1
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Islam S, Parves MR, Islam MJ, Ali MA, Efaz FM, Hossain MS, Ullah MO, Halim MA. Structural and functional effects of the L84S mutant in the SARS-COV-2 ORF8 dimer based on microsecond molecular dynamics study. J Biomol Struct Dyn 2024; 42:5770-5787. [PMID: 37403295 DOI: 10.1080/07391102.2023.2228919] [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: 01/10/2023] [Accepted: 06/17/2023] [Indexed: 07/06/2023]
Abstract
The L84S mutation has been observed frequently in the ORF8 protein of SARS-CoV-2, which is an accessory protein involved in various important functions such as virus propagation, pathogenesis, and evading the immune response. However, the specific effects of this mutation on the dimeric structure of ORF8 and its impacts on interactions with host components and immune responses are not well understood. In this study, we performed one microsecond molecular dynamics (MD) simulation and analyzed the dimeric behavior of the L84S and L84A mutants in comparison to the native protein. The MD simulations revealed that both mutations caused changes in the conformation of the ORF8 dimer, influenced protein folding mechanisms, and affected the overall structural stability. In particular, the 73YIDI76 motif has found to be significantly affected by the L84S mutation, leading to structural flexibility in the region connecting the C-terminal β4 and β5 strands. This flexibility might be responsible for virus immune modulation. The free energy landscape (FEL) and principle component analysis (PCA) have also supported our investigation. Overall, the L84S and L84A mutations affect the ORF8 dimeric interfaces by reducing the frequency of protein-protein interacting residues (Arg52, Lys53, Arg98, Ile104, Arg115, Val117, Asp119, Phe120, and Ile121) in the ORF8 dimer. Our findings provide detail insights for further research in designing structure-based therapeutics against the SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shafiqul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Rimon Parves
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Jahirul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Faiyaz Md Efaz
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Shahadat Hossain
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
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2
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Defective ORF8 dimerization in SARS-CoV-2 delta variant leads to a better adaptive immune response due to abrogation of ORF8-MHC1 interaction. Mol Divers 2023; 27:45-57. [PMID: 35243596 PMCID: PMC8893242 DOI: 10.1007/s11030-022-10405-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/08/2022] [Indexed: 02/08/2023]
Abstract
In India, during the second wave of the COVID-19 pandemic, the breakthrough infections were mainly caused by the SARS-COV-2 delta variant (B.1.617.2). It was reported that, among majority of the infections due to the delta variant, only 9.8% percent cases required hospitalization, whereas only 0.4% fatality was observed. Sudden dropdown in COVID-19 infections cases were observed within a short timeframe, suggesting better host adaptation with evolved delta variant. Downregulation of host immune response against SARS-CoV-2 by ORF8 induced MHC-I degradation has been reported earlier. The Delta variant carried mutations (deletion) at Asp119 and Phe120 amino acids which are critical for ORF8 dimerization. The deletions of amino acids Asp119 and Phe120 in ORF8 of delta variant resulted in structural instability of ORF8 dimer caused by disruption of hydrogen bonds and salt bridges as revealed by structural analysis and MD simulation studies. Further, flexible docking of wild type and mutant ORF8 dimer revealed reduced interaction of mutant ORF8 dimer with MHC-I as compared to wild-type ORF8 dimer with MHC-1, thus implicating its possible role in MHC-I expression and host immune response against SARS-CoV-2. We thus propose that mutant ORF8 of SARS-CoV-2 delta variant may not be hindering the MHC-I expression thereby resulting in a better immune response against the SARS-CoV-2 delta variant, which partly explains the possible reason for sudden drop of SARS-CoV-2 infection rate in the second wave of SARS-CoV-2 predominated by delta variant in India.
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3
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Geographical distribution of host's specific SARS-CoV-2 mutations in the early phase of the COVID-19 pandemic. Gene 2022; 851:147020. [PMCID: PMC9635256 DOI: 10.1016/j.gene.2022.147020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
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4
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Jasim SA, Mahdi RS, Bokov DO, Najm MAA, Sobirova GN, Bafoyeva ZO, Taifi A, Alkadir OKA, Mustafa YF, Mirzaei R, Karampoor S. The deciphering of the immune cells and marker signature in COVID-19 pathogenesis: An update. J Med Virol 2022; 94:5128-5148. [PMID: 35835586 PMCID: PMC9350195 DOI: 10.1002/jmv.28000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/28/2022] [Accepted: 07/13/2022] [Indexed: 12/15/2022]
Abstract
The precise interaction between the immune system and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical in deciphering the pathogenesis of coronavirus disease 2019 (COVID-19) and is also vital for developing novel therapeutic tools, including monoclonal antibodies, antivirals drugs, and vaccines. Viral infections need innate and adaptive immune reactions since the various immune components, such as neutrophils, macrophages, CD4+ T, CD8+ T, and B lymphocytes, play different roles in various infections. Consequently, the characterization of innate and adaptive immune reactions toward SARS-CoV-2 is crucial for defining the pathogenicity of COVID-19. In this study, we explain what is currently understood concerning the conventional immune reactions to SARS-CoV-2 infection to shed light on the protective and pathogenic role of immune response in this case. Also, in particular, we investigate the in-depth roles of other immune mediators, including neutrophil elastase, serum amyloid A, and syndecan, in the immunopathogenesis of COVID-19.
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Affiliation(s)
| | - Roaa Salih Mahdi
- Department of Pathology, College of MedicineUniversity of BabylonHillaIraq
| | - Dmitry Olegovich Bokov
- Institute of PharmacySechenov First Moscow State Medical UniversityMoscowRussian Federation,Laboratory of Food ChemistryFederal Research Center of Nutrition, Biotechnology and Food SafetyMoscowRussian Federation
| | - Mazin A. A. Najm
- Pharmaceutical Chemistry Department, College of PharmacyAl‐Ayen UniversityThi‐QarIraq
| | - Guzal N. Sobirova
- Department of Rehabilitation, Folk Medicine and Physical EducationTashkent Medical AcademyTashkentUzbekistan
| | - Zarnigor O. Bafoyeva
- Department of Rehabilitation, Folk Medicine and Physical EducationTashkent Medical AcademyTashkentUzbekistan
| | | | | | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of PharmacyUniversity of MosulMosulIraq
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research CenterPasteur Institute of IranTehranIran
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research CenterIran University of Medical SciencesTehranIran
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5
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Sheikh A, Huang H, Parvin S, Badruzzaman M, Ahamed T, Hossain E, Baran IS, Saud ZA. A multi-population-based genomic analysis uncovers unique haplotype variants and crucial mutant genes in SARS-CoV-2. J Genet Eng Biotechnol 2022; 20:149. [PMID: 36318347 PMCID: PMC9626712 DOI: 10.1186/s43141-022-00431-3] [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: 10/25/2021] [Accepted: 10/12/2022] [Indexed: 11/05/2022]
Abstract
Background COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rigorous detection and treatment strategies against SARS-CoV-2 have become very challenging due to continuous evolutions to the viral genome. Therefore, careful genomic analysis is sorely needed to understand transmission, the cellular mechanism of pathogenicity, and the development of vaccines or drugs. Objective In this study, we intended to identify SARS-CoV-2 genome variants that may help understand the cellular and molecular foundation of coronavirus infections required to develop effective intervention strategies. Methods SARS-CoV-2 genome sequences were downloaded from an open-source public database, processed, and analyzed for variants in target detection sites and genes. Results We have identified six unique variants, G---AAC, T---AAC---T, AAC---T, AAC--------T, C----------T, and C--------C, at the nucleocapsid region and eleven major hotspot mutant genes: nsp3, surface glycoprotein, nucleocapsid phosphoprotein, ORF8, nsp6, nsp2, nsp4, helicase, membrane glycoprotein, 3′-5′ exonuclease, and 2′-O-ribose methyltransferases. In addition, we have identified eleven major mutant genes that may have a crucial role in SARS-CoV-2 pathogenesis. Conclusion Studying haplotype variants and 11 major mutant genes to understand the mechanism of action of fatal pathogenicity and inter-individual variations in immune responses is inevitable for managing target patient groups with identified variants and developing effective anti-viral drugs and vaccines. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00431-3.
