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Abebe EC, Dejenie TA. Protective roles and protective mechanisms of neutralizing antibodies against SARS-CoV-2 infection and their potential clinical implications. Front Immunol 2023; 14:1055457. [PMID: 36742320 PMCID: PMC9892939 DOI: 10.3389/fimmu.2023.1055457] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023] Open
Abstract
Neutralizing antibodies (NAbs) are central players in the humoral immunity that defends the body from SARS-CoV-2 infection by blocking viral entry into host cells and neutralizing their biological effects. Even though NAbs primarily work by neutralizing viral antigens, on some occasions, they may also combat the SARS-CoV-2 virus escaping neutralization by employing several effector mechanisms in collaboration with immune cells like natural killer (NK) cells and phagocytes. Besides their prophylactic and therapeutic roles, antibodies can be used for COVID-19 diagnosis, severity evaluation, and prognosis assessment in clinical practice. Furthermore, the measurement of NAbs could have key implications in determining individual or herd immunity against SARS-CoV-2, vaccine effectiveness, and duration of the humoral protective response, as well as aiding in the selection of suitable individuals who can donate convalescent plasma to treat infected people. Despite all these clinical applications of NAbs, using them in clinical settings can present some challenges. This review discusses the protective functions, possible protective mechanisms against SARS-CoV-2, and potential clinical applications of NAbs in COVID-19. This article also highlights the possible challenges and solutions associated with COVID-19 antibody-based prophylaxis, therapy, and vaccination.
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Affiliation(s)
- Endeshaw Chekol Abebe
- Department of Medical Biochemistry, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Tadesse Asmamaw Dejenie
- Department of Medical Biochemistry, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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2
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de Moura HL, Menon RG, Zibetti MVW, Regatte RR. Optimization of spin-lock times for T 1ρ mapping of human knee cartilage with bi- and stretched-exponential models. Sci Rep 2022; 12:16829. [PMID: 36207361 PMCID: PMC9546896 DOI: 10.1038/s41598-022-21269-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/26/2022] [Indexed: 02/05/2023] Open
Abstract
Two optimization criteria based on Cramér-Rao Bounds are compared between each other and with non-optimized schedules for T1ρ mapping using synthetic data, model phantoms, and in-vivo knee cartilage. The curve fitting is done on complex-valued data using an iterative Nonlinear Least Squares (NLS) approach. The optimization criteria are compared based on the Mean Normalized Absolute Error (MNAE) and variance of the estimated parameters. The optimized spin-lock time (TSL) schedules provided improved results over the non-optimized schedules for all cases that were tested. The simulations showed that optimized schedules can reach the same precision and reduce acquisition times by 16.5 min (42%) for the bi-exponential model, and 6.6 min (22%) for the stretched-exponential model. In the model phantoms experiments, the bi-exponential MNAE was reduced from 0.47 to 0.36, while stretched-exponential from 0.28 to 0.20 with a Modified Cramér-Rao Lower Bound (MCRLB). In-vivo knee cartilage experiments show a reduction in bi-exponential MNAE from 0.47 to 0.31, and stretched-exponential from 0.047 to 0.039. The optimized spin-lock times criteria reduced the error in all cases, being more significant in the synthetic data and model phantoms. The optimized TSL schedules can be either used to improve the quality of parameter maps or reduce scan time.
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Affiliation(s)
- Hector L. de Moura
- grid.137628.90000 0004 1936 8753Department of Radiology, Center for Biomedical Imaging, New York University Grossman School of Medicine, New York, NY USA
| | - Rajiv G. Menon
- grid.137628.90000 0004 1936 8753Department of Radiology, Center for Biomedical Imaging, New York University Grossman School of Medicine, New York, NY USA
| | - Marcelo V. W. Zibetti
- grid.137628.90000 0004 1936 8753Department of Radiology, Center for Biomedical Imaging, New York University Grossman School of Medicine, New York, NY USA
| | - Ravinder R. Regatte
- grid.137628.90000 0004 1936 8753Department of Radiology, Center for Biomedical Imaging, New York University Grossman School of Medicine, New York, NY USA
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3
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Zhang M, He Y, Jie Z. Delta Variant: Partially Sensitive To Vaccination, but Still Worth Global Attention. J Transl Int Med 2022; 10:227-235. [PMID: 36776232 PMCID: PMC9901554 DOI: 10.2478/jtim-2022-0026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pandemic coronavirus disease 2019 (COVID-19) has rapidly spread to all countries worldwide. The emergence of its variants has exacerbated this problem. To date, many variants have been identified across the viral genome; the variants of concern are the focus of attention due to their higher transmissibility and resistance to vaccines, especially the delta variant. The delta variant has become the dominant severe acute respiratory syndrome novel coronavirus (SARS-CoV-2) variant worldwide, causing severe panic as it is highly infectious. A better understanding of these variants may help in the development of possible treatments and save more lives. In this study, we summarize the characteristics of the variants of concern. More importantly, we summarize the results of previous studies on the delta variant. The delta variant has a high transmissibility rate and increases the risk of hospitalization and death. However, it is partially sensitive to vaccines. In addition, nonpharmaceutical interventions are valuable during epidemics. These interventions can be used against the delta variant, but managing this variant should still be taken seriously.
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Affiliation(s)
- Meng Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai200240, China
| | - Yanchao He
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai200240, China
| | - Zhijun Jie
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai200240, China
- Center of Community-Based Health Research, Fudan University, Shanghai200240, China
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4
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López-Cortés GI, Palacios-Pérez M, Veledíaz HF, Hernández-Aguilar M, López-Hernández GR, Zamudio GS, José MV. The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures. Vaccines (Basel) 2022; 10:864. [PMID: 35746472 PMCID: PMC9230601 DOI: 10.3390/vaccines10060864] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/14/2022] [Accepted: 05/19/2022] [Indexed: 02/06/2023] Open
Abstract
The global scale of the COVID-19 pandemic has demonstrated the evolution of SARS-CoV-2 and the clues of adaptation. After two years and two months since the declaration of the pandemic, several variants have emerged and become fixed in the human population thanks to extrinsic selective pressures but also to the inherent mutational capacity of the virus. Here, we applied a neutral substitution evolution test to the spike (S) protein of Omicron's protein and compared it to the others' variant of concern (VOC) neutral evolution. We carried out comparisons among the interactions between the S proteins from the VOCs (Alpha, Beta, Gamma, Delta and Omicron) and the receptor ACE2. The shared amino acids among all the ACE2 binding S proteins remain constant, indicating that these amino acids are essential for the accurate binding to the receptor. The complexes of the RBD for every variant with the receptor were used to identify the amino acids involved in the protein-protein interaction (PPI). The RBD of Omicron establishes 82 contacts, compared to the 74 of the Wuhan original viral protein. Hence, the mean number of contacts per residue is higher, making the contact thermodynamically more stable. The RBDs of the VOCs are similar in sequence and structure; however, Omicron's RBD presents the largest deviation from the structure by 1.11 Å RMSD, caused by a set of mutations near the glycosylation N343. The chemical properties and structure near the glycosylation N343 of the Omicron S protein are different from the original protein, which provoke reduced recognition by the neutralizing antibodies. Our results hint that selective pressures are induced by mass vaccination throughout the world and by the persistence of recurrent infections in immunosuppressed individuals, who did not eliminate the infection and ended up facilitating the selection of viruses whose characteristics are different from the previous VOCs, less pathogenic but with higher transmissibility.
