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Maqbool ME, Farhan A, Qamar MA. Global impact of COVID-19 on food safety and environmental sustainability: Pathways to face the pandemic crisis. Heliyon 2024; 10:e35154. [PMID: 39170381 PMCID: PMC11336433 DOI: 10.1016/j.heliyon.2024.e35154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/23/2024] Open
Abstract
The COVID-19 pandemic poses ongoing challenges to the sustainability of various socioeconomic sectors, including agriculture, the food supply chain, the food business, and environmental sustainability. This study employs data obtained from the World Health Organization (WHO), and Food and Agriculture Organization (FAO), as well as scientific and technical research publications, to evaluate the impacts of COVID-19 on agriculture and food security. This article seeks to highlight the profound influence of the COVID-19 pandemic on agriculture, the supply and demand of food, and the overall safety of food. The article also explores the several pathways by which COVID-19 can be transmitted in these areas and the various technologies employed for its detection. The ongoing and post-pandemic ramifications are substantial since they could decrease agricultural output due to limitations on migration, a downturn in international trade, less buying capacity, and disturbances in food production and processing. Therefore, based on this thorough investigation, recommendations are issued for mitigating and controlling the pandemic's effects.
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Affiliation(s)
- Muhammad Ehsan Maqbool
- Departmentof Zoology, Wildlife and Fisheries, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Ahmad Farhan
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Muhammad Azam Qamar
- Department of Chemistry, School of Science, University of Management and Technology, Lahore, 54770, Pakistan
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2
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Carter T, Iqbal M. The Influenza A Virus Replication Cycle: A Comprehensive Review. Viruses 2024; 16:316. [PMID: 38400091 PMCID: PMC10892522 DOI: 10.3390/v16020316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Influenza A virus (IAV) is the primary causative agent of influenza, colloquially called the flu. Each year, it infects up to a billion people, resulting in hundreds of thousands of human deaths, and causes devastating avian outbreaks with worldwide losses worth billions of dollars. Always present is the possibility that a highly pathogenic novel subtype capable of direct human-to-human transmission will spill over into humans, causing a pandemic as devastating if not more so than the 1918 influenza pandemic. While antiviral drugs for influenza do exist, they target very few aspects of IAV replication and risk becoming obsolete due to antiviral resistance. Antivirals targeting other areas of IAV replication are needed to overcome this resistance and combat the yearly epidemics, which exact a serious toll worldwide. This review aims to summarise the key steps in the IAV replication cycle, along with highlighting areas of research that need more focus.
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Affiliation(s)
- Toby Carter
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK;
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3
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Mo C, Li X, Wu Q, Fan Y, Liu D, Zhu Y, Yang Y, Liao X, Zhou Z, Zhou L, Li Q, Zhang Q, Liu W, Zhou R, Tian X. SARS-CoV-2 mRNA vaccine requires signal peptide to induce antibody responses. Vaccine 2023; 41:6863-6869. [PMID: 37821314 DOI: 10.1016/j.vaccine.2023.09.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/15/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]
Abstract
New SARS-CoV-2 variants continue to prevail worldwide, and effective vaccines are needed to prevent an epidemic. mRNA vaccines are gradually being applied to the prevention and control of infectious diseases with significant safety and effectiveness. The spike (S) protein of SARS-CoV-2 is the main target of mRNA vaccine design, but the impact of the signal peptide (SP), transmembrane region (TM), and cytoplasmic tail (CT) on mRNA vaccine remains unclear. In this study, we constructed three forms of mRNA vaccines related to the S protein: full-length, deletion of the TM and CT, and simultaneous deletion of the SP, TM and CT, and compared their immunogenicity. Our experimental data show that full-length S protein and deletion of the TM and CT could effectively induce neutralizing antibody production in mice, while S protein without the SP and TM could not. This indicates that the S protein SP is necessary for the design of mRNA vaccine.
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MESH Headings
- Animals
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- Mice
- COVID-19 Vaccines/immunology
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Protein Sorting Signals/genetics
- mRNA Vaccines/immunology
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- COVID-19/prevention & control
- COVID-19/immunology
- Mice, Inbred BALB C
- Female
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/administration & dosage
- Humans
- Immunogenicity, Vaccine
- Antibody Formation/immunology
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Affiliation(s)
- Chuncong Mo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China; Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Xiao Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Qianying Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Ye Fan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China; Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Donglan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yuhui Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yujie Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Xiaohong Liao
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Zhichao Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Liling Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Qiuru Li
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Qiong Zhang
- Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Rong Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China; Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China.
| | - Xingui Tian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China.
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4
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Chadha A, Dara R, Pearl DL, Sharif S, Poljak Z. Predictive analysis for pathogenicity classification of H5Nx avian influenza strains using machine learning techniques. Prev Vet Med 2023; 216:105924. [PMID: 37224663 DOI: 10.1016/j.prevetmed.2023.105924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 03/17/2023] [Accepted: 04/21/2023] [Indexed: 05/26/2023]
Abstract
Over the past decades, avian influenza (AI) outbreaks have been reported across different parts of the globe, resulting in large-scale economic and livestock loss and, in some cases raising concerns about their zoonotic potential. The virulence and pathogenicity of H5Nx (e.g., H5N1, H5N2) AI strains for poultry could be inferred through various approaches, and it has been frequently performed by detecting certain pathogenicity markers in their haemagglutinin (HA) gene. The utilization of predictive modeling methods represents a possible approach to exploring this genotypic-phenotypic relationship for assisting experts in determining the pathogenicity of circulating AI viruses. Therefore, the main objective of this study was to evaluate the predictive performance of different machine learning (ML) techniques for in-silico prediction of pathogenicity of H5Nx viruses in poultry, using complete genetic sequences of the HA gene. We annotated 2137 H5Nx HA gene sequences based on the presence of the polybasic HA cleavage site (HACS) with 46.33% and 53.67% of sequences previously identified as highly pathogenic (HP) and low pathogenic (LP), respectively. We compared the performance of different ML classifiers (e.g., logistic regression (LR) with the lasso and ridge regularization, random forest (RF), K-nearest neighbor (KNN), Naïve Bayes (NB), support vector machine (SVM), and convolutional neural network (CNN)) for pathogenicity classification of raw H5Nx nucleotide and protein sequences using a 10-fold cross-validation technique. We found that different ML techniques can be successfully used for the pathogenicity classification of H5 sequences with ∼99% classification accuracy. Our results indicate that for pathogenicity classification of (1) aligned deoxyribonucleic acid (DNA) and protein sequences, with NB classifier had the lowest accuracies of 98.41% (+/-0.89) and 98.31% (+/-1.06), respectively; (2) aligned DNA and protein sequences, with LR (L1/L2), KNN, SVM (radial basis function (RBF)) and CNN classifiers had the highest accuracies of 99.20% (+/-0.54) and 99.20% (+/-0.38), respectively; (3) unaligned DNA and protein sequences, with CNN's achieved accuracies of 98.54% (+/-0.68) and 99.20% (+/-0.50), respectively. ML methods show potential for regular classification of H5Nx virus pathogenicity for poultry species, particularly when sequences containing regular markers were frequently present in the training dataset.
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Affiliation(s)
- Akshay Chadha
- School of Computer Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
| | - Rozita Dara
- School of Computer Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - David L Pearl
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Shayan Sharif
- Department of Pathobiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Zvonimir Poljak
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Rana R, Kant R, Kumra T, Gupta S, Rana DS, Ganguly NK. An update on SARS-CoV-2 immunization and future directions. Front Pharmacol 2023; 14:1125305. [PMID: 36969857 PMCID: PMC10033701 DOI: 10.3389/fphar.2023.1125305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/09/2023] [Indexed: 03/29/2023] Open
Abstract
Millions of people have died as a result of SARS-CoV-2, which was first discovered in China and has since spread globally. Patients with SARS-CoV-2 infection may show a range of symptoms, including fever, coughing, and shortness of breath, or they may show no symptoms at all. To treat COVID-19 symptoms and avoid serious infections, many medications and vaccinations have been employed. However, to entirely eradicate COVID-19 from the world, next-generation vaccine research is required because of the devastating consequences it is having for humanity and every nation's economy. Scientists are working hard to eradicate this dangerous virus across the world. SARS-CoV-2 has also undergone significant mutation, leading to distinct viral types such as the alpha, beta, gamma, delta, and omicron variants. This has sparked discussion about the effectiveness of current vaccines for the newly formed variants. A proper comparison of these vaccinations is required to compare their efficacy as the number of people immunized against SARS-CoV-2 globally increases. Population-level statistics evaluating the capacity of these vaccines to reduce infection are therefore being developed. In this paper, we analyze the many vaccines on the market in terms of their production process, price, dosage needed, and efficacy. This article also discusses the challenges of achieving herd immunity, the likelihood of reinfection, and the importance of convalescent plasma therapy in reducing infection.
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Affiliation(s)
- Rashmi Rana
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | - Ravi Kant
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | - Tanya Kumra
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | - Sneha Gupta
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
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Structural patterns of SARS-CoV-2 variants of concern (alpha, beta, gamma, delta) spike protein are influenced by variant-specific amino acid mutations: A computational study with implications on viral evolution. J Theor Biol 2023; 558:111376. [PMID: 36473508 PMCID: PMC9721161 DOI: 10.1016/j.jtbi.2022.111376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 (SARS2) regularly mutates resulting to variants of concern (VOC) which have higher virulence and transmissibility rates while concurrently evading available therapeutic strategies. This highlights the importance of amino acid mutations occurring in the SARS2 spike protein structure since it may affect virus biology. However, this was never fully elucidated. Here, network analysis was performed based on the COVID-19 genomic epidemiology network between December 2019-July 2021. Representative SARS2 VOC spike protein models were generated and quality checked, protein model superimposition was done, and common contact based on contact mapping was established. Throughout this study, we found that: (1) certain individual variant-specific amino acid mutations can affect the spike protein structural pattern; (2) certain individual variant-specific amino acid mutations had no affect on the spike protein structural pattern; and (3) certain combination of variant-specific amino acids are putatively epistatic mutations that can potentially influence the VOC spike protein structural pattern. This manuscript was submitted as part of a theme issue on "Modelling COVID-19 and Preparedness for Future Pandemics".
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7
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Influence of viral genome properties on polymerase fidelity. Trends Genet 2023; 39:9-14. [PMID: 36402624 DOI: 10.1016/j.tig.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/27/2022] [Accepted: 10/30/2022] [Indexed: 11/17/2022]
Abstract
The first step of viral evolution takes place during genome replication via the error-prone viral polymerase. Among the mutants that arise through this process, only a few well-adapted variants will be selected by natural selection, renewing the viral genome population. Viral polymerase-mediated errors are thought to occur stochastically. However, accumulating evidence suggests that viral polymerase-mediated mutations are heterogeneously distributed throughout the viral genome. Here, we review work that supports this concept and provides mechanistic insights into how specific features of the viral genome could modulate viral polymerase-mediated errors. A predisposition to accumulate viral polymerase-mediated errors at specific loci in the viral genome may guide evolution to specific pathways, thus opening new directions of research to better understand viral evolutionary dynamics.