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Affiliation(s)
- Afzal Sheikh
- grid.443108.a0000 0000 8550 5526Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Dhaka 1706 Bangladesh
| | - He Huang
- Research and Development Department, Bioengineering Lab. Co., Ltd, 657 Nagatake Midori-ku, Sagamihara-shi, Kanagawa-ken 252-0154 Japan
| | - Sultana Parvin
- grid.263023.60000 0001 0703 3735Department of Biology, Faculty of Science and Engineering, Saitama University, Saitama, Japan
| | - Mohammad Badruzzaman
- grid.443108.a0000 0000 8550 5526Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Dhaka 1706 Bangladesh
| | - Tofayel Ahamed
- grid.443108.a0000 0000 8550 5526Department of Agroforestry and Environment, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Dhaka 1706 Bangladesh
| | - Ekhtear Hossain
- grid.263880.70000 0004 0386 0655Department of Biological Sciences and Chemistry, Southern University and A&M College, 244 William James Hall, Baton Rouge, LA 70813 USA
| | - Iri Sato Baran
- Genesis Institute of Genetic Research, Genesis Healthcare Corporation, Yebisu Garden Place Tower 15F/26F 4-20-3 Ebisu, Shibuya-ku, Tokyo, Japan
| | - Zahangir Alam Saud
- grid.412656.20000 0004 0451 7306Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205 Bangladesh
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6
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Alsafar H, Albreiki M, Mousa M, Azman SK, Vurivi H, Waasia F, Ruta D, Alhosani F, Almazrouei S, Abuyadek R, Selvaraj F, Chaves-Coira I, Zvereff V, Abdel-Malek MAY, Alkaabi N, Uddin M, Al Awadhi T, Al Marzouqi N, Al Attar F, Al Shamsi S, Al Shehhi F, Alteneiji H, Mohamed K, Al Muhairi N, AlRand H, Fikri A, Henschel A. Genomic epidemiology and emergence of SARS-CoV-2 variants of concern in the United Arab Emirates. Sci Rep 2022; 12:14669. [PMID: 36038563 PMCID: PMC9421632 DOI: 10.1038/s41598-022-16967-w] [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: 10/25/2021] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
Since the declaration of SARS-CoV-2 outbreak as a pandemic, the United Arab Emirates (UAE) public health authorities have adopted strict measures to reduce transmission as early as March 2020. As a result of these measures, flight suspension, nationwide RT-PCR and surveillance of viral sequences were extensively implemented. This study aims to characterize the epidemiology, transmission pattern, and emergence of variants of concerns (VOCs) and variants of interests (VOIs) of SARS-CoV-2 in the UAE, followed by the investigation of mutations associated with hospitalized cases. A total of 1274 samples were collected and sequenced from all seven emirates between the period of 25 April 2020 to 15 February 2021. Phylogenetic analysis demonstrated multiple introductions of SARS-CoV-2 into the UAE in the early pandemic, followed by a local spread of root clades (A, B, B.1 and B.1.1). As the international flight resumed, the frequencies of VOCs surged indicating the January peak of positive cases. We observed that the hospitalized cases were significantly associated with the presence of B.1.1.7 (p < 0.001), B.1.351 (p < 0.001) and A.23.1 (p = 0.009). Deceased cases are more likely to occur in the presence of B.1.351 (p < 0.001) and A.23.1 (p = 0.022). Logistic and ridge regression showed that 51 mutations are significantly associated with hospitalized cases with the highest proportion originated from S and ORF1a genes (31% and 29% respectively). Our study provides an epidemiological insight of the emergence of VOCs and VOIs following the borders reopening and worldwide travels. It provides reassurance that hospitalization is markedly more associated with the presence of VOCs. This study can contribute to understand the global transmission of SARS-CoV-2 variants.
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Affiliation(s)
- Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Emirates Bio-Research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
| | - Mohammed Albreiki
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates
| | - Mira Mousa
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates.,Nuffield Department of Women's and Reproduction Health, Oxford University, Oxford, UK
| | - Syafiq Kamarul Azman
- Department of Electrical Engineering and Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Hema Vurivi
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates
| | - Fathimathuz Waasia
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates
| | - Dymitr Ruta
- Emirates ICT Innovation Center (EBTIC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Farida Alhosani
- Abu Dhabi Public Health Center, Abu Dhabi Department of Health, Abu Dhabi, United Arab Emirates
| | - Shereena Almazrouei
- Abu Dhabi Public Health Center, Abu Dhabi Department of Health, Abu Dhabi, United Arab Emirates
| | - Rowan Abuyadek
- Abu Dhabi Public Health Center, Abu Dhabi Department of Health, Abu Dhabi, United Arab Emirates.,High Institute of Public Health, Alexandria University, Alexandria, Egypt
| | - Francis Selvaraj
- Department Laboratory Medicine Services, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Irene Chaves-Coira
- Molecular and Genetics Department, UniLabs, Abu Dhabi, United Arab Emirates
| | - Val Zvereff
- Department of Molecular Diagnostics, National Reference Laboratory, Abu Dhabi, United Arab Emirates.,Department of Pathology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mohamed A Y Abdel-Malek
- Molecular Biology Laboratory, Mediclinic Alnoor Hospital, Abu Dhabi, United Arab Emirates.,Clinical Pathology Department, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Nawal Alkaabi
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Maimunah Uddin
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Tayba Al Awadhi
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | | | - Fatma Al Attar
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | | | | | - Hala Alteneiji
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | | | - Noor Al Muhairi
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Hussain AlRand
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Asma Fikri
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Andreas Henschel
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates. .,Department of Electrical Engineering and Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
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7
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Mekawy AS, Alaswad Z, Ibrahim AA, Mohamed AA, AlOkda A, Elserafy M. The consequences of viral infection on host DNA damage response: a focus on SARS-CoVs. J Genet Eng Biotechnol 2022; 20:104. [PMID: 35829826 PMCID: PMC9277982 DOI: 10.1186/s43141-022-00388-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/04/2022] [Indexed: 12/03/2022]
Abstract
DNA damage and genome instability in host cells are introduced by many viruses during their life cycles. Severe acute respiratory syndrome coronaviruses (SARS-CoVs) manipulation of DNA damage response (DDR) is an important area of research that is still understudied. Elucidation of the direct and indirect interactions between SARS-CoVs and DDR not only provides important insights into how the viruses exploit DDR pathways in host cells but also contributes to our understanding of their pathogenicity. Here, we present the known interactions of both SARS-CoV and SARS-CoV-2 with DDR pathways of the host cells, to further understand the consequences of infection on genome integrity. Since this area of research is in its early stages, we try to connect the unlinked dots to speculate and propose different consequences on DDR mechanisms. This review provides new research scopes that can be further investigated in vitro and in vivo, opening new avenues for the development of anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Asmaa S Mekawy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Zina Alaswad
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Aya A Ibrahim
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Ahmed A Mohamed
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Abdelrahman AlOkda
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada.,Metabolic Disorders and Complications Program and Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt. .,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt.