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Affiliation(s)
- Georgina I. López-Cortés
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (M.P.-P.); (H.F.V.); (M.H.-A.); (G.R.L.-H.); (G.S.Z.)
- Network of Researchers on the Chemical Evolution of Life, NoRCEL, Leeds LS7 3RB, UK
| | - Miryam Palacios-Pérez
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (M.P.-P.); (H.F.V.); (M.H.-A.); (G.R.L.-H.); (G.S.Z.)
- Network of Researchers on the Chemical Evolution of Life, NoRCEL, Leeds LS7 3RB, UK
| | - Hannya F. Veledíaz
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (M.P.-P.); (H.F.V.); (M.H.-A.); (G.R.L.-H.); (G.S.Z.)
| | - Margarita Hernández-Aguilar
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (M.P.-P.); (H.F.V.); (M.H.-A.); (G.R.L.-H.); (G.S.Z.)
| | - Gerardo R. López-Hernández
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (M.P.-P.); (H.F.V.); (M.H.-A.); (G.R.L.-H.); (G.S.Z.)
| | - Gabriel S. Zamudio
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (M.P.-P.); (H.F.V.); (M.H.-A.); (G.R.L.-H.); (G.S.Z.)
| | - Marco V. José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (M.P.-P.); (H.F.V.); (M.H.-A.); (G.R.L.-H.); (G.S.Z.)
- Network of Researchers on the Chemical Evolution of Life, NoRCEL, Leeds LS7 3RB, UK
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5
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Tian D, Sun Y, Zhou J, Ye Q. The global epidemic of SARS-CoV-2 variants and their mutational immune escape. J Med Virol 2022; 94:847-857. [PMID: 34609003 PMCID: PMC8661756 DOI: 10.1002/jmv.27376] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/23/2021] [Accepted: 10/01/2021] [Indexed: 12/16/2022]
Abstract
During the COVID-19 pandemic, genetic variants of SARS-CoV-2 have been emerging and spreading around the world. Several SARS-CoV-2 endemic variants were found in United Kingdom, South Africa, Japan, and India between 2020 and April 2021. Studies have shown that many SARS-CoV-2 variants are more infectious than early wild strain and produce immune escape. These SARS-CoV-2 variants have brought new challenges to the prevention and control of COVID-19. This review summarizes and analyzes the biological characteristics of different amino acid mutations and the epidemic characteristics and immune escape of different SARS-CoV-2 variants. We hope to provide scientific reference for the monitoring, prevention, and control measures of new SARS-CoV-2 variants and the development strategy of the second-generation vaccine.
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Affiliation(s)
- Dandan Tian
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's HospitalZhejiang University School of MedicineHangzhouChina
| | - YanHong Sun
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's HospitalZhejiang University School of MedicineHangzhouChina
| | - JianMing Zhou
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's HospitalZhejiang University School of MedicineHangzhouChina
| | - Qing Ye
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's HospitalZhejiang University School of MedicineHangzhouChina
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6
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Qiu C, Xiao C, Wang Z, Zhu G, Mao L, Chen X, Gao L, Deng J, Su J, Su H, Fang EF, Zhang ZJ, Zhang J, Xie C, Yuan J, Luo OJ, Huang L, Wang P, Chen G. CD8+ T-Cell Epitope Variations Suggest a Potential Antigen HLA-A2 Binding Deficiency for Spike Protein of SARS-CoV-2. Front Immunol 2022; 12:764949. [PMID: 35116022 PMCID: PMC8804355 DOI: 10.3389/fimmu.2021.764949] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/14/2021] [Indexed: 12/15/2022] Open
Abstract
We identified SARS-CoV-2 specific antigen epitopes by HLA-A2 binding affinity analysis and characterized their ability to activate T cells. As the pandemic continues, variations in SARS-CoV-2 virus strains have been found in many countries. In this study, we directly assess the immune response to SARS-CoV-2 epitope variants. We first predicted potential HLA-A*02:01-restricted CD8+ T-cell epitopes of SARS-CoV-2. Using the T2 cell model, HLA-A*02:01-restricted T-cell epitopes were screened for their binding affinity and ability to activate T cells. Subsequently, we examined the identified epitope variations and analyzed their impact on immune response. Here, we identified specific HLA-A2-restricted T-cell epitopes in the spike protein of SARS-CoV-2. Seven epitope peptides were confirmed to bind with HLA-A*02:01 and potentially be presented by antigen-presenting cells to induce host immune responses. Tetramers containing these peptides could interact with specific CD8+ T cells from convalescent COVID-19 patients, and one dominant epitope (n-Sp1) was defined. These epitopes could activate and generate epitope-specific T cells in vitro, and those activated T cells showed cytolytic activity toward target cells. Meanwhile, n-Sp1 epitope variant 5L>F significantly decreased the proportion of specific T-cell activation; n-Sp1 epitope 8L>V variant showed significantly reduced binding to HLA-A*02:01 and decreased proportion of n-Sp1-specific CD8+ T cell, which potentially contributes to the immune escape of SARS-CoV-2. Our data indicate that the variation of a dominant epitope will cause the deficiency of HLA-A*02:01 binding and T-cell activation, which subsequently requires the formation of a new CD8+ T-cell immune response in COVID-19 patients.
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Affiliation(s)
- Congling Qiu
- Department of Neurology, Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
| | - Chanchan Xiao
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
| | - Zhigang Wang
- Department of Neurology, Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
| | - Guodong Zhu
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
- Department of Geriatrics, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Lipeng Mao
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
| | - Xiongfei Chen
- Department of Primary Public Health, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Lijuan Gao
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
| | - Jieping Deng
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
| | - Jun Su
- Department of Neurology, Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
| | - Huanxing Su
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, Macau SAR, China
| | - Evandro Fei Fang
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Zhang-Jin Zhang
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
- School of Chinese Medicine, Li Ka Shing (LKS) Faculty of Medicine, the University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jikai Zhang
- Department of Biological Products and Materia Medica, Institute of Biologics and Pharmaceuticals Research, Guangzhou, China
| | - Caojun Xie
- Department of Primary Public Health, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Jun Yuan
- Department of Primary Public Health, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Oscar Junhong Luo
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, China
| | - Li`an Huang
- Department of Neurology, Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
| | - Pengcheng Wang
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
- *Correspondence: Pengcheng Wang, ; Guobing Chen,
| | - Guobing Chen
- Department of Neurology, Affiliated Huaqiao Hospital, Jinan University, Guangzhou, China
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Department of Microbiology and Immunology, Jinan University, Guangzhou, China
- *Correspondence: Pengcheng Wang, ; Guobing Chen,
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Chérifi F, Laraba-Djebari F. Bioactive Molecules Derived from Snake Venoms with Therapeutic Potential for the Treatment of Thrombo-Cardiovascular Disorders Associated with COVID-19. Protein J 2021; 40:799-841. [PMID: 34499333 PMCID: PMC8427918 DOI: 10.1007/s10930-021-10019-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 01/08/2023]
Abstract
As expected, several new variants of Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2) emerged and have been detected around the world throughout this Coronavirus Disease of 2019 (COVID-19) pandemic. Currently, there is no specific developed drug against COVID-19 and the challenge of developing effective antiviral strategies based on natural agents with different mechanisms of action becomes an urgent need and requires identification of genetic differences among variants. Such data is used to improve therapeutics to combat SARS-CoV-2 variants. Nature is known to offer many biotherapeutics from animal venoms, algae and plant that have been historically used in traditional medicine. Among these bioresources, snake venom displays many bioactivities of interest such as antiviral, antiplatelet, antithrombotic, anti-inflammatory, antimicrobial and antitumoral. COVID-19 is a viral respiratory sickness due to SARS-CoV-2 which induces thrombotic disorders due to cytokine storm, platelet hyperactivation and endothelial dysfunction. This review aims to: (1) present an overview on the infection, the developed thrombo-inflammatory responses and mechanisms of induced thrombosis of COVID-19 compared to other similar pathogenesis; (2) underline the role of natural compounds such as anticoagulant, antiplatelet and thrombolytic agents; (3) investigate the management of coagulopathy related to COVID-19 and provide insight on therapeutic such as venom compounds. We also summarize the updated advances on antiviral proteins and peptides derived from snake venoms that could weaken coagulopathy characterizing COVID-19.