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8
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Naidu SAG, Clemens RA, Naidu AS. SARS-CoV-2 Infection Dysregulates Host Iron (Fe)-Redox Homeostasis (Fe-R-H): Role of Fe-Redox Regulators, Ferroptosis Inhibitors, Anticoagulants, and Iron-Chelators in COVID-19 Control. J Diet Suppl 2023; 20:312-371. [PMID: 35603834 DOI: 10.1080/19390211.2022.2075072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Severe imbalance in iron metabolism among SARS-CoV-2 infected patients is prominent in every symptomatic (mild, moderate to severe) clinical phase of COVID-19. Phase-I - Hypoxia correlates with reduced O2 transport by erythrocytes, overexpression of HIF-1α, altered mitochondrial bioenergetics with host metabolic reprogramming (HMR). Phase-II - Hyperferritinemia results from an increased iron overload, which triggers a fulminant proinflammatory response - the acute cytokine release syndrome (CRS). Elevated cytokine levels (i.e. IL6, TNFα and CRP) strongly correlates with altered ferritin/TF ratios in COVID-19 patients. Phase-III - Thromboembolism is consequential to erythrocyte dysfunction with heme release, increased prothrombin time and elevated D-dimers, cumulatively linked to severe coagulopathies with life-threatening outcomes such as ARDS, and multi-organ failure. Taken together, Fe-R-H dysregulation is implicated in every symptomatic phase of COVID-19. Fe-R-H regulators such as lactoferrin (LF), hemoxygenase-1 (HO-1), erythropoietin (EPO) and hepcidin modulators are innate bio-replenishments that sequester iron, neutralize iron-mediated free radicals, reduce oxidative stress, and improve host defense by optimizing iron metabolism. Due to its pivotal role in 'cytokine storm', ferroptosis is a potential intervention target. Ferroptosis inhibitors such as ferrostatin-1, liproxstatin-1, quercetin, and melatonin could prevent mitochondrial lipid peroxidation, up-regulate antioxidant/GSH levels and abrogate iron overload-induced apoptosis through activation of Nrf2 and HO-1 signaling pathways. Iron chelators such as heparin, deferoxamine, caffeic acid, curcumin, α-lipoic acid, and phytic acid could protect against ferroptosis and restore mitochondrial function, iron-redox potential, and rebalance Fe-R-H status. Therefore, Fe-R-H restoration is a host biomarker-driven potential combat strategy for an effective clinical and post-recovery management of COVID-19.
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Affiliation(s)
| | - Roger A Clemens
- Department of International Regulatory Science, University of Southern California School of Pharmacy, Los Angeles, CA, USA
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Haghighi M, Khorasani A, Karimi P, Keshavarz R, Mahdavi M. Different Formulations of Inactivated SARS-CoV-2 Vaccine Candidates in Human Compatible Adjuvants: Potency Studies in Mice Showed Different Platforms of Immune Responses. Viral Immunol 2022; 35:663-672. [PMID: 36534465 DOI: 10.1089/vim.2022.0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Several inactivated SARS-CoV-2 vaccines have been approved for human use, but are not highly potent. In this study, different formulations of the inactivated SARS-CoV-2 virus were developed in Alum, Montanide 51VG, and Montanide ISA720VG adjuvants, followed by assessment of immune responses. The SARS-CoV-2 virus was inactivated with formalin and formulated in the adjuvants. BALB/c mice were immunized subcutaneously with 4 μg of vaccines on days 0 and 14; (IL-4) and (IFN-g), cytotoxic T lymphocyte (CTL) activity, and specific immunoglobulin G (IgG) titer and IgG1, IgG2a, and IgG2a/IgG1 ratio, and anti-receptor-binding domain (RBD) IgG response were assessed 2 weeks after the final immunization. Immunization with SARS-CoV-2-Montanide ISA51VG showed a significant increase in the IFN-γ cytokine versus SARS-CoV-2-Alum, SARS-CoV-2-Montanide ISA720VG, and control groups (p < 0.0033). Cytokine IL-4 response in SARS-CoV-2-Alum group showed a significant increase compared with SARS-CoV-2-Montanide ISA51VG, SARS-CoV-2-Montanide ISA720VG, and control groups (p < 0.0206). In addition, SARS-CoV-2-Montanide ISA51VG vaccine induced the highest IFN-γ/IL-4 cytokine ratio versus other groups (p < 0.0004). CTL activity in SARS-CoV-2-Montanide ISA51VG and SARS-CoV-2-Montanide ISA720VG groups showed a significant increase compared with SARS-CoV-2-Alum and control groups (p < 0.0075). Specific IgG titer in SARS-CoV-2-Montanide ISA51 VG and SARS-CoV-2-Montanide ISA720VG showed a significant increase compared with SARS-CoV-2-Alum and control groups (p < 0.0143). Results from specific IgG1and IgG2a in SARS-CoV-2-Alum, SARS-CoV-2-Montanide ISA51VG, and SARS-CoV-2-Montanide ISA720VG vaccine showed a significant increase compared with phosphate buffer saline (PBS) group (p < 0.0001), but SARS-CoV-2-Montanide ISA51VG and SARS-CoV-2-Montanide ISA 720VG groups showed the highest IgG2a/IgG1 ratio and a significant increase compared with SARS-CoV-2-Alum group (p < 0.0379). Moreover, inactivated SARS-CoV-2+Alum and SARS-CoV-2-Montanide ISA 720VG groups demonstrated a significant increase in anti-RBD IgG response versus the SARS-CoV-2-Montanide ISA51VG group. It seems that the type of vaccine formulation is a critical parameter, influencing the immunologic pattern and vaccine potency and human-compatible oil-based adjuvants were more potent than Alum adjuvant in the vaccine formulation.
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Affiliation(s)
- Melika Haghighi
- Department of FMD Vaccine Production, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Akbar Khorasani
- Department of FMD Vaccine Production, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Pegah Karimi
- Department of Biochemistry, Faculty of Basic Sciences, Islamic Azad University, Tehran, Iran
| | - Rouhollah Keshavarz
- PPD Tuberculin Department, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mehdi Mahdavi
- Advanced Therapy Medicinal Product (ATMP) Department, Breast Cancer Research Center, Motamed Cancer Institute, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran.,Recombinant Vaccine Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Immunotherapy Group, The Institute of Pharmaceutical Science (TIPS), Tehran University of Medical Science, Tehran, Iran
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Jose AM. Analyzing the Impermeable Structure and Myriad of Antiviral Therapies for SARS-CoV-2. JOURNAL OF THE ASSOCIATION OF PHYSICIANS OF INDIA 2022. [DOI: 10.5005/japi-11001-0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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11
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de Bruin ACM, Funk M, Spronken MI, Gultyaev AP, Fouchier RAM, Richard M. Hemagglutinin Subtype Specificity and Mechanisms of Highly Pathogenic Avian Influenza Virus Genesis. Viruses 2022; 14:v14071566. [PMID: 35891546 PMCID: PMC9321182 DOI: 10.3390/v14071566] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/04/2023] Open
Abstract
Highly Pathogenic Avian Influenza Viruses (HPAIVs) arise from low pathogenic precursors following spillover from wild waterfowl into poultry populations. The main virulence determinant of HPAIVs is the presence of a multi-basic cleavage site (MBCS) in the hemagglutinin (HA) glycoprotein. The MBCS allows for HA cleavage and, consequently, activation by ubiquitous proteases, which results in systemic dissemination in terrestrial poultry. Since 1959, 51 independent MBCS acquisition events have been documented, virtually all in HA from the H5 and H7 subtypes. In the present article, data from natural LPAIV to HPAIV conversions and experimental in vitro and in vivo studies were reviewed in order to compile recent advances in understanding HA cleavage efficiency, protease usage, and MBCS acquisition mechanisms. Finally, recent hypotheses that might explain the unique predisposition of the H5 and H7 HA sequences to obtain an MBCS in nature are discussed.
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Affiliation(s)
- Anja C. M. de Bruin
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Mathis Funk
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Monique I. Spronken
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Alexander P. Gultyaev
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
- Group Imaging and Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, The Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
- Correspondence:
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12
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Gass JD, Kellogg HK, Hill NJ, Puryear WB, Nutter FB, Runstadler JA. Epidemiology and Ecology of Influenza A Viruses among Wildlife in the Arctic. Viruses 2022; 14:v14071531. [PMID: 35891510 PMCID: PMC9315492 DOI: 10.3390/v14071531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/10/2022] [Accepted: 07/10/2022] [Indexed: 02/01/2023] Open
Abstract
Arctic regions are ecologically significant for the environmental persistence and geographic dissemination of influenza A viruses (IAVs) by avian hosts and other wildlife species. Data describing the epidemiology and ecology of IAVs among wildlife in the arctic are less frequently published compared to southern temperate regions, where prevalence and subtype diversity are more routinely documented. Following PRISMA guidelines, this systematic review addresses this gap by describing the prevalence, spatiotemporal distribution, and ecological characteristics of IAVs detected among wildlife and the environment in this understudied region of the globe. The literature search was performed in PubMed and Google Scholar using a set of pre-defined search terms to identify publications reporting on IAVs in Arctic regions between 1978 and February 2022. A total of 2125 articles were initially screened, 267 were assessed for eligibility, and 71 articles met inclusion criteria. IAVs have been detected in multiple wildlife species in all Arctic regions, including seabirds, shorebirds, waterfowl, seals, sea lions, whales, and terrestrial mammals, and in the environment. Isolates from wild birds comprise the majority of documented viruses derived from wildlife; however, among all animals and environmental matrices, 26 unique low and highly pathogenic subtypes have been characterized in the scientific literature from Arctic regions. Pooled prevalence across studies indicates 4.23% for wild birds, 3.42% among tested environmental matrices, and seroprevalences of 9.29% and 1.69% among marine and terrestrial mammals, respectively. Surveillance data are geographically biased, with most data from the Alaskan Arctic and many fewer reports from the Russian, Canadian, North Atlantic, and Western European Arctic. We highlight multiple important aspects of wildlife host, pathogen, and environmental ecology of IAVs in Arctic regions, including the role of avian migration and breeding cycles for the global spread of IAVs, evidence of inter-species and inter-continental reassortment at high latitudes, and how climate change-driven ecosystem shifts, including changes in the seasonal availability and distribution of dietary resources, have the potential to alter host–pathogen–environment dynamics in Arctic regions. We conclude by identifying gaps in knowledge and propose priorities for future research.