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8
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Piri-Gharaghie T, Doosti A, Mirzaei SA. Fabrication and Characterization of pcDNA3.1(+) Location within Chitosan/Nanoparticles Complexes for Enhanced Gene Delivery. IRANIAN JOURNAL OF BIOTECHNOLOGY 2022; 20:e3110. [PMID: 36381280 PMCID: PMC9618014 DOI: 10.30498/ijb.2022.297534.3110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
BACKGROUND Chitosan nanoparticles (CSNP) are becoming a popular alternative for delivering nucleic acids to tissues for gene transfer (gene therapy). The size and morphology of these biodegradable nano-carriers are adjustable, and their positive charge allows them to interact strongly with negatively charged nucleic acids. OBJECTIVE This study aimed to fabricate and characterize pcDNA3.1 (+) plasmid (pDNA) and CSNP complexes and determine the plasmid location in these vehicles. MATERIALS AND METHODS The characteristics of the pDNA/CSNP complex after production were investigated by SEM, XRD, DLS, TGA, and FTIR. The capacity of CSNP to form complexes with pDNA was investigated by labeling free plasmids with the fluorescent intercalating dye OliGreen. The stability of pDNA/CSNP in the presence of chitosanase was evaluated. Surface-Enhanced Raman Spectroscopy (SERS) for pDNA localization was performed, and absorption rate in BALB/c mice was assessed by real-time PCR. RESULTS The optimum pDNA/CSNP ratio for plasmid complex formation was established to be 1:2 (w.w) by measuring spectroscopy. At these optimum complex formation ratios, spectroscopy, and gel digest experiments, SERS indicated that a part of the pDNA was present on the complex outer surface. The findings of plasmid absorption in mouse thigh tissue by real-time PCR revealed that the rate of gene uptake was significantly greater at a dose of 1:2 (w.w) of pDNA/CSNP than in other groups (P< 0.001). CONCLUSIONS The findings of this study reveal exactly pDNA fits into polymer nanostructured delivery systems, allowing the formulation to be adjusted for selective distribution. This understanding will aid future research into the system's functioning in vitro and in vivo.
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Affiliation(s)
- Tohid Piri-Gharaghie
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Abbas Doosti
- Biotechnology Research Center, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Seyed Abbas Mirzaei
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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9
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Wang Q, Wu X, Mao Q, Gao F, Liu M, Song Z, Bian L, Liang Z. How SARS-CoV-2 dodges immune surveillance and facilitates infection: an analytical review. Expert Rev Anti Infect Ther 2022; 20:1119-1127. [PMID: 35574688 DOI: 10.1080/14787210.2022.2078307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Effective treatments for the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic are limited. The virus has evolved strategies to evade the immune system or hijack immune responses to facilitate infection and escape immune surveillance. Mechanistically, SARS-CoV-2 takes advantage of TLR4 and cytokine-induced integrins to promote its entrance into the cell. Furthermore, the activation of pattern recognition receptors (PRR)-mediated signaling pathways is compromised by SARS-CoV-2 non-structural proteins (NSPs), accessory protein open reading frames (ORFs), and structural proteins upon infection, contributing to viral infection and replication. Host factors necessary for cellular protein synthesis, metabolism, and viral replication can also be inhibited by the SARS-CoV-2 proteins. Exploring specific mechanisms would optimize the therapy methods and benefit drug research and development. AREAS COVERED : We describe pathways and mechanisms by which SARS-CoV-2 evades immune system; these include the mechanisms that operate during virus entry, signaling pathways involved, and processes at RNA and protein levels. EXPERT OPINION : Increased understanding of how viruses interfere with immune responses would provide more evidence for drug development. Drugs targeting conserved viral proteins to inhibit their replication or host factors to enhance immune responses would minimize the impact of virus mutations and prepare for future coronavirus outbreaks.
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Affiliation(s)
- Qian Wang
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
| | - Xing Wu
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
| | - Qunying Mao
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
| | - Fan Gao
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
| | - Mingchen Liu
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
| | - Ziyang Song
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
| | - Lianlian Bian
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
| | - Zhenglun Liang
- National Institutes for Food and Drug Control, Beijing, People's Republic of China.,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, Beijing, People's Republic of China.,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Beijing, People's Republic of China
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10
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Zhang Z, Shen Q, Chang H. Vaccines for COVID-19: A Systematic Review of Immunogenicity, Current Development, and Future Prospects. Front Immunol 2022; 13:843928. [PMID: 35572592 PMCID: PMC9092649 DOI: 10.3389/fimmu.2022.843928] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/21/2022] [Indexed: 01/09/2023] Open
Abstract
The persistent coronavirus disease 2019 (COVID-19), characterized by severe respiratory syndrome, is caused by coronavirus 2 (SARS-CoV-2), and it poses a major threat to public health all over the world. Currently, optimal COVID-19 management involves effective vaccination. Vaccination is known to greatly enhance immune response against viral infections and reduce public transmission of COVID-19. However, although current vaccines offer some benefits, viral variations and other factors demand the continuous development of vaccines to eliminate this virus from host. Hence, vaccine research and development is crucial and urgent to the elimination of this pandemic. Herein, we summarized the structural and replicatory features of SARS-CoV-2, and focused on vaccine-mediated disease prevention strategies like vaccine antigen selection, vaccine research, and vaccine application. We also evaluated the latest literature on COVID-19 and extensively reviewed action mechanisms, clinical trial (CT) progresses, advantages, as well as disadvantages of various vaccine candidates against SARS-CoV-2. Lastly, we discussed the current viral treatment, prevention trends, and future prospects.