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Affiliation(s)
- Fatah Chérifi
- USTHB, Faculty of Biological Sciences, Laboratory of Cellular and Molecular Biology, USTHB, BP 32, El-Alia, Bab Ezzouar, Algiers, Algeria
| | - Fatima Laraba-Djebari
- USTHB, Faculty of Biological Sciences, Laboratory of Cellular and Molecular Biology, USTHB, BP 32, El-Alia, Bab Ezzouar, Algiers, Algeria.
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8
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Neerukonda SN, Vassell R, Lusvarghi S, Wang R, Echegaray F, Bentley L, Eakin AE, Erlandson KJ, Katzelnick LC, Weiss CD, Wang W. SARS-COV-2 Delta variant displays moderate resistance to neutralizing antibodies and spike protein properties of higher soluble ACE2 sensitivity, enhanced cleavage and fusogenic activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.11.05.467523. [PMID: 34790980 PMCID: PMC8597883 DOI: 10.1101/2021.11.05.467523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The SARS-CoV-2 B.1.617 lineage variants, Kappa (B.1.617.1) and Delta (B.1.617.2, AY) emerged during the second wave of infections in India, but the Delta variants have become dominant worldwide and continue to evolve. The spike proteins of B.1.617.1, B.1.617.2, and AY.1 variants have several substitutions in the receptor binding domain (RBD), including L452R+E484Q, L452R+T478K, and K417N+L452R+T478K, respectively, that could potentially reduce effectiveness of therapeutic antibodies and current vaccines. Here we compared B.1.617 variants, and their single and double RBD substitutions for resistance to neutralization by convalescent sera, mRNA vaccine-elicited sera, and therapeutic neutralizing antibodies using a pseudovirus neutralization assay. Pseudoviruses with the B.1.617.1, B.1.617.2, and AY.1 spike showed a modest 1.5 to 4.4-fold reduction in neutralization titer by convalescent sera and vaccine-elicited sera. In comparison, similar modest reductions were also observed for pseudoviruses with C.37, P.1, R.1, and B.1.526 spikes, but seven- and sixteen-fold reduction for vaccine-elicited and convalescent sera, respectively, was seen for pseudoviruses with the B.1.351 spike. Four of twenty-three therapeutic neutralizing antibodies showed either complete or partial loss of neutralization against B.1.617.2 pseudoviruses due to the L452R substitution, whereas six of twenty-three therapeutic neutralizing antibodies showed either complete or partial loss of neutralization against B.1.617.1 pseudoviruses due to either the E484Q or L452R substitution. Against AY.1 pseudoviruses, the L452R and K417N substitutions accounted for the loss of neutralization by four antibodies and one antibody, respectively, whereas one antibody lost potency that could not be fully accounted for by a single RBD substitution. The modest resistance of B.1.617 variants to vaccine-elicited sera suggest that current mRNA-based vaccines will likely remain effective in protecting against B.1.617 variants, but the therapeutic antibodies need to be carefully selected based on their resistance profiles. Finally, the spike proteins of B.1.617 variants are more efficiently cleaved due to the P681R substitution, and the spike of Delta variants exhibited greater sensitivity to soluble ACE2 neutralization, as well as fusogenic activity, which may contribute to enhanced spread of Delta variants.
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Pang X, Li P, Zhang L, Que L, Dong M, Xie B, Wang Q, Wei Y, Xie X, Li L, Yin C, Wei L, Huang K, Hua Y, Zhou Q, Li Y, Yu L, Li W, Mo Z, Zhang M, Leng J, Hu Y. Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. Front Microbiol 2021; 12:753823. [PMID: 34733263 PMCID: PMC8558435 DOI: 10.3389/fmicb.2021.753823] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/20/2021] [Indexed: 12/28/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Understanding the influence of mutations in the SARS-CoV-2 gene on clinical outcomes is critical for treatment and prevention. Here, we analyzed all high-coverage complete SARS-CoV-2 sequences from GISAID database from January 1, 2020, to January 1, 2021, to mine the mutation hotspots associated with clinical outcome and developed a model to predict the clinical outcome in different epidemic strains. Exploring the cause of mutation based on RNA-dependent RNA polymerase (RdRp) and RNA-editing enzyme, mutation was more likely to occur in severe and mild cases than in asymptomatic cases, especially A > G, C > T, and G > A mutations. The mutations associated with asymptomatic outcome were mainly in open reading frame 1ab (ORF1ab) and N genes; especially R6997P and V30L mutations occurred together and were correlated with asymptomatic outcome with high prevalence. D614G, Q57H, and S194L mutations were correlated with mild and severe outcome with high prevalence. Interestingly, the single-nucleotide variant (SNV) frequency was higher with high percentage of nt14408 mutation in RdRp in severe cases. The expression of ADAR and APOBEC was associated with clinical outcome. The model has shown that the asymptomatic percentage has increased over time, while there is high symptomatic percentage in Alpha, Beta, and Gamma. These findings suggest that mutation in the SARS-CoV-2 genome may have a direct association with clinical outcomes and pandemic. Our result and model are helpful to predict the prevalence of epidemic strains and to further study the mechanism of mutation causing severe disease.
