square deviation = 10.90 Å), yet it still masks the important antigen-binding residues by 57.3%-88.4%, explaining its 250-folded antigen-blocking efficiency. The introduced protease accessible surface area method affirmed better protease efficiency for light chain (33.03 Å2) over heavy chain (5.06 Å2), which aligns with the experiments. Overall, we developed MD-SWAXS validation method to study the dynamics of flexible blocking segments and introduced methodologies to estimate their antigen-blocking and protease-restoring efficiencies, which would potentially be advancing the clinical applications of any spatial hindrance-based pro-Ab.
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Affiliation(s)
- Jun Min Liao
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shih-Ting Hong
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yeng-Tseng Wang
- Department of Biochemistry, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-An Cheng
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Precisemab Biotech Co. Ltd, Taipei, Taiwan
| | - Kai-Wen Ho
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shu-Ing Toh
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, Taiwan
- Department of Chemical Engineering &College of Semiconductor Research, National Tsing Hua University, Hsinchu, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - I-Chen Hu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ming-Yii Huang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chin-Yuan Chang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Tian-Lu Cheng
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
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3
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Merrett JE, Nolan M, Hartman L, John N, Flynn B, Baker L, Schang C, McCarthy D, Lister D, Cheng NN, Crosbie N, Poon R, Jex A. Highly sensitive wastewater surveillance of SARS-CoV-2 variants by targeted next-generation amplicon sequencing provides early warning of incursion in Victoria, Australia. Appl Environ Microbiol 2024; 90:e0149723. [PMID: 39012098 PMCID: PMC11337797 DOI: 10.1128/aem.01497-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 06/06/2024] [Indexed: 07/17/2024] Open
Abstract
The future of the COVID pandemic and its public health and societal impact will be determined by the profile and spread of emerging variants and the timely identification and response to them. Wastewater surveillance of SARS-CoV-2 has been widely adopted in many countries across the globe and has played an important role in tracking infection levels and providing useful epidemiological information that cannot be adequately captured by clinical testing alone. However, novel variants can emerge rapidly, spread globally, and markedly alter the trajectory of the pandemic, as exemplified by the Delta and Omicron variants. Most mutations linked to the emergence of new SARS-CoV-2 variants are found within variable regions of the SARS-CoV-2 Spike protein. We have developed a duplex hemi-nested PCR method that, coupled with short amplicon sequencing, allows simultaneous typing of two of the most highly variable and informative regions of the Spike gene: the N-terminal domain and the receptor binding motif. Using this method in an operationalized public health program, we identified the first known incursion of Omicron BA.1 into Victoria, Australia and demonstrated how sensitive amplicon sequencing methods can be combined with wastewater surveillance as a relatively low-cost solution for early warning of variant incursion and spread.IMPORTANCEThis study offers a rapid, cost-effective, and sensitive approach for monitoring SARS-CoV-2 variants in wastewater. The method's flexibility permits timely modifications, enabling the integration of emerging variants and adaptations to evolving SARS-CoV-2 genetics. Of particular significance for low- and middle-income regions with limited surveillance capabilities, this technique can potentially be utilized to study a range of pathogens or viruses that possess diverse genetic sequences, similar to influenza.
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Affiliation(s)
- James E. Merrett
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Monica Nolan
- Victorian Department of Health, Melbourne, Victoria, Australia
| | - Leon Hartman
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Nijoy John
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Brianna Flynn
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Louise Baker
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Christelle Schang
- Environmental and Public Health Microbiology Lab, Monash University, Clayton, Victoria, Australia
| | - David McCarthy
- Environmental and Public Health Microbiology Lab, Monash University, Clayton, Victoria, Australia
- School of Civil and Environmental Engineering, Queensland University of Technology, Brisbane, Queensland, Australia
| | - David Lister
- Victorian Department of Health, Melbourne, Victoria, Australia
| | - Ngai Ning Cheng
- Victorian Department of Health, Melbourne, Victoria, Australia
- South Australian Water Corporation, Adelaide, South Australia, Australia
| | - Nick Crosbie
- Melbourne Water Corporation, Docklands, Victoria, Australia
| | - Rachael Poon
- Victorian Department of Health, Melbourne, Victoria, Australia
| | - Aaron Jex
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
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4
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Samrat SK, Kumar P, Liu Y, Chen K, Lee H, Li Z, Chen Y, Li H. An ISG15-Based High-Throughput Screening Assay for Identification and Characterization of SARS-CoV-2 Inhibitors Targeting Papain-like Protease. Viruses 2024; 16:1239. [PMID: 39205213 PMCID: PMC11359932 DOI: 10.3390/v16081239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/18/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
Emergence of newer variants of SARS-CoV-2 underscores the need for effective antivirals to complement the vaccination program in managing COVID-19. The multi-functional papain-like protease (PLpro) of SARS-CoV-2 is an essential viral protein that not only regulates the viral replication but also modulates the host immune system, making it a promising therapeutic target. To this end, we developed an in vitro interferon stimulating gene 15 (ISG15)-based Förster resonance energy transfer (FRET) assay and screened the National Cancer Institute (NCI) Diversity Set VI compound library, which comprises 1584 small molecules. Subsequently, we assessed the PLpro enzymatic activity in the presence of screened molecules. We identified three potential PLpro inhibitors, namely, NSC338106, 651084, and 679525, with IC50 values in the range from 3.3 to 6.0 µM. These molecules demonstrated in vitro inhibition of the enzyme activity and exhibited antiviral activity against SARS-CoV-2, with EC50 values ranging from 0.4 to 4.6 µM. The molecular docking of all three small molecules to PLpro suggested their specificity towards the enzyme's active site. Overall, our study contributes promising prospects for further developing potential antivirals to combat SARS-CoV-2 infection.
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Affiliation(s)
- Subodh Kumar Samrat
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (P.K.); (Y.L.); (K.C.); (Z.L.); (Y.C.)
| | - Prashant Kumar
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (P.K.); (Y.L.); (K.C.); (Z.L.); (Y.C.)
| | - Yuchen Liu
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (P.K.); (Y.L.); (K.C.); (Z.L.); (Y.C.)
| | - Ke Chen
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (P.K.); (Y.L.); (K.C.); (Z.L.); (Y.C.)
| | - Hyun Lee
- Department of Pharmaceutical Sciences, College of Pharmacy and Biophysics Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL 60607, USA;
| | - Zhong Li
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (P.K.); (Y.L.); (K.C.); (Z.L.); (Y.C.)
| | - Yin Chen
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (P.K.); (Y.L.); (K.C.); (Z.L.); (Y.C.)
| | - Hongmin Li
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (P.K.); (Y.L.); (K.C.); (Z.L.); (Y.C.)
- Department of Chemistry and Biochemistry, College of Science & College of Medicine, The University of Arizona, Tucson, AZ 85721, USA
- The BIO5 Institute, The University of Arizona, Tucson, AZ 85721, USA
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5
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Li X, Mi Z, Liu Z, Rong P. SARS-CoV-2: pathogenesis, therapeutics, variants, and vaccines. Front Microbiol 2024; 15:1334152. [PMID: 38939189 PMCID: PMC11208693 DOI: 10.3389/fmicb.2024.1334152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/29/2024] [Indexed: 06/29/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in December 2019 with staggering economic fallout and human suffering. The unique structure of SARS-CoV-2 and its underlying pathogenic mechanism were responsible for the global pandemic. In addition to the direct damage caused by the virus, SARS-CoV-2 triggers an abnormal immune response leading to a cytokine storm, culminating in acute respiratory distress syndrome and other fatal diseases that pose a significant challenge to clinicians. Therefore, potential treatments should focus not only on eliminating the virus but also on alleviating or controlling acute immune/inflammatory responses. Current management strategies for COVID-19 include preventative measures and supportive care, while the role of the host immune/inflammatory response in disease progression has largely been overlooked. Understanding the interaction between SARS-CoV-2 and its receptors, as well as the underlying pathogenesis, has proven to be helpful for disease prevention, early recognition of disease progression, vaccine development, and interventions aimed at reducing immunopathology have been shown to reduce adverse clinical outcomes and improve prognosis. Moreover, several key mutations in the SARS-CoV-2 genome sequence result in an enhanced binding affinity to the host cell receptor, or produce immune escape, leading to either increased virus transmissibility or virulence of variants that carry these mutations. This review characterizes the structural features of SARS-CoV-2, its variants, and their interaction with the immune system, emphasizing the role of dysfunctional immune responses and cytokine storm in disease progression. Additionally, potential therapeutic options are reviewed, providing critical insights into disease management, exploring effective approaches to deal with the public health crises caused by SARS-CoV-2.
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Affiliation(s)
- Xi Li
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ze Mi
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhenguo Liu
- Department of Infectious Disease, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Pengfei Rong
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
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6
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Xue S, Han Y, Wu F, Wang Q. Mutations in the SARS-CoV-2 spike receptor binding domain and their delicate balance between ACE2 affinity and antibody evasion. Protein Cell 2024; 15:403-418. [PMID: 38442025 PMCID: PMC11131022 DOI: 10.1093/procel/pwae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Intensive selection pressure constrains the evolutionary trajectory of SARS-CoV-2 genomes and results in various novel variants with distinct mutation profiles. Point mutations, particularly those within the receptor binding domain (RBD) of SARS-CoV-2 spike (S) protein, lead to the functional alteration in both receptor engagement and monoclonal antibody (mAb) recognition. Here, we review the data of the RBD point mutations possessed by major SARS-CoV-2 variants and discuss their individual effects on ACE2 affinity and immune evasion. Many single amino acid substitutions within RBD epitopes crucial for the antibody evasion capacity may conversely weaken ACE2 binding affinity. However, this weakened effect could be largely compensated by specific epistatic mutations, such as N501Y, thus maintaining the overall ACE2 affinity for the spike protein of all major variants. The predominant direction of SARS-CoV-2 evolution lies neither in promoting ACE2 affinity nor evading mAb neutralization but in maintaining a delicate balance between these two dimensions. Together, this review interprets how RBD mutations efficiently resist antibody neutralization and meanwhile how the affinity between ACE2 and spike protein is maintained, emphasizing the significance of comprehensive assessment of spike mutations.
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Affiliation(s)
- Song Xue
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yuru Han
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Fan Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
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7
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Lado S, Thannesberger J, Spettel K, Arpović J, Ferreira BI, Lavitrano M, Steininger C. Unveiling Inter- and Intra-Patient Sequence Variability with a Multi-Sample Coronavirus Target Enrichment Approach. Viruses 2024; 16:786. [PMID: 38793667 PMCID: PMC11125942 DOI: 10.3390/v16050786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/08/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Amid the global challenges posed by the COVID-19 pandemic, unraveling the genomic intricacies of SARS-CoV-2 became crucial. This study explores viral evolution using an innovative high-throughput next-generation sequencing (NGS) approach. By taking advantage of nasal swab and mouthwash samples from patients who tested positive for COVID-19 across different geographical regions during sequential infection waves, our study applied a targeted enrichment protocol and pooling strategy to increase detection sensitivity. The approach was extremely efficient, yielding a large number of reads and mutations distributed across 10 distinct viral gene regions. Notably, the genes Envelope, Nucleocapsid, and Open Reading Frame 8 had the highest number of unique mutations per 1000 nucleotides, with both spike and Nucleocapsid genes showing evidence for positive selection. Focusing on the spike protein gene, crucial in virus replication and immunogenicity, our findings show a dynamic SARS-CoV-2 evolution, emphasizing the virus-host interplay. Moreover, the pooling strategy facilitated subtle sequence variability detection. Our findings painted a dynamic portrait of SARS-CoV-2 evolution, emphasizing the intricate interplay between the virus and its host populations and accentuating the importance of continuous genomic surveillance to understand viral dynamics. As SARS-CoV-2 continues to evolve, this approach proves to be a powerful, versatile, fast, and cost-efficient screening tool for unraveling emerging variants, fostering understanding of the virus's genetic landscape.
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Affiliation(s)
- Sara Lado
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine 1, Medical University of Vienna, 1090 Vienna, Austria; (S.L.); (J.T.)
| | - Jakob Thannesberger
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine 1, Medical University of Vienna, 1090 Vienna, Austria; (S.L.); (J.T.)
| | - Kathrin Spettel
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria;
- Division of Biomedical Science, University of Applied Sciences, FH Campus Wien, 1100 Vienna, Austria
| | - Jurica Arpović
- Department of Medical Biology, School of Medicine, University of Mostar, Bijeli Brijeg b.b., 88000 Mostar, Bosnia and Herzegovina
| | - Bibiana I. Ferreira
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Campus de Gambelas, Edf. 2, 8005-139 Faro, Portugal;
- Algarve Biomedical Center Research Institute, Campus de Gambelas, Edf. 2, lab 3.67, 8005-139 Faro, Portugal
| | | | - Christoph Steininger
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine 1, Medical University of Vienna, 1090 Vienna, Austria; (S.L.); (J.T.)
- Karl-Landsteiner Institute for Microbiome Research, Medical University of Vienna, 1090 Vienna, Austria
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8
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Faraji N, Zeinali T, Joukar F, Aleali MS, Eslami N, Shenagari M, Mansour-Ghanaei F. Mutational dynamics of SARS-CoV-2: Impact on future COVID-19 vaccine strategies. Heliyon 2024; 10:e30208. [PMID: 38707429 PMCID: PMC11066641 DOI: 10.1016/j.heliyon.2024.e30208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024] Open
Abstract
The rapid emergence of multiple strains of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has sparked profound concerns regarding the ongoing evolution of the virus and its potential impact on global health. Classified by the World Health Organization (WHO) as variants of concern (VOC), these strains exhibit heightened transmissibility and pathogenicity, posing significant challenges to existing vaccine strategies. Despite widespread vaccination efforts, the continual evolution of SARS-CoV-2 variants presents a formidable obstacle to achieving herd immunity. Of particular concern is the coronavirus spike (S) protein, a pivotal viral surface protein crucial for host cell entry and infectivity. Mutations within the S protein have been shown to enhance transmissibility and confer resistance to antibody-mediated neutralization, undermining the efficacy of traditional vaccine platforms. Moreover, the S protein undergoes rapid molecular evolution under selective immune pressure, leading to the emergence of diverse variants with distinct mutation profiles. This review underscores the urgent need for vigilance and adaptation in vaccine development efforts to combat the evolving landscape of SARS-CoV-2 mutations and ensure the long-term effectiveness of global immunization campaigns.