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Affiliation(s)
- Zhan Zhang
- Ministry of Education (MOE) Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Qi Shen
- Ministry of Education (MOE) Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Haocai Chang
- Ministry of Education (MOE) Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
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11
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Rochman ND, Faure G, Wolf YI, Freddolino PL, Zhang F, Koonin EV. Epistasis at the SARS-CoV-2 Receptor-Binding Domain Interface and the Propitiously Boring Implications for Vaccine Escape. mBio 2022; 13:e0013522. [PMID: 35289643 PMCID: PMC9040817 DOI: 10.1128/mbio.00135-22] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/08/2022] [Indexed: 12/13/2022] Open
Abstract
At the time of this writing, December 2021, potential emergence of vaccine escape variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a grave global concern. The interface between the receptor-binding domain (RBD) of SARS-CoV-2 spike (S) protein and the host receptor (ACE2) overlaps the binding site of principal neutralizing antibodies (NAb), limiting the repertoire of viable mutations. Nonetheless, variants with multiple RBD mutations have risen to dominance. Nonadditive, epistatic relationships among RBD mutations are apparent, and assessing the impact of such epistasis on the mutational landscape, particularly the risk of vaccine escape, is crucial. We employed protein structure modeling using Rosetta to compare the effects of all single mutants at the RBD-NAb and RBD-ACE2 interfaces for the wild type and Delta, Gamma, and Omicron variants. Overall, epistasis at the RBD interface appears to be limited, and the effects of most multiple mutations are additive. Epistasis at the Delta variant interface weakly stabilizes NAb interaction relative to ACE2 interaction, whereas in Gamma, epistasis more substantially destabilizes NAb interaction. Despite bearing many more RBD mutations, the epistatic landscape of Omicron closely resembles that of Gamma. Thus, although Omicron poses new risks not observed with Delta, structural constraints on the RBD appear to hamper continued evolution toward more complete vaccine escape. The modest ensemble of mutations relative to the wild type that are currently known to reduce vaccine efficacy is likely to contain the majority of all possible escape mutations for future variants, predicting the continued efficacy of the existing vaccines. IMPORTANCE Emergence of vaccine escape variants of SARS-CoV-2 is arguably the most pressing problem during the COVID-19 pandemic as vaccines are distributed worldwide. We employed a computational approach to assess the risk of antibody escape resulting from mutations in the receptor-binding domain of the spike protein of the wild-type SARS-CoV-2 virus as well as the Delta, Gamma, and Omicron variants. The efficacy of the existing vaccines against Omicron could be substantially reduced relative to the wild type, and the potential for vaccine escape is of grave concern. Our results suggest that although Omicron poses new evolutionary risks not observed for Delta, structural constraints on the RBD make continued evolution toward more complete vaccine escape from either Delta or Omicron unlikely. The modest set of escape-enhancing mutations already identified for the wild type likely include the majority of all possible mutations with this effect.
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Affiliation(s)
- Nash D. Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
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12
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Zeng H, Gao X, Xu G, Zhang S, Cheng L, Xiao T, Zu W, Zhang Z. SARS-CoV-2 helicase NSP13 hijacks the host protein EWSR1 to promote viral replication by enhancing RNA unwinding activity. INFECTIOUS MEDICINE 2022. [PMCID: PMC8868009 DOI: 10.1016/j.imj.2021.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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13
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Shindo N, Toyoshiba H. [Drug repositioning to combat COVID-19 using artificial intelligence system]. Nihon Yakurigaku Zasshi 2022; 157:41-46. [PMID: 34980812 DOI: 10.1254/fpj.21042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Although months have passed since WHO declared COVID-19 a global pandemic, only a limited number of clinically effective drugs are available, and the development of drugs to treat COVID-19 has become an urgent issue worldwide. The pace of new research on COVID-19 is extremely high and it is impossible to read every report. In order to tackle these problems, we leveraged our artificial intelligence (AI) system, Concept Encoder, to accelerate the process of drug repositioning. Concept Encoder is a patented AI system based on natural language processing technology and by deeply learning papers on COVID-19, the system identified a large group of genes implicated in COVID-19 pathogenesis. The AI system then generated a molecular linkage map for COVID-19, connecting the genes by learning the molecular relationship comprehensively. By thoroughly reviewing the resulting map and list of the genes with rankings, we found potential key players for disease progression and existing drugs that might improve COVID-19 survival. Here, we focus on potential targets and discuss the perspective of our approach.
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14
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Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Pal Choudhury P, Abd El-Aziz TM, Takayama K, Kandimalla R, Lal A, Serrano-Aroca Á, Azad GK, Aljabali AAA, Palù G, Chauhan G, Adadi P, Tambuwala M, Brufsky AM, Baetas-da-Cruz W, Barh D, Azevedo V, Bazan NG, Andrade BS, Santana Silva RJ, Uversky VN. An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. PeerJ 2022. [PMID: 35341060 DOI: 10.1101/2021.05.25.445557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Abstract
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, India
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Mumbai, India
| | - Elrashdy M Redwan
- Faculty of Science, Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic Rochester, Rochester, NY, United States
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Catolica de Valencia San Vicente Martir, Valencia, Spain
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical, Yarmouk University, Irbid, Jordan
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
| | - Parise Adadi
- Department of Food Science, University of Otago, University of Otago, Dunedin, New Zealand
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK
| | - Adam M Brufsky
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and 46 Applied Biotechnology (IIOAB), Nonakuri, India
| | - Vasco Azevedo
- Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Nikolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA, United States
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Raner José Santana Silva
- Departamento de Ciencias Biologicas (DCB), Programa de Pos-Graduacao em Genetica e Biologia Molecular (PPGGBM), Universidade Estadual de Santa Cruz (UESC), Ilheus, Brazil
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
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15
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Rochman ND, Faure G, Wolf YI, Freddolino PL, Zhang F, Koonin EV. Epistasis at the SARS-CoV-2 RBD Interface and the Propitiously Boring Implications for Vaccine Escape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.30.458225. [PMID: 34494024 PMCID: PMC8423221 DOI: 10.1101/2021.08.30.458225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
At the time of this writing, December 2021, potential emergence of vaccine escape variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a grave global concern. The interface between the receptor-binding domain (RBD) of SARS-CoV-2 spike (S) protein and the host receptor (ACE2) overlap with the binding site of principal neutralizing antibodies (NAb), limiting the repertoire of viable mutations. Nonetheless, variants with multiple mutations in the RBD have rose to dominance. Non-additive, epistatic relationships among RBD mutations are apparent, and assessing the impact of such epistasis on the mutational landscape is crucial. Epistasis can substantially increase the risk of vaccine escape and cannot be completely characterized through the study of the wild type (WT) alone. We employed protein structure modeling using Rosetta to compare the effects of all single mutants at the RBD-NAb and RBD-ACE2 interfaces for the WT, Delta, Gamma, and Omicron variants. Overall, epistasis at the RBD interface appears to be limited and the effects of most multiple mutations are additive. Epistasis at the Delta variant interface weakly stabilizes NAb interaction relative to ACE2 interaction, whereas in the Gamma variant, epistasis more substantially destabilizes NAb interaction. Although a small, systematic trend towards NAb destabilization not observed for Delta or Gamma was detected for Omicron, and despite bearing significantly more RBD mutations, the epistatic landscape of the Omicron variant closely resembles that of Gamma. These results suggest that, although Omicron poses new risks not observed with Delta, structural constraints on the RBD hamper continued evolution towards more complete vaccine escape. The modest ensemble of mutations relative to the WT that are currently known to reduce vaccine efficacy is likely to comprise the majority of all possible escape mutations for future variants, predicting continued efficacy of the existing vaccines.