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Affiliation(s)
- Xianwu Pang
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
| | - Pu Li
- PFOMIC Bioinformatics Company, Nanning, China
| | - Lifeng Zhang
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases With Integrative Medicine, Guangxi University of Chinese Medicine, Nanning, China
| | - Lusheng Que
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Min Dong
- School of Pharmacy, Guangxi Medical University, Nanning, China
| | - Bo Xie
- School of Information and Management, Guangxi Medical University, Nanning, China
| | - Qihui Wang
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Yinfeng Wei
- Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Xing Xie
- Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Lanxiang Li
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Chunyue Yin
- The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, China
| | - Liuchun Wei
- The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, China
| | - Kexin Huang
- School of Information and Management, Guangxi Medical University, Nanning, China
| | - Yiming Hua
- School of Information and Management, Guangxi Medical University, Nanning, China
| | - Qingniao Zhou
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Yingfang Li
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Lei Yu
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Weidong Li
- Life Sciences Institute, Guangxi Medical University, Nanning, China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Maosheng Zhang
- School of Information and Management, Guangxi Medical University, Nanning, China
| | - Jing Leng
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases With Integrative Medicine, Guangxi University of Chinese Medicine, Nanning, China
| | - Yanling Hu
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
- School of Information and Management, Guangxi Medical University, Nanning, China
- Life Sciences Institute, Guangxi Medical University, Nanning, China
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
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10
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Meekins DA, Gaudreault NN, Richt JA. Natural and Experimental SARS-CoV-2 Infection in Domestic and Wild Animals. Viruses 2021; 13:1993. [PMID: 34696423 PMCID: PMC8540328 DOI: 10.3390/v13101993] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 is the etiological agent responsible for the ongoing COVID-19 pandemic, which continues to spread with devastating effects on global health and socioeconomics. The susceptibility of domestic and wild animal species to infection is a critical facet of SARS-CoV-2 ecology, since reverse zoonotic spillover events resulting in SARS-CoV-2 outbreaks in animal populations could result in the establishment of new virus reservoirs. Adaptive mutations in the virus to new animal species could also complicate ongoing mitigation strategies to combat SARS-CoV-2. In addition, animal species susceptible to SARS-CoV-2 infection are essential as standardized preclinical models for the development and efficacy testing of vaccines and therapeutics. In this review, we summarize the current findings regarding the susceptibility of different domestic and wild animal species to experimental SARS-CoV-2 infection and provide detailed descriptions of the clinical disease and transmissibility in these animals. In addition, we outline the documented natural infections in animals that have occurred at the human-animal interface. A comprehensive understanding of animal susceptibility to SARS-CoV-2 is crucial to inform public health, veterinary, and agricultural systems, and to guide environmental policies.
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Affiliation(s)
- David A. Meekins
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (D.A.M.); (N.N.G.)
- Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (D.A.M.); (N.N.G.)
- Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (D.A.M.); (N.N.G.)
- Center of Excellence for Emerging and Zoonotic Animal Diseases (CEEZAD), College of Veterinary Medicine, Kansas State University, Manhattan, KS 66502, USA
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11
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López-Cortés GI, Palacios-Pérez M, Zamudio GS, Veledíaz HF, Ortega E, José MV. Neutral evolution test of the spike protein of SARS-CoV-2 and its implications in the binding to ACE2. Sci Rep 2021; 11:18847. [PMID: 34552110 PMCID: PMC8458503 DOI: 10.1038/s41598-021-96950-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/18/2021] [Indexed: 12/11/2022] Open
Abstract
As the SARS-CoV-2 has spread and the pandemic has dragged on, the virus continued to evolve rapidly resulting in the emergence of new highly transmissible variants that can be of public health concern. The evolutionary mechanisms that drove this rapid diversity are not well understood but neutral evolution should open the first insight. The neutral theory of evolution states that most mutations in the nucleic acid sequences are random and they can be fixed or disappear by purifying selection. Herein, we performed a neutrality test to better understand the selective pressures exerted over SARS-CoV-2 spike protein from homologue proteins of Betacoronavirus, as well as to the spikes from human clinical isolates of the virus. Specifically, Tyr and Asn have higher occurrence rates on the Receptor Binding Domain (RBD) and in the overall sequence of spike proteins of Betacoronavirus, whereas His and Arg have lower occurrence rates. The in vivo evolutionary phenomenon of SARS-CoV-2 shows that Glu, Lys, Phe, and Val have the highest probability of occurrence in the emergent viral particles. Amino acids that have higher occurrence than the expected by the neutral control, are favorable and are fixed in the sequence while the ones that have lower occurrence than expected, influence the stability and/or functionality of the protein. Our results show that most unique mutations either for SARS-CoV-2 or its variants of health concern are under selective pressures, which could be related either to the evasion of the immune system, increasing the virus' fitness or altering protein - protein interactions with host proteins. We explored the consequences of those selected mutations in the structure and protein - protein interaction with the receptor. Altogether all these forces have shaped the spike protein and the continually evolving variants.
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Affiliation(s)
- Georgina I López-Cortés
- Department of Immunology, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico
| | - Miryam Palacios-Pérez
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico
| | - Gabriel S Zamudio
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico
| | - Hannya F Veledíaz
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico
- Universidad Latinoamericana, Nutrición, Campus Cuernavaca, Morelos, Mexico
| | - Enrique Ortega
- Department of Immunology, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico.
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, CDMX, Mexico.
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12
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Bilinska K, von Bartheld CS, Butowt R. Expression of the ACE2 Virus Entry Protein in the Nervus Terminalis Reveals the Potential for an Alternative Route to Brain Infection in COVID-19. Front Cell Neurosci 2021; 15:674123. [PMID: 34290590 PMCID: PMC8287262 DOI: 10.3389/fncel.2021.674123] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/09/2021] [Indexed: 12/11/2022] Open
Abstract
Previous studies suggested that the SARS-CoV-2 virus may gain access to the brain by using a route along the olfactory nerve. However, there is a general consensus that the obligatory virus entry receptor, angiotensin converting enzyme 2 (ACE2), is not expressed in olfactory receptor neurons, and the timing of arrival of the virus in brain targets is inconsistent with a neuronal transfer along olfactory projections. We determined whether nervus terminalis neurons and their peripheral and central projections should be considered as a potential alternative route from the nose to the brain. Nervus terminalis neurons in postnatal mice were double-labeled with antibodies against ACE2 and two nervus terminalis markers, gonadotropin-releasing hormone (GnRH) and choline acetyltransferase (CHAT). We show that a small fraction of CHAT-labeled nervus terminalis neurons, and the large majority of GnRH-labeled nervus terminalis neurons with cell bodies in the region between the olfactory epithelium and the olfactory bulb express ACE2 and cathepsins B and L. Nervus terminalis neurons therefore may provide a direct route for the virus from the nasal epithelium, possibly via innervation of Bowman's glands, to brain targets, including the telencephalon and diencephalon. This possibility needs to be examined in suitable animal models and in human tissues.
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Affiliation(s)
- Katarzyna Bilinska
- L. Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Christopher S. von Bartheld
- Department of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV, United States
| | - Rafal Butowt
- L. Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
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13
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Shi AC, Xie X. Making sense of spike D614G in SARS-CoV-2 transmission. SCIENCE CHINA. LIFE SCIENCES 2021; 64:1062-1067. [PMID: 33587268 PMCID: PMC7882856 DOI: 10.1007/s11427-020-1893-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/25/2021] [Indexed: 11/26/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of the current coronavirus disease 2019 (COVID-19) pandemic, has evolved to adapt to human host and transmission over the past 12 months. One prominent adaptive mutation is the asparagine-to-glycine substitution at amino acid position 614 in the viral spike protein (D614G), which has become dominant in the currently circulating virus strains. Since spike protein determines host ranges, tissue tropism, and pathogenesis through binding to the cellular receptor of angiotensin converting enzyme 2 (ACE2), the D614G mutation is hypothesized to enhance viral fitness in human host, leading to increased transmission during the global pandemic. Here we summarize the recent progress on the role of the D614G mutation in viral replication, pathogenesis, transmission, and vaccine and therapeutic antibody development. These findings underscore the importance in closely monitoring viral evolution and defining their functions to ensure countermeasure efficacy against newly emerging variants.
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Affiliation(s)
- Aria C Shi
- School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77550, USA.