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Affiliation(s)
- Niloofar Faraji
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Tahereh Zeinali
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Farahnaz Joukar
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Maryam Sadat Aleali
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Narges Eslami
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Shenagari
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Fariborz Mansour-Ghanaei
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
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9
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Shim K, Hwang EH, Kim G, Woo YM, An YJ, Baek SH, Oh T, Kim Y, Jang K, Hong JJ, Koo BS. Molecular evolutionary characteristics of severe acute respiratory syndrome coronavirus 2 and the relatedness of epidemiological and socio-environmental factors. Heliyon 2024; 10:e30222. [PMID: 38737246 PMCID: PMC11088249 DOI: 10.1016/j.heliyon.2024.e30222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
After the first outbreak, SARS-CoV-2 infection continues to occur due to the emergence of new variants. There is limited information available on the comparative evaluation of evolutionary characteristics of SARS-CoV-2 among different countries over time, and its relatedness to epidemiological and socio-environmental factors within those countries. We assessed comparative Bayesian evolutionary characteristics for SARS-CoV-2 in eight countries from 2020 to 2022 using BEAST version 2.6.7. Additionally, the relatedness between virus evolution factors and both epidemiological and socio-environmental factors was analyzed using Pearson's correlation coefficient. The estimated substitution rates in the gene encoding S protein of SARS-CoV-2 exhibited a continuous increase from 2020 to 2022 and were divided into two distinct groups in 2022 (p value < 0.05). Effective population size (Ne) generally showed decreased patterns by time. Notably, the change rates of the substitution rates were negatively correlated with the cumulative vaccination rates in 2021. A strict and rapid vaccination policy in the United Arab Emirates dramatically reduced the evolution of the virus, compared to other countries. Also, the average yearly temperature in countries were negatively correlated with the substitution rates. The changes of six epitopes in SARS-CoV-2 were related to various socio-environmental factors. We figured out comparative virus evolutionary traits and the association of epidemiological and socio-environmental factors especially cumulative vaccination rates and average temperature.
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Affiliation(s)
- Kyuyoung Shim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Eun-Ha Hwang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Green Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Young Min Woo
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - You Jung An
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Seung Ho Baek
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Taehwan Oh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Yujin Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Kiwon Jang
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jung Joo Hong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Bon-Sang Koo
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
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10
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Guo H, Ha S, Botten JW, Xu K, Zhang N, An Z, Strohl WR, Shiver JW, Fu TM. SARS-CoV-2 Omicron: Viral Evolution, Immune Evasion, and Alternative Durable Therapeutic Strategies. Viruses 2024; 16:697. [PMID: 38793580 PMCID: PMC11125895 DOI: 10.3390/v16050697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Since the SARS-CoV-2 Omicron virus has gained dominance worldwide, its continual evolution with unpredictable mutations and patterns has revoked all authorized immunotherapeutics. Rapid viral evolution has also necessitated several rounds of vaccine updates in order to provide adequate immune protection. It remains imperative to understand how Omicron evolves into different subvariants and causes immune escape as this could help reevaluate the current intervention strategies mostly implemented in the clinics as emergency measures to counter the pandemic and, importantly, develop new solutions. Here, we provide a review focusing on the major events of Omicron viral evolution, including the features of spike mutation that lead to immune evasion against monoclonal antibody (mAb) therapy and vaccination, and suggest alternative durable options such as the ACE2-based experimental therapies superior to mAbs to address this unprecedented evolution of Omicron virus. In addition, this type of unique ACE2-based virus-trapping molecules can counter all zoonotic SARS coronaviruses, either from unknown animal hosts or from established wild-life reservoirs of SARS-CoV-2, and even seasonal alpha coronavirus NL63 that depends on human ACE2 for infection.
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Affiliation(s)
- Hailong Guo
- IGM Biosciences, Mountain View, CA 94043, USA
| | - Sha Ha
- IGM Biosciences, Mountain View, CA 94043, USA
| | - Jason W. Botten
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, USA
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Kai Xu
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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11
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Qian J, Zhang S, Wang F, Li J, Zhang J. What makes SARS-CoV-2 unique? Focusing on the spike protein. Cell Biol Int 2024; 48:404-430. [PMID: 38263600 DOI: 10.1002/cbin.12130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.
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Affiliation(s)
- Jingbo Qian
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shichang Zhang
- Department of Clinical Laboratory Medicine, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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12
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Zhang R, Yan H, Zhou J, Yan G, Liu X, Shang C, Chen Y. Improved fluorescence-based assay for rapid screening and evaluation of SARS-CoV-2 main protease inhibitors. J Med Virol 2024; 96:e29498. [PMID: 38436148 DOI: 10.1002/jmv.29498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global threat to human health. In parallel with vaccines, efficacious antivirals are urgently needed. SARS-CoV-2 main protease (Mpro) is an attractive drug target for antiviral development owing to its key roles in virus replication and host immune evasion. Due to the limitations of currently available methods, the development of novel high-throughput screening assays is of the highest importance for the discovery of Mpro inhibitors. In this study, we first developed an improved fluorescence-based assay for rapid screening of Mpro inhibitors from an anti-infection compound library using a versatile dimerization-dependent red fluorescent protein (ddRFP) biosensor. Utilizing this assay, we identified MG-101 as a competitive Mpro inhibitor in vitro. Moreover, our results revealed that ensitrelvir is a potent Mpro inhibitor, but baicalein, chloroquine, ebselen, echinatin, and silibinin are not. Therefore, this robust ddRFP assay provides a faithful avenue for rapid screening and evaluation of Mpro inhibitors to fight against COVID-19.
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Affiliation(s)
- Rui Zhang
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Haohao Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Jiahao Zhou
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Gangan Yan
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Xiaoping Liu
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
| | - Chao Shang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yunyu Chen
- Institute for Drug Screening and Evaluation, Wannan Medical College, Wuhu, China
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13
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Yu X, Li X, Xia S, Lu T, Zong M, Suo C, Man Q, Xiong L. Development and validation of a prognostic model based on clinical laboratory biomarkers to predict admission to ICU in Omicron variant-infected hospitalized patients complicated with myocardial injury. Front Immunol 2024; 15:1268213. [PMID: 38361939 PMCID: PMC10868580 DOI: 10.3389/fimmu.2024.1268213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/03/2024] [Indexed: 02/17/2024] Open
Abstract
Aims The aim of this study was to develop and validate a prognostic model based on clinical laboratory biomarkers for the early identification of high-risk patients who require intensive care unit (ICU) admission among those hospitalized with the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and complicated with myocardial injury (MI). Methods This single-center study enrolled 263 hospitalized patients with confirmed Omicron variant infection and concurrent MI. The patients were randomly divided into training and validation cohorts. Relevant variables were collected upon admission, and the least absolute shrinkage and selection operator (LASSO) was used to select candidate variables for constructing a Cox regression prognostic model. The model's performance was evaluated in both training and validating cohorts based on discrimination, calibration, and net benefit. Results Of the 263 eligible patients, 210 were non-ICU patients and 53 were ICU patients. The prognostic model was built using four selected predictors: white blood cell (WBC) count, procalcitonin (PCT) level, C-reactive protein (CRP) level, and blood urea nitrogen (BUN) level. The model showed good discriminative ability in both the training cohort (concordance index: 0.802, 95% CI: 0.716-0.888) and the validation cohort (concordance index: 0.799, 95% CI: 0.681-0.917). For calibration, the predicted probabilities and observed proportions were highly consistent, indicating the model's reliability in predicting outcomes. In the 21-day decision curve analysis, the model had a positive net benefit for threshold probability ranges of 0.2 to 0.8 in the training cohort and nearly 0.2 to 1 in the validation cohort. Conclusion In this study, we developed a clinically practical model with high discrimination, calibration, and net benefit. It may help to early identify severe and critical cases among Omicron variant-infected hospitalized patients with MI.
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Affiliation(s)
- Xueying Yu
- Department of Clinical Laboratory, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaoguang Li
- Department of Thyroid, Breast and Vascular Surgery, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shuai Xia
- Key Laboratory of Medical Molecular Virology (Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences, MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, China
| | - Tianyu Lu
- Key Laboratory of Medical Molecular Virology (Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences, MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Fudan University, Shanghai, China
| | - Ming Zong
- Department of Clinical Laboratory, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Chen Suo
- Department of Epidemiology and Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Qiuhong Man
- Department of Clinical Laboratory, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lize Xiong
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
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14
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Avila-Herrera A, Kimbrel JA, Manuel Martí J, Thissen J, Saada EA, Weisenberger T, Arrildt KT, Segelke BW, Allen JE, Zemla A, Borucki MK. Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies. PLoS One 2024; 19:e0289198. [PMID: 38271318 PMCID: PMC10810540 DOI: 10.1371/journal.pone.0289198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Viral populations in natural infections can have a high degree of sequence diversity, which can directly impact immune escape. However, antibody potency is often tested in vitro with a relatively clonal viral populations, such as laboratory virus or pseudotyped virus stocks, which may not accurately represent the genetic diversity of circulating viral genotypes. This can affect the validity of viral phenotype assays, such as antibody neutralization assays. To address this issue, we tested whether recombinant virus carrying SARS-CoV-2 spike (VSV-SARS-CoV-2-S) stocks could be made more genetically diverse by passage, and if a stock passaged under selective pressure was more capable of escaping monoclonal antibody (mAb) neutralization than unpassaged stock or than viral stock passaged without selective pressures. We passaged VSV-SARS-CoV-2-S four times concurrently in three cell lines and then six times with or without polyclonal antiserum selection pressure. All three of the monoclonal antibodies tested neutralized the viral population present in the unpassaged stock. The viral inoculum derived from serial passage without antiserum selection pressure was neutralized by two of the three mAbs. However, the viral inoculum derived from serial passage under antiserum selection pressure escaped neutralization by all three mAbs. Deep sequencing revealed the rapid acquisition of multiple mutations associated with antibody escape in the VSV-SARS-CoV-2-S that had been passaged in the presence of antiserum, including key mutations present in currently circulating Omicron subvariants. These data indicate that viral stock that was generated under polyclonal antiserum selection pressure better reflects the natural environment of the circulating virus and may yield more biologically relevant outcomes in phenotypic assays. Thus, mAb assessment assays that utilize a more genetically diverse, biologically relevant, virus stock may yield data that are relevant for prediction of mAb efficacy and for enhancing biosurveillance.
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Affiliation(s)
- Aram Avila-Herrera
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Jeffrey A. Kimbrel
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Jose Manuel Martí
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - James Thissen
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Edwin A. Saada
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Tracy Weisenberger
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Kathryn T. Arrildt
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Brent W. Segelke
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Jonathan E. Allen
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Adam Zemla
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Monica K. Borucki
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
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15
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Gao X, Wang F, Liu H, Chai J, Tian G, Yao L, Chen C, Huo P, Yao Y, Wen J, Zhao N, Sun D. BF.7: a new Omicron subvariant characterized by rapid transmission. Clin Microbiol Infect 2024; 30:137-141. [PMID: 37802303 DOI: 10.1016/j.cmi.2023.09.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 08/20/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023]
Abstract
OBJECTIVES BF.7 (BA.5.2.1.7) is a novel sublineage of Omicron BA.5, whose clinical characteristics are not yet established. METHODS From 28 September 2022 to 3 October 2022, the first 421 patients with BF.7 were assessed in Hohhot China and the clinical data were extracted and analysed. The basic reproduction number (R0) was estimated using a statistical model calculation method. RESULTS The R0 value was determined to be 13.79 (95% confidence interval: 12.44-15.24). The mean age was 33.43 ± 18.78 years. Asymptomatic, mild, moderate, severe, and critical patients accounted for 12.35% (52/421), 82.42% (347/421), 4.75% (20/421), 0.24% (1/421), and 0.24% (1/421) proportion, respectively. The main clinical symptoms were fever accounting for 41.09% (173/421), cough accounting for 41.09% (173/421), and throat dryness and soreness accounting for 30.88% (130/421). In the 3-dose vaccination subgroup, 31.22% (64) cases had a fever, which were significantly lower than 51.37% (96) cases of the 2-dose vaccination subgroup (p 0.000). The rates of abnormally increased C-reactive protein level in the 2-dose and 3-dose vaccination subgroups were 10.16% (19/187) and 4.88% (10/205), significantly lower than 66.67% (10/15) of the 1-dose vaccination subgroup (1-dose vs. 2-dose: p 0.000, 1-dose vs. 3-dose: p 0.000). Notably, the population with complete 3 doses of vaccination did not exhibit any severe or critical status. DISCUSSION BF.7 exhibited a higher transmission than previously emerged SARS-CoV-2. The vaccine against COVID-19 was found to relieve fever, nausea, and vomiting as well as reduce the abnormal ratio of lymphocytes, eosinophils, neutrophils, and the C-reactive protein level.
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Affiliation(s)
- Xiaoyu Gao
- Inner Mongolia People's Hospital NHC Key Laboratory of Diagnosis & Treatment of COPD/Inner Mongolia Key Laboratory of Respiratory Diseases, Inner Mongolia Autonomous Region Hohhot, China; Inner Mongolia People's Hospital Inner Mongolia Academy of Medical Sciences, Inner Mongolia Autonomous Region Hohhot, China
| | - Furong Wang
- Inner Mongolia Fourth Hospital, Inner Mongolia Autonomous Region Hohhot, China
| | - Huizhao Liu
- Inner Mongolia People's Hospital NHC Key Laboratory of Diagnosis & Treatment of COPD/Inner Mongolia Key Laboratory of Respiratory Diseases, Inner Mongolia Autonomous Region Hohhot, China
| | - Jun Chai
- Inner Mongolia People's Hospital NHC Key Laboratory of Diagnosis & Treatment of COPD/Inner Mongolia Key Laboratory of Respiratory Diseases, Inner Mongolia Autonomous Region Hohhot, China
| | - Guangyuan Tian
- Inner Mongolia People's Hospital NHC Key Laboratory of Diagnosis & Treatment of COPD/Inner Mongolia Key Laboratory of Respiratory Diseases, Inner Mongolia Autonomous Region Hohhot, China
| | - Lili Yao
- Inner Mongolia People's Hospital NHC Key Laboratory of Diagnosis & Treatment of COPD/Inner Mongolia Key Laboratory of Respiratory Diseases, Inner Mongolia Autonomous Region Hohhot, China
| | - Chen Chen
- Inner Mongolia Fourth Hospital, Inner Mongolia Autonomous Region Hohhot, China
| | - Peng Huo
- Inner Mongolia People's Hospital NHC Key Laboratory of Diagnosis & Treatment of COPD/Inner Mongolia Key Laboratory of Respiratory Diseases, Inner Mongolia Autonomous Region Hohhot, China
| | - Yingxi Yao
- Inner Mongolia People's Hospital NHC Key Laboratory of Diagnosis & Treatment of COPD/Inner Mongolia Key Laboratory of Respiratory Diseases, Inner Mongolia Autonomous Region Hohhot, China
| | - Jing Wen
- Inner Mongolia People's Hospital NHC Key Laboratory of Diagnosis & Treatment of COPD/Inner Mongolia Key Laboratory of Respiratory Diseases, Inner Mongolia Autonomous Region Hohhot, China
| | - Na Zhao
- Inner Mongolia People's Hospital NHC Key Laboratory of Diagnosis & Treatment of COPD/Inner Mongolia Key Laboratory of Respiratory Diseases, Inner Mongolia Autonomous Region Hohhot, China
| | - Dejun Sun
- Inner Mongolia People's Hospital NHC Key Laboratory of Diagnosis & Treatment of COPD/Inner Mongolia Key Laboratory of Respiratory Diseases, Inner Mongolia Autonomous Region Hohhot, China; Inner Mongolia People's Hospital Inner Mongolia Academy of Medical Sciences, Inner Mongolia Autonomous Region Hohhot, China.