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Affiliation(s)
- Nash D. Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
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16
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Hossain ME, Rahman MM, Alam MS, Sarmin M, Karim Y, Hasan M, Hoque AF, Hasan MM, Rahman MZ, Chisti MJ, Rahman M. A Case Report: Genetically Distinct Severe Acute Respiratory Syndrome Coronavirus-2 Variant Causing Reinfection. Front Microbiol 2021; 12:792514. [PMID: 34956160 PMCID: PMC8696118 DOI: 10.3389/fmicb.2021.792514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/11/2021] [Indexed: 11/29/2022] Open
Abstract
Background: The emergence of novel variants has been a great deal of international concern since the recently published data suggest that previous infections with SARS-CoV-2 may not protect an individual from new variants. We report a patient had two distinct episodes of COVID-19 with different variants of SARS-CoV-2. Methods: The nasopharyngeal samples collected from the two episodes were subjected to whole-genome sequencing and comparative genome analysis. Results: The first infection presented with mild symptoms, while the second infection presented with severe outcomes which occurred 74 days after the patient recovered from the first episode. He had elevated C-reactive protein, ferritin, and bilateral consolidation as a sign of acute infection. Genome analysis revealed that the strains from the first and second episodes belonged to two distinct Nexstrain clades 20B and 20I and Pangolin lineages B.1.1.25 and B.1.1.7, respectively. A total of 36 mutations were observed in the episode-2 strain when compared with the reference strain Wuhan-Hu-1. Among them, eight mutations were identified in the receptor-binding domain (RBD). Conclusion: Our findings concern whether the immunity acquired by natural infection or mass vaccination could confer adequate protection against the constantly evolving SARS-CoV-2. Therefore, continuous monitoring of genetic variations of SARS-CoV-2 strains is crucial for interventions such as vaccine and drug designs, treatment using monoclonal antibodies, and patient management.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Mustafizur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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17
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Patel M, Shahjin F, Cohen JD, Hasan M, Machhi J, Chugh H, Singh S, Das S, Kulkarni TA, Herskovitz J, Meigs DD, Chandra R, Hettie KS, Mosley RL, Kevadiya BD, Gendelman HE. The Immunopathobiology of SARS-CoV-2 Infection. FEMS Microbiol Rev 2021; 45:fuab035. [PMID: 34160586 PMCID: PMC8632753 DOI: 10.1093/femsre/fuab035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022] Open
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can lead to coronavirus disease 2019 (COVID-19). Virus-specific immunity controls infection, transmission and disease severity. With respect to disease severity, a spectrum of clinical outcomes occur associated with age, genetics, comorbidities and immune responses in an infected person. Dysfunctions in innate and adaptive immunity commonly follow viral infection. These are heralded by altered innate mononuclear phagocyte differentiation, activation, intracellular killing and adaptive memory, effector, and regulatory T cell responses. All of such affect viral clearance and the progression of end-organ disease. Failures to produce effective controlled antiviral immunity leads to life-threatening end-organ disease that is typified by the acute respiratory distress syndrome. The most effective means to contain SARS-CoV-2 infection is by vaccination. While an arsenal of immunomodulators were developed for control of viral infection and subsequent COVID-19 disease, further research is required to enable therapeutic implementation.
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Affiliation(s)
- Milankumar Patel
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Farah Shahjin
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Jacob D Cohen
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Mahmudul Hasan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, NE 68198, USA
| | - Jatin Machhi
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Heerak Chugh
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Snigdha Singh
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Srijanee Das
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Tanmay A Kulkarni
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, NE 68198, USA
| | - Jonathan Herskovitz
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Douglas D Meigs
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Ramesh Chandra
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
| | - Kenneth S Hettie
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology, Department of Otolaryngology –Head & Neck Surgery, Stanford University, Palo Alto, CA 94304, USA
| | - R Lee Mosley
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Bhavesh D Kevadiya
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Howard E Gendelman
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, NE 68198, USA
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
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18
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Constantino FB, Cury SS, Nogueira CR, Carvalho RF, Justulin LA. Prediction of Non-canonical Routes for SARS-CoV-2 Infection in Human Placenta Cells. Front Mol Biosci 2021; 8:614728. [PMID: 34820418 PMCID: PMC8606885 DOI: 10.3389/fmolb.2021.614728] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 10/15/2021] [Indexed: 02/02/2023] Open
Abstract
The SARS-CoV-2 is the causative agent of the COVID-19 pandemic. The data available about COVID-19 during pregnancy have demonstrated placental infection; however, the mechanisms associated with intrauterine transmission of SARS-CoV-2 is still debated. Intriguingly, while canonical SARS-CoV-2 cell entry mediators are expressed at low levels in placental cells, the receptors for viruses that cause congenital infections such as the cytomegalovirus and Zika virus are highly expressed in these cells. Here we analyzed the transcriptional profile (microarray and single-cell RNA-Seq) of proteins potentially interacting with coronaviruses to identify non- canonical mediators of SARS-CoV-2 infection and replication in the placenta. Despite low levels of the canonical cell entry mediators ACE2 and TMPRSS2, we show that cells of the syncytiotrophoblast, villous cytotrophoblast, and extravillous trophoblast co-express high levels of the potential non-canonical cell-entry mediators DPP4 and CTSL. We also found changes in the expression of DAAM1 and PAICS genes during pregnancy, which are translated into proteins also predicted to interact with coronaviruses proteins. These results provide new insight into the interaction between SARS-CoV-2 and host proteins that may act as non-canonical routes for SARS-CoV-2 infection and replication in the placenta cells.
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Affiliation(s)
- Flávia Bessi Constantino
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Sarah Santiloni Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Celia Regina Nogueira
- Department of Internal Clinic, Botucatu Medicine School, São Paulo State University (UNESP), Botucatu, Brazil
| | - Robson Francisco Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Luis Antonio Justulin
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
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19
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Paula Junior WD, Freitas CSD, Lima Neto FFD, Santana NA, Soares NZD, Fonseca VLM, Nascimento RCRMD, Grabe-Guimarães A. Immune response in acute respiratory syndrome induced by the new coronavirus. ABCS HEALTH SCIENCES 2021. [DOI: 10.7322/abcshs.2020256.1704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Coronaviruses (CoVs) belong to the family Coronaviridae, which are enveloped and have a single-stranded RNA genome. The new coronavirus (SARS-CoV-2) is the seventh known coronavirus that can infect humans and cause serious illness, such as acute respiratory syndrome. The coronaviruses already identified have contributed to the understanding of the clinical manifestations caused by SARS-CoV-2, as well as their associations with the immune system. The aim of the present study was to carry out a narrative review of the literature on the host's immune response to infection by the new coronavirus. The review contains basic and summarized information on the main mechanisms involved in the immune response to SARS-CoV-2. The characteristics of the infection were considered according to the following: from the initial contact with the host through binding to angiotensin-converting enzyme 2 (ACE-2); the recognition of the pathogen by innate immunity cells; its containment mechanisms, including the production of effector cytokines and chemokines important in the development of the inflammatory process; and the participation of the complement system until the activation of the adaptive immune response. The probable occurrence of a host dysfunctional immune response and the escape mechanisms of the virus were also addressed. Despite numerous studies on the pathogenesis of SARS-CoV-2 infection, knowledge about the host's immune response in COVID-19 is not fully understood. The present work established the relationship between the new coronavirus and the immune system, but further studies are needed for all the mechanisms of the process to be elucidated.