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14
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Gurzawska-Comis K, Becker K, Brunello G, Klinge B. COVID-19: Review of European recommendations and experts' opinion on dental care. Summary and consensus statements of group 5. The 6th EAO Consensus Conference 2021. Clin Oral Implants Res 2021; 32 Suppl 21:382-388. [PMID: 34196063 PMCID: PMC8444925 DOI: 10.1111/clr.13780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/14/2021] [Indexed: 11/27/2022]
Abstract
Objectives The present work reports the EAO workshop group 5 and consensus plenary discussions and statements based on two reviews summarising European guidelines and experts’ opinion on infection control and prevention (ICP) in dentistry during the pandemic. Material Two manuscripts were presented at the 6th EAO Consensus Conference. The first study compared the most recent national guidelines/recommendations of European countries. The second paper was an experts’ opinion‐based survey on application of ICP regulation during the second wave. The outcome of COVID‐19 group discussion was presented to all participants of the consensus to come to an agreement about the consensus statements and clinical recommendation. Results The dynamic of the pandemic had an impact on rapidly published and frequently updated national guidelines in Europe. As guidelines were not based on solid evidence, they were supplemented by experts’ opinion on ICP in dentistry. The dental care should be guaranteed during the pandemic; however, in case of suspected or confirmed COVID‐19 disease, the treatment should be postponed if possible. Remote triage and patient‐related measures (i.e., social distancing, hand hygiene and mask wearing) were recommended to be the most efficient to reduce SARS‐CoV‐2 transmission. The type of personal protective equipment for dental staff should be adequate to the procedure and infection risk. Conclusions Adequate infection control protocols have to be followed by healthcare professionals and patients to minimise the spreading of COVID‐19. We foresee the importance of continuously updating the national dental guidelines, considering the evolution of the pandemic and new scientific evidence becoming available.
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Affiliation(s)
- Katarzyna Gurzawska-Comis
- Department of Oral Surgery, University of Birmingham, 5 Mill Pool Way, Edgbaston, Birmingham, B5 7EG, United Kingdom.,Birmingham Community Healthcare NHS Foundation Trust, Birmingham Dental Hospital, Oral Surgery Department
| | - Kathrin Becker
- Department of Orthodontics, Universitätsklinikum Düsseldorf, Düsseldorf, Germany
| | - Giulia Brunello
- Department of Neurosciences, Dentistry Section, University of Padova, Padova, Italy.,Department of Oral Surgery, Universitätsklinikum Düsseldorf, Düsseldorf, Germany
| | - Björn Klinge
- Faculty of Odontology, Malmo University, Malmo, Sweden.,Karolinska Institutet, Department of Dental Medicine, Stockholm, Sweden
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15
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Notable and Emerging Variants of SARS-CoV-2 Virus: A Quick Glance. Indian J Clin Biochem 2021; 36:451-458. [PMID: 34219999 PMCID: PMC8237041 DOI: 10.1007/s12291-021-00991-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/15/2021] [Indexed: 12/27/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiological agent of coronavirus disease-2019 (COVID-19), is a highly contagious pathogenic coronavirus to emerge and spread in human populations. Although substantial exertions have been laid to avert spread of COVID-19 by therapeutic and preventive countermeasures, but emergence of SARS-CoV-2 variants as a result of mutations make the infection more ominous. New viral confers a higher nasopharyngeal viral load, increased viral transmissibility, higher infectiousness, immune escape, increased resistance to monoclonal/polyclonal antibodies from convalescence sera/vaccine, and an enhanced virulence. Thus, it is pertinent to monitor evolving mutations and genetic diversity of SARS-CoV-2 as it is decisive for understanding the viral variants. In this review we provide an overview of colloquial nomenclature and the genetic characteristics of different SARS-CoV-2 variants in the context of mutational changes of the circulating strains, transmissibility potential, virulence and infectivity.
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16
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Martínez Arbas S, Busi SB, Queirós P, de Nies L, Herold M, May P, Wilmes P, Muller EEL, Narayanasamy S. Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies. Front Genet 2021; 12:666244. [PMID: 34194470 PMCID: PMC8236828 DOI: 10.3389/fgene.2021.666244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/30/2021] [Indexed: 12/21/2022] Open
Abstract
In recent years, multi-omic studies have enabled resolving community structure and interrogating community function of microbial communities. Simultaneous generation of metagenomic, metatranscriptomic, metaproteomic, and (meta) metabolomic data is more feasible than ever before, thus enabling in-depth assessment of community structure, function, and phenotype, thus resulting in a multitude of multi-omic microbiome datasets and the development of innovative methods to integrate and interrogate those multi-omic datasets. Specifically, the application of reference-independent approaches provides opportunities in identifying novel organisms and functions. At present, most of these large-scale multi-omic datasets stem from spatial sampling (e.g., water/soil microbiomes at several depths, microbiomes in/on different parts of the human anatomy) or case-control studies (e.g., cohorts of human microbiomes). We believe that longitudinal multi-omic microbiome datasets are the logical next step in microbiome studies due to their characteristic advantages in providing a better understanding of community dynamics, including: observation of trends, inference of causality, and ultimately, prediction of community behavior. Furthermore, the acquisition of complementary host-derived omics, environmental measurements, and suitable metadata will further enhance the aforementioned advantages of longitudinal data, which will serve as the basis to resolve drivers of community structure and function to understand the biotic and abiotic factors governing communities and specific populations. Carefully setup future experiments hold great potential to further unveil ecological mechanisms to evolution, microbe-microbe interactions, or microbe-host interactions. In this article, we discuss the challenges, emerging strategies, and best-practices applicable to longitudinal microbiome studies ranging from sampling, biomolecular extraction, systematic multi-omic measurements, reference-independent data integration, modeling, and validation.
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Affiliation(s)
- Susana Martínez Arbas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Susheel Bhanu Busi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Pedro Queirós
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laura de Nies
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Malte Herold
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Emilie E. L. Muller
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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17
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Bilinska K, von Bartheld CS, Butowt R. Expression of the ACE2 virus entry protein in the nervus terminalis reveals the potential for an alternative route to brain infection in COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.11.439398. [PMID: 33880469 PMCID: PMC8057234 DOI: 10.1101/2021.04.11.439398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Previous studies suggested that the SARS-CoV-2 virus may gain access to the brain by using a route along the olfactory nerve. However, there is a general consensus that the obligatory virus entry receptor, angiotensin converting enzyme 2 (ACE2), is not expressed in olfactory receptor neurons, and the timing of arrival of the virus in brain targets is inconsistent with a neuronal transfer along olfactory projections. We determined whether nervus terminalis neurons and their peripheral and central projections should be considered as a potential alternative route from the nose to the brain. Nervus terminalis neurons in postnatal mice were double-labeled with antibodies against ACE2 and two nervus terminalis markers, gonadotropin-releasing hormone (GnRH) and choline acetyltransferase (CHAT). We show that a small fraction of CHAT-labeled nervus terminalis neurons, and the large majority of GnRH-labeled nervus terminalis neurons with cell bodies in the region between the olfactory epithelium and the olfactory bulb express ACE2 and cathepsins B and L. Nervus terminalis neurons therefore may provide a direct route for the virus from the nasal epithelium, possibly via innervation of Bowman's glands, to brain targets, including the telencephalon and diencephalon. This possibility needs to be examined in suitable animal models and in human tissues.