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Affiliation(s)
- Jonathon D. Gass
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
- Correspondence:
| | - Hunter K. Kellogg
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Nichola J. Hill
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA;
| | - Wendy B. Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
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13
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Fofana AM, Hurford A. Parasite-induced shifts in host movement may explain the transient coexistence of high- and low-pathogenic disease strains. J Evol Biol 2022; 35:1072-1086. [PMID: 35789020 DOI: 10.1111/jeb.14053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 11/27/2022]
Abstract
Many parasites induce decreased host movement, known as lethargy, which can impact disease spread and the evolution of virulence. Mathematical models have investigated virulence evolution when parasites cause host death, but disease-induced decreased host movement has received relatively less attention. Here, we consider a model where, due to the within-host parasite replication rate, an infected host can become lethargic and shift from a moving to a resting state, where it can die. We find that when the lethargy and disease-induced mortality costs to the parasites are not high, then evolutionary bistability can arise, and either moderate or high virulence can evolve depending on the initial virulence and the magnitude of mutation. These results suggest, firstly, the coexistence of strains with different virulence, which may explain the transient coexistence of low- and high-pathogenic strains of avian influenza viruses, and secondly, that medical interventions to treat the symptoms of lethargy or prevent disease-induced host deaths can result in a large jump in virulence and the rapid evolution of high virulence. In complement to existing results that show bistability when hosts are heterogeneous at the population level, we show that evolutionary bistability may arise due to transmission heterogeneity at the individual host level.
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Affiliation(s)
- Abdou Moutalab Fofana
- Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Amy Hurford
- Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada.,Mathematics and Statistics, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
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14
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Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, is a global pandemic impacting 254 million people in 190 countries. Comorbidities, particularly cardiovascular disease, diabetes, and hypertension, increase the risk of infection and poor outcomes. SARS-CoV-2 enters host cells through the angiotensin-converting enzyme-2 receptor, generating inflammation and cytokine storm, often resulting in multiorgan failure. The mechanisms and effects of COVID-19 on patients with high-risk diabetes are not yet completely understood. In this review, we discuss the variety of coronaviruses, structure of SARS-CoV-2, mutations in SARS-CoV-2 spike proteins, receptors associated with viral host entry, and disease progression. Furthermore, we focus on possible mechanisms of SARS-CoV-2 in diabetes, leading to inflammation and heart failure. Finally, we discuss existing therapeutic approaches, unanswered questions, and future directions.
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Affiliation(s)
- Chandrakala Aluganti Narasimhulu
- Division of Metabolic and Cardiovascular Sciences, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States
| | - Dinender K Singla
- Division of Metabolic and Cardiovascular Sciences, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States
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15
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Funk M, de Bruin ACM, Spronken MI, Gultyaev AP, Richard M. In Silico Analyses of the Role of Codon Usage at the Hemagglutinin Cleavage Site in Highly Pathogenic Avian Influenza Genesis. Viruses 2022; 14:v14071352. [PMID: 35891333 PMCID: PMC9316147 DOI: 10.3390/v14071352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 02/01/2023] Open
Abstract
A vast diversity of 16 influenza hemagglutinin (HA) subtypes are found in birds. Interestingly, viruses from only two subtypes, H5 and H7, have so far evolved into highly pathogenic avian influenza viruses (HPAIVs) following insertions or substitutions at the HA cleavage site by the viral polymerase. The mechanisms underlying this striking subtype specificity are still unknown. Here, we compiled a comprehensive dataset of 20,488 avian influenza virus HA sequences to investigate differences in nucleotide and amino acid usage at the HA cleavage site between subtypes and how these might impact the genesis of HPAIVs by polymerase stuttering and realignment. We found that sequences of the H5 and H7 subtypes stand out by their high purine content at the HA cleavage site. In addition, fewer substitutions were necessary in H5 and H7 HAs than in HAs from other subtypes to acquire an insertion-prone HA cleavage site sequence, as defined based on in vitro and in vivo data from the literature. Codon usage was more favorable for HPAIV genesis in sequences of viruses isolated from species or geographical regions in which HPAIV genesis is more frequently observed in nature. The results of the present analyses suggest that the subtype restriction of HPAIV genesis to H5 and H7 influenza viruses might be due to the particular codon usage at the HA cleavage site in these subtypes.
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Affiliation(s)
- Mathis Funk
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (M.F.); (A.C.M.d.B.); (M.I.S.); (A.P.G.)
| | - Anja C. M. de Bruin
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (M.F.); (A.C.M.d.B.); (M.I.S.); (A.P.G.)
| | - Monique I. Spronken
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (M.F.); (A.C.M.d.B.); (M.I.S.); (A.P.G.)
| | - Alexander P. Gultyaev
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (M.F.); (A.C.M.d.B.); (M.I.S.); (A.P.G.)
- Group Imaging and Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, The Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (M.F.); (A.C.M.d.B.); (M.I.S.); (A.P.G.)
- Correspondence:
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16
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Insight towards the effect of the multi basic cleavage site of SARS-CoV-2 spike protein on cellular proteases. Virus Res 2022; 318:198845. [PMID: 35680004 PMCID: PMC9170277 DOI: 10.1016/j.virusres.2022.198845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/27/2022] [Accepted: 06/06/2022] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection presents an immense global health problem. Spike (S) protein of coronavirus is the primary determinant of its entry into the host as it consists of both receptor binding and fusion domain. Besides tissue tropism, and host range, coronavirus pathogenesis are primarily controlled by the interaction of S protein with the cell receptor. Moreover, the proteolytic activation of S protein by host cell proteases plays a decisive role. The host-cell proteases have shown to be involved in the proteolysis of S protein and cleaving it into two functional subunits, S1 and S2, during the maturation process. In the present study, the interaction of the S protein of SARS-CoV-2 with different host proteases like furin, cathepsin B, and plasmin has been analyzed using molecular docking and molecular dynamics (MD) simulation. Incorporation of the furin cleavage site (R-R-A-R) in the S protein of SARS-CoV-2 has been studied by mutating the individual amino acid. MD simulation results suggest the polytropic nature of the S protein. Our analysis indicated that a single amino acid substitution in the polybasic cleavage site of S protein perturb the binding of cellular proteases. This mutation study might help to generate an attenuated SARS-CoV-2. Besides, targeting host proteases by inhibitors may result in a practical approach to stop the cellular spread of SARS-CoV-2 and develop its antiviral.
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17
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Souza PF, Mesquita FP, Amaral JL, Landim PG, Lima KR, Costa MB, Farias IR, Belém MO, Pinto YO, Moreira HH, Magalhaes IC, Castelo-Branco DS, Montenegro RC, de Andrade CR. The spike glycoprotein of SARS-CoV-2: A review of how mutations of spike glycoproteins have driven the emergence of variants with high transmissibility and immune escape. Int J Biol Macromol 2022; 208:105-125. [PMID: 35300999 PMCID: PMC8920968 DOI: 10.1016/j.ijbiomac.2022.03.058] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 12/23/2022]
Abstract
Late in 2019, SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) emerged, causing an unknown type of pneumonia today called coronaviruses disease 2019 (COVID-19). COVID-19 is still an ongoing global outbreak that has claimed and threatened many lives worldwide. Along with the fastest vaccine developed in history to fight SARS-CoV-2 came a critical problem, SARS-CoV-2. These new variants are a result of the accumulation of mutations in the sequence and structure of spike (S) glycoprotein, which is by far the most critical protein for SARS-CoV-2 to recognize cells and escape the immune system, in addition to playing a role in SARS-CoV-2 infection, pathogenicity, transmission, and evolution. In this review, we discuss mutation of S protein and how these mutations have led to new variants that are usually more transmissible and can thus mitigate the immunity produced by vaccination. Here, analysis of S protein sequences and structures from variants point out the mutations among them, how they emerge, and the behavior of S protein from each variant. This review brings details in an understandable way about how the variants of SARS-CoV-2 are a result of mutations in S protein, making them more transmissible and even more aggressive than their relatives.
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Affiliation(s)
- Pedro F.N. Souza
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil,Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil,Corresponding author at: Drug research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Brazil, Rua Coronel Nunes de Melo 100, Caixa 60430-275 Fortaleza, CE, Brazil
| | - Felipe P. Mesquita
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Jackson L. Amaral
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil
| | - Patrícia G.C. Landim
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil
| | - Karollyny R.P. Lima
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil
| | - Marília B. Costa
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Izabelle R. Farias
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Mônica O. Belém
- Laboratory of Translational Research, Christus University Center, Fortaleza, Ceará 60192, Brazil
| | - Yago O. Pinto
- Medical Education Institution-Idomed, Canindé, Ceará, Brazil
| | | | | | - Débora S.C.M. Castelo-Branco
- Department of Pathology and Legal Medicine, Postgraduate Program in Medical Microbiology, Group of Applied Medical Microbiology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Raquel C. Montenegro
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Claudia R. de Andrade
- Laboratory of Translational Research, Christus University Center, Fortaleza, Ceará 60192, Brazil
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18
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Genomic determinants of Furin cleavage in diverse European SARS-related bat coronaviruses. Commun Biol 2022; 5:491. [PMID: 35637279 PMCID: PMC9151638 DOI: 10.1038/s42003-022-03421-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/27/2022] [Indexed: 12/11/2022] Open
Abstract
The furin cleavage site (FCS) in SARS-CoV-2 is unique within the Severe acute respiratory syndrome–related coronavirus (SrC) species. We re-assessed diverse SrC from European horseshoe bats and analyzed the spike-encoding genomic region harboring the FCS in SARS-CoV-2. We reveal molecular features in SrC such as purine richness and RNA secondary structures that resemble those required for FCS acquisition in avian influenza viruses. We discuss the potential acquisition of FCS through molecular mechanisms such as nucleotide substitution, insertion, or recombination, and show that a single nucleotide exchange in two European bat-associated SrC may suffice to enable furin cleavage. Furthermore, we show that FCS occurrence is variable in bat- and rodent-borne counterparts of human coronaviruses. Our results suggest that furin cleavage sites can be acquired in SrC via conserved molecular mechanisms known in other reservoir-bound RNA viruses and thus support a natural origin of SARS-CoV-2. Genomic analyses of spike glycoprotein genes of European bat SARS-related coronaviruses suggest that furin cleavage sites can be acquired in the bat reservoir via conserved molecular mechanisms, supporting a natural origin of SARS-CoV-2.
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19
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Xu W, Navarro-López R, Solis-Hernandez M, Liljehult-Fuentes F, Molina-Montiel M, Lagunas-Ayala M, Rocha-Martinez M, Ferrara-Tijera E, Pérez de la Rosa J, Berhane Y. Evolutionary Dynamics of Mexican Lineage H5N2 Avian Influenza Viruses. Viruses 2022; 14:v14050958. [PMID: 35632700 PMCID: PMC9146523 DOI: 10.3390/v14050958] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
We have demonstrated for the first time a comprehensive evolutionary analysis of the Mexican lineage H5N2 avian influenza virus (AIV) using complete genome sequences (n = 189), from its first isolation in 1993 until 2019. Our study showed that the Mexican lineage H5N2 AIV originated from the North American wild bird gene pool viruses around 1990 and is currently circulating in poultry populations of Mexico, the Dominican Republic, and Taiwan. Since the implementation of vaccination in 1995, the highly pathogenic AIV (HPAIV) H5N2 virus was eradicated from Mexican poultry in mid-1995. However, the low pathogenic AIV (LPAIV) H5N2 virus has continued to circulate in domestic poultry populations in Mexico, eventually evolving into five distinct clades. In the current study, we demonstrate that the evolution of Mexican lineage H5N2 AIVs involves gene reassortments and mutations gained over time. The current circulating Mexican lineage H5N2 AIVs are classified as LPAIV based on the amino acid sequences of the hemagglutinin (HA) protein cleavage site motif as well as the results of the intravenous pathogenicity index (IVPI). The immune pressure from vaccinations most likely has played a significant role in the positive selection of antigenic drift mutants within the Mexican H5N2 AIVs. Most of the identified substitutions in these viruses are located on the critical antigenic residues of the HA protein and as a result, might have contributed to vaccine failures. This study highlights and stresses the need for vaccine updates while emphasizing the importance of continued molecular monitoring of the HA protein for its antigenic changes compared to the vaccines used.