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20
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Fong SW, Yeo NKW, Chan YH, Goh YS, Amrun SN, Ang N, Rajapakse MP, Lum J, Foo S, Lee CYP, Carissimo G, Chee RSL, Torres-Ruesta A, Tay MZ, Chang ZW, Poh CM, Young BE, Tambyah PA, Kalimuddin S, Leo YS, Lye DC, Lee B, Biswas S, Howland SW, Renia L, Ng LFP. Robust Virus-Specific Adaptive Immunity in COVID-19 Patients with SARS-CoV-2 Δ382 Variant Infection. J Clin Immunol 2021; 42:214-229. [PMID: 34716845 PMCID: PMC8556776 DOI: 10.1007/s10875-021-01142-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/17/2021] [Indexed: 01/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) that have become dominant as the pandemic progresses bear the ORF8 mutation together with multiple spike mutations. A 382-nucleotide deletion (Δ382) in the ORF7b and ORF8 regions has been associated with milder disease phenotype and less systemic inflammation in COVID-19 patients. However, its impact on host immunity against SARS-CoV-2 remains undefined. Here, RNA-sequencing was performed to elucidate whole blood transcriptomic profiles and identify contrasting immune signatures between patients infected with either wildtype or Δ382 SARS-CoV-2 variant. Interestingly, the immune landscape of Δ382 SARS-CoV-2 infected patients featured an increased adaptive immune response, evidenced by enrichment of genes related to T cell functionality, a more robust SARS-CoV-2-specific T cell immunity, as well as a more rapid antibody response. At the molecular level, eukaryotic initiation factor 2 signaling was found to be upregulated in patients bearing Δ382, and its associated genes were correlated with systemic levels of T cell-associated and pro-inflammatory cytokines. This study provides more in-depth insight into the host–pathogen interactions of ORF8 with great promise as a therapeutic target to combat SARS-CoV-2 infection.
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Affiliation(s)
- Siew-Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Nicholas Kim-Wah Yeo
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Yi-Hao Chan
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Yun Shan Goh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Siti Naqiah Amrun
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Nicholas Ang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | | | - Josephine Lum
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Shihui Foo
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Cheryl Yi-Pin Lee
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Guillaume Carissimo
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Rhonda Sin-Ling Chee
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Anthony Torres-Ruesta
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - Matthew Zirui Tay
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Zi Wei Chang
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Chek Meng Poh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore City, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore City, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore City, Singapore
| | - Paul A Tambyah
- National Centre for Infectious Diseases, Singapore City, Singapore
- Department of Medicine, National University Hospital, Singapore City, Singapore
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - Shirin Kalimuddin
- Department of Infectious Diseases, Singapore General Hospital, Singapore City, Singapore
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore City, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore City, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore City, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore City, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore City, Singapore
| | - David C Lye
- National Centre for Infectious Diseases, Singapore City, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore City, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore City, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore City, Singapore
| | - Bernett Lee
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Subhra Biswas
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Shanshan Wu Howland
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore City, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore.
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
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21
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Kaur A, Chopra M, Bhushan M, Gupta S, Kumari P H, Sivagurunathan N, Shukla N, Rajagopal S, Bhalothia P, Sharma P, Naravula J, Suravajhala R, Gupta A, Abbasi BA, Goswami P, Singh H, Narang R, Polavarapu R, Medicherla KM, Valadi J, Kumar S A, Chaubey G, Singh KK, Bandapalli OR, Kavi Kishor PB, Suravajhala P. The Omic Insights on Unfolding Saga of COVID-19. Front Immunol 2021; 12:724914. [PMID: 34745097 PMCID: PMC8564481 DOI: 10.3389/fimmu.2021.724914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
The year 2019 has seen an emergence of the novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease of 2019 (COVID-19). Since the onset of the pandemic, biological and interdisciplinary research is being carried out across the world at a rapid pace to beat the pandemic. There is an increased need to comprehensively understand various aspects of the virus from detection to treatment options including drugs and vaccines for effective global management of the disease. In this review, we summarize the salient findings pertaining to SARS-CoV-2 biology, including symptoms, hosts, epidemiology, SARS-CoV-2 genome, and its emerging variants, viral diagnostics, host-pathogen interactions, alternative antiviral strategies and application of machine learning heuristics and artificial intelligence for effective management of COVID-19 and future pandemics.
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Affiliation(s)
- Arvinpreet Kaur
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Punjab, India
- Bioclues.org, Hyderabad, India
| | - Mehak Chopra
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Mahak Bhushan
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, India
| | - Sonal Gupta
- Bioclues.org, Hyderabad, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | | | - Narmadhaa Sivagurunathan
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Nidhi Shukla
- Bioclues.org, Hyderabad, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Shalini Rajagopal
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Purva Bhalothia
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Purnima Sharma
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Punjab, India
| | - Jalaja Naravula
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Renuka Suravajhala
- Bioclues.org, Hyderabad, India
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
| | - Ayam Gupta
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Bilal Ahmed Abbasi
- Functional Genomics Unit, Council of Scientific and Industrial Research- Institute of Genomics & Integrative Biology (CSIR-IGIB), Delhi, India
| | - Prittam Goswami
- Department of Biotechnology, Haldia Institute of Technology, West Bengal, India
| | - Harpreet Singh
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Punjab, India
- Bioclues.org, Hyderabad, India
| | - Rahul Narang
- Department of Microbiology, All India Institute of Medical Sciences, Bibinagar, Hyderabad, India
| | | | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Jayaraman Valadi
- Bioclues.org, Hyderabad, India
- Department of Computer Science, Flame University, Pune, India
| | - Anil Kumar S
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Benaras Hindu University, Varanasi, India
| | - Keshav K. Singh
- Department of Genetics, University of Alabama, Birmingham, AL, United States
| | - Obul Reddy Bandapalli
- Bioclues.org, Hyderabad, India
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Department of Applied Biology, Council of Scientific and Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, India
| | - Polavarapu Bilhan Kavi Kishor
- Bioclues.org, Hyderabad, India
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kerala, India
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22
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Zahn T, Mhedhbi I, Hein S, Raupach J, Miskey C, Husria Y, Bayanga K, Bartel D, Vieths S, Ivics Z, Oberle D, Keller‐Stanislawski B, Herrlein M, Maier TJ, Hildt E. Persistence of infectious SARS-CoV-2 particles for up to 37 days in patients with mild COVID-19. Allergy 2021; 77:2053-2066. [PMID: 34637150 PMCID: PMC8652783 DOI: 10.1111/all.15138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/19/2021] [Accepted: 10/01/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND People suffering from COVID-19 are typically considered non-infectious 14 days after diagnosis if symptoms have disappeared for at least 48 h. We describe three patients who independently acquired their infection. These three patients experienced mild COVID-19 and completely recovered symptomatically within 10 days, but remained PCR-positive in deep pharyngeal samples for at least 38 days. We attempted to isolate virus from pharyngeal swabs to investigate whether these patients still carried infectious virus. METHODS Infectious virus was amplified in Vero E6 cells and characterized by electron microscopy and WGS. The immune response was investigated by ELISA and peptide arrays. RESULTS In all three cases, infectious and replication-competent virus was isolated and amplified in Vero E6 cells. Virus replication was detected by RT-PCR and immunofluorescence microscopy. Electron microscopy confirmed the formation of intact SARS-CoV-2 particles. For a more detailed analysis, all three isolates were characterized by whole-genome sequencing (WGS). The sequence data revealed that the isolates belonged to the 20A or 20C clade, and two mutations in ORF8 were identified among other mutations that could be relevant for establishing a long-term infection. Characterization of the humoral immune response in comparison to patients that had fully recovered from mild COVID-19 revealed a lack of antibodies binding to sequential epitopes of the receptor-binding domain (RBD) for the long-term infected patients. CONCLUSION Thus, a small portion of COVID-19 patients displays long-term infectivity and termination of quarantine periods after 14 days, without PCR-based testing, should be reconsidered critically.