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Affiliation(s)
- Katarzyna Bilinska
- L. Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Christopher S. von Bartheld
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, United States
| | - Rafal Butowt
- L. Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
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18
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Butowt R, Meunier N, Bryche B, von Bartheld CS. The olfactory nerve is not a likely route to brain infection in COVID-19: a critical review of data from humans and animal models. Acta Neuropathol 2021; 141:809-822. [PMID: 33903954 PMCID: PMC8075028 DOI: 10.1007/s00401-021-02314-2] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 12/12/2022]
Abstract
One of the most frequent symptoms of COVID-19 is the loss of smell and taste. Based on the lack of expression of the virus entry proteins in olfactory receptor neurons, it was originally assumed that the new coronavirus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) does not infect olfactory neurons. Recent studies have reported otherwise, opening the possibility that the virus can directly infect the brain by traveling along the olfactory nerve. Multiple animal models have been employed to assess mechanisms and routes of brain infection of SARS-CoV-2, often with conflicting results. We here review the current evidence for an olfactory route to brain infection and conclude that the case for infection of olfactory neurons is weak, based on animal and human studies. Consistent brain infection after SARS-CoV-2 inoculation in mouse models is only seen when the virus entry proteins are expressed abnormally, and the timeline and progression of rare neuro-invasion in these and in other animal models points to alternative routes to the brain, other than along the olfactory projections. COVID-19 patients can be assured that loss of smell does not necessarily mean that the SARS-CoV-2 virus has gained access to and has infected their brains.
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Affiliation(s)
- Rafal Butowt
- L. Rydygier Collegium Medicum, Nicolaus Copernicus University, 85-094, Bydgoszcz, Poland.
| | - Nicolas Meunier
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Bertrand Bryche
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Christopher S von Bartheld
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, Reno, NV, 89557, USA.
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19
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The Identification of the SARS-CoV-2 Whole Genome: Nine Cases Among Patients in Banten Province, Indonesia. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.2.52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the strain of virus that causes coronavirus disease 2019 (COVID-19), the respiratory illness responsible for the current pandemic. Viral genome sequencing has been widely applied during outbreaks to study the relatedness of this virus to other viruses, its transmission mode, pace, evolution and geographical spread, and also its adaptation to human hosts. To date, more than 90,000 SARS-CoV-2 genome sequences have been uploaded to the GISAID database. The availability of sequencing data along with clinical and geographical data may be useful for epidemiological investigations. In this study, we aimed to analyse the genetic background of SARS-CoV-2 from patients in Indonesia by whole genome sequencing. We examined nine samples from COVID-19 patients with RT-PCR cycle threshold (Ct) of less than 25 using ARTIC Network protocols for Oxford Nanopore’s Gridi On sequencer. The analytical methods were based on the ARTIC multiplex PCR sequencing protocol for COVID-19. In this study, we found that several genetic variants within the nine COVID-19 patient samples. We identified a mutation at position 614 P323L mutation in the ORF1ab gene often found in our severe patient samples. The number of SNPs and their location within the SARS-CoV-2 genome seems to vary. This diversity might be responsible for the virulence of the virus and its clinical manifestation.
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20
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Yesudhas D, Srivastava A, Gromiha MM. COVID-19 outbreak: history, mechanism, transmission, structural studies and therapeutics. Infection 2021; 49:199-213. [PMID: 32886331 PMCID: PMC7472674 DOI: 10.1007/s15010-020-01516-2] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/25/2020] [Indexed: 01/08/2023]
Abstract
PURPOSE The coronavirus outbreak emerged as a severe pandemic, claiming more than 0.8 million lives across the world and raised a major global health concern. We survey the history and mechanism of coronaviruses, and the structural characteristics of the spike protein and its key residues responsible for human transmissions. METHODS We have carried out a systematic review to summarize the origin, transmission and etiology of COVID-19. The structural analysis of the spike protein and its disordered residues explains the mechanism of the viral transmission. A meta-data analysis of the therapeutic compounds targeting the SARS-CoV-2 is also included. RESULTS Coronaviruses can cross the species barrier and infect humans with unexpected consequences for public health. The transmission rate of SARS-CoV-2 infection is higher compared to that of the closely related SARS-CoV infections. In SARS-CoV-2 infection, intrinsically disordered regions are observed at the interface of the spike protein and ACE2 receptor, providing a shape complementarity to the complex. The key residues of the spike protein have stronger binding affinity with ACE2. These can be probable reasons for the higher transmission rate of SARS-CoV-2. In addition, we have also discussed the therapeutic compounds and the vaccines to target SARS-CoV-2, which can help researchers to develop effective drugs/vaccines for COVID-19. The overall history and mechanism of entry of SARS-CoV-2 along with structural study of spike-ACE2 complex provide insights to understand disease pathogenesis and development of vaccines and drugs.
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Affiliation(s)
- Dhanusha Yesudhas
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
| | - Ambuj Srivastava
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
- School of Computing, Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.
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21
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Klaus J, Palizzotto C, Zini E, Meli ML, Leo C, Egberink H, Zhao S, Hofmann-Lehmann R. SARS-CoV-2 Infection and Antibody Response in a Symptomatic Cat from Italy with Intestinal B-Cell Lymphoma. Viruses 2021; 13:527. [PMID: 33806922 PMCID: PMC8004793 DOI: 10.3390/v13030527] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023] Open
Abstract
Since the coronavirus disease (COVID-19) pandemic was first identified in early 2020, rare cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in pet cats have been reported worldwide. Some reports of cats with SARS-CoV-2 showed self-limiting respiratory or gastrointestinal disease after suspected human-to-feline transmission via close contact with humans with SARS-CoV-2. In the present study, we investigated a cat with SARS-CoV-2 that was presented to a private animal clinic in Northern Italy in May 2020 in a weak clinical condition due to an underlying intestinal B-cell lymphoma. The cat developed signs of respiratory tract disease, including a sneeze, a cough and ocular discharge, three days after an oropharyngeal swab tested positive for SARS-CoV-2 viral RNA using two real-time reverse transcriptase polymerase chain reaction (RT-qPCR) assays for the envelope (E) and RNA-dependent RNA polymerase (RdRp) gene. Thus, SARS-CoV-2 viral RNA was detectable prior to the onset of clinical signs. Five and six months after positive molecular results, the serological testing substantiated the presence of a SARS-CoV-2 infection in the cat with the detection of anti-SARS-CoV-2 receptor binding domain (RBD) immunoglobulin (IgG) antibodies and neutralizing activity in a surrogate virus neutralization assay (sVNT). To the best of our knowledge, this extends the known duration of seropositivity of SARS-CoV-2 in a cat. Our study provides further evidence that cats are susceptible to SARS-CoV-2 under natural conditions and strengthens the assumption that comorbidities may play a role in the development of clinical disease.
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Affiliation(s)
- Julia Klaus
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (M.L.M.); (R.H.-L.)
| | - Carlo Palizzotto
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara, Italy; (E.Z.); (C.L.)
| | - Eric Zini
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara, Italy; (E.Z.); (C.L.)
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
- Department of Animal Medicine, Production and Health, University of Padova, Viale dell’Università 16, 35020 Legnaro, Padova, Italy
| | - Marina L. Meli
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (M.L.M.); (R.H.-L.)
| | - Chiara Leo
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara, Italy; (E.Z.); (C.L.)
| | - Herman Egberink
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, University of Utrecht, 3584 CL Utrecht, The Netherlands; (H.E.); (S.Z.)
| | - Shan Zhao
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, University of Utrecht, 3584 CL Utrecht, The Netherlands; (H.E.); (S.Z.)
| | - Regina Hofmann-Lehmann
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (M.L.M.); (R.H.-L.)