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16
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Zhao Z, Zhu Q, Zhou X, Li W, Yin X, Li J. Structural Basis for the Inhibition of SARS-CoV-2 M pro D48N Mutant by Shikonin and PF-07321332. Viruses 2023; 16:65. [PMID: 38257765 PMCID: PMC10818409 DOI: 10.3390/v16010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/24/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Preventing the spread of SARS-CoV-2 and its variants is crucial in the fight against COVID-19. Inhibition of the main protease (Mpro) of SARS-CoV-2 is the key to disrupting viral replication, making Mpro a promising target for therapy. PF-07321332 and shikonin have been identified as effective broad-spectrum inhibitors of SARS-CoV-2 Mpro. The crystal structures of SARS-CoV-2 Mpro bound to PF-07321332 and shikonin have been resolved in previous studies. However, the exact mechanism regarding how SARS-CoV-2 Mpro mutants impact their binding modes largely remains to be investigated. In this study, we expressed a SARS-CoV-2 Mpro mutant, carrying the D48N substitution, representing a class of mutations located near the active sites of Mpro. The crystal structures of Mpro D48N in complex with PF-07321332 and shikonin were solved. A detailed analysis of the interactions between Mpro D48N and two inhibitors provides key insights into the binding pattern and its structural determinants. Further, the binding patterns of the two inhibitors to Mpro D48N mutant and wild-type Mpro were compared in detail. This study illustrates the possible conformational changes when the Mpro D48N mutant is bound to inhibitors. Structural insights derived from this study will inform the development of new drugs against novel coronaviruses.
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Affiliation(s)
- Zhenyu Zhao
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China; (Z.Z.); (X.Z.); (W.L.)
| | - Qinyao Zhu
- Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang 110142, China;
| | - Xuelan Zhou
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China; (Z.Z.); (X.Z.); (W.L.)
| | - Wenwen Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China; (Z.Z.); (X.Z.); (W.L.)
| | - Xiushan Yin
- Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang 110142, China;
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China; (Z.Z.); (X.Z.); (W.L.)
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17
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Altorki TA, Abdulal RH, Suliman BA, Aljeraisi TM, Alsharef A, Abdulaal WH, Alfaleh MA, Algaissi AA, Alhabbab RY, Ozbak H, Eid HM, Almutawif YA, Li X, Al-Rabia MW, Zhang Q, Mahmoud AB, Mahallawi WH, Hashem AM. Robust memory humoral immune response to SARS-CoV-2 in the tonsils of adults and children. Front Immunol 2023; 14:1291534. [PMID: 38149243 PMCID: PMC10750384 DOI: 10.3389/fimmu.2023.1291534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 11/17/2023] [Indexed: 12/28/2023] Open
Abstract
Background Adaptive humoral immunity against SARS-CoV-2 has mainly been evaluated in peripheral blood. Human secondary lymphoid tissues (such as tonsils) contain large numbers of plasma cells that secrete immunoglobulins at mucosal sites. Yet, the role of mucosal memory immunity induced by vaccines or natural infection against SARS-CoV-2 and its variants is not fully understood. Methods Tonsillar mononuclear cells (TMNCs) from adults (n=10) and children (n=11) were isolated and stimulated using positive SARS-CoV-2 nasal swabs. We used endpoint enzyme-linked immunosorbent assays (ELISAs) for the measurement of anti-S1, -RBD, and -N IgG antibody levels and a pseudovirus microneutralization assay to assess neutralizing antibodies (nAbs) in paired serum and supernatants from stimulated TMNCs. Results Strong systemic humoral response in previously SARS-CoV-2 infected and vaccinated adults and children was observed in accordance with the reported history of the participants. Interestingly, we found a significant increase in anti-RBD IgG (305 and 834 folds) and anti-S1 IgG (475 and 443 folds) in the stimulated TMNCs from adults and children, respectively, compared to unstimulated cells. Consistently, the stimulated TMNCs secreted higher levels of nAbs against the ancestral Wuhan strain and the Omicron BA.1 variant compared to unstimulated cells by several folds. This increase was seen in all participants including children with no known history of infection, suggesting that these participants might have been previously exposed to SARS-CoV-2 and that not all asymptomatic cases necessarily could be detected by serum antibodies. Furthermore, nAb levels against both strains were significantly correlated in adults (r=0.8788; p = 0.0008) and children (r = 0.7521; p = 0.0076), and they strongly correlated with S1 and RBD-specific IgG antibodies. Conclusion Our results provide evidence for persistent mucosal humoral memory in tonsils from previously infected and/or vaccinated adults and children against recent and old variants upon re-exposure. They also highlight the importance of targeting mucosal sites with vaccines to help control infection at the primary sites and prevent potential breakthrough infections.
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Affiliation(s)
- Tarfa A. Altorki
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rwaa H. Abdulal
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bandar A. Suliman
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
| | - Talal M. Aljeraisi
- Otorhinolaryngology, Head and Neck Surgery Department, Faculty of Medicine, Taibah University, Madinah, Saudi Arabia
| | - Asem Alsharef
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wesam H. Abdulaal
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohamed A. Alfaleh
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdullah A. Algaissi
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Rowa Y. Alhabbab
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hani Ozbak
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
| | - Hamza Mohammed Eid
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
| | - Yahya Ahmad Almutawif
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
| | - Xuguang Li
- Centre for Oncology and Regulatory Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada and World Health Organization Collaborating Center for Standardization and Evaluation of Biologicals, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Mohammed W. Al-Rabia
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Qibo Zhang
- Academic and Research Departments, Section of Immunology, School of Biosciences and Medicine University of Surrey, Surrey, United Kingdom
| | - Ahmed Bakur Mahmoud
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
- Health and Life Research Center, Taibah University, Madinah, Saudi Arabia
| | - Waleed H. Mahallawi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
| | - Anwar M. Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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18
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Yang L, Guo S, Hou C, Jiang S, Shi L, Ma X, Zheng B, Fang Y, Ye L, He X. Low-Entropy Hydration Shells at the Spike RBD's Binding Site May Reveal the Contagiousness of SARS-CoV-2 Variants. Biomolecules 2023; 13:1628. [PMID: 38002310 PMCID: PMC10669249 DOI: 10.3390/biom13111628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/29/2023] [Accepted: 11/05/2023] [Indexed: 11/26/2023] Open
Abstract
The infectivity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is primarily determined by the binding affinity between the receptor-binding domain (RBD) of the spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor. Here, through screening off pseudo hydrophilic groups on protein surfaces, the distribution of low-entropy regions on hydration shells of the ACE2 receptor and the RBDs of multiple SARS-CoV-2 variants was demonstrated. Shape matching between the low-entropy hydration shells of multiple SARS-CoV-2 variants and the ACE2 receptor has been identified as a mechanism that drives hydrophobic attraction between the RBDs and the ACE2 receptor, which estimates the binding affinity. Low-entropy regions of the hydration shells, which play important roles in determining the binding of other viruses and their receptors, are demonstrated. The RBD-ACE2 binding is thus found to be guided by hydrophobic collapse between the shape-matched low-entropy regions of the hydration shells of the proteins. A measure of the low-entropy status of the hydration shells can be estimated by calculating genuine hydrophilic groups within the binding sites. An important indicator of the contagiousness of SARS-CoV-2 variants is the low-entropy level of its hydration shells at the spike protein binding site.
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Affiliation(s)
- Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (S.G.); (S.J.); (L.S.); (X.M.)
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (S.G.); (S.J.); (L.S.); (X.M.)
| | - Chengyu Hou
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China;
| | - Shenda Jiang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (S.G.); (S.J.); (L.S.); (X.M.)
| | - Liping Shi
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (S.G.); (S.J.); (L.S.); (X.M.)
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (S.G.); (S.J.); (L.S.); (X.M.)
| | - Bing Zheng
- Key Laboratory of Functional Inorganic Material Chemistry (Ministry of Education) and School of Chemistry and Materials Science, Heilongjiang University, Harbin 150001, China;
| | - Yi Fang
- Department of Mathematics, Nanchang University, Nanchang 330031, China;
| | - Lin Ye
- School of System Design and Intelligent Manufacturing, Southern University of Science and Technology, Shenzhen 518055, China;
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (S.G.); (S.J.); (L.S.); (X.M.)
- Shenzhen STRONG Advanced Materials Research Institute Co., Ltd., Shenzhen 518035, China
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19
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Treeza M M, Augustine S, Mathew AA, Kanthlal S, Panonummal R. Targeting Viral ORF3a Protein: A New Approach to Mitigate COVID-19 Induced Immune Cell Apoptosis and Associated Respiratory Complications. Adv Pharm Bull 2023; 13:678-687. [PMID: 38022818 PMCID: PMC10676557 DOI: 10.34172/apb.2023.069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/15/2022] [Accepted: 01/20/2023] [Indexed: 12/01/2023] Open
Abstract
Infection with SARS-CoV-2 is a growing concern to the global well-being of the public at present. Different amino acid mutations alter the biological and epidemiological characteristics, as well as immune resistance of SARS-CoV-2. The virus-induced pulmonary impairment and inflammatory cytokine storm are directly related to its clinical manifestations. But, the fundamental mechanisms of inflammatory responses are found to be the reason for the death of immune cells which render the host immune system failure. Apoptosis of immune cells is one of the most common forms of programmed cell death induced by the virus for its survival and virulence property. ORF3a, a SARS-CoV-2 accessory viral protein, induces apoptosis in host cells and suppress the defense mechanism. This suggests, inhibiting SARS-CoV-2 ORF3a protein is a good therapeutic strategy for the treatment in COVID-19 infection by promoting the host immune defense mechanism.
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Affiliation(s)
- Minu Treeza M
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
| | - Sanu Augustine
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
| | | | - S.K. Kanthlal
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
| | - Rajitha Panonummal
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
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20
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Yang J, Lin S, Chen Z, Yang F, Guo L, Wang L, Duan Y, Zhang X, Dai Y, Yin K, Yu C, Yuan X, Sun H, He B, Cao Y, Ye H, Dong H, Liu X, Chen B, Li J, Zhao Q, Lu G. Development of a bispecific nanobody conjugate broadly neutralizes diverse SARS-CoV-2 variants and structural basis for its broad neutralization. PLoS Pathog 2023; 19:e1011804. [PMID: 38033141 PMCID: PMC10688893 DOI: 10.1371/journal.ppat.1011804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/07/2023] [Indexed: 12/02/2023] Open
Abstract
The continuous emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased transmissibility and profound immune-escape capacity makes it an urgent need to develop broad-spectrum therapeutics. Nanobodies have recently attracted extensive attentions due to their excellent biochemical and binding properties. Here, we report two high-affinity nanobodies (Nb-015 and Nb-021) that target non-overlapping epitopes in SARS-CoV-2 S-RBD. Both nanobodies could efficiently neutralize diverse viruses of SARS-CoV-2. The neutralizing mechanisms for the two nanobodies are further delineated by high-resolution nanobody/S-RBD complex structures. In addition, an Fc-based tetravalent nanobody format is constructed by combining Nb-015 and Nb-021. The resultant nanobody conjugate, designated as Nb-X2-Fc, exhibits significantly enhanced breadth and potency against all-tested SARS-CoV-2 variants, including Omicron sub-lineages. These data demonstrate that Nb-X2-Fc could serve as an effective drug candidate for the treatment of SARS-CoV-2 infection, deserving further in-vivo evaluations in the future.
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Affiliation(s)
- Jing Yang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Sheng Lin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zimin Chen
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fanli Yang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liyan Guo
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lingling Wang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanping Duan
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xindan Zhang
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yushan Dai
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Keqing Yin
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chongzhang Yu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xin Yuan
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Honglu Sun
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bin He
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Cao
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Disaster Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Haoyu Ye
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Haohao Dong
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xianbo Liu
- CHENGDU NB BIOLAB CO., LTD, Chengdu, Sichuan, China
| | - Bo Chen
- CHENGDU NB BIOLAB CO., LTD, Chengdu, Sichuan, China
| | - Jian Li
- School of Basic Medical Sciences, Chengdu University, Chengdu, Sichuan, China
| | - Qi Zhao
- College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Guangwen Lu
- Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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21
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Wahid M, Jawed A, Mandal RK, Areeshi MY, El-Shall NA, Mohapatra RK, Tuli HS, Dhama K, Pellicano R, Fagoonee S, Haque S. Role of available COVID-19 vaccines in reducing deaths and perspective for next generation vaccines and therapies to counter emerging viral variants: an update. Minerva Med 2023; 114:683-697. [PMID: 37293890 DOI: 10.23736/s0026-4806.23.08509-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The COVID-19 disease wreaked havoc all over the world causing more than 6 million deaths out of over 519 million confirmed cases. It not only disturbed the human race health-wise but also caused huge economic losses and social disturbances. The utmost urgency to counter pandemic was to develop effective vaccines as well as treatments that could reduce the incidences of infection, hospitalization and deaths. The most known vaccines that could help in managing these parameters are Oxford-AstraZeneca (AZD1222), Pfizer-BioNTech (BNT162b2), Moderna (mRNA-1273) and Johnson & Johnson (Ad26.COV2.S). The effectiveness of AZD1222 vaccine in reducing deaths is 88% in the age group 40-59 years, touching 100% in the age group 16-44 years & 65-84 years. BNT162b2 vaccine also did well in reducing deaths due to COVID-19 (95% in the age group 40-49 years and 100% in the age group 16-44 years. Similarly, mRNA-1273 vaccine showed potential in reducing COVID-19 deaths with effectiveness ranging from 80.3 to 100% depending upon age group of the vaccinated individuals. Ad26.COV2.S vaccine was also 100% effective in reducing COVID-19 deaths. The SARS-CoV-2 emerging variants have emphasized the need of booster vaccine doses to enhance protective immunity in vaccinated individuals. Additionally, therapeutic effectiveness of Molnupiravir, Paxlovid and Evusheld are also providing resistance against the spread of COVID-19 disease as well as may be effective against emerging variants. This review highlights the progress in developing COVID-19 vaccines, their protective efficacies, advances being made to design more efficacious vaccines, and presents an overview on advancements in developing potent drugs and monoclonal antibodies for countering COVID-19 and emerging variants of SARS-CoV-2 including the most recently emerged and highly mutated Omicron variant.