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Affiliation(s)
- Wanhong Xu
- National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada;
| | - Roberto Navarro-López
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Mario Solis-Hernandez
- United States-Mexico Commission for the Prevention of Foot-and-Mouth Disease and Other Exotic Diseases of Animals, Mexico City 64590, Mexico; (M.S.-H.); (F.L.-F.)
| | - Francisco Liljehult-Fuentes
- United States-Mexico Commission for the Prevention of Foot-and-Mouth Disease and Other Exotic Diseases of Animals, Mexico City 64590, Mexico; (M.S.-H.); (F.L.-F.)
| | - Miguel Molina-Montiel
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - María Lagunas-Ayala
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Marisol Rocha-Martinez
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Eduardo Ferrara-Tijera
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Juan Pérez de la Rosa
- Animal Health General Directorate, Animal and Plant Health, Food Inspection and Food Safety National Services (SENASICA), Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), Mexico City 06470, Mexico; (R.N.-L.); (M.M.-M.); (M.L.-A.); (M.R.-M.); (E.F.-T.); (J.P.d.l.R.)
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada;
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2S2, Canada
- Correspondence: ; Tel.: +1-204-789-7062
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20
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Functionalized graphene oxide based nanocarrier for enhanced cytotoxicity of Juniperus squamata root essential oil against breast cancer cells. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103370] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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21
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Annotating Spike Protein Polymorphic Amino Acids of Variants of SARS-CoV-2, Including Omicron. Biochem Res Int 2022; 2022:2164749. [PMID: 35450296 PMCID: PMC9017565 DOI: 10.1155/2022/2164749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/24/2022] [Indexed: 11/18/2022] Open
Abstract
The prolonged global spread and community transmission of severe acute respiratory syndrome virus 2 (SARS-CoV-2) has led to the emergence of variants and brought questions regarding disease severity and vaccine effectiveness. We conducted simple bioinformatics on the spike gene of a representative of each variant. The data show that a number of polymorphic amino acids are located mostly on the amino-terminal side of the S1/S2 cleavage site. The Omicron variant diverges from the others, with the highest number of amino acid substitutions, including the receptor-binding site (RBS), epitopes, S1/S2 cleavage site, fusion peptide, and heptad repeat 1. The current sharp global increase in the frequency of the Omicron genome constitutes evidence of its high community transmissibility. In conclusion, the proposed guideline could give an immediate insight of the probable biological nature of any variant of SARS-Cov-2. As the Omicron diverged the farthest from the original pandemic strain, Wuhan-Hu-1, we expect different epidemiological and clinical patterns of Omicron cases. On vaccine efficacy, slight changes in some epitopes while others are conserved should not lead to a significant reduction in the effectiveness of an approved vaccine.
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22
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Novel Low Pathogenic Avian Influenza H6N1 in Backyard Chicken in Easter Island (Rapa Nui), Chilean Polynesia. Viruses 2022; 14:v14040718. [PMID: 35458448 PMCID: PMC9031230 DOI: 10.3390/v14040718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 01/08/2023] Open
Abstract
Little is known about the prevalence of avian influenza viruses (AIV) in wildlife and domestic animals in Polynesia. Here, we present the results of active AIV surveillance performed during two sampling seasons in 2019 on Easter Island (Rapa Nui). Tracheal and cloacal swabs as well as sera samples were obtained from domestic backyard poultry, while fresh faeces were collected from wild birds. In addition to detecting antibodies against AIV in 46% of the domestic chickens in backyard production systems tested, we isolated a novel low pathogenic H6N1 virus from a chicken. Phylogenetic analysis of all genetic segments revealed that the virus was closely related to AIV’s circulating in South America. Our analysis showed different geographical origins of the genetic segments, with the PA, HA, NA, NP, and MP gene segments coming from central Chile and the PB2, PB1, and NS being closely related to viruses isolated in Argentina. While the route of introduction can only be speculated, our analysis shows the persistence and independent evolution of this strain in the island since its putative introduction between 2015 and 2016. The results of this research are the first evidence of AIV circulation in domestic birds on a Polynesian island and increase our understanding of AIV ecology in region, warranting further surveillance on Rapa Nui and beyond.
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Muhammad YA. Reconciling differences pertaining to the origin of SARS-CoV-2. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2022; 46:28. [PMID: 35153468 PMCID: PMC8824583 DOI: 10.1186/s42269-022-00712-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND At the time of this writing, SARS-CoV-2 has reportedly claimed the lives of millions of people worldwide. However, there is still disagreement concerning the origin of SARS-CoV-2, its true nature, and the extent of its pathogenicity. Thus, the purpose of this manuscript is to highlight and critically analyze these differences so that research efforts can be geared toward addressing these concerns. MAIN BODY For this purpose, the author studied the perspectives of both conventional and non-conventional scientists, physicians, and researchers in an attempt to understand the points of contention and the reasons for the vast gulf in perspective. CONCLUSION After reviewing the varying but divergent perspective pertaining to the origin of SARS-CoV-2 and the premises used to justify them, it has become clear that if the scientific community is to put a halt to the spread of misinformation pertaining to the origin of SARS-CoV-2 and COVID-19, the predominant scientific community (particularly the microbiologist/immunologist) must carry out the requisite scientific procedures and encourage governmental/academic transparency.
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Affiliation(s)
- Yasin Ali Muhammad
- Department of Biological Sciences, Winston-Salem State University, Winston-Salem, NC USA
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24
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Abstract
The field of molecular epidemiology responded to the SARS-CoV-2 pandemic with an unrivaled amount of whole viral genome sequencing. By the time this sentence is published we will have well surpassed 1.5 million whole genomes, more than 4 times the number of all microbial whole genomes deposited in GenBank and 35 times the total number of viral genomes. This extraordinary dataset that accrued in near real time has also given us an opportunity to chart the global and local evolution of a virus as it moves through the world population. The data itself presents challenges that have never been dealt with in molecular epidemiology, and tracking a virus that is changing so rapidly means that we are often running to catch up. Here we review what is known about the evolution of the virus, and the critical impact that whole genomes have had on our ability to trace back and track forward the spread of lineages of SARS-CoV-2. We then review what whole genomes have told us about basic biological properties of the virus such as transmissibility, virulence, and immune escape with a special emphasis on pediatric disease. We couch this discussion within the framework of systematic biology and phylogenetics, disciplines that have proven their worth again and again for identifying and deciphering the spread of epidemics, though they were largely developed in areas far removed from infectious disease and medicine.
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Affiliation(s)
- Ahmed M Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Paul J Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
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Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Viruses 2021; 13:v13122511. [PMID: 34960779 PMCID: PMC8705554 DOI: 10.3390/v13122511] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
Genotype screening was implemented in Italy and showed a significant prevalence of new SARS-CoV-2 mutants carrying Q675H mutation, near the furin cleavage site of spike protein. Currently, this mutation, which is expressed on different SARS-CoV-2 lineages circulating worldwide, has not been thoughtfully investigated. Therefore, we performed phylogenetic and biocomputational analysis to better understand SARS-CoV-2 Q675H mutants’ evolutionary relationships with other circulating lineages and Q675H function in its molecular context. Our studies reveal that Q675H spike mutation is the result of parallel evolution because it arose independently in separate evolutionary clades. In silico data show that the Q675H mutation gives rise to a hydrogen-bonds network in the spike polar region. This results in an optimized directionality of arginine residues involved in interaction of spike with the furin binding pocket, thus improving proteolytic exposure of the viral protein. Furin was predicted to have a greater affinity for Q675H than Q675 substrate conformations. As a consequence, Q675H mutation could confer a fitness advantage to SARS-CoV-2 by promoting a more efficient viral entry. Interestingly, here we have shown that Q675H spike mutation is documented in all the VOCs. This finding highlights that VOCs are still evolving to enhance viral fitness and to adapt to the human host. At the same time, it may suggest Q675H spike mutation involvement in SARS-CoV-2 evolution.
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Delgadillo-Gutiérrez K, Castelán-Vega JA, Jiménez-Alberto A, Fernández-Lizárraga MDC, Aparicio-Ozores G, Monterrubio-López GP, Ribas-Aparicio RM. Characterization and use in neutralization assays of avian influenza codon-optimized H5 and H7 retroviral pseudotypes. J Virol Methods 2021; 300:114391. [PMID: 34890710 DOI: 10.1016/j.jviromet.2021.114391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/12/2021] [Accepted: 11/27/2021] [Indexed: 10/19/2022]
Abstract
Influenza is a relevant problem for public and animal health, with a significant economic impact. In recent years, outbreaks of avian influenza virus have resulted in devastating losses in the poultry industry worldwide, and although its transmission to humans is very rare, there is always a potential risk for an even more severe outbreak. Currently, vaccination is considered the most effective tool for the control and prevention of influenza infections in both humans and animals. The maintenance of animal welfare and the successful implementation of animal health programs depend on the timely administration of vaccines, which must comply with quality specifications indicated by health authorities; for example, the capability to ensure a minimum antibody titer. The production of viral antigens used in these tests can pose a biosafety risk, and some viral strains can be difficult to grow. Therefore, new biotechnological alternatives are required to overcome these disadvantages. In this study, we produced pseudotypes carrying H5 and H7 hemagglutinins from lowly and highly pathogenic avian influenza viruses. These pseudotypes were used in neutralization assays to detect neutralizing antibodies in avian sera, which were confirmed positive by inhibition of the hemagglutination test. Our results showed that the pseudotype neutralization assay is a viable alternative for the detection of neutralizing antibodies, by demonstrating subtype specificity and requiring reduced biosafety requirements. Therefore, it represents a versatile platform that can facilitate technology transfer protocols between laboratories, and an immediate application in serological tools for quality control of veterinary vaccines against avian influenza.
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Affiliation(s)
- Karen Delgadillo-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Juan Arturo Castelán-Vega
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Alicia Jiménez-Alberto
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | | | - Gerardo Aparicio-Ozores
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Gloria Paulina Monterrubio-López
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City, Mexico.