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22
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Garcia-Beltran WF, Lam EC, St. Denis K, Nitido AD, Garcia ZH, Hauser BM, Feldman J, Pavlovic MN, Gregory DJ, Poznansky MC, Sigal A, Schmidt AG, Iafrate AJ, Naranbhai V, Balazs AB. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.14.21251704. [PMID: 33619506 PMCID: PMC7899476 DOI: 10.1101/2021.02.14.21251704] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Vaccination elicits immune responses capable of potently neutralizing SARS-CoV-2. However, ongoing surveillance has revealed the emergence of variants harboring mutations in spike, the main target of neutralizing antibodies. To understand the impact of these variants, we evaluated the neutralization potency of 99 individuals that received one or two doses of either BNT162b2 or mRNA-1273 vaccines against pseudoviruses representing 10 globally circulating strains of SARS-CoV-2. Five of the 10 pseudoviruses, harboring receptor-binding domain mutations, including K417N/T, E484K, and N501Y, were highly resistant to neutralization. Crossneutralization of B.1.351 variants was comparable to SARS-CoV and bat-derived WIV1-CoV, suggesting that a relatively small number of mutations can mediate potent escape from vaccine responses. While the clinical impact of neutralization resistance remains uncertain, these results highlight the potential for variants to escape from neutralizing humoral immunity and emphasize the need to develop broadly protective interventions against the evolving pandemic.
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Affiliation(s)
- Wilfredo F. Garcia-Beltran
- These authors contributed equally
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | - Evan C. Lam
- These authors contributed equally
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Kerri St. Denis
- These authors contributed equally
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Adam D. Nitido
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Zeidy H. Garcia
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Blake M. Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Maia N. Pavlovic
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, 02129, USA
| | - David J. Gregory
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, 02129, USA
- Pedriatric Infectious Disease, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Mark C. Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, 02129, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban, 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4041 South Africa
- Max Planck Institute for Infection Biology, Berlin, 10117, Germany
| | - Aaron G. Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - A. John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Vivek Naranbhai
- Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for the AIDS Programme of Research in South Africa, Durban, 4001, South Africa
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23
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Pitol AK, Julian TR. Community Transmission of SARS-CoV-2 by Surfaces: Risks and Risk Reduction Strategies. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2021; 8:263-269. [PMID: 37566313 PMCID: PMC7805599 DOI: 10.1021/acs.estlett.0c00966] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 05/19/2023]
Abstract
SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is perceived to be primarily transmitted via person-to-person contact through droplets produced while talking, coughing, and sneezing. Transmission may also occur through other routes, including contaminated surfaces; nevertheless, the role that surfaces have on the spread of the disease remains contested. Here, we use the Quantitative Microbial Risk Assessment framework to examine the risks of community transmission of SARS-CoV-2 through surfaces and to evaluate the effectiveness of hand and surface disinfection as potential interventions. Using conservative assumptions on input parameters of the model (e.g., dose-response relationship, ratio of genome copies to infective virus), the average of the median risks for single hand-to-surface contact followed by hand-to-face contact range from 1.6 × 10-4 to 5.6 × 10-9 for modeled prevalence rates of 0.2%-5%. For observed prevalence rates (0.2%, 1%), this corresponds to a low risk of infection (<10-6). Hand disinfection substantially reduces risks of transmission independently of the disease's prevalence and contact frequency. In contrast, the effectiveness of surface disinfection is highly dependent on the prevalence and the frequency of contacts. The work supports the current perception that contaminated surfaces are not a primary mode of transmission of SARS-CoV-2 and affirms the benefits of making hand disinfectants widely available.
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Affiliation(s)
- Ana K. Pitol
- Department of Civil and Environmental Engineering,
Imperial College London, London SW7 2AZ, United
Kingdom
| | - Timothy R. Julian
- Eawag, Swiss Federal Institute of Aquatic
Science and Technology, Dübendorf CH-8600,
Switzerland
- Swiss Tropical and Public Health
Institute, Basel CH-4051, Switzerland
- University of Basel, Basel
CH-4055, Switzerland
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24
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Shukla AK, Banerjee M. Angiotensin-Converting-Enzyme 2 and Renin-Angiotensin System Inhibitors in COVID-19: An Update. High Blood Press Cardiovasc Prev 2021; 28:129-139. [PMID: 33635533 PMCID: PMC7908946 DOI: 10.1007/s40292-021-00439-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/10/2021] [Indexed: 02/07/2023] Open
Abstract
Ever since its outbreak, Corona Virus Disease 2019(COVID-19) caused by SARS-CoV-2 has affected more than 26 million individuals in more than 200 countries. Although the mortality rate of COVID-19 is low, but several clinical studies showed, patients with diabetes mellitus (DM) or other major complication at high risk of COVID-19 and reported more severe disease and increased fatality. The angiotensin-converting-enzyme 2 (ACE2), a component of renin-angiotensin-system (RAS); acts on ACE/Ang-II/AT1recptor axis, and regulates pathological processes like hypertension, cardiac dysfunction, Acute Respiratory Distress Syndrome (ARDS) etc. The progression of T2DM and hypertension show decreased expression and activity of ACE2. There are several treatment strategies for controlling diabetes, hypertension, etc; like ACE2 gene therapies, endogenous ACE2 activators, human recombinant ACE2 (hrACE2), Angiotensin-II receptor blockers (ARBs) and ACE inhibitors (ACEi) medications. ACE2, the receptors for SARS-CoV2, facilitates virus entry inside host cell. Clinicians are using two classes of medications for the treatment of COVID-19; one targets the SARS-CoV-2-ACE2 interaction, while other targets human immune system. The aim of this review is to discuss the role of ACE2 in diabetes and in COVID-19 and to provide an analysis of data proposing harm and benefit of RAS inhibitor treatment in COVID-19 infection as well as showing no association whatsoever. This review also highlights some candidate vaccines which are undergoing clinical trials.
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Affiliation(s)
- Ashwin Kumar Shukla
- Molecular and Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow, Uttar Pradesh, India
| | - Monisha Banerjee
- Molecular and Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow, Uttar Pradesh, India.
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25
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Everett HE, Lean FZX, Byrne AMP, van Diemen PM, Rhodes S, James J, Mollett B, Coward VJ, Skinner P, Warren CJ, Bewley KR, Watson S, Hurley S, Ryan KA, Hall Y, Simmons H, Núñez A, Carroll MW, Brown IH, Brookes SM. Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection. Viruses 2021; 13:113. [PMID: 33467732 PMCID: PMC7830262 DOI: 10.3390/v13010113] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/07/2021] [Accepted: 01/10/2021] [Indexed: 02/07/2023] Open
Abstract
Ferrets were experimentally inoculated with SARS-CoV-2 (severe acute respiratory syndrome (SARS)-related coronavirus 2) to assess infection dynamics and host response. During the resulting subclinical infection, viral RNA was monitored between 2 and 21 days post-inoculation (dpi), and reached a peak in the upper respiratory cavity between 4 and 6 dpi. Viral genomic sequence analysis in samples from three animals identified the Y453F nucleotide substitution relative to the inoculum. Viral RNA was also detected in environmental samples, specifically in swabs of ferret fur. Microscopy analysis revealed viral protein and RNA in upper respiratory tract tissues, notably in cells of the respiratory and olfactory mucosae of the nasal turbinates, including olfactory neuronal cells. Antibody responses to the spike and nucleoprotein were detected from 21 dpi, but virus-neutralizing activity was low. A second intranasal inoculation (re-exposure) of two ferrets after a 17-day interval did not produce re-initiation of viral RNA shedding, but did amplify the humoral response in one animal. Therefore, ferrets can be experimentally infected with SARS-CoV-2 to model human asymptomatic infection.