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Affiliation(s)
- Mohd Wahid
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, University of Jazan, Jazan, Saudi Arabia
| | - Arshad Jawed
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, University of Jazan, Jazan, Saudi Arabia
| | - Raju K Mandal
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, University of Jazan, Jazan, Saudi Arabia
| | - Mohammed Y Areeshi
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, University of Jazan, Jazan, Saudi Arabia
| | - Nahed A El-Shall
- Department of Poultry and Fish Diseases, Faculty of Veterinary Medicine, Alexandria University, Edfina, Egypt
| | - Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar, India
| | - Hardeep S Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Rinaldo Pellicano
- Unit of Gastroenterology, Molinette Hospital, Città della Salute e della Scienza, Turin, Italy -
| | - Sharmila Fagoonee
- Institute of Biostructure and Bioimaging (CNR), Molecular Biotechnology Center, Turin, Italy
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, University of Jazan, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Center of Medical and Bio-Allied Health Sciences Research, University of Ajman, Ajman, United Arab Emirates
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22
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Ma Y, Wu H, Chen S, Xie C, Hu J, Qi X, Ma X, Chu Y, Shan J, Lu Y, Cui L, Zou B, Zhou G. FEN1-aided recombinase polymerase amplification (FARPA) for one-pot and multiplex detection of nucleic acids with an ultra-high specificity and sensitivity. Biosens Bioelectron 2023; 237:115456. [PMID: 37354713 DOI: 10.1016/j.bios.2023.115456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/26/2023]
Abstract
Recombinase polymerase amplification (RPA) running at 37-42 °C is fast, efficient and less-implemented; however, the existing technologies of nucleic acid testing based on RPA have some limitations in specificity of single-base recognition and multiplexing capability. Herein, we report a highly specific and multiplex RPA-based nucleic acid detection platform by combining flap endonuclease 1 (FEN1)-catalysed invasive reactions with RPA, termed as FEN1-aided RPA (FARPA). The optimal conditions enable RPA and FEN1-based fluorescence detection to occur automatically and sequentially within a 25-min turnaround time and FARPA exhibits sensitivity to 5 target molecules. Due to the ability of invasive reactions in discriminating single-base variation, this one-pot FARPA is much more specific than the Exo probe-based or CRISPR-based RPA methods. Using a universal primer pair derived from tags in reverse transcription primers, multiplex FARPA was successfully demonstrated by the 3-plex assay for the detection of SARS-CoV-2 pathogen (the ORF1ab, the N gene, and the human RNase P gene as the internal control), the 2-plex assay for the discrimination of SARS-CoV-2 wild-type from variants (Alpha, Beta, Epsilon, Delta, or Omicrons), and the 4-plex assay for the screening of arboviruses (zika virus, tick-borne encephalitis virus, yellow fever virus, and chikungunya virus). We have validated multiplex FARPA with 103 nasopharyngeal swabs for SARS-CoV-2 detection. The results showed a 100% agreement with RT-qPCR assays. Moreover, a hand-held FARPA analyser was constructed for the visualized FARPA due to the switch-like endpoint read-out. This FARPA is very suitable for pathogen screening and discrimination of viral variants, greatly facilitating point-of-care diagnostics.
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Affiliation(s)
- Yi Ma
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Haiping Wu
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China; Department of Clinical Pharmacy, Nanjing Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Shan Chen
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Chunmei Xie
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Jingjing Hu
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Xiemin Qi
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Xueping Ma
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Jingwen Shan
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yan Lu
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China
| | - Lunbiao Cui
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210009, China
| | - Bingjie Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Guohua Zhou
- Department of Clinical Pharmacy, Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210002, China.
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23
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Li C, Ma L, Zou D, Zhang R, Bai X, Li L, Wu G, Huang T, Zhao W, Jin E, Bao Y, Song S. RCoV19: A One-stop Hub for SARS-CoV-2 Genome Data Integration, Variant Monitoring, and Risk Pre-warning. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1066-1079. [PMID: 37898309 PMCID: PMC10928372 DOI: 10.1016/j.gpb.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
The Resource for Coronavirus 2019 (RCoV19) is an open-access information resource dedicated to providing valuable data on the genomes, mutations, and variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this updated implementation of RCoV19, we have made significant improvements and advancements over the previous version. Firstly, we have implemented a highly refined genome data curation model. This model now features an automated integration pipeline and optimized curation rules, enabling efficient daily updates of data in RCoV19. Secondly, we have developed a global and regional lineage evolution monitoring platform, alongside an outbreak risk pre-warning system. These additions provide a comprehensive understanding of SARS-CoV-2 evolution and transmission patterns, enabling better preparedness and response strategies. Thirdly, we have developed a powerful interactive mutation spectrum comparison module. This module allows users to compare and analyze mutation patterns, assisting in the detection of potential new lineages. Furthermore, we have incorporated a comprehensive knowledgebase on mutation effects. This knowledgebase serves as a valuable resource for retrieving information on the functional implications of specific mutations. In summary, RCoV19 serves as a vital scientific resource, providing access to valuable data, relevant information, and technical support in the global fight against COVID-19. The complete contents of RCoV19 are available to the public at https://ngdc.cncb.ac.cn/ncov/.
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Affiliation(s)
- Cuiping Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Lina Ma
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Rongqin Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue Bai
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Lun Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Gangao Wu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianhao Huang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Enhui Jin
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shuhui Song
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China.
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24
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Makowski JA, Kensinger AH, Cunningham CL, Frye CJ, Shine M, Lackey PE, Mihailescu MR, Evanseck JD. Delta SARS-CoV-2 s2m Structure, Dynamics, and Entropy: Consequences of the G15U Mutation. ACS PHYSICAL CHEMISTRY AU 2023; 3:434-443. [PMID: 37780540 PMCID: PMC10540284 DOI: 10.1021/acsphyschemau.3c00008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 10/03/2023]
Abstract
Bioinformatic analysis of the Delta SARS-CoV-2 genome reveals a single nucleotide mutation (G15U) in the stem-loop II motif (s2m) relative to ancestral SARS-CoV-2. Despite sequence similarity, unexpected differences between SARS-CoV-2 and Delta SARS-CoV-2 s2m homodimerization experiments require the discovery of unknown structural and thermodynamic changes necessary to rationalize the data. Using our reported SARS-CoV-2 s2m model, we induced the G15U substitution and performed 3.5 microseconds of unbiased molecular dynamics simulation at 283 and 310 K. The resultant Delta s2m adopted a secondary structure consistent with our reported NMR data, resulting in significant deviations in the tertiary structure and dynamics from our SARS-CoV-2 s2m model. First, we find differences in the overall three-dimensional structure, where the characteristic 90° L-shaped kink of the SARS-CoV-2 s2m did not form in the Delta s2m resulting in a "linear" hairpin with limited bending dynamics. Delta s2m helical parameters are calculated to align closely with A-form RNA, effectively eliminating a hinge point to form the L-shape kink by correcting an upper stem defect in SARS-CoV-2 induced by a noncanonical and dynamic G:A base pair. Ultimately, the shape difference rationalizes the migration differences in reported electrophoresis experiments. Second, increased fluctuation of the Delta s2m palindromic sequence, within the terminal loop, compared to SARS-CoV-2 s2m results in an estimated increase of entropy of 6.8 kcal/mol at 310 K relative to the SARS-CoV-2 s2m. The entropic difference offers a unique perspective on why the Delta s2m homodimerizes less spontaneously, forming fewer kissing dimers and extended duplexes compared to SARS-CoV-2. In this work, both the L-shape reduction and palindromic entropic penalty provides an explanation of our reported in vitro electrophoresis homodimerization results. Ultimately, the structural, dynamical, and entropic differences between the SARS-CoV-2 s2m and Delta s2m serve to establish a foundation for future studies of the s2m function in the viral lifecycle.
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Affiliation(s)
- Joseph A. Makowski
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Adam H. Kensinger
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Caylee L. Cunningham
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Caleb J. Frye
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Morgan Shine
- Department
of Biochemistry and Chemistry, Westminster
College, New Wilmington, Pennsylvania 16172, United States
| | - Patrick E. Lackey
- Department
of Biochemistry and Chemistry, Westminster
College, New Wilmington, Pennsylvania 16172, United States
| | - Mihaela Rita Mihailescu
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Jeffrey D. Evanseck
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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25
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Esposito S, Deolmi M, Ramundo G, Puntoni M, Caminiti C, Principi N. True prevalence of long COVID in children: a narrative review. Front Microbiol 2023; 14:1225952. [PMID: 37789860 PMCID: PMC10543413 DOI: 10.3389/fmicb.2023.1225952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/23/2023] [Indexed: 10/05/2023] Open
Abstract
Contrary to what is true for adults, little is known about pediatric long COVID (LC). Studies enrolling children are relatively few and extremely heterogeneous. This does not allow to draw definitive conclusions on the frequency and pathogenesis of pediatric LC and limits the development of appropriate and effective measures to contain the clinical, social and economic impact of this condition on the pediatric population. Depending on the methods used to collect and analyze data, studies have found that the incidence rate of pediatric LC may vary from about 25% to less than 5%. However, despite true prevalence of pediatric LC cannot be exactly defined, studies comparing children with previous COVID-19 and uninfected controls have shown that most of the clinical manifestations detected in infected children, mainly mood symptoms, mental health disorders and heart abnormalities could be diagnosed with similar frequency and severity in uninfected subjects also. This seems to indicate that SARS-CoV-2 is the cause of pediatric LC only in a part of children and other factors play a relevant role in this regard. Pandemic itself with the persistent disruption of child lives may have caused persistent stress in all the pediatric population causing mood symptoms, mental health disorders or several organ and body system functional alterations, regardless SARS-CoV-2 infection. These suppositions suggest the need for long-term physical control of all the children after COVID-19 especially when they were already suffering from an underlying disease or have had a severe disease. Moreover, attention should be paid to the assessment of change in children's emotional and behavioral functioning in order to assure adequate interventions for the best emotional and behavioral well being. However, whatever its origin, it seems highly likely that the prevalence of the pediatric LC is set to decline in the future. Preliminary observations seem to suggest that recently developed SARS-CoV-2 variants are associated with less severe COVID-19. This suggests that, as already seen in adults, a lower number of pediatric virus-associated LC cases should occur. Furthermore, the use of COVID-19 vaccines, reducing incidence and severity of SARS-CoV-2 infection, may reduce risk of LC development. Finally, elimination of restrictive measures should significantly reduce mood symptoms and mental health disorders.
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Affiliation(s)
- Susanna Esposito
- Pediatric Clinic, Pietro Barilla Children’s Hospital, Department of Medicine and Surgery, University Hospital of Parma, Parma, Italy
| | - Michela Deolmi
- Pediatric Clinic, Pietro Barilla Children’s Hospital, Department of Medicine and Surgery, University Hospital of Parma, Parma, Italy
| | - Greta Ramundo
- Pediatric Clinic, Pietro Barilla Children’s Hospital, Department of Medicine and Surgery, University Hospital of Parma, Parma, Italy
| | - Matteo Puntoni
- Clinical and Epidemiological Research Unit, University Hospital of Parma, Parma, Italy
| | - Caterina Caminiti
- Clinical and Epidemiological Research Unit, University Hospital of Parma, Parma, Italy
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Zhan Y, Ye L, Ouyang Q, Yin J, Cui J, Liu K, Guo C, Zhang H, Zhai J, Zheng C, Guo A, Sun B. The binding profile of SARS-CoV-2 with human leukocyte antigen polymorphisms reveals critical alleles involved in immune evasion. J Med Virol 2023; 95:e29113. [PMID: 37750416 DOI: 10.1002/jmv.29113] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/26/2023] [Accepted: 09/11/2023] [Indexed: 09/27/2023]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), astonished the world and led to millions of deaths. Due to viral new mutations and immune evasion, SARS-CoV-2 ranked first in transmission and influence. The binding affinity of human leukocyte antigen (HLA) polymorphisms to SARS-CoV-2 might be related to immune escape, but the mechanisms remained unclear. In this study, we obtained the binding affinity of SARS-CoV-2 strains with different HLA proteins and identified 31 risk alleles. Subsequent structural predictions identified 10 active binding sites in these HLA proteins that may promote immune evasion. Particularly, we also found that the weak binding ability with HLA class I polymorphisms could contribute to the immune evasion of Omicron. These findings suggest important implications for preventing the immune evasion of SARS-CoV-2 and providing new insights for the vaccine design.
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Affiliation(s)
- Yan Zhan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Beijing, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Ling Ye
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qianying Ouyang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Beijing, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Jiye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Beijing, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Jiajia Cui
- Department of Geriatric Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Ke Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Beijing, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Chengxian Guo
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| | | | - Jingbo Zhai
- Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Medical College, Inner Mongolia Minzu University, Tongliao, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Aoxiang Guo
- Department of Pharmacy, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- Shenzhen Key Laboratory of Chinese Medicine Active substance screening and Translational Research, Shenzhen, China
| | - Bao Sun
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
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Li J, Zhang Q, Xu C, Zhang Y, Lu Y, Ai M, Tan X. Differences in clinical characteristics and liver injury between patients diagnosed with the Omicron subvariant BA.5.2 and the prototype of SARS-CoV-2: a single center retrospective study. BMC Gastroenterol 2023; 23:271. [PMID: 37553605 PMCID: PMC10408107 DOI: 10.1186/s12876-023-02907-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND The purpose of this study was to investigate the differences between the clinical characteristics and the factors influencing liver injury in patients with the Omicron subvariant BA.5.2 (Omicron BA.5.2) and the prototype of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS Between December 30, 2019 and November 30, 2022, 157 patients infected with the SARS-CoV-2 prototype and 199 patients infected with the Omicron BA.5.2 were included in this case-control, single-center, retrospective study. Differences in clinical characteristics and liver injury between the Omicron BA.5.2 patients and the prototype patients were subsequently analyzed. RESULTS None of the Omicron BA.5.2 patients reached the critical state, and showed relatively milder symptoms including fever, cough, headache, muscle soreness, nausea or vomiting, diarrhea, anorexia and hypoxia. The Omicron BA.5.2 had a lower effect on body temperature (T), white blood cell (WBC) count, hematocrit (HCT), C-reactive protein (CRP) level, D-dimer, finger pulse oxygen saturation (SpO2) and lung lesions. The differences in liver injury between the two groups were related to the severity of the disease, T, blood oxygen levels, albumin (ALB), CRP, and medication usage. Gender, body mass index, and CRP levels influenced liver damage in the Omicron BA.5.2 patients. In particular, CRP was an independent risk factor for liver injury. Because the severity of liver function damage was considerably low, only a small number of Omicron BA.5.2 patients required liver-protective treatment. CONCLUSION Liver injury is expected in the COVID-19 patients. The Omicron BA.5.2 patients showed milder symptoms of liver injury than the prototype patients. However, dynamic monitoring of liver function is warranted, especially for individuals presenting with elevated levels of CRP.