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Kida Y, Okuya K, Saito T, Yamagishi J, Ohnuma A, Hattori T, Miyamoto H, Manzoor R, Yoshida R, Nao N, Kajihara M, Watanabe T, Takada A. Structural Requirements in the Hemagglutinin Cleavage Site-Coding RNA Region for the Generation of Highly Pathogenic Avian Influenza Virus. Pathogens 2021; 10:1597. [PMID: 34959552 PMCID: PMC8707032 DOI: 10.3390/pathogens10121597] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) with H5 and H7 hemagglutinin (HA) subtypes are derived from their low pathogenic counterparts following the acquisition of multiple basic amino acids in their HA cleavage site. It has been suggested that consecutive adenine residues and a stem-loop structure in the viral RNA region that encodes the cleavage site are essential for the acquisition of the polybasic cleavage site. By using a reporter assay to detect non-templated nucleotide insertions, we found that insertions more frequently occurred in the RNA region (29 nucleotide-length) encoding the cleavage site of an H5 HA gene that was predicted to have a stem-loop structure containing consecutive adenines than in a mutated corresponding RNA region that had a disrupted loop structure with fewer adenines. In virus particles generated by using reverse genetics, nucleotide insertions that created additional codons for basic amino acids were found in the RNA region encoding the cleavage site of an H5 HA gene but not in the mutated RNA region. We confirmed the presence of virus clones with the ability to replicate without trypsin in a plaque assay and to cause lethal infection in chicks. These results demonstrate that the stem-loop structure containing consecutive adenines in HA genes is a key molecular determinant for the emergence of H5 HPAIVs.
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Affiliation(s)
- Yurie Kida
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Kosuke Okuya
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Takeshi Saito
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Junya Yamagishi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
| | - Aiko Ohnuma
- Technical Office, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
| | - Takanari Hattori
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Hiroko Miyamoto
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Rashid Manzoor
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Reiko Yoshida
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
- One Health Research Center, Hokkaido University, Sapporo 060-0818, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan;
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; (Y.K.); (K.O.); (T.S.); (T.H.); (H.M.); (R.M.); (R.Y.); (M.K.)
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
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Zamperin G, Bianco A, Smith J, Bortolami A, Vervelde L, Schivo A, Fortin A, Marciano S, Panzarin V, Mazzetto E, Milani A, Berhane Y, Digard P, Bonfante F, Monne I. Heterogeneity of Early Host Response to Infection with Four Low-Pathogenic H7 Viruses with a Different Evolutionary History in the Field. Viruses 2021; 13:2323. [PMID: 34835129 PMCID: PMC8620788 DOI: 10.3390/v13112323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Once low-pathogenic avian influenza viruses (LPAIVs) of the H5 and H7 subtypes from wild birds enter into poultry species, there is the possibility of them mutating into highly pathogenic avian influenza viruses (HPAIVs), resulting in severe epizootics with up to 100% mortality. This mutation from a LPAIV to HPAIV strain is the main cause of an AIV's major economic impact on poultry production. Although AIVs are inextricably linked to their hosts in their evolutionary history, the contribution of host-related factors in the emergence of HPAI viruses has only been marginally explored so far. In this study, transcriptomic sequencing of tracheal tissue from chickens infected with four distinct LP H7 viruses, characterized by a different history of pathogenicity evolution in the field, was implemented. Despite the inoculation of a normalized infectious dose of viruses belonging to the same subtype (H7) and pathotype (LPAI), the use of animals of the same age, sex and species as well as the identification of a comparable viral load in the target samples, the analyses revealed a heterogeneity in the gene expression profile in response to infection with each of the H7 viruses administered.
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Affiliation(s)
- Gianpiero Zamperin
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Alice Bianco
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Jacqueline Smith
- Easter Bush Campus, The University of Edinburgh, Roslin EH25 9RG, UK; (J.S.); (L.V.); (P.D.)
| | - Alessio Bortolami
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Lonneke Vervelde
- Easter Bush Campus, The University of Edinburgh, Roslin EH25 9RG, UK; (J.S.); (L.V.); (P.D.)
| | - Alessia Schivo
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Andrea Fortin
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Sabrina Marciano
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Valentina Panzarin
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Eva Mazzetto
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Adelaide Milani
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, 1015 Arlington, Winnipeg, MB R3E 3M4, Canada;
| | - Paul Digard
- Easter Bush Campus, The University of Edinburgh, Roslin EH25 9RG, UK; (J.S.); (L.V.); (P.D.)
| | - Francesco Bonfante
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, 35020 Padua, Italy; (A.B.); (A.B.); (A.S.); (A.F.); (S.M.); (V.P.); (E.M.); (A.M.); (F.B.); (I.M.)
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29
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Gong Y, Qin S, Dai L, Tian Z. The glycosylation in SARS-CoV-2 and its receptor ACE2. Signal Transduct Target Ther 2021; 6:396. [PMID: 34782609 PMCID: PMC8591162 DOI: 10.1038/s41392-021-00809-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/24/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
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Affiliation(s)
- Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
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Dupré G, Hoede C, Figueroa T, Bessière P, Bertagnoli S, Ducatez M, Gaspin C, Volmer R. Phylodynamic Study of the Conserved RNA Structure Encompassing the Hemagglutinin Cleavage Site Encoding Region of H5 and H7 Low Pathogenic Avian Influenza Viruses. Virus Evol 2021; 7:veab093. [PMID: 35299790 PMCID: PMC8923263 DOI: 10.1093/ve/veab093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/07/2021] [Accepted: 10/29/2021] [Indexed: 11/14/2022] Open
Abstract
Abstract
Highly Pathogenic Avian Influenza Viruses (HPAIV) evolve from Low Pathogenic Avian Influenza Viruses (LPAIV) of the H5 and H7 subtypes. This evolution is characterized by the acquisition of a multi-basic cleavage site (MBCS) motif in the hemagglutinin (HA) that leads to an extended viral tropism and severe disease in poultry. One key unanswered question is whether the risk of transition to HPAIV is similar for all LPAIV H5 or H7 strains, or whether specific determinants in the HA sequence of some H5 or H7 LPAIV strains correlate with a higher risk of transition to HPAIV. Here we determined if specific features of the conserved RNA stem loop located at the hemagglutinin cleavage site-encoding region could be detected along the LPAIV to HPAIV evolutionary pathway. Analysis of the thermodynamic stability of the predicted RNA structures showed no specific patterns common to HA sequences leading to HPAIV and distinct from those remaining LPAIV. However, RNA structure clustering analysis revealed that most of the American lineage ancestors leading to H7 emergences via recombination shared the same vRNA structure topology at the HA1/HA2 boundary region. Our study thus identified predicted secondary RNA structures present in the HA of H7 viruses, which could promote genetic recombination and acquisition of a MBCS.
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Affiliation(s)
- Gabriel Dupré
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Claire Hoede
- INRAE, UR875 Mathématiques et Informatique Appliquées Toulouse, Plateforme GenoToul BioInfo, F-31326 Castanet-Tolosan, France
| | - Thomas Figueroa
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Pierre Bessière
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Stéphane Bertagnoli
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Mariette Ducatez
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
| | - Christine Gaspin
- INRAE, UR875 Mathématiques et Informatique Appliquées Toulouse, Plateforme GenoToul BioInfo, F-31326 Castanet-Tolosan, France
| | - Romain Volmer
- Ecole nationale vétérinaire de Toulouse, Université de Toulouse, ENVT, INRAE, IHAP, UMR 1225, Toulouse, France
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Sarker MT, Hasan AQF, Rafi MO, Hossain MJ, El-Mageed HRA, Elsapagh RM, Capasso R, Emran TB. A Comprehensive Overview of the Newly Emerged COVID-19 Pandemic: Features, Origin, Genomics, Epidemiology, Treatment, and Prevention. BIOLOGICS 2021; 1:357-383. [DOI: 10.3390/biologics1030021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The coronavirus disease 2019 (COVID-19), a life-threatening pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has resulted in massive destruction and is still continuously adding to its death toll. The advent of this global outbreak has not yet been confirmed; however, investigation for suitable prophylaxis against this lethal virus is being carried out by experts all around the globe. The SARS-CoV-2 belongs to the Coronaviridae superfamily, like the other previously occurring human coronavirus variants. To better understand a new virus variant, such as the SARS-CoV-2 delta variant, it is vital to investigate previous virus strains, including their genomic composition and functionality. Our study aimed at addressing the basic overview of the virus’ profile that may provide the scientific community with evidence-based insights into COVID-19. Therefore, this study accomplished a comprehensive literature review that includes the virus’ origin, classification, structure, life cycle, genome, mutation, epidemiology, and subsequent essential factors associated with host–virus interaction. Moreover, we summarized the considerable diagnostic measures, treatment options, including multiple therapeutic approaches, and prevention, as well as future directions that may reduce the impact and misery caused by this devastating pandemic. The observations and data provided here have been screened and accumulated through extensive literature study, hence this study will help the scientific community properly understand this new virus and provide further leads for therapeutic interventions.
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32
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In silico study of some selective phytochemicals against a hypothetical SARS-CoV-2 spike RBD using molecular docking tools. Comput Biol Med 2021. [DOI: 10.1016/j.compbiomed.2021.104818
expr 849028860 + 881472580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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Sharma HN, Latimore COD, Matthews QL. Biology and Pathogenesis of SARS-CoV-2: Understandings for Therapeutic Developments against COVID-19. Pathogens 2021; 10:1218. [PMID: 34578250 PMCID: PMC8470303 DOI: 10.3390/pathogens10091218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 01/18/2023] Open
Abstract
Coronaviruses are positive sense, single-stranded, enveloped, and non-segmented RNA viruses that belong to the Coronaviridae family within the order Nidovirales and suborder Coronavirinae. Two Alphacoronavirus strains: HCoV-229E and HCoV-NL63 and five Betacoronaviruses: HCoV-HKU1, HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2 have so far been recognized as Human Coronaviruses (HCoVs). Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 is currently the greatest concern for humanity. Despite the overflow of research on SARS-CoV-2 and other HCoVs published every week, existing knowledge in this area is insufficient for the complete understanding of the viruses and the diseases caused by them. This review is based on the analysis of 210 published works, and it attempts to cover the basic biology of coronaviruses, including the genetic characteristics, life cycle, and host-pathogen interaction, pathogenesis, the antiviral drugs, and vaccines against HCoVs, especially focusing on SARS-CoV-2. Furthermore, we will briefly discuss the potential link between extracellular vesicles (EVs) and SARS-CoV-2/COVID-19 pathophysiology.