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Affiliation(s)
- Tobias Zahn
- Division of Virology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Ines Mhedhbi
- Division of Virology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Sascha Hein
- Division of Virology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Jan Raupach
- Division of Virology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Csaba Miskey
- Division of Medical Biotechnology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Younes Husria
- Division of Virology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Kathrin Bayanga
- Division of Transfusion Medicine Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Detlef Bartel
- Division of Allergology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Stefan Vieths
- Management board Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Zoltan Ivics
- Division of Medical Biotechnology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Doris Oberle
- Division of Pharmacovigilance Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Brigitte Keller‐Stanislawski
- Division of Pharmacovigilance Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Marie‐Luise Herrlein
- Division of Virology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Thorsten Jürgen Maier
- Division of Pharmacovigilance Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Eberhard Hildt
- Division of Virology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
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23
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Desforges M, Gurdasani D, Hamdy A, Leonardi AJ. Uncertainty around the Long-Term Implications of COVID-19. Pathogens 2021; 10:1267. [PMID: 34684216 PMCID: PMC8536991 DOI: 10.3390/pathogens10101267] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than 231 million people globally, with more than 4.7 million deaths recorded by the World Health Organization as of 26 September 2021. In response to the pandemic, some countries (New Zealand, Vietnam, Taiwan, South Korea and others) have pursued suppression strategies, so-called Zero COVID policies, to drive and maintain infection rates as close to zero as possible and respond aggressively to new cases. In comparison, European countries and North America have adopted mitigation strategies (of varying intensity and effectiveness) that aim primarily to prevent health systems from being overwhelmed. With recent advances in our understanding of SARS-CoV-2 and its biology, and the increasing recognition there is more to COVID-19 beyond the acute infection, we offer a perspective on some of the long-term risks of mutational escape, viral persistence, reinfection, immune dysregulation and neurological and multi-system complications (Long COVID).
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Affiliation(s)
- Marc Desforges
- Centre Hospitalier Universitaire Ste-Justine and Faculté de Médecine, Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | | | - Adam Hamdy
- Panres Pandemic Research, Newport TF10 8PG, UK;
| | - Anthony J. Leonardi
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA;
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24
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Valcarcel A, Bensussen A, Álvarez-Buylla ER, Díaz J. Structural Analysis of SARS-CoV-2 ORF8 Protein: Pathogenic and Therapeutic Implications. Front Genet 2021; 12:693227. [PMID: 34552615 PMCID: PMC8450498 DOI: 10.3389/fgene.2021.693227] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/29/2021] [Indexed: 12/27/2022] Open
Abstract
Current therapeutic strategies and vaccines against SARS-CoV-2 are mainly focused on the Spike protein despite there are other viral proteins with important roles in COVID-19 pathogenicity. For example, ORF8 restructures vesicular trafficking in the host cell, impacts intracellular immunity through the IFN-I signaling, and growth pathways through the mitogen-activated protein kinases (MAPKs). In this mini-review, we analyze the main structural similarities of ORF8 with immunological molecules such as IL-1, contributing to the immunological deregulation observed in COVID-19. We also propose that the blockage of some effector functions of ORF8 with Rapamycin, such as the mTORC1 activation through MAPKs 40 pathway, with Rapamycin, can be a promising approach to reduce COVID-19 mortality.
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Affiliation(s)
- Antonio Valcarcel
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Antonio Bensussen
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Elena R Álvarez-Buylla
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.,Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evoluciónde Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - José Díaz
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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25
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Brandt D, Simunovic M, Busche T, Haak M, Belmann P, Jünemann S, Schulz T, Klages LJ, Vinke S, Beckstette M, Pohl E, Scherer C, Sczyrba A, Kalinowski J. Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines. Viruses 2021; 13:1870. [PMID: 34578452 PMCID: PMC8518987 DOI: 10.3390/v13091870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/20/2022] Open
Abstract
Genomic surveillance of the SARS-CoV-2 pandemic is crucial and mainly achieved by amplicon sequencing protocols. Overlapping tiled-amplicons are generated to establish contiguous SARS-CoV-2 genome sequences, which enable the precise resolution of infection chains and outbreaks. We investigated a SARS-CoV-2 outbreak in a local hospital and used nanopore sequencing with a modified ARTIC protocol employing 1200 bp long amplicons. We detected a long deletion of 168 nucleotides in the ORF8 gene in 76 samples from the hospital outbreak. This deletion is difficult to identify with the classical amplicon sequencing procedures since it removes two amplicon primer-binding sites. We analyzed public SARS-CoV-2 sequences and sequencing read data from ENA and identified the same deletion in over 100 genomes belonging to different lineages of SARS-CoV-2, pointing to a mutation hotspot or to positive selection. In almost all cases, the deletion was not represented in the virus genome sequence after consensus building. Additionally, further database searches point to other deletions in the ORF8 coding region that have never been reported by the standard data analysis pipelines. These findings and the fact that ORF8 is especially prone to deletions, make a clear case for the urgent necessity of public availability of the raw data for this and other large deletions that might change the physiology of the virus towards endemism.
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Affiliation(s)
- David Brandt
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
| | - Marina Simunovic
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
| | - Markus Haak
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
| | - Peter Belmann
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Sebastian Jünemann
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Tizian Schulz
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Levin Joe Klages
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
| | - Svenja Vinke
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
| | - Michael Beckstette
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Ehmke Pohl
- Department of Biosciences, Durham University, Durham DH1 3LE, UK;
| | - Christiane Scherer
- Evangelisches Klinikum Bethel, Institut für Laboratoriumsmedizin, Mikrobiologie und Hygiene, 33617 Bielefeld, Germany;
- Universitätsklinikum OWL der Universität Bielefeld, 33615 Bielefeld, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
- Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (D.B.); (M.S.); (T.B.); (M.H.); (P.B.); (S.J.); (T.S.); (L.J.K.); (S.V.); (M.B.); (A.S.)