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Affiliation(s)
- Jie Li
- Department of Gastroenterology, Jingzhou of Hubei Province, First Hospital of Yangtze University, Jingzhou, China
- Digestive Disease Research Institution of Yangtze University, Jingzhou, China
| | - Qing Zhang
- Department of Gastroenterology, Jingzhou of Hubei Province, First Hospital of Yangtze University, Jingzhou, China
- Digestive Disease Research Institution of Yangtze University, Jingzhou, China
- Clinical medical college, Jingzhou of Hubei Province, Yangtze University, Jingzhou, China
| | - Chao Xu
- Department of Gastroenterology, Jingzhou of Hubei Province, First Hospital of Yangtze University, Jingzhou, China
- Digestive Disease Research Institution of Yangtze University, Jingzhou, China
| | - Yan Zhang
- Department of Gastroenterology, Jingzhou of Hubei Province, First Hospital of Yangtze University, Jingzhou, China
- Digestive Disease Research Institution of Yangtze University, Jingzhou, China
| | - Yueyue Lu
- Department of Gastroenterology, Jingzhou of Hubei Province, First Hospital of Yangtze University, Jingzhou, China
- Digestive Disease Research Institution of Yangtze University, Jingzhou, China
| | - Minghua Ai
- Department of Gastroenterology, Jingzhou of Hubei Province, First Hospital of Yangtze University, Jingzhou, China
- Digestive Disease Research Institution of Yangtze University, Jingzhou, China
| | - Xiaoping Tan
- Department of Gastroenterology, Jingzhou of Hubei Province, First Hospital of Yangtze University, Jingzhou, China.
- Digestive Disease Research Institution of Yangtze University, Jingzhou, China.
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Mocci S, Littera R, Chessa L, Campagna M, Melis M, Ottelio CM, Piras IS, Lai S, Firinu D, Tranquilli S, Mascia A, Vacca M, Schirru D, Lecca LI, Rassu S, Cannas F, Sanna C, Carta MG, Sedda F, Giuressi E, Cipri S, Miglianti M, Perra A, Giglio S. A review of the main genetic factors influencing the course of COVID-19 in Sardinia: the role of human leukocyte antigen-G. Front Immunol 2023; 14:1138559. [PMID: 37342325 PMCID: PMC10277491 DOI: 10.3389/fimmu.2023.1138559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Introduction A large number of risk and protective factors have been identified during the SARS-CoV-2 pandemic which may influence the outcome of COVID-19. Among these, recent studies have explored the role of HLA-G molecules and their immunomodulatory effects in COVID-19, but there are very few reports exploring the genetic basis of these manifestations. The present study aims to investigate how host genetic factors, including HLA-G gene polymorphisms and sHLA-G, can affect SARS-CoV-2 infection. Materials and Methods We compared the immune-genetic and phenotypic characteristics between COVID-19 patients (n = 381) with varying degrees of severity of the disease and 420 healthy controls from Sardinia (Italy). Results HLA-G locus analysis showed that the extended haplotype HLA-G*01:01:01:01/UTR-1 was more prevalent in both COVID-19 patients and controls. In particular, this extended haplotype was more common among patients with mild symptoms than those with severe symptoms [22.7% vs 15.7%, OR = 0.634 (95% CI 0.440 - 0.913); P = 0.016]. Furthermore, the most significant HLA-G 3'UTR polymorphism (rs371194629) shows that the HLA-G 3'UTR Del/Del genotype frequency decreases gradually from 27.6% in paucisymptomatic patients to 15.9% in patients with severe symptoms (X2 = 7.095, P = 0.029), reaching the lowest frequency (7.0%) in ICU patients (X2 = 11.257, P = 0.004). However, no significant differences were observed for the soluble HLA-G levels in patients and controls. Finally, we showed that SARS-CoV-2 infection in the Sardinian population is also influenced by other genetic factors such as β-thalassemia trait (rs11549407C>T in the HBB gene), KIR2DS2/HLA-C C1+ group combination and the HLA-B*58:01, C*07:01, DRB1*03:01 haplotype which exert a protective effect [P = 0.005, P = 0.001 and P = 0.026 respectively]. Conversely, the Neanderthal LZTFL1 gene variant (rs35044562A>G) shows a detrimental consequence on the disease course [P = 0.001]. However, by using a logistic regression model, HLA-G 3'UTR Del/Del genotype was independent from the other significant variables [ORM = 0.4 (95% CI 0.2 - 0.7), PM = 6.5 x 10-4]. Conclusion Our results reveal novel genetic variants which could potentially serve as biomarkers for disease prognosis and treatment, highlighting the importance of considering genetic factors in the management of COVID-19 patients.
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Affiliation(s)
- Stefano Mocci
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
| | - Roberto Littera
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Luchino Chessa
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- Liver Unit, University Hospital, Cagliari, Italy
| | - Marcello Campagna
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Maurizio Melis
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
| | - Carla Maria Ottelio
- Anesthesia and Intensive Care Unit, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Ignazio S. Piras
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Sara Lai
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Davide Firinu
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Stefania Tranquilli
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Alessia Mascia
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Monica Vacca
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Daniele Schirru
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Luigi Isaia Lecca
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Stefania Rassu
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Federica Cannas
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Celeste Sanna
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Mauro Giovanni Carta
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Francesca Sedda
- Section of Pathology, Oncology and Molecular Pathology Unit, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Erika Giuressi
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
| | - Selene Cipri
- GeneMos-APS (Association for Social Advancement), Reggio Calabria, Italy
| | - Michela Miglianti
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Andrea Perra
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
- Section of Pathology, Oncology and Molecular Pathology Unit, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Sabrina Giglio
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Cagliari, Italy
- Centre for Research University Services (CeSAR, Centro Servizi di Ateneo per la Ricerca), University of Cagliari, Monserrato, Italy
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Ning S, Chang HC, Fan KC, Hsiao PY, Feng C, Shoemaker D, Chen RT. A point-of-care biosensor for rapid detection and differentiation of COVID-19 virus (SARS-CoV-2) and influenza virus using subwavelength grating micro-ring resonator. APPLIED PHYSICS REVIEWS 2023; 10:021410. [PMID: 37265478 PMCID: PMC10228026 DOI: 10.1063/5.0146079] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/05/2023] [Indexed: 06/03/2023]
Abstract
In the context of continued spread of coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 and the emergence of new variants, the demand for rapid, accurate, and frequent detection is increasing. Moreover, the new predominant strain, Omicron variant, manifests more similar clinical features to those of other common respiratory infections. The concurrent detection of multiple potential pathogens helps distinguish SARS-CoV-2 infection from other diseases with overlapping symptoms, which is significant for providing tailored treatment to patients and containing the outbreak. Here, we report a lab-on-a-chip biosensing platform for SARS-CoV-2 detection based on the subwavelength grating micro-ring resonator. The sensing surface is functionalized by specific antibody against SARS-CoV-2 spike protein, which could produce redshifts of resonant peaks by antigen-antibody combination, thus achieving quantitative detection. Additionally, the sensor chip is integrated with a microfluidic chip featuring an anti-backflow Y-shaped structure that enables the concurrent detection of two analytes. In this study, we realized the detection and differentiation of COVID-19 and influenza A H1N1. Experimental results indicate that the limit of detection of our device reaches 100 fg/ml (1.31 fM) within 15 min detecting time, and cross-reactivity tests manifest the specificity of the optical diagnostic assay. Furthermore, the integrated packaging and streamlined workflow facilitate its use for clinical applications. Thus, the biosensing platform presents a promising approach for attaining highly sensitive, selective, multiplexed, and quantitative point-of-care diagnosis and distinction between COVID-19 and influenza.
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Affiliation(s)
- Shupeng Ning
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas 78758, USA
| | - Hao-Chen Chang
- Omega Optics, Inc., 8500 Shoal Creek Blvd., Austin, Texas 78757, USA
| | - Kang-Chieh Fan
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas 78758, USA
| | - Po-Yu Hsiao
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas 78758, USA
| | - Chenghao Feng
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas 78758, USA
| | - Devan Shoemaker
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas 78758, USA
| | - Ray T. Chen
- Author to whom correspondence should be addressed:
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30
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Lyoo KS, Lee H, Lee SG, Yeom M, Lee JY, Kim KC, Yang JS, Song D. Experimental Infection and Transmission of SARS-CoV-2 Delta and Omicron Variants among Beagle Dogs. Emerg Infect Dis 2023; 29:782-785. [PMID: 36848871 PMCID: PMC10045707 DOI: 10.3201/eid2904.221727] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
We assessed susceptibility of dogs to SARS-COV-2 Delta and Omicron variants by experimentally inoculating beagle dogs. Moreover, we investigated transmissibility of the variants from infected to naive dogs. The dogs were susceptible to infection without clinical signs and transmitted both strains to other dogs through direct contact.
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Chen R, Guo Y, Deng S, Wang J, Gao M, Han H, Wang L, Jiang H, Huang K. All-cause mortality in moderate and severe COVID-19 patients with myocardial injury receiving versus not receiving azvudine: a propensity score-matched analysis. CARDIOLOGY PLUS 2023; 8:103-110. [PMID: 37539021 PMCID: PMC10364645 DOI: 10.1097/cp9.0000000000000049] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/27/2023] [Indexed: 08/05/2023] Open
Abstract
Omicron is currently the dominant strain of severe acute respiratory syndrome coronavirus 2, but little is known about the characteristics and management of omicron related myocardial injury, particularly the potential benefit of the antiviral agent azvudine. Methods Patients with confirmed and suspected coronavirus disease 2019 (COVID-19) admitted to Wuhan Union Hospital from December 7, 2022, to December 30, 2022, were included in this study. Cox regression was conducted to identify risk factors for all-cause mortality. A propensity score-matched analysis was performed at a 1:1 ratio with a caliper of 0.1 pooled standard deviations of relevant confounders. Results The final analysis included a total of 332 patients (167 confirmed cases and 165 suspected cases), 42.77% (142/332) of the patients were 80 years of age or older and 68.67% (228/332) of them were men, 158 patients were treated with azvudine. In the matched cohort, the total mortality was 30.30% (60/198), 40 (20.20%, 40/198) patients received noninvasive ventilation and 22 (11.11%, 22/198) received invasive ventilation, 34 (17.17%, 34/198) patients were admitted to intensive care unit (ICU). The rate of shock, multiple organ damages and arrhythmia were 11.62% (23/198), 20.20% (40/198), and 12.12% (24/198), respectively. There was no significant difference on these clinical outcomes in patients treated with azvudine or not. Azvudine reduced early mortality (within 14 days from admission) (hazard ratio: 0.37, 95% confidence interval: 0.18-0.77) even after adjusting for other treatments including glucocorticoids, immunoglobin and anticoagulant therapy, but not the final in-hospital mortality of patients. Conclusions Patients with COVID-19-related myocardial injury had a high mortality of about 30.30% (60/198). Azvudine improved the early survival of the patients but not final mortality.
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Affiliation(s)
- Ru Chen
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yi Guo
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shan Deng
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jian Wang
- Department of Clinical Laboratory, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Meng Gao
- Liyuan Cardiovascular Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hongli Han
- Liyuan Cardiovascular Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Lin Wang
- Department of Clinical Laboratory, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hongwei Jiang
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Kai Huang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei clinical research center of metabolic and cardiovascular disease, Huazhong University of Science and Technology, Wuhan 430022, China
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Shi J, Zhao Y, Peng M, Zhu S, Wu Y, Ji R, Shen C. Screening of Efficient Adjuvants for the RBD-Based Subunit Vaccine of SARS-CoV-2. Vaccines (Basel) 2023; 11:vaccines11040713. [PMID: 37112625 PMCID: PMC10147067 DOI: 10.3390/vaccines11040713] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/12/2023] [Accepted: 03/17/2023] [Indexed: 04/29/2023] Open
Abstract
The variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are more transmissible, with a reduced sensitivity to vaccines targeting the original virus strain. Therefore, developing an effective vaccine against both the original SARS-CoV-2 strain and its variants is an urgent need. It is known that the receptor-binding domain (RBD) in the S protein of SARS-CoV-2 is an important vaccine target, but subunit vaccines usually have lower immunogenicity and efficacy. Thus, selecting appropriate adjuvants to enhance the immunogenicity of protein-based subunit vaccine antigens is necessary. Here, an RBD-Fc subunit vaccine of SARS-CoV-2 has been generated, followed by vaccination in B6 mice, and four adjuvant regimens were investigated, including aluminum salts (Alum) + 3-O-desacyl-4'-monophosphoryl lipid A (MPL), AddaVax, QS21 + MPL, and Imiquimod. The adjuvant potency was evaluated by comparing the elicited polyclonal antibodies titers with measuring binding to RBD and S protein in ELISA and Western blot analysis, and also the cross-neutralizing antibodies titers using a pseudovirus infection assay of hACE2-expressing 293T cells, with pseudoviruses expressing the S protein of the SARS-CoV-2 original strain and Delta strain. The presence of QS21 + MPL adjuvant induced stronger polyclonal antibody response and neutralization potency blocking the original strain and Delta strain, as compared with the non-adjuvant RBD-Fc group and other adjuvant groups. Meanwhile, Imiquimod even had a negative effect in inducing specific antibodies and cross-neutralizing antibody production as an adjuvant.
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Affiliation(s)
- Juan Shi
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing 210009, China
| | - Yu Zhao
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing 210009, China
| | - Min Peng
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing 210009, China
| | - Suyue Zhu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing 210009, China
| | - Yandan Wu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing 210009, China
| | - Ruixue Ji
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing 210009, China
| | - Chuanlai Shen
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing 210009, China
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Liang S, Jiang T, Jiao Z, Zhou Z. A model simulation on the SARS-CoV-2 Omicron variant containment in Beijing, China. INTELLIGENT MEDICINE 2023; 3:10-15. [PMID: 36438437 PMCID: PMC9677562 DOI: 10.1016/j.imed.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/08/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022]
Abstract
Objective The Omicron variant of SARS-COV-2 is replacing previously circulating variants around the world in 2022. Sporadic outbreaks of the Omicron variant into China have posed a concern how to properly response to battle against evolving coronavirus disease 2019 (COVID-19). Methods Based on the epidemic data from website announced by Beijing Center for Disease Control and Prevention for the recent outbreak in Beijing from April 22nd to June 8th in 2022, we developed a modified SEPIR model to mathematically simulate the customized dynamic COVID-zero strategy and project transmissions of the Omicron epidemic. To demonstrate the effectiveness of dynamic-changing policies deployment during this outbreak control, we modified the transmission rate into four parts according to policy-changing dates as April 22nd to May 2nd, May 3rd to 11st, May 12th to 21st, May 22nd to June 8th, and we adopted Markov chain Monte Carlo (MCMC) to estimate different transmission rate. Then we altered the timing and scaling of these measures used to understand the effectiveness of these policies on the Omicron variant. Results The estimated effective reproduction number of four parts were 1.75 (95% CI 1.66-1.85), 0.89 (95% CI 0.79-0.99), 1.15 (95% CI 1.05-1.26) and 0.53 (95% CI 0.48 -0.60), respectively. In the experiment, we found that till June 8th the cumulative cases would rise to 132,609 (95% CI 59,667-250,639), 73.39 times of observed cumulative cases number 1,807 if no policy were implemented on May 3rd, and would be 3,235 (95% CI 1,909 - 4,954), increased by 79.03% if no policy were implemented on May 22nd. A 3-day delay of the implementation of policies would led to increase of cumulative cases by 58.28% and a 7-day delay would led to increase of cumulative cases by 187.00%. On the other hand, taking control measures 3 or 7 days in advance would result in merely 38.63% or 68.62% reduction of real cumulative cases. And if lockdown implemented 3 days before May 3rd, the cumulative cases would be 289 (95% CI 211-378), reduced by 84%, and the cumulative cases would be 853 (95% CI 578-1,183), reduced by 52.79% if lockdown implemented 3 days after May 3rd. Conclusion The dynamic COVID-zero strategy might be able to effectively minimize the scale of the transmission, shorten the epidemic period and reduce the total number of infections.