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Affiliation(s)
- Homa Nath Sharma
- Microbiology Program, Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA;
| | | | - Qiana L. Matthews
- Microbiology Program, Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA;
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA;
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34
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Song W, Huang X, Guan W, Chen P, Wang P, Zheng M, Li Z, Wang Y, Yang Z, Chen H, Wang X. Multiple basic amino acids in the cleavage site of H7N9 hemagglutinin contribute to high virulence in mice. J Thorac Dis 2021; 13:4650-4660. [PMID: 34527306 PMCID: PMC8411188 DOI: 10.21037/jtd-21-226] [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: 02/04/2021] [Accepted: 06/18/2021] [Indexed: 11/25/2022]
Abstract
Background Avian influenza A (H7N9) virus has caused more than 1,500 cases of human infection since its emergence in early 2013. Displaying little or no pathogenicity in poultry, but a 40% case-fatality rate in humans, five waves of H7N9 human infections occurred in China during 2013–2017, caused solely by a low pathogenicity strain. However, avian isolates possessing a polybasic connecting peptide in the hemagglutinin (HA) protein were detected in mid-2016, indicating that a highly pathogenic virus had emerged and was co-circulating with the low pathogenicity strains. Methods Here we characterize the pathogenicity of a newly emerged human H7N9 variant with a PEVPKRKRTAR/GLF insertion motif at the cleavage site of the HA protein in vitro and in vivo. Results This variant replicates in MDCK cells independently of TPCK-trypsin, which is indicative of high pathogenicity in chickens. The 50% mouse lethal dose (MLD50) of this novel isolate was less than 10 plaque forming units (PFU), compared with 3.16×104 for an identical virus lacking the polybasic insertion, indicating a high virulence phenotype. Conclusions Our results demonstrate that the multiple basic amino acid insertion in the HA protein of the H7N9 variant confers high virulence in mammals, highlighting a potential risk to humans. Continuous viral surveillance is therefore necessary in the China region to improve pandemic preparedness.
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Affiliation(s)
- Wenjun Song
- State Key Laboratory of Respiratory Disease, Institute of Integration of Traditional and Western Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, and the Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaofeng Huang
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, and the Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China
| | - Wenda Guan
- State Key Laboratory of Respiratory Disease, Institute of Integration of Traditional and Western Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Pin Chen
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, and the Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China
| | - Pui Wang
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, and the Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China
| | - Min Zheng
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, and the Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China
| | - Zhengtu Li
- State Key Laboratory of Respiratory Disease, Institute of Integration of Traditional and Western Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yutao Wang
- State Key Laboratory of Respiratory Disease, Institute of Integration of Traditional and Western Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, Institute of Integration of Traditional and Western Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Honglin Chen
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, and the Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China
| | - Xinhua Wang
- State Key Laboratory of Respiratory Disease, Institute of Integration of Traditional and Western Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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35
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Nag A, Paul S, Banerjee R, Kundu R. In silico study of some selective phytochemicals against a hypothetical SARS-CoV-2 spike RBD using molecular docking tools. Comput Biol Med 2021; 137:104818. [PMID: 34481181 PMCID: PMC8401086 DOI: 10.1016/j.compbiomed.2021.104818] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 02/07/2023]
Abstract
Background This world is currently witnessing a pandemic outbreak of ‘COVID-19′ caused by a positive-strand RNA virus ‘SARS-CoV-2’. Millions have succumbed globally to the disease, and the numbers are increasing day by day. The viral genome enters into the human host through interaction between the spike protein (S) and host angiotensin-converting enzyme-2 (ACE2) proteins. S is the common target for most recently rolled-out vaccines across regions. A recent surge in single/multiple mutations in S region is of great concern as it may escape vaccine induced immunity. So far, the treatment regime with repurposed drugs has not been too successful. Hypothesis Natural compounds are capable of targeting mutated spike protein by binding to its active site and destabilizing the spike-host ACE2 interaction. Materials and methods A hypothetical mutated spike protein was constructed by incorporating twelve different mutations from twelve geographical locations simultaneously into the receptor-binding domain (RBD) and docked with ACE2 and seven phytochemicals namely allicin, capsaicin, cinnamaldehyde, curcumin, gingerol, piperine and zingeberene. Molecular Dynamic (MD) simulation and Principal Component Analysis (PCA) were finally used for validation of the docking results. Result The docking results showed that curcumin and piperine were most potent to bind ACE2, mutated spike, and mutated spike-ACE2 complex, thereby restricting viral entry. ADME analysis also proved their drug candidature. The docking complexes were found to be stable by MD simulation. Conclusion This result provides a significant insight about the phytochemicals' role, namely curcumin and piperine, as the potential therapeutic entities against mutated spike protein of SARS-CoV-2.
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Affiliation(s)
- Anish Nag
- Department of Life Sciences, CHRIST (Deemed to Be University), Bangalore 560029, India
| | - Subhabrata Paul
- School of Biotechnology, Presidency University, Canal Bank Rd, DG Block, Action Area 1D, New Town, West Bengal 700156, India
| | - Ritesh Banerjee
- School of Biological and Environmental Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Rita Kundu
- Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, India.
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36
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Briand FX, Niqueux E, Schmitz A, Martenot C, Cherbonnel M, Massin P, Kerbrat F, Chatel M, Guillemoto C, Guillou-Cloarec C, Ogor K, Le Prioux A, Allée C, Beven V, Hirchaud E, Blanchard Y, Scoizec A, Le Bouquin S, Eterradossi N, Grasland B. Highly Pathogenic Avian Influenza A(H5N8) Virus Spread by Short- and Long-Range Transmission, France, 2016-17. Emerg Infect Dis 2021; 27:508-516. [PMID: 33496244 PMCID: PMC7853534 DOI: 10.3201/eid2702.202920] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We detected 3 genotypes of highly pathogenic avian influenza A(H5N8) virus in France during winter 2016–17. Genotype A viruses caused dramatic economic losses in the domestic duck farm industry in southwestern France. Our phylogenetic analysis suggests that genotype A viruses formed 5 distinct geographic clusters in southwestern France. In some clusters, local secondary transmission might have been started by a single introduction. The intensity of the viral spread seems to correspond to the density of duck holdings in each production area. To avoid the introduction of disease into an unaffected area, it is crucial that authorities limit the movements of potentially infected birds.
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Chiara M, Horner DS, Gissi C, Pesole G. Comparative Genomics Reveals Early Emergence and Biased Spatiotemporal Distribution of SARS-CoV-2. Mol Biol Evol 2021; 38:2547-2565. [PMID: 33605421 PMCID: PMC7928790 DOI: 10.1093/molbev/msab049] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Effective systems for the analysis of molecular data are fundamental for monitoring the spread of infectious diseases and studying pathogen evolution. The rapid identification of emerging viral strains, and/or genetic variants potentially associated with novel phenotypic features is one of the most important objectives of genomic surveillance of human pathogens and represents one of the first lines of defense for the control of their spread. During the COVID 19 pandemic, several taxonomic frameworks have been proposed for the classification of SARS-Cov-2 isolates. These systems, which are typically based on phylogenetic approaches, represent essential tools for epidemiological studies as well as contributing to the study of the origin of the outbreak. Here, we propose an alternative, reproducible, and transparent phenetic method to study changes in SARS-CoV-2 genomic diversity over time. We suggest that our approach can complement other systems and facilitate the identification of biologically relevant variants in the viral genome. To demonstrate the validity of our approach, we present comparative genomic analyses of more than 175,000 genomes. Our method delineates 22 distinct SARS-CoV-2 haplogroups, which, based on the distribution of high-frequency genetic variants, fall into four major macrohaplogroups. We highlight biased spatiotemporal distributions of SARS-CoV-2 genetic profiles and show that seven of the 22 haplogroups (and of all of the four haplogroup clusters) showed a broad geographic distribution within China by the time the outbreak was widely recognized—suggesting early emergence and widespread cryptic circulation of the virus well before its isolation in January 2020. General patterns of genomic variability are remarkably similar within all major SARS-CoV-2 haplogroups, with UTRs consistently exhibiting the greatest variability, with s2m, a conserved secondary structure element of unknown function in the 3′-UTR of the viral genome showing evidence of a functional shift. Although several polymorphic sites that are specific to one or more haplogroups were predicted to be under positive or negative selection, overall our analyses suggest that the emergence of novel types is unlikely to be driven by convergent evolution and independent fixation of advantageous substitutions, or by selection of recombined strains. In the absence of extensive clinical metadata for most available genome sequences, and in the context of extensive geographic and temporal biases in the sampling, many questions regarding the evolution and clinical characteristics of SARS-CoV-2 isolates remain open. However, our data indicate that the approach outlined here can be usefully employed in the identification of candidate SARS-CoV-2 genetic variants of clinical and epidemiological importance.
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Affiliation(s)
- Matteo Chiara
- Department of Biosciences, University of Milan, Milan, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - David S Horner
- Department of Biosciences, University of Milan, Milan, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Carmela Gissi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari A. Moro, Bari,Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari A. Moro, Bari,Italy
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38
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Millet JK, Jaimes JA, Whittaker GR. Molecular diversity of coronavirus host cell entry receptors. FEMS Microbiol Rev 2021; 45:fuaa057. [PMID: 33118022 PMCID: PMC7665467 DOI: 10.1093/femsre/fuaa057] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/24/2020] [Indexed: 12/11/2022] Open
Abstract
Coronaviruses are a group of viruses causing disease in a wide range of animals, and humans. Since 2002, the successive emergence of bat-borne severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), swine acute diarrhea syndrome coronavirus (SADS-CoV) and SARS-CoV-2 has reinforced efforts in uncovering the molecular and evolutionary mechanisms governing coronavirus cell tropism and interspecies transmission. Decades of studies have led to the discovery of a broad set of carbohydrate and protein receptors for many animal and human coronaviruses. As the main determinant of coronavirus entry, the spike protein binds to these receptors and mediates membrane fusion. Prone to mutations and recombination, spike evolution has been studied extensively. The interactions between spike proteins and their receptors are often complex and despite many advances in the field, there remains many unresolved questions concerning coronavirus tropism modification and cross-species transmission, potentially leading to delays in outbreak responses. The emergence of SARS-CoV-2 underscores the need to address these outstanding issues in order to better anticipate new outbreaks. In this review, we discuss the latest advances in the field of coronavirus receptors emphasizing on the molecular and evolutionary processes that underlie coronavirus receptor usage and host range expansion.
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Affiliation(s)
- Jean K Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, 78352 Jouy-en-Josas, France
| | - Javier A Jaimes
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
- Master of Public Health Program, Cornell University, Ithaca, NY 14853, USA
- Cornell Feline Health Center, Ithaca, NY 14853, USA
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39
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Malik YS, Ansari MI, Kattoor JJ, Kaushik R, Sircar S, Subbaiyan A, Tiwari R, Dhama K, Ghosh S, Tomar S, Zhang KYJ. Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. Brief Bioinform 2021; 22:1006-1022. [PMID: 33377145 PMCID: PMC7953982 DOI: 10.1093/bib/bbaa383] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Interaction of SARS-CoV-2 spike glycoprotein with the ACE2 cell receptor is very crucial for virus attachment to human cells. Selected mutations in SARS-CoV-2 S-protein are reported to strengthen its binding affinity to mammalian ACE2. The N501T mutation in SARS-CoV-2-CTD furnishes better support to hotspot 353 in comparison with SARS-CoV and shows higher affinity for receptor binding. Recombination analysis exhibited higher recombination events in SARS-CoV-2 strains, irrespective of their geographical origin or hosts. Investigation further supports a common origin among SARS-CoV-2 and its predecessors, SARS-CoV and bat-SARS-like-CoV. The recombination events suggest a constant exchange of genetic material among the co-infecting viruses in possible reservoirs and human hosts before SARS-CoV-2 emerged. Furthermore, a comprehensive analysis of codon usage bias (CUB) in SARS-CoV-2 revealed significant CUB among the S-genes of different beta-coronaviruses governed majorly by natural selection and mutation pressure. Various indices of codon usage of S-genes helped in quantifying its adaptability in other animal hosts. These findings might help in identifying potential experimental animal models for investigating pathogenicity for drugs and vaccine development experiments.