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Affiliation(s)
- Helen E. Everett
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Fabian Z. X. Lean
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Alexander M. P. Byrne
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Pauline M. van Diemen
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Shelley Rhodes
- Bacteriology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK;
| | - Joe James
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Benjamin Mollett
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Vivien J. Coward
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Paul Skinner
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Caroline J. Warren
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Kevin R. Bewley
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
| | - Samantha Watson
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Shellene Hurley
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Kathryn A. Ryan
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
| | - Yper Hall
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
| | - Hugh Simmons
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Alejandro Núñez
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Miles W. Carroll
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
- Nuffield Department of Medicine, Oxford University, Oxford OX1 3SY, UK
| | - Ian H. Brown
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Sharon M. Brookes
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
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26
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Chen S, Ren LZ, Ouyang HS, Liu S, Zhang LY. Necessary problems in re-emergence of COVID-19. World J Clin Cases 2021; 9:1-7. [PMID: 33511167 PMCID: PMC7809654 DOI: 10.12998/wjcc.v9.i1.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/05/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 poses a great threat to human beings. Although numerous patients have recovered, re-positive cases have been reported in several countries. Till now, we still know very little about the disease and its pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, more attention should be paid to the following aspects, such as post-discharge surveillance, asymptomatic infection, re-evaluation of influenza-like symptoms, and dynamic monitoring of genomic mutation of SARS-CoV-2.
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Affiliation(s)
- Si Chen
- College of Animal Sciences, Jilin University, Changchun 130062, Jilin Province, China
| | - Lin-Zhu Ren
- College of Animal Sciences, Jilin University, Changchun 130062, Jilin Province, China
| | - Hong-Sheng Ouyang
- College of Animal Sciences, Jilin University, Changchun 130062, Jilin Province, China
| | - Shen Liu
- Department of Pharmacy, Jilin Cancer Hospital, Changchun 130000, Jilin Province, China
| | - Li-Ying Zhang
- College of Animal Sciences, Jilin University, Changchun 130062, Jilin Province, China
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27
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Abstract
The cGAS-STING signalling pathway has emerged as a key mediator of inflammation in the settings of infection, cellular stress and tissue damage. Underlying this broad involvement of the cGAS-STING pathway is its capacity to sense and regulate the cellular response towards microbial and host-derived DNAs, which serve as ubiquitous danger-associated molecules. Insights into the structural and molecular biology of the cGAS-STING pathway have enabled the development of selective small-molecule inhibitors with the potential to target the cGAS-STING axis in a number of inflammatory diseases in humans. Here, we outline the principal elements of the cGAS-STING signalling cascade and discuss the general mechanisms underlying the association of cGAS-STING activity with various autoinflammatory, autoimmune and degenerative diseases. Finally, we outline the chemical nature of recently developed cGAS and STING antagonists and summarize their potential clinical applications.
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28
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SARS-CoV‑2, a virus with many faces: a series of cases with prolonged persistence of COVID-19 symptoms. Wien Med Wochenschr 2020; 171:3-6. [PMID: 33315163 PMCID: PMC7734614 DOI: 10.1007/s10354-020-00793-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/16/2020] [Indexed: 01/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as the causative agent of the ongoing pandemic, has spread into more than 200 countries to date. The disease which is caused by the virus is termed COVID-19. In most cases, it presents at first like common flu with cough and other respiratory symptoms. Nevertheless, other symptoms have been reported, such as a feeling of extreme fatigue, gastrointestinal symptoms, or acute onset of olfactory and gustatory dysfunction. Here we report a series of 10 cases (1 male, 9 females) observed between February and April 2020, with an undulating appearance and disappearance of symptoms. Weeks passed before the diagnosis was established. Symptoms resolved rapidly after treatment with hydroxychloroquine. It seems that the course of COVID-19 can be mild or moderate but with a long persistence of symptoms, and may therefore remain obscure. This may cause a public health issue because of the long infectivity of these patients.
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29
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Soliman MS, AbdelFattah M, Aman SMN, Ibrahim LM, Aziz RK. A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 25:123-128. [PMID: 33253058 DOI: 10.1089/omi.2020.0194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The novel severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is causing an unprecedented pandemic, threatening planetary health, society, and economy. Genomic surveillance continues to be a critical effort toward tracking the virus and containing its spread, and more genomes from diverse geographical areas and different time points are needed to provide an appropriate representation of the virus evolution. In this study, we report the successful assembly of one single gapless, unambiguous contiguous sequence representing the complete viral genome from a nasopharyngeal swab of an infected health care worker in Cairo, Egypt. The sequence has all typical features of SARS-CoV-2 genomes, with no protein-disrupting mutations. However, three mutations are worth highlighting and future tracking: a synonymous mutation causing a rare spike S813I variation and two less frequent ones leading to an A41V variation in NSP3, encoded by ORF1a (ORF1a A895V), and a Q677H variation in the spike protein. Both affected proteins, S and NSP3, are relevant to vaccine and drug development. Although the genome, named CU_S3, belongs to the prevalent global genotype, marked by the D614G spike variation, the combined variations in the spike proteins and ORF1a do not co-occur in any of the 197,000 genomes reported to date. Future studies will assess the biological, pathogenic, and epidemiological implications of this set of genetic variations. This line of research is needed to inform vaccine and therapeutic innovation to stem the COVID-19 pandemic.
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Affiliation(s)
- May S Soliman
- Clinical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - May AbdelFattah
- Clinical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt.,Cairo University Pediatric Hospital, Cairo, Egypt
| | - Soad M N Aman
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Lamyaa M Ibrahim
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt.,Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt
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30
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Zhang Z, Ye S, Wu A, Jiang T, Peng Y. Prediction of the Receptorome for the Human-Infecting Virome. Virol Sin 2020; 36:133-140. [PMID: 32725480 PMCID: PMC7385468 DOI: 10.1007/s12250-020-00259-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/01/2020] [Indexed: 11/26/2022] Open
Abstract
The virus receptors are key for the viral infection of host cells. Identification of the virus receptors is still challenging at present. Our previous study has shown that human virus receptor proteins have some unique features including high N-glycosylation level, high number of interaction partners and high expression level. Here, a random-forest model was built to identify human virus receptorome from human cell membrane proteins with an accepted accuracy based on the combination of the unique features of human virus receptors and protein sequences. A total of 1424 human cell membrane proteins were predicted to constitute the receptorome of the human-infecting virome. In addition, the combination of the random-forest model with protein–protein interactions between human and viruses predicted in previous studies enabled further prediction of the receptors for 693 human-infecting viruses, such as the enterovirus, norovirus and West Nile virus. Finally, the candidate alternative receptors of the SARS-CoV-2 were also predicted in this study. As far as we know, this study is the first attempt to predict the receptorome for the human-infecting virome and would greatly facilitate the identification of the receptors for viruses.
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Affiliation(s)
- Zheng Zhang
- Bioinformatics Center of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Sifan Ye
- Bioinformatics Center of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Taijiao Jiang
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yousong Peng
- Bioinformatics Center of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China.
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