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Affiliation(s)
- Shihao Liang
- Yidu Cloud Technology Inc, Beijing 100089, China
| | - Tianhong Jiang
- Changshu Center for Disease Control and Prevention, Jiangsu 215501, China
| | - Zengtao Jiao
- Yidu Cloud Technology Inc, Beijing 100089, China
| | - Zhengyuan Zhou
- Changshu Center for Disease Control and Prevention, Jiangsu 215501, China
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Li S, Wu J, Jiang W, He H, Zhou Y, Wu W, Gao Y, Xie M, Xia A, He J, Zhang Q, Han Y, Wang N, Zhu G, Wang Q, Zhang Z, Mayer CT, Wang K, Wang X, Wang J, Chen Z, Jiang S, Sun L, Xia R, Wang Q. Characterization of cross-reactive monoclonal antibodies against SARS-CoV-1 and SARS-CoV-2: Implication for rational design and development of pan-sarbecovirus vaccines and neutralizing antibodies. J Med Virol 2023; 95:e28440. [PMID: 36573441 PMCID: PMC9880677 DOI: 10.1002/jmv.28440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
Emergence of various circulating SARS-CoV-2 variants of concern (VOCs) promotes the identification of pan-sarbecovirus vaccines and broadly neutralizing antibodies (bNAbs). Here, to characterize monoclonal antibodies cross-reactive against both SARS-CoV-1 and SARS-CoV-2 and to search the criterion for bNAbs against all emerging SARS-CoV-2, we isolated several SARS-CoV-1-cross-reactive monoclonal antibodies (mAbs) from a wildtype SARS-CoV-2 convalescent donor. These antibodies showed broad binding capacity and cross-neutralizing potency against various SARS-CoV-2 VOCs, including B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), and B.1.617.2 (Delta), but failed to efficiently neutralize Omicron variant and its sublineages. Structural analysis revealed how Omicron sublineages, but not other VOCs, efficiently evade an antibody family cross-reactive against SARS-CoV-1 through their escape mutations. Further evaluation of a series of SARS-CoV-1/2-cross-reactive bNAbs showed a negative correlation between the neutralizing activities against SARS-CoV-1 and SARS-CoV-2 Omicron variant. Together, these results suggest the necessity of using cross-neutralization against SARS-CoV-1 and SARS-CoV-2 Omicron as criteria for rational design and development of potent pan-sarbecovirus vaccines and bNAbs.
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Affiliation(s)
- Shibo Li
- Department of Infectious DiseaseZhoushan Hospital, Wenzhou Medical UniversityZhoushanChina
| | - Jianbo Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Weiyu Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Haiyan He
- Department of Hematology, Myeloma & Lymphoma Center, Shanghai Changzheng HospitalNaval Medical UniversityShanghaiChina
| | - Yunjiao Zhou
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Wei Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Yidan Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Minxiang Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Anqi Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Jiaying He
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Qianqian Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Yuru Han
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Nan Wang
- Department of General Surgery, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Guangqi Zhu
- Department of Infectious DiseaseZhoushan Hospital, Wenzhou Medical UniversityZhoushanChina
| | - Qiujing Wang
- Department of Infectious DiseaseZhoushan Hospital, Wenzhou Medical UniversityZhoushanChina
| | - Zheen Zhang
- Department of Infectious DiseaseZhoushan Hospital, Wenzhou Medical UniversityZhoushanChina
| | - Christian T. Mayer
- Experimental Immunology Branch, Center for Cancer Research, National Cancer InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Kang Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of BiophysicsChinese Academy of SciencesBeijingChina
| | - Junqing Wang
- Department of General Surgery, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Zhenguo Chen
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Fifth People's HospitalFudan UniversityShanghaiChina
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Lei Sun
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical SciencesFudan UniversityShanghaiChina,Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Fifth People's HospitalFudan UniversityShanghaiChina
| | - Rong Xia
- Department of Transfusion Medicine, Shanghai Huashan HospitalFudan UniversityShanghaiChina
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical SciencesFudan UniversityShanghaiChina
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Zhou Y, Zhi H, Teng Y. The outbreak of SARS-CoV-2 Omicron lineages, immune escape, and vaccine effectivity. J Med Virol 2023; 95:e28138. [PMID: 36097349 PMCID: PMC9538491 DOI: 10.1002/jmv.28138] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/03/2022] [Accepted: 09/07/2022] [Indexed: 01/11/2023]
Abstract
As of November 2021, several SARS-CoV-2 variants appeared and became dominant epidemic strains in many countries, including five variants of concern (VOCs) Alpha, Beta, Gamma, Delta, and Omicron defined by the World Health Organization during the COVID-19 pandemic. As of August 2022, Omicron is classified into five main lineages, BA.1, BA.2, BA.3, BA.4, BA.5 and some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6) (https://www.gisaid.org/). Compared to the previous VOCs (Alpha, Beta, Gamma, and Delta), all the Omicron lineages have the most highly mutations in the spike protein, and with 50 mutations accumulated throughout the genome. Early data indicated that Omicron BA.2 sublineage had higher infectivity and more immune escape than the early wild-type (WT) strain, the previous VOCs, and BA.1. Recently, global surveillance data suggest a higher transmissibility of BA.4/BA.5 than BA.1, BA.1.1 and BA.2, and BA.4/BA.5 is becoming dominant strain in many countries globally.
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Affiliation(s)
- Yongbing Zhou
- Department of Clinical Laboratory, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huilin Zhi
- Department of Dermatology, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Teng
- Department of Clinical Laboratory, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
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36
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Ye Q, Liu H, Mao J, Shu Q. Nonpharmaceutical interventions for COVID-19 disrupt the dynamic balance between influenza A virus and human immunity. J Med Virol 2023; 95:e28292. [PMID: 36367115 PMCID: PMC9877879 DOI: 10.1002/jmv.28292] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
During the COVID-19 epidemic, nonpharmaceutical interventions (NPIs) blocked the transmission route of respiratory diseases. This study aimed to investigate the impact of NPIs on the influenza A virus (IAV) outbreak. The present study enrolled all children with respiratory tract infections who came to the Children's Hospital of Zhejiang University between January 2019 and July 2022. A direct immunofluorescence assay kit detected IAV. Virus isolation and Sanger sequencing were performed. From June to July 2022, in Hangzhou, China, the positive rate of IAV infection in children has increased rapidly, reaching 30.41%, and children over 3 years old are the main infected population, accounting for 75% of the total number of infected children. Influenza A (H3N2) viruses are representative strains during this period. In this outbreak, H3N2 was isolated from a cluster of its own and is highly homologous with A/South_Dakota/22/2022 (2021-2022 Northern Hemisphere). Between isolated influenza A (H3N2) viruses and A/South_Dakota/22/2022, the nucleotide homology of the HA gene ranged from 97.3% to 97.5%; the amino acid homology was 97%-97.2%, and the genetic distance of nucleotides ranged from 0.05 to 0.052. Compared with A/South_Dakota/22/2022, the isolated H3N2 showed S156H, N159Y, I160T, D186S, S198P, I48T, S53D, and K171N mutations. There was no variation in 13 key amino acid sites associated with neuraminidase inhibitor resistance in NA protein. Long-term NPIs have significantly affected the evolution and transmission of the influenza virus and human immunity, breaking the dynamic balance between the IAV and human immunity.
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Affiliation(s)
- Qing Ye
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Huihui Liu
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Jianhua Mao
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Qiang Shu
- Department of Thoracic & Cardiovascular Surgery, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
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37
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Effect of Double Mutation (L452R and E484Q) on the Binding Affinity of Monoclonal Antibodies (mAbs) against the RBD-A Target for Vaccine Development. Vaccines (Basel) 2022; 11:vaccines11010023. [PMID: 36679867 PMCID: PMC9860914 DOI: 10.3390/vaccines11010023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, emerges as a global health problem, as the viral genome is evolving rapidly to form several variants. Advancement and progress in the development of effective vaccines and neutralizing monoclonal antibodies are promising to combat viral infections. In the current scenario, several lineages containing "co-mutations" in the receptor-binding domain (RBD) region of the spike (S) protein are imposing new challenges. Co-occurrence of some co-mutations includes delta (L452R/T478K), kappa (L452R/E484Q), and a common mutation in both beta and gamma variants (E484K/N501Y). The effect of co-mutants (L452R/E484Q) on human angiotensin-converting enzyme 2 (hACE2) binding has already been elucidated. Here, for the first time, we investigated the role of these RBD co-mutations (L452R/E484Q) on the binding affinity of mAbs by adopting molecular dynamics (MD) simulation and free-energy binding estimation. The results obtained from our study suggest that the structural and dynamic changes introduced by these co-mutations reduce the binding affinity of the viral S protein to monoclonal antibodies (mAbs). The structural changes imposed by L452R create a charged patch near the interfacial surface that alters the affinity towards mAbs. In E484Q mutation, polar negatively charged E484 helps in the formation of electrostatic interaction, while the neutrally charged Q residue affects the interaction by forming repulsive forces. MD simulations along with molecular mechanics-generalized Born surface area (MMGBSA) studies revealed that the REGN 10933, BD-368-2, and S2M11 complexes have reduced binding affinity towards the double-mutant RBD. This indicates that their mutant (MT) structures have a stronger ability to escape from most antibodies than the wild type (WT). However, EY6A Ab showed higher affinity towards the double MT-RBD complex as compared to the WT. However, no significant effect of the per-residue contribution of double-mutated residues was observed, as this mAb does not interact with the region harboring L452 and E484 residues.
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38
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Hughes E, Binny R, Hendy S, James A. Predicting elimination of evolving virus variants. MATHEMATICAL MEDICINE AND BIOLOGY : A JOURNAL OF THE IMA 2022; 39:410-424. [PMID: 35975450 DOI: 10.1093/imammb/dqac012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/14/2022] [Accepted: 07/26/2022] [Indexed: 01/01/2023]
Abstract
As the SARS-CoV-2 virus spreads around the world new variants are appearing regularly. Although some countries have achieved very swift and successful vaccination campaigns, on a global scale the vast majority of the population is unvaccinated and new variants are proving more resistant to the current set of vaccines. We present a simple model of disease spread, which includes the evolution of new variants of a novel virus and varying vaccine effectiveness to these new strains. We show that rapid vaccine updates to target new strains are more effective than slow updates and containing spread through non-pharmaceutical interventions is vital while these vaccines are delivered. Finally, when measuring the key model inputs, e.g. the rate at which new mutations and variants of concern emerge, is difficult we show how an observable model output, the number of new variants that have been seen, is strongly correlated with the probability the virus is eliminated.
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Affiliation(s)
- Elliott Hughes
- School of Mathematics and Statistics, University of Canterbury, Christchurch 8140, New Zealand.,Te Pūnaha Matatini: the Centre for Complex Systems and Networks, Auckland 1010, New Zealand
| | - Rachelle Binny
- Manaaki Whenua, Lincoln 7640, New Zealand.,Te Pūnaha Matatini: the Centre for Complex Systems and Networks, Auckland 1010, New Zealand
| | - Shaun Hendy
- Te Pūnaha Matatini: the Centre for Complex Systems and Networks, Auckland 1010, New Zealand.,Department of Physics, University of Auckland, Auckland 1010, New Zealand
| | - Alex James
- School of Mathematics and Statistics, University of Canterbury, Christchurch 8140, New Zealand.,Te Pūnaha Matatini: the Centre for Complex Systems and Networks, Auckland 1010, New Zealand
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39
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Moore JS, Robertson LJ, Price R, Curry G, Farnan J, Black A, Nesbit MA, McLaughlin JA, Moore T. Evaluation of the performance of a lateral flow device for quantitative detection of anti-SARS-CoV-2 IgG. CLINICAL IMMUNOLOGY COMMUNICATIONS 2022; 2:130-135. [PMID: 38013966 PMCID: PMC9472806 DOI: 10.1016/j.clicom.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022]
Abstract
INTRODUCTION The AbC-19™ lateral flow immunoassay (LFIA) performance was evaluated on plasma samples from a SARS-CoV-2 vaccination cohort, WHO international standards for anti-SARS-CoV-2 IgG (human), individuals ≥2 weeks from infection of RT-PCR confirmed SARS-CoV-2 genetic variants, as well as microorganism serology. METHODS Pre-vaccination to three weeks post-booster samples were collected from a cohort of 111 patients (including clinically extremely vulnerable patients) from Northern Ireland. All patients received Oxford-AstraZeneca COVID-19 vaccination for the first and second dose, and Pfizer-BioNTech for the third (first booster). WHO international standards, 15 samples from 2 variants of concern (Delta and Omicron) and cross-reactivity with plasma samples from other microorganism infections were also assessed on AbC-19™. RESULTS All 80 (100%) participants sampled post-booster had high positive IgG responses, compared to 38/95 (40%) participants at 6 months post-first vaccination. WHO standard results correlated with information from corresponding biological data sheets, and antibodies to all genetic variants were detected by LFIA. No cross-reactivity was found with exception of one (of five) Dengue virus samples. CONCLUSION These findings suggest BNT162b2 booster vaccination enhanced humoral immunity to SARS-CoV-2 from pre-booster levels, and that this antibody response was detectable by the LFIA. In combination with cross-reactivity, standards and genetic variant results would suggest LFIA may be a cost-effective measure to assess SARS-CoV-2 antibody status.