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Affiliation(s)
| | | | | | - Rahul Kaushik
- Laboratory for Structural Bioinformatics, RIKEN Center for Biosystems Dynamics Research, Japan
| | | | | | - Ruchi Tiwari
- Department of Vet erinary Microbiology, DUVASU, Mathura, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Souvik Ghosh
- Health Center for Zoonoses and Tropical Veterinary Medicine, Basseterre, St. Kitts, West Indies
| | | | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Japan
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40
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Dey D, Dey N, Ghosh S, Chandrasekaran N, Mukherjee A, Thomas J. Potential combination therapy using twenty phytochemicals from twenty plants to prevent SARS- CoV-2 infection: An in silico Approach. Virusdisease 2021; 32:108-116. [PMID: 33842675 PMCID: PMC8021291 DOI: 10.1007/s13337-021-00658-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
Covid 19 caused by novel strain SARS- CoV-2 has become a pandemic due to its contagious nature of infection. It enters by binding with ACE2 receptor present on the outer surface of a cell by cleaving S1/S2 with proteolytic protein Furin. Further viral replication or transcription then takes place with the help of main protease 3CLpro and polymerase RdRp. This in silco study was carried out to block ACE2, Furin, 3CLpro and RdRP with various phytochemicals to prevent SARS- CoV-2 entry and replication or transcription. Twenty different phytochemicals were screened to understand the drug-likeliness obeying Lipinski’s rule 5 and further, molecular docking was performed using these phytochemicals to block their respective target proteins. All the phytochemicals follow Lipinski’s rule of five and molecular docking result shows best binding affinity of Podofilox − 7.54 kcal/mol with ACE2, Psoralidin − 8.04 kcal/mol with Furin, Ursolic acid − 8.88 kcal/mol with 3CLpro and Epiafzelechin − 8.26 kcal/mol with RdRp. Thus, blocking two human receptors ACE2 and Furin with Podofilox and Psoralidin respectively may prevent the viral entry into the cells. Also blocking viral proteins 3CLpro and RdRp with Ursolic acid and Epiafzelechin may prevent viral replication or transcription. Using this combination therapy of blocking the receptors responsible for viral entry and viral proteins responsible for replication or transcription may prevent SARS- CoV-2 infection.
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Affiliation(s)
- Dipjyoti Dey
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | - Nirban Dey
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | - Shalini Ghosh
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | | | - Amitava Mukherjee
- Centre for Nanobiotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | - John Thomas
- Centre for Nanobiotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu India
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41
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High B, Hixon AM, Tyler KL, Piquet AL, Pelak VS. Neurology and the COVID-19 Pandemic: Gathering Data for an Informed Response. Neurol Clin Pract 2021; 11:e48-e63. [PMID: 33842072 PMCID: PMC8032425 DOI: 10.1212/cpj.0000000000000908] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/18/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW The current coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the greatest medical crises faced by our current generation of health care providers. Although much remains to be learned about the pathophysiology of SARS-CoV-2, there is both historical precedent from other coronaviruses and a growing number of case reports and series that point to neurologic consequences of COVID-19. RECENT FINDINGS Olfactory/taste disturbances and increased risk of strokes and encephalopathies have emerged as potential consequences of COVID-19 infection. Evidence regarding whether these sequelae result indirectly from systemic infection or directly from neuroinvasion by SARS-CoV-2 is emerging. SUMMARY This review summarizes the current understanding of SARS-CoV-2 placed in context with our knowledge of other human coronaviruses. Evidence and data regarding neurologic sequelae of COVID-19 and the neuroinvasive potential of human coronaviruses are provided along with a summary of patient registries of interest to the Neurology community.
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Affiliation(s)
- Brigit High
- Medical Scientist Training Program (BH, AMH), Rocky Mountain Taste and Smell Center (BH), Department of Neurology (KLT, ALP, VSP), and Department of Ophthalmology (VSP), University of Colorado School of Medicine, Aurora
| | - Alison M Hixon
- Medical Scientist Training Program (BH, AMH), Rocky Mountain Taste and Smell Center (BH), Department of Neurology (KLT, ALP, VSP), and Department of Ophthalmology (VSP), University of Colorado School of Medicine, Aurora
| | - Kenneth L Tyler
- Medical Scientist Training Program (BH, AMH), Rocky Mountain Taste and Smell Center (BH), Department of Neurology (KLT, ALP, VSP), and Department of Ophthalmology (VSP), University of Colorado School of Medicine, Aurora
| | - Amanda L Piquet
- Medical Scientist Training Program (BH, AMH), Rocky Mountain Taste and Smell Center (BH), Department of Neurology (KLT, ALP, VSP), and Department of Ophthalmology (VSP), University of Colorado School of Medicine, Aurora
| | - Victoria S Pelak
- Medical Scientist Training Program (BH, AMH), Rocky Mountain Taste and Smell Center (BH), Department of Neurology (KLT, ALP, VSP), and Department of Ophthalmology (VSP), University of Colorado School of Medicine, Aurora
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42
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Peacock TP, Penrice-Randal R, Hiscox JA, Barclay WS. SARS-CoV-2 one year on: evidence for ongoing viral adaptation. J Gen Virol 2021; 102:001584. [PMID: 33855951 PMCID: PMC8290271 DOI: 10.1099/jgv.0.001584] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/16/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is thought to have originated in the human population from a zoonotic spillover event. Infection in humans results in a variety of outcomes ranging from asymptomatic cases to the disease COVID-19, which can have significant morbidity and mortality, with over two million confirmed deaths worldwide as of January 2021. Over a year into the pandemic, sequencing analysis has shown that variants of SARS-CoV-2 are being selected as the virus continues to circulate widely within the human population. The predominant drivers of genetic variation within SARS-CoV-2 are single nucleotide polymorphisms (SNPs) caused by polymerase error, potential host factor driven RNA modification, and insertion/deletions (indels) resulting from the discontinuous nature of viral RNA synthesis. While many mutations represent neutral 'genetic drift' or have quickly died out, a subset may be affecting viral traits such as transmissibility, pathogenicity, host range, and antigenicity of the virus. In this review, we summarise the current extent of genetic change in SARS-CoV-2, particularly recently emerging variants of concern, and consider the phenotypic consequences of this viral evolution that may impact the future trajectory of the pandemic.
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Affiliation(s)
- Thomas P. Peacock
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
| | | | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wendy S. Barclay
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
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43
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Saeed NM, Rashid PMA, Dyary HO. Genetic characterization of highly pathogenic avian influenza A (H5N8) virus isolated from domestic geese in Iraq, 2018. BMC Vet Res 2021; 17:124. [PMID: 33740981 PMCID: PMC7980536 DOI: 10.1186/s12917-021-02831-y] [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: 02/28/2021] [Accepted: 03/10/2021] [Indexed: 12/25/2022] Open
Abstract
Background Influenza viruses are a continuous threat to avian and mammalian species, causing epidemics and pandemics. After the circulation of H5N1 in 2006, 2015, and 2016 in Iraq, an H5N8 influenza virus emerged in domestic geese in Sulaymaniyah Province, Iraq. This study analyzed the genetic characteristics of the Iraqi H5N8 viruses. Results An HPAI virus subtype H5N8 was identified from domestic backyard geese in the Kurdistan Region, north Iraq. Phylogenic analyses of the hemagglutinin (HA) and neuraminidase (NA) genes indicated that Iraq H5N8 viruses belonged to clade 2.3.4.4 group B and clustered with isolates from Iran, Israel, and Belgium. Genetic analysis of the HA gene indicated molecular markers for avian-type receptors. Characterization of the NA gene showed that the virus had sensitive molecular markers for antiviral drugs. Conclusions This is the first study ever on H5N8 in Iraq, and it is crucial to understand the epidemiology of the viruses in Iraq and the Middle East. The results suggest a possible role of migratory birds in the introduction of HPAI subtype H5N8 into Iraq.
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Affiliation(s)
- Nahla Muhammad Saeed
- College of Veterinary Medicine, University of Sulaimani, Sulaymaniyah, Kurdistan Region, Iraq
| | - Peshnyar Muhammad Atta Rashid
- Molecular Diagnostic Laboratory, Directorate of Veterinary Services, Sulaymaniyah, Kurdistan Region, Iraq.,Kurdistan Institution for Strategic Studies and Scientific Research, Sulaymaniyah, Kurdistan Region, Iraq
| | - Hiewa Othman Dyary
- College of Veterinary Medicine, University of Sulaimani, Sulaymaniyah, Kurdistan Region, Iraq.
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Cueno ME, Ueno M, Iguchi R, Harada T, Miki Y, Yasumaru K, Kiso N, Wada K, Baba K, Imai K. Insights on the Structural Variations of the Furin-Like Cleavage Site Found Among the December 2019-July 2020 SARS-CoV-2 Spike Glycoprotein: A Computational Study Linking Viral Evolution and Infection. Front Med (Lausanne) 2021; 8:613412. [PMID: 33777970 PMCID: PMC7987684 DOI: 10.3389/fmed.2021.613412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
The SARS-CoV-2 (SARS2) is the cause of the coronavirus disease 2019 (COVID-19) pandemic. One unique structural feature of the SARS2 spike protein is the presence of a furin-like cleavage site (FLC) which is associated with both viral pathogenesis and host tropism. Specifically, SARS2 spike protein binds to the host ACE-2 receptor which in-turn is cleaved by furin proteases at the FLC site, suggesting that SARS2 FLC structural variations may have an impact on viral infectivity. However, this has not yet been fully elucidated. This study designed and analyzed a COVID-19 genomic epidemiology network for December 2019 to July 2020, and subsequently generated and analyzed representative SARS2 spike protein models from significant node clusters within the network. To distinguish possible structural variations, a model quality assessment was performed before further protein model analyses and superimposition of the protein models, particularly in both the receptor-binding domain (RBD) and FLC. Mutant spike models were generated with the unique 681PRRA684 amino acid sequence found within the deleted FLC. We found 9 SARS2 FLC structural patterns that could potentially correspond to nine node clusters encompassing various countries found within the COVID-19 genomic epidemiology network. Similarly, we associated this with the rapid evolution of the SARS2 genome. Furthermore, we observed that either in the presence or absence of the unique 681PRRA684 amino acid sequence no structural changes occurred within the SARS2 RBD, which we believe would mean that the SARS2 FLC has no structural influence on SARS2 RBD and may explain why host tropism was maintained.