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Affiliation(s)
- J S Moore
- Biomedical Sciences Research Institute, Ulster University, Northern Ireland, United Kingdom
- Integrated Diagnostics Laboratory, Ulster University, 3-5a Frederick St, Belfast, Northern Ireland, United Kingdom
| | - L J Robertson
- Biomedical Sciences Research Institute, Ulster University, Northern Ireland, United Kingdom
- Integrated Diagnostics Laboratory, Ulster University, 3-5a Frederick St, Belfast, Northern Ireland, United Kingdom
| | - R Price
- Biomedical Sciences Research Institute, Ulster University, Northern Ireland, United Kingdom
| | - G Curry
- Biomedical Sciences Research Institute, Ulster University, Northern Ireland, United Kingdom
- Integrated Diagnostics Laboratory, Ulster University, 3-5a Frederick St, Belfast, Northern Ireland, United Kingdom
| | - J Farnan
- The Group Surgery, 257 North Queen Street, Belfast, Northern Ireland, United Kingdom
| | - A Black
- The Group Surgery, 257 North Queen Street, Belfast, Northern Ireland, United Kingdom
| | - M A Nesbit
- Biomedical Sciences Research Institute, Ulster University, Northern Ireland, United Kingdom
- Integrated Diagnostics Laboratory, Ulster University, 3-5a Frederick St, Belfast, Northern Ireland, United Kingdom
| | - J A McLaughlin
- Integrated Diagnostics Laboratory, Ulster University, 3-5a Frederick St, Belfast, Northern Ireland, United Kingdom
- Nanotechnology and Integrated Bioengineering Centre, Ulster University, Northern Ireland, United Kingdom
| | - T Moore
- Biomedical Sciences Research Institute, Ulster University, Northern Ireland, United Kingdom
- Integrated Diagnostics Laboratory, Ulster University, 3-5a Frederick St, Belfast, Northern Ireland, United Kingdom
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Amendola A, Canuti M, Bianchi S, Kumar S, Fappani C, Gori M, Colzani D, Kosakovsky Pond SL, Miura S, Baggieri M, Marchi A, Borghi E, Zuccotti G, Raviglione MC, Magurano F, Tanzi E. Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy. ENVIRONMENTAL RESEARCH 2022; 215:113979. [PMID: 36029839 PMCID: PMC9404229 DOI: 10.1016/j.envres.2022.113979] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/07/2022] [Accepted: 07/21/2022] [Indexed: 05/12/2023]
Abstract
As a reference laboratory for measles and rubella surveillance in Lombardy, we evaluated the association between SARS-CoV-2 infection and measles-like syndromes, providing preliminary evidence for undetected early circulation of SARS-CoV-2. Overall, 435 samples from 156 cases were investigated. RNA from oropharyngeal swabs (N = 148) and urine (N = 141) was screened with four hemi-nested PCRs and molecular evidence for SARS-CoV-2 infection was found in 13 subjects. Two of the positive patients were from the pandemic period (2/12, 16.7%, March 2020-March 2021) and 11 were from the pre-pandemic period (11/44, 25%, August 2019-February 2020). Sera (N = 146) were tested for anti-SARS-CoV-2 IgG, IgM, and IgA antibodies. Five of the RNA-positive individuals also had detectable anti-SARS-CoV-2 antibodies. No strong evidence of infection was found in samples collected between August 2018 and July 2019 from 100 patients. The earliest sample with evidence of SARS-CoV-2 RNA was from September 12, 2019, and the positive patient was also positive for anti-SARS-CoV-2 antibodies (IgG and IgM). Mutations typical of B.1 strains previously reported to have emerged in January 2020 (C3037T, C14408T, and A23403G), were identified in samples collected as early as October 2019 in Lombardy. One of these mutations (C14408T) was also identified among sequences downloaded from public databases that were obtained by others from samples collected in Brazil in November 2019. We conclude that a SARS-CoV-2 progenitor capable of producing a measles-like syndrome may have emerged in late June-late July 2019 and that viruses with mutations characterizing B.1 strain may have been spreading globally before the first Wuhan outbreak. Our findings should be complemented by high-throughput sequencing to obtain additional sequence information. We highlight the importance of retrospective surveillance studies in understanding the early dynamics of COVID-19 spread and we encourage other groups to perform retrospective investigations to seek confirmatory proofs of early SARS-CoV-2 circulation.
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Affiliation(s)
- Antonella Amendola
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Marta Canuti
- Department of Health Sciences, University of Milan, 20142, Milan, Italy.
| | - Silvia Bianchi
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, 19122, Philadelphia, USA; Department of Biology, Temple University, 19122, Philadelphia, USA; Center for Excellence in Genome Medicine and Research, King Abdulaziz University, 22252, Jeddah, Saudi Arabia.
| | - Clara Fappani
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Maria Gori
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Daniela Colzani
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, 19122, Philadelphia, USA; Department of Biology, Temple University, 19122, Philadelphia, USA.
| | - Sayaka Miura
- Institute for Genomics and Evolutionary Medicine, Temple University, 19122, Philadelphia, USA; Department of Biology, Temple University, 19122, Philadelphia, USA.
| | - Melissa Baggieri
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Antonella Marchi
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Elisa Borghi
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Gianvincenzo Zuccotti
- Department of Paediatrics, Children Hospital V. Buzzi, University of Milan, 20154, Milan, Italy; Romeo and Enrica Invernizzi Pediatric Research Center, University of Milan, 20154, Milan, Italy.
| | - Mario C Raviglione
- Centre for Multidisciplinary Research in Health Science, University of Milan, 20122, Milan, Italy.
| | - Fabio Magurano
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Elisabetta Tanzi
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
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Li H, Arcalas C, Song J, Rahmati M, Park S, Koyanagi A, Lee SW, Yon DK, Shin JI, Smith L. Genetics, structure, transmission, epidemiology, immune response, and vaccine efficacies of the SARS‐CoV‐2 Delta variant: A comprehensive review. Rev Med Virol 2022; 33:e2408. [PMID: 36420676 DOI: 10.1002/rmv.2408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 10/29/2022] [Accepted: 11/02/2022] [Indexed: 11/25/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant (B.1.617.2) was the predominant variant behind the surges of COVID-19 in the United States, Europe, and India in the second half of 2021. The information available regarding the defining mutations and their effects on the structure, transmission, and vaccine efficacy of SARS-CoV-2 is constantly evolving. With waning vaccine immunity and relaxation of social distancing policies across the globe driving the increased spread of the Delta variant, there is a great need for a resource aggregating the most recent information for clinicians and researchers concerning the Delta variant. Accordingly, this narrative review comprehensively reviews the genetics, structure, epidemiology, clinical course, and vaccine efficacy of the Delta variant. Comparison with the omicron variant is also discussed. The Delta variant is defined by 15 mutations in the Spike protein, most of which increase affinity for the ACE-2 receptor or enhance immune escape. The Delta variant causes similar symptoms to prototypical COVID-19, but it is more likely to be severe, with a greater inflammatory phenotype and viral load. The reproduction number is estimated to be approximately twice the prototypical strains present during the early pandemic, and numerous breakthrough infections have been reported. Despite studies demonstrating breakthrough infection and reduced antibody neutralisation, full vaccination effectively reduces the likelihood of severe illness and hospitalisation.
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Affiliation(s)
- Han Li
- University of Florida College of Medicine Gainesville Florida USA
| | | | - Junmin Song
- Keimyung University School of Medicine Daegu Republic of Korea
| | - Masoud Rahmati
- Department of Physical Education and Sport Sciences Faculty of Literature and Human Sciences Lorestan University Khoramabad Iran
| | - Seoyeon Park
- Yonsei University College of Medicine Seoul Republic of Korea
| | - Ai Koyanagi
- Parc Sanitari Sant Joan de Deu/CIBERSAM Fundacio Sant Joan de Deu Universitat de Barcelona Sant Boi de Llobregat, Barcelona Spain
- ICREA (Catalan Institution for Research and Advanced Studies) Barcelona Spain
| | - Seung Won Lee
- Department of Precision Medicine Sungkyunkwan University School of Medicine Suwon Republic of Korea
| | - Dong Keon Yon
- Center for Digital Health, Medical Science Research Institute Kyung Hee University College of Medicine Seoul Republic of Korea
- Department of Pediatrics Kyung Hee University Medical Center Kyung Hee University College of Medicine Seoul Republic of Korea
| | - Jae Il Shin
- Department of Pediatrics Yonsei University College of Medicine Seoul Republic of Korea
| | - Lee Smith
- Centre for Health, Performance, and Wellbeing Anglia Ruskin University Cambridge UK
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Chavda VP, Bezbaruah R, Deka K, Nongrang L, Kalita T. The Delta and Omicron Variants of SARS-CoV-2: What We Know So Far. Vaccines (Basel) 2022; 10:1926. [PMID: 36423021 PMCID: PMC9698608 DOI: 10.3390/vaccines10111926] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 07/30/2023] Open
Abstract
The world has not yet completely overcome the fear of the havoc brought by SARS-CoV-2. The virus has undergone several mutations since its initial appearance in China in December 2019. Several variations (i.e., B.1.616.1 (Kappa variant), B.1.617.2 (Delta variant), B.1.617.3, and BA.2.75 (Omicron variant)) have emerged throughout the pandemic, altering the virus's capacity to spread, risk profile, and even symptoms. Humanity faces a serious threat as long as the virus keeps adapting and changing its fundamental function to evade the immune system. The Delta variant has two escape alterations, E484Q and L452R, as well as other mutations; the most notable of these is P681R, which is expected to boost infectivity, whereas the Omicron has about 60 mutations with certain deletions and insertions. The Delta variant is 40-60% more contagious in comparison to the Alpha variant. Additionally, the AY.1 lineage, also known as the "Delta plus" variant, surfaced as a result of a mutation in the Delta variant, which was one of the causes of the life-threatening second wave of coronavirus disease 2019 (COVID-19). Nevertheless, the recent Omicron variants represent a reminder that the COVID-19 epidemic is far from ending. The wave has sparked a fervor of investigation on why the variant initially appeared to propagate so much more rapidly than the other three variants of concerns (VOCs), whether it is more threatening in those other ways, and how its type of mutations, which induce minor changes in its proteins, can wreck trouble. This review sheds light on the pathogenicity, mutations, treatments, and impact on the vaccine efficacy of the Delta and Omicron variants of SARS-CoV-2.
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad 380008, Gujarat, India
| | - Rajashri Bezbaruah
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Kangkan Deka
- NETES Institute of Pharmaceutical Science, Mirza, Guwahati 781125, Assam, India
| | - Lawandashisha Nongrang
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Tutumoni Kalita
- Girijananda Chowdhury Institute of Pharmaceutical Science, Azara, Guwahati 781017, Assam, India
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Sharma S, Vercruysse T, Sanchez-Felipe L, Kerstens W, Rasulova M, Bervoets L, De Keyzer C, Abdelnabi R, Foo CS, Lemmens V, Van Looveren D, Maes P, Baele G, Weynand B, Lemey P, Neyts J, Thibaut HJ, Dallmeier K. Updated vaccine protects against SARS-CoV-2 variants including Omicron (B.1.1.529) and prevents transmission in hamsters. Nat Commun 2022; 13:6644. [PMID: 36333374 PMCID: PMC9636174 DOI: 10.1038/s41467-022-34439-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Current COVID-19 vaccines are based on prototypic spike sequences from ancestral 2019 SARS-CoV-2 strains. However, the ongoing pandemic is fueled by variants of concern (VOC) escaping vaccine-mediated protection. Here we demonstrate how immunization in hamsters using prototypic spike expressed from yellow fever 17D (YF17D) as vector blocks ancestral virus (B lineage) and VOC Alpha (B.1.1.7) yet fails to fully protect from Beta (B.1.351). However, the same YF17D vectored vaccine candidate with an evolved antigen induced considerably improved neutralizing antibody responses against VOCs Beta, Gamma (P.1) and the recently predominant Omicron (B.1.1.529), while maintaining immunogenicity against ancestral virus and VOC Delta (B.1.617.2). Thus vaccinated animals resisted challenge by all VOCs, including vigorous high titre exposure to the most difficult to cover Beta, Delta and Omicron variants, eliminating detectable virus and markedly improving lung pathology. Finally, vaccinated hamsters did not transmit Delta variant to non-vaccinated cage mates. Overall, our data illustrate how current first-generation COVID-19 vaccines may need to be updated to maintain efficacy against emerging VOCs and their spread at community level.
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Affiliation(s)
- Sapna Sharma
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, BE-3000, Leuven, Belgium
| | - Thomas Vercruysse
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, BE-3000, Leuven, Belgium
| | - Lorena Sanchez-Felipe
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, BE-3000, Leuven, Belgium
| | - Winnie Kerstens
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, BE-3000, Leuven, Belgium
| | - Madina Rasulova
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, BE-3000, Leuven, Belgium
| | - Lindsey Bervoets
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, BE-3000, Leuven, Belgium
| | - Carolien De Keyzer
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, BE-3000, Leuven, Belgium
| | - Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, BE-3000, Leuven, Belgium
| | - Caroline S Foo
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, BE-3000, Leuven, Belgium
| | - Viktor Lemmens
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, BE-3000, Leuven, Belgium
| | - Dominique Van Looveren
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, BE-3000, Leuven, Belgium
| | - Piet Maes
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, Zoonotic Infectious Diseases Unit, BE-3000, Leuven, Belgium
| | - Guy Baele
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, Evolutionary and Computational Virology, BE-3000, Leuven, Belgium
| | - Birgit Weynand
- KU Leuven Department of Imaging and Pathology, Translational Cell and Tissue Research, BE-3000, Leuven, Belgium
| | - Philippe Lemey
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, Evolutionary and Computational Virology, BE-3000, Leuven, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, BE-3000, Leuven, Belgium
- Global Virus Network (GVN), Baltimore, MD, USA
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, BE-3000, Leuven, Belgium
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology, Molecular Vaccinology and Vaccine Discovery, BE-3000, Leuven, Belgium.
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Lazarus JV, Romero D, Kopka CJ, Karim SA, Abu-Raddad LJ, Almeida G, Baptista-Leite R, Barocas JA, Barreto ML, Bar-Yam Y, Bassat Q, Batista C, Bazilian M, Chiou ST, Del Rio C, Dore GJ, Gao GF, Gostin LO, Hellard M, Jimenez JL, Kang G, Lee N, Matičič M, McKee M, Nsanzimana S, Oliu-Barton M, Pradelski B, Pyzik O, Rabin K, Raina S, Rashid SF, Rathe M, Saenz R, Singh S, Trock-Hempler M, Villapol S, Yap P, Binagwaho A, Kamarulzaman A, El-Mohandes A. A multinational Delphi consensus to end the COVID-19 public health threat. Nature 2022; 611:332-345. [PMID: 36329272 PMCID: PMC9646517 DOI: 10.1038/s41586-022-05398-2] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022]
Abstract
Despite notable scientific and medical advances, broader political, socioeconomic and behavioural factors continue to undercut the response to the COVID-19 pandemic1,2. Here we convened, as part of this Delphi study, a diverse, multidisciplinary panel of 386 academic, health, non-governmental organization, government and other experts in COVID-19 response from 112 countries and territories to recommend specific actions to end this persistent global threat to public health. The panel developed a set of 41 consensus statements and 57 recommendations to governments, health systems, industry and other key stakeholders across six domains: communication; health systems; vaccination; prevention; treatment and care; and inequities. In the wake of nearly three years of fragmented global and national responses, it is instructive to note that three of the highest-ranked recommendations call for the adoption of whole-of-society and whole-of-government approaches1, while maintaining proven prevention measures using a vaccines-plus approach2 that employs a range of public health and financial support measures to complement vaccination. Other recommendations with at least 99% combined agreement advise governments and other stakeholders to improve communication, rebuild public trust and engage communities3 in the management of pandemic responses. The findings of the study, which have been further endorsed by 184 organizations globally, include points of unanimous agreement, as well as six recommendations with >5% disagreement, that provide health and social policy actions to address inadequacies in the pandemic response and help to bring this public health threat to an end.