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Affiliation(s)
- Marni E Cueno
- Department of Microbiology, Nihon University School of Dentistry, Tokyo, Japan.,Immersion Biology Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, Japan.,Immersion Physics Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, Japan
| | - Miu Ueno
- Immersion Physics Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, Japan
| | - Rinako Iguchi
- Immersion Physics Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, Japan
| | - Tsubasa Harada
- Immersion Physics Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, Japan
| | - Yoshifumi Miki
- Immersion Biology Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, Japan
| | - Kanae Yasumaru
- Immersion Biology Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, Japan
| | - Natsumi Kiso
- Immersion Biology Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, Japan
| | - Kanta Wada
- Immersion Biology Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, Japan
| | - Koki Baba
- Immersion Biology Class, Department of Science, Tokyo Gakugei University International Secondary School, Tokyo, Japan
| | - Kenichi Imai
- Department of Microbiology, Nihon University School of Dentistry, Tokyo, Japan
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Shahhosseini N, Wong G, Kobinger GP, Chinikar S. SARS-CoV-2 spillover transmission due to recombination event. GENE REPORTS 2021; 23:101045. [PMID: 33615041 PMCID: PMC7884226 DOI: 10.1016/j.genrep.2021.101045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/21/2021] [Accepted: 01/31/2021] [Indexed: 01/08/2023]
Abstract
In late 2019, a novel Coronavirus emerged in China. Perceiving the modulating factors of cross-species virus transmission is critical to elucidate the nature of virus emergence. Using bioinformatics tools, we analyzed the mapping of the SARS-CoV-2 genome, modeling of protein structure, and analyze the evolutionary origin of SARS-CoV-2, as well as potential recombination events. Phylogenetic tree analysis shows that SARS-CoV-2 has the closest evolutionary relationship with Bat-SL-CoV-2 (RaTG13) at the scale of the complete virus genome, and less similarity to Pangolin-CoV. However, the Receptor Binding Domain (RBD) of SARS-CoV-2 is almost identical to Pangolin-CoV at the aa level, suggesting that spillover transmission probably occurred directly from pangolins, but not bats. Further recombination analysis revealed the pathway for spillover transmission from Bat-SL-CoV-2 and Pangolin-CoV. Here, we provide evidence for recombination event between Bat-SL-CoV-2 and Pangolin-CoV that resulted in the emergence of SARS-CoV-2. Nevertheless, the role of mutations should be noted as another influencing factor in the continuing evolution and resurgence of novel SARS-CoV-2 variants.
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Affiliation(s)
- Nariman Shahhosseini
- Département de Microbiologie-Infectiologie et d'Immunologie, Université Laval, Québec City, Québec, Canada
| | - Gary Wong
- Département de Microbiologie-Infectiologie et d'Immunologie, Université Laval, Québec City, Québec, Canada.,Pasteur Institute of Shanghai, China
| | - Gary P Kobinger
- Département de Microbiologie-Infectiologie et d'Immunologie, Université Laval, Québec City, Québec, Canada.,Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Sadegh Chinikar
- Institute of Virology, University of Veterinary Medicine, Vienna, Austria.,Pasteur Institute of Tehran, Iran
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Lee DH, Criado MF, Swayne DE. Pathobiological Origins and Evolutionary History of Highly Pathogenic Avian Influenza Viruses. Cold Spring Harb Perspect Med 2021; 11:a038679. [PMID: 31964650 PMCID: PMC7849344 DOI: 10.1101/cshperspect.a038679] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
High-pathogenicity avian influenza (HPAI) viruses have arisen from low-pathogenicity avian influenza (LPAI) viruses via changes in the hemagglutinin proteolytic cleavage site, which include mutation of multiple nonbasic to basic amino acids, duplication of basic amino acids, or recombination with insertion of cellular or viral amino acids. Between 1959 and 2019, a total of 42 natural, independent H5 (n = 15) and H7 (n = 27) LPAI to HPAI virus conversion events have occurred in Europe (n = 16), North America (n = 9), Oceania (n = 7), Asia (n = 5), Africa (n = 4), and South America (n = 1). Thirty-eight of these HPAI outbreaks were limited in the number of poultry premises affected and were eradicated. However, poultry outbreaks caused by A/goose/Guangdong/1/1996 (H5Nx), Mexican H7N3, and Chinese H7N9 HPAI lineages have continued. Active surveillance and molecular detection and characterization efforts will provide the best opportunity for early detection and eradication from domestic birds.
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Affiliation(s)
- Dong-Hun Lee
- Department of Pathobiology & Veterinary Science, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Miria Ferreira Criado
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia 30605, USA
| | - David E Swayne
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia 30605, USA
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A risk marker of tribasic hemagglutinin cleavage site in influenza A (H9N2) virus. Commun Biol 2021; 4:71. [PMID: 33452423 PMCID: PMC7811019 DOI: 10.1038/s42003-020-01589-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/06/2020] [Indexed: 01/10/2023] Open
Abstract
Low pathogenic avian influenza A(H9N2) virus is endemic worldwide and continually recruit internal genes to generate human-infecting H5N1, H5N6, H7N9, and H10N8 influenza variants. Here we show that hemagglutinin cleavage sites (HACS) of H9N2 viruses tended to mutate towards hydrophilic via evolutionary transition, and the tribasic HACS were found at high prevalence in Asia and the Middle East. Our finding suggested that the tribasic H9N2 viruses increased the viral replication, stability, pathogenicity and transmission in chickens and the virulence of mice compared to the monobasic H9N2 viruses. Notably, the enlarged stem-loop structures of HACS in the RNA region were found in the increasing tribasic H9N2 viruses. The enlarged HACS RNA secondary structures of H9N2 viruses did not influence the viral replication but accelerated the frequency of nucleotide insertion in HACS. With the prevailing tendency of the tribasic H9N2 viruses, the tribasic HACS in H9N2 viruses should be paid more attention.
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Telwatte S, Kumar N, Vallejo-Gracia A, Kumar GR, Lu CM, Ott M, Wong JK, Yukl SA. Novel RT-ddPCR Assays for determining the transcriptional profile of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.12.425991. [PMID: 33469579 PMCID: PMC7814816 DOI: 10.1101/2021.01.12.425991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The exact mechanism of coronavirus replication and transcription is not fully understood; however, a hallmark of coronavirus transcription is the generation of negative-sense RNA intermediates that serve as the templates for the synthesis of positive-sense genomic RNA (gRNA) and an array of subgenomic mRNAs (sgRNAs) encompassing sequences arising from discontinuous transcription. Existing PCR-based diagnostic assays for SAR-CoV-2 are qualitative or semi-quantitative and do not provide the resolution needed to assess the complex transcription dynamics of SARS-CoV-2 over the course of infection. We developed and validated a novel panel of specially designed SARS-CoV-2 ddPCR-based assays to map the viral transcription profile. Application of these assays to clinically relevant samples will enhance our understanding of SARS-CoV-2 replication and transcription and may also inform the development of improved diagnostic tools and therapeutics.
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Affiliation(s)
- Sushama Telwatte
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Nitasha Kumar
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
| | | | - G. Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
| | - Chuanyi M. Lu
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Melanie Ott
- Department of Medicine, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
| | - Joseph K. Wong
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Steven A. Yukl
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Infectious Diseases, San Francisco VA Health Care System, San Francisco, CA, USA
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Senapati S, Banerjee P, Bhagavatula S, Kushwaha PP, Kumar S. Contributions of human ACE2 and TMPRSS2 in determining host-pathogen interaction of COVID-19. J Genet 2021; 100:12. [PMID: 33707363 PMCID: PMC7904510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/16/2020] [Accepted: 10/05/2020] [Indexed: 09/20/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is at present an emerging global public health crisis. Angiotensin converting enzyme 2 (ACE2) and trans-membrane protease serine 2 (TMPRSS2) are the two major host factors that contribute to the virulence of SARS-CoV-2 and pathogenesis of coronavirus disease-19 (COVID-19). Transmission of SARS-CoV-2 from animal to human is considered a rare event that necessarily requires strong evolutionary adaptations. Till date no other human cellular receptors are identified beside ACE2 for SARS-CoV-2 entry inside the human cell. Proteolytic cleavage of viral spike (S)-protein and ACE2 by TMPRSS2 began the entire host-pathogen interaction initiated with the physical binding of ACE2 to S-protein. SARS-CoV-2 S-protein binds to ACE2 with much higher affinity and stability than that of SARS-CoVs. Molecular interactions between ACE2-S and TMPRSS2-S are crucial and preciously mediated by specific residues. Structural stability, binding affinity and level of expression of these three interacting proteins are key susceptibility factors for COVID-19. Specific protein-protein interactions (PPI) are being identified that explains uniqueness of SARS-CoV-2 infection. Amino acid substitutions due to naturally occurring genetic polymorphisms potentially alter these PPIs and poses further clinical heterogeneity of COVID-19. Repurposing of several phytochemicals and approved drugs against ACE2, TMPRSS2 and S-protein have been proposed that could inhibit PPI between them. We have also identified some novel lead phytochemicals present in Azadirachta indica and Aloe barbadensis which could be utilized for further in vitro and in vivo anti-COVID-19 drug discovery. Uncovering details of ACE2-S and TMPRSS2-S interactions would further contribute to future research on COVID-19.
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Affiliation(s)
- Sabyasachi Senapati
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda 151 401, India.
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da Silva PG, Mesquita JR, de São José Nascimento M, Ferreira VAM. Viral, host and environmental factors that favor anthropozoonotic spillover of coronaviruses: An opinionated review, focusing on SARS-CoV, MERS-CoV and SARS-CoV-2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:141483. [PMID: 32829257 PMCID: PMC7405882 DOI: 10.1016/j.scitotenv.2020.141483] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 05/21/2023]
Abstract
Environmental factors play a key role in the zoonotic transmission of emerging pathogenic viruses as mankind is constantly disturbing wildlife's ecosystems usually by cutting down forests to build human settlements or by catching wild animals for food, which deprives the viruses of their natural hosts and gives them opportunity to infect humans. In December 2019, a new coronavirus emerged from bats and was named SARS-CoV-2 by the International Committee for Taxonomy of Viruses, and the disease it causes named COVID-19 by the World Health Organization. Disease outbreaks such as SARS in 2002-2003, MERS in 2012 and the current COVID-19 pandemic are the result of higher mutation rates of coronaviruses and their unique capacity for genetic recombination, resulting in adaptations that make them more suitable to cross the species barriers and infect other species. This ability for host switching and interspecies infection is often attributed to the great diversity of these viruses, which is a result of viral and host factors such as the low fidelity of their RNA-dependent RNA polymerase, the high frequency of their homologous RNA recombination, and the adaptation of the S protein to bind host receptors like the angiotensin converting enzyme 2 (ACE2) in the case of SARS-CoV and SARS-CoV-2, and dipeptidyl peptidase 4 (DDP4) in MERS-CoV. This review presents an overview of the zoonotic transmission of SARS, MERS and COVID-19, focusing on the viral, host and environmental factors that favor the spillover of these viruses into humans, as well as the biological and ecological factors that make bats the perfect animal reservoir of infection for these viruses.
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Affiliation(s)
| | - João Rodrigo Mesquita
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal; Epidemiology Research Unit (EPIUnit), Institute of Public Health, University of Porto, Porto, Portugal
| | - Maria de São José Nascimento
- Epidemiology Research Unit (EPIUnit), Institute of Public Health, University of Porto, Porto, Portugal; Faculty of Pharmacy, University of Porto (FFUP), Porto, Portugal
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