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Affiliation(s)
- Jeffrey V Lazarus
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.
- Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.
- City University of New York Graduate School of Public Health and Health Policy (CUNY SPH), New York City, NY, USA.
| | - Diana Romero
- City University of New York Graduate School of Public Health and Health Policy (CUNY SPH), New York City, NY, USA
| | | | - Salim Abdool Karim
- University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Program of Research in South Africa (CAPRISA), Durban, South Africa
| | - Laith J Abu-Raddad
- Weill Cornell Medicine, Cornell University, Ithaca, NY, USA
- Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation-Education City, Doha, Qatar
| | | | - Ricardo Baptista-Leite
- UNITE Global Parliamentarians Network, Lisbon, Portugal
- Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
- Institute of Health Sciences (CIIS), Catholic University of Portugal, Lisbon, Portugal
| | | | - Mauricio L Barreto
- Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
- University of Bahia, Salvador, Brazil
| | - Yaneer Bar-Yam
- New England Complex Systems Institute, Cambridge, MA, USA
| | - Quique Bassat
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Manhiça Health Research Center (CISM), Maputo, Mozambique
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
- Pediatrics Department, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
- Biomedical Research Consortium in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Carolina Batista
- Doctors Without Borders (MSF), Geneva, Switzerland
- Baraka Impact Finance, Geneva, Switzerland
| | | | - Shu-Ti Chiou
- National Yang Ming Chiao Tung University, Taipei, Taiwan
| | | | - Gregory J Dore
- University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - George F Gao
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lawrence O Gostin
- The O'Neill Institute for National and Global Health Law, Georgetown University, Washington, DC, USA
| | | | - Jose L Jimenez
- Department of Chemistry, University of Colorado Boulder, Boulder, CO, USA
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado Boulder, Boulder, CO, USA
| | | | | | - Mojca Matičič
- Clinic for Infectious Diseases and Febrile Illnesses, University Medical Centre, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Martin McKee
- The London School of Hygiene & Tropical Medicine, London, UK
| | | | | | - Bary Pradelski
- French National Centre for Scientific Research (CNRS), Grenoble, France
| | | | - Kenneth Rabin
- City University of New York Graduate School of Public Health and Health Policy (CUNY SPH), New York City, NY, USA
| | - Sunil Raina
- Dr. Rajendra Prasad Government Medical College, Himachal Pradesh, India
| | - Sabina Faiz Rashid
- James P. Grant School of Public Health, BRAC University, Dhaka, Bangladesh
| | | | - Rocio Saenz
- University of Costa Rica, San José, Costa Rica
| | - Sudhvir Singh
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | | | - Sonia Villapol
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Peiling Yap
- International Digital Health & AI Research Collaborative (I-DAIR), Geneva, Switzerland
| | | | | | - Ayman El-Mohandes
- City University of New York Graduate School of Public Health and Health Policy (CUNY SPH), New York City, NY, USA
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Tian D, Nie W, Sun Y, Ye Q. The Epidemiological Features of the SARS-CoV-2 Omicron Subvariant BA.5 and Its Evasion of the Neutralizing Activity of Vaccination and Prior Infection. Vaccines (Basel) 2022; 10:1699. [PMID: 36298564 PMCID: PMC9612321 DOI: 10.3390/vaccines10101699] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/21/2022] Open
Abstract
From December 2021 to May 2022, the Omicron BA.1 and BA.2 subvariants successively became the most dominant strains in many countries around the world. Subsequently, Omicron subvariants have emerged, and Omicron has been classified into five main lineages, including BA.1, BA.2, BA.3, BA.4, BA.5, and some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6, BA.5.1, and BA.5.2). The recent emergence of several Omicron subvariants has generated new concerns about further escape from immunity induced by prior infection and vaccination and the creation of new COVID-19 waves globally. In particular, BA.5 (first found in southern Africa, February 2022) displays a higher transmissibility than other Omicron subvariants and is replacing the previously circulating BA.1 and BA.2 in several countries.
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Affiliation(s)
| | | | | | - Qing Ye
- Department of Clinical Laboratory, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Hangzhou 310052, China
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Jaago M, Rähni A, Pupina N, Pihlak A, Sadam H, Tuvikene J, Avarlaid A, Planken A, Planken M, Haring L, Vasar E, Baćević M, Lambert F, Kalso E, Pussinen P, Tienari PJ, Vaheri A, Lindholm D, Timmusk T, Ghaemmaghami AM, Palm K. Differential patterns of cross-reactive antibody response against SARS-CoV-2 spike protein detected for chronically ill and healthy COVID-19 naïve individuals. Sci Rep 2022; 12:16817. [PMID: 36207326 PMCID: PMC9540097 DOI: 10.1038/s41598-022-20849-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
Immunity to previously encountered viruses can alter response to unrelated pathogens. We reasoned that similar mechanism may also involve SARS-CoV-2 and thereby affect the specificity and the quality of the immune response against the virus. Here, we employed high-throughput next generation phage display method to explore the link between antibody immune response to previously encountered antigens and spike (S) glycoprotein. By profiling the antibody response in COVID-19 naïve individuals with a diverse clinical history (including cardiovascular, neurological, or oncological diseases), we identified 15 highly antigenic epitopes on spike protein that showed cross-reactivity with antigens of seasonal, persistent, latent or chronic infections from common human viruses. We observed varying degrees of cross-reactivity of different viral antigens with S in an epitope-specific manner. The data show that pre-existing SARS-CoV-2 S1 and S2 cross-reactive serum antibody is readily detectable in pre-pandemic cohort. In the severe COVID-19 cases, we found differential antibody response to the 15 defined antigenic and cross-reactive epitopes on spike. We also noted that despite the high mutation rates of Omicron (B.1.1.529) variants of SARS-CoV-2, some of the epitopes overlapped with the described mutations. Finally, we propose that the resolved epitopes on spike if targeted by re-called antibody response from SARS-CoV-2 infections or vaccinations can function in chronically ill COVID-19 naïve/unvaccinated individuals as immunogenic targets to boost antibodies augmenting the chronic conditions. Understanding the relationships between prior antigen exposure at the antibody epitope level and the immune response to subsequent infections with viruses from a different strain is paramount to guiding strategies to exit the COVID-19 pandemic.
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Affiliation(s)
- Mariliis Jaago
- Protobios LLC, Tallinn, Estonia
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Annika Rähni
- Protobios LLC, Tallinn, Estonia
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | | | | | - Helle Sadam
- Protobios LLC, Tallinn, Estonia
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Jürgen Tuvikene
- Protobios LLC, Tallinn, Estonia
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- DXLabs LLC, Tallinn, Estonia
| | - Annela Avarlaid
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Anu Planken
- North Estonia Medical Centre Foundation, Tallinn, Estonia
| | - Margus Planken
- North Estonia Medical Centre Foundation, Tallinn, Estonia
| | - Liina Haring
- Institute of Clinical Medicine, Psychiatry Clinic of Tartu University Hospital, University of Tartu, Tartu, Estonia
| | - Eero Vasar
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Center of Excellence for Genomics and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Miljana Baćević
- Dental Biomaterial Research Unit (d-BRU), Faculty of Medicine, University of Liege, Liege, Belgium
| | - France Lambert
- Department of Periodontology and Oral Surgery, Faculty of Medicine, University of Liege, Liege, Belgium
| | - Eija Kalso
- Department of Anaesthesiology, Intensive Care and Pain Medicine, Helsinki University Hospital, Helsinki, Finland
- SleepWell Research Programme, Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Pirkko Pussinen
- Oral and Maxillofacial Diseases, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Pentti J Tienari
- Translational Immunology Research Program, Department of Neurology, Neurocenter, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Antti Vaheri
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Dan Lindholm
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Tõnis Timmusk
- Protobios LLC, Tallinn, Estonia
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Amir M Ghaemmaghami
- Immunology and Immuno-Bioengineering Group, School of Life Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, United Kingdom
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A Vaccine with Multiple Receptor-Binding Domain Subunit Mutations Induces Broad-Spectrum Immune Response against SARS-CoV-2 Variants of Concern. Vaccines (Basel) 2022; 10:vaccines10101653. [PMID: 36298518 PMCID: PMC9609383 DOI: 10.3390/vaccines10101653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
With the emergence of more variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the immune evasion of these variants from existing vaccines, the development of broad-spectrum vaccines is urgently needed. In this study, we designed a novel SARS-CoV-2 receptor-binding domain (RBD) subunit (RBD5m) by integrating five important mutations from SARS-CoV-2 variants of concern (VOCs). The neutralization activities of antibodies induced by the RBD5m candidate vaccine are more balanced and effective for neutralizing different SARS-CoV-2 VOCs in comparison with those induced by the SARS-CoV-2 prototype strain RBD. Our results suggest that the RBD5m vaccine is a good broad-spectrum vaccine candidate able to prevent disease from several different SARS-CoV-2 VOCs.
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48
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Hu Q, Xiong Y, Zhu G, Zhang Y, Zhang Y, Huang P, Ge G. The SARS-CoV-2 main protease (M pro): Structure, function, and emerging therapies for COVID-19. MedComm (Beijing) 2022; 3:e151. [PMID: 35845352 PMCID: PMC9283855 DOI: 10.1002/mco2.151] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 12/21/2022] Open
Abstract
The main proteases (Mpro), also termed 3-chymotrypsin-like proteases (3CLpro), are a class of highly conserved cysteine hydrolases in β-coronaviruses. Increasing evidence has demonstrated that 3CLpros play an indispensable role in viral replication and have been recognized as key targets for preventing and treating coronavirus-caused infectious diseases, including COVID-19. This review is focused on the structural features and biological function of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease Mpro (also known as 3CLpro), as well as recent advances in discovering and developing SARS-CoV-2 3CLpro inhibitors. To better understand the characteristics of SARS-CoV-2 3CLpro inhibitors, the inhibition activities, inhibitory mechanisms, and key structural features of various 3CLpro inhibitors (including marketed drugs, peptidomimetic, and non-peptidomimetic synthetic compounds, as well as natural compounds and their derivatives) are summarized comprehensively. Meanwhile, the challenges in this field are highlighted, while future directions for designing and developing efficacious 3CLpro inhibitors as novel anti-coronavirus therapies are also proposed. Collectively, all information and knowledge presented here are very helpful for understanding the structural features and inhibitory mechanisms of SARS-CoV-2 3CLpro inhibitors, which offers new insights or inspiration to medicinal chemists for designing and developing more efficacious 3CLpro inhibitors as novel anti-coronavirus agents.
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Affiliation(s)
- Qing Hu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Yuan Xiong
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Guang‐Hao Zhu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Ya‐Ni Zhang
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Yi‐Wen Zhang
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Ping Huang
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Guang‐Bo Ge
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
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Dhanasooraj D, Viswanathan P, Saphia S, Jose BP, Parambath FC, Sivadas S, Akash NP, Vimisha TV, Nair PR, Mohan A, Hafeez N, Poovullathi JK, Vadekkandiyil S, Govindan SKK, Khobragade R, Aravindan KP, Radhakrishnan C. Genomic surveillance of SARS-CoV-2 by sequencing the RBD region using Sanger sequencing from North Kerala. Front Public Health 2022; 10:974667. [PMID: 36091505 PMCID: PMC9454329 DOI: 10.3389/fpubh.2022.974667] [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] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/08/2022] [Indexed: 01/21/2023] Open
Abstract
Next Generation Sequencing (NGS) is the gold standard for the detection of new variants of SARS-CoV-2 including those which have immune escape properties, high infectivity, and variable severity. This test is helpful in genomic surveillance, for planning appropriate and timely public health interventions. But labs with NGS facilities are not available in small or medium research settings due to the high cost of setting up such a facility. Transportation of samples from many places to few centers for NGS testing also produces delays due to transportation and sample overload leading in turn to delays in patient management and community interventions. This becomes more important for patients traveling from hotspot regions or those suspected of harboring a new variant. Another major issue is the high cost of NGS-based tests. Thus, it may not be a good option for an economically viable surveillance program requiring immediate result generation and patient follow-up. The current study used a cost-effective facility which can be set up in a common research lab and which is replicable in similar centers with expertise in Sanger nucleotide sequencing. More samples can be processed at a time and can generate the results in a maximum of 2 days (1 day for a 24 h working lab). We analyzed the nucleotide sequence of the Receptor Binding Domain (RBD) region of SARS-CoV-2 by the Sanger sequencing using in-house developed methods. The SARS-CoV-2 variant surveillance was done during the period of March 2021 to May 2022 in the Northern region of Kerala, a state in India with a population of 36.4 million, for implementing appropriate timely interventions. Our findings broadly agree with those from elsewhere in India and other countries during the period.
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Affiliation(s)
| | - Prasanth Viswanathan
- Virus Research and Diagnostic Laboratory, Government Medical College, Kozhikode, Kerala, India
| | - Shammy Saphia
- Multidisciplinary Research Unit, Government Medical College, Kozhikode, Kerala, India
| | - Beena Philomina Jose
- Department of Microbiology, Government Medical College, Kozhikode, Kerala, India
| | | | - Saritha Sivadas
- Virus Research and Diagnostic Laboratory, Government Medical College, Kozhikode, Kerala, India
| | - N. P. Akash
- Virus Research and Diagnostic Laboratory, Government Medical College, Kozhikode, Kerala, India
| | - T. V. Vimisha
- Virus Research and Diagnostic Laboratory, Government Medical College, Kozhikode, Kerala, India
| | | | - Anuja Mohan
- Virus Research and Diagnostic Laboratory, Government Medical College, Kozhikode, Kerala, India
| | - Nimin Hafeez
- Virus Research and Diagnostic Laboratory, Government Medical College, Kozhikode, Kerala, India
| | | | - Shameer Vadekkandiyil
- Department of General Medicine, Government Medical College, Kozhikode, Kerala, India
| | | | - Rajan Khobragade
- Department of Health and Family Welfare, Government of Kerala, Thiruvananthapuram, India
| | | | - Chandni Radhakrishnan
- Department of Emergency Medicine, Government Medical College, Kozhikode, Kerala, India
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Abidi M, Soheilifard R, Ghasemi RH. Comparison of the unbinding process of RBD-ACE2 complex between SARS-CoV-2 variants (Delta, delta plus, and Lambda): A steered molecular dynamics simulation. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2114599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Mohadese Abidi
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
| | - Reza Soheilifard
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
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