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26
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Kaklamanos A, Belogiannis K, Skendros P, Gorgoulis VG, Vlachoyiannopoulos PG, Tzioufas AG. COVID-19 Immunobiology: Lessons Learned, New Questions Arise. Front Immunol 2021; 12:719023. [PMID: 34512643 PMCID: PMC8427766 DOI: 10.3389/fimmu.2021.719023] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/09/2021] [Indexed: 12/17/2022] Open
Abstract
There is strong evidence that COVID-19 pathophysiology is mainly driven by a spatiotemporal immune deregulation. Both its phenotypic heterogeneity, spanning from asymptomatic to severe disease/death, and its associated mortality, are dictated by and linked to maladaptive innate and adaptive immune responses against SARS-CoV-2, the etiologic factor of the disease. Deregulated interferon and cytokine responses, with the contribution of immune and cellular stress-response mediators (like cellular senescence or uncontrolled inflammatory cell death), result in innate and adaptive immune system malfunction, endothelial activation and inflammation (endothelitis), as well as immunothrombosis (with enhanced platelet activation, NET production/release and complement hyper-activation). All these factors play key roles in the development of severe COVID-19. Interestingly, another consequence of this immune deregulation, is the production of autoantibodies and the subsequent development of autoimmune phenomena observed in some COVID-19 patients with severe disease. These new aspects of the disease that are now emerging (like autoimmunity and cellular senescence), could offer us new opportunities in the field of disease prevention and treatment. Simultaneously, lessons already learned from the immunobiology of COVID-19 could offer new insights, not only for this disease, but also for a variety of chronic inflammatory responses observed in autoimmune and (auto)inflammatory diseases.
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Affiliation(s)
- Aimilios Kaklamanos
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Institute for Autoimmune Systemic and Neurological Diseases, Athens, Greece
| | - Konstantinos Belogiannis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Skendros
- First Department of Internal Medicine and Laboratory of Molecular Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Vassilis G. Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Faculty Institute for Cancer Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
- Basic Research Center, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
- Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Panayiotis G. Vlachoyiannopoulos
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Institute for Autoimmune Systemic and Neurological Diseases, Athens, Greece
| | - Athanasios G. Tzioufas
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Institute for Autoimmune Systemic and Neurological Diseases, Athens, Greece
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27
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Singh J, Pandit P, McArthur AG, Banerjee A, Mossman K. Evolutionary trajectory of SARS-CoV-2 and emerging variants. Virol J 2021; 18:166. [PMID: 34389034 PMCID: PMC8361246 DOI: 10.1186/s12985-021-01633-w] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.
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Affiliation(s)
- Jalen Singh
- School of Interdisciplinary Science, McMaster University, Hamilton, ON, Canada
| | - Pranav Pandit
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
| | - Karen Mossman
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Medicine, McMaster University, Hamilton, ON, Canada.
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada.
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28
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Rochman ND, Wolf YI, Faure G, Mutz P, Zhang F, Koonin EV. Ongoing global and regional adaptive evolution of SARS-CoV-2. Proc Natl Acad Sci U S A 2021; 118:e2104241118. [PMID: 34292871 PMCID: PMC8307621 DOI: 10.1073/pnas.2104241118] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Understanding the trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution is paramount to control the COVID-19 pandemic. We analyzed more than 300,000 high-quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ongoing evolution of SARS-CoV-2 during the pandemic is characterized primarily by purifying selection, but a small set of sites appear to evolve under positive selection. The receptor-binding domain of the spike protein and the region of the nucleocapsid protein associated with nuclear localization signals (NLS) are enriched with positively selected amino acid replacements. These replacements form a strongly connected network of apparent epistatic interactions and are signatures of major partitions in the SARS-CoV-2 phylogeny. Virus diversity within each geographic region has been steadily growing for the entirety of the pandemic, but analysis of the phylogenetic distances between pairs of regions reveals four distinct periods based on global partitioning of the tree and the emergence of key mutations. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. The NLS-associated variants across multiple partitions rose to global prominence in March to July, during a period of stasis in terms of interregional diversity. Finally, beginning in July 2020, multiple mutations, some of which have since been demonstrated to enable antibody evasion, began to emerge associated with ongoing regional diversification, which might be indicative of speciation.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142;
- HHMI, Massachusetts Institute of Technology, Cambridge, MA 02139
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;
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Redondo N, Zaldívar-López S, Garrido JJ, Montoya M. SARS-CoV-2 Accessory Proteins in Viral Pathogenesis: Knowns and Unknowns. Front Immunol 2021; 12:708264. [PMID: 34305949 PMCID: PMC8293742 DOI: 10.3389/fimmu.2021.708264] [Citation(s) in RCA: 171] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/22/2021] [Indexed: 12/23/2022] Open
Abstract
There are still many unanswered questions concerning viral SARS-CoV-2 pathogenesis in COVID-19. Accessory proteins in SARS-CoV-2 consist of eleven viral proteins whose roles during infection are still not completely understood. Here, a review on the current knowledge of SARS-CoV-2 accessory proteins is summarized updating new research that could be critical in understanding SARS-CoV-2 interaction with the host. Some accessory proteins such as ORF3b, ORF6, ORF7a and ORF8 have been shown to be important IFN-I antagonists inducing an impairment in the host immune response. In addition, ORF3a is involved in apoptosis whereas others like ORF9b and ORF9c interact with cellular organelles leading to suppression of the antiviral response in infected cells. However, possible roles of ORF7b and ORF10 are still awaiting to be described. Also, ORF3d has been reassigned. Relevant information on the knowns and the unknowns in these proteins is analyzed, which could be crucial for further understanding of SARS-CoV-2 pathogenesis and to design strategies counteracting their actions evading immune responses in COVID-19.
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Affiliation(s)
- Natalia Redondo
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
| | - Sara Zaldívar-López
- Animal Breeding and Genomics Group, Department of Genetics, Faculty of Veterinary Medicine, University of Córdoba, Córdoba, Spain
- Immunogenomics and Molecular Pathogenesis GA14 Group, Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Juan J. Garrido
- Animal Breeding and Genomics Group, Department of Genetics, Faculty of Veterinary Medicine, University of Córdoba, Córdoba, Spain
- Immunogenomics and Molecular Pathogenesis GA14 Group, Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Maria Montoya
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
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Laneri S, Brancaccio M, Mennitti C, De Biasi MG, Pero ME, Pisanelli G, Scudiero O, Pero R. Antimicrobial Peptides and Physical Activity: A Great Hope against COVID 19. Microorganisms 2021; 9:1415. [PMID: 34209064 PMCID: PMC8304224 DOI: 10.3390/microorganisms9071415] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/07/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial peptides (AMPs), α- and β-defensins, possess antiviral properties. These AMPs achieve viral inhibition through different mechanisms of action. For example, they can: (i) bind directly to virions; (ii) bind to and modulate host cell-surface receptors, disrupting intracellular signaling; (iii) function as chemokines to augment and alter adaptive immune responses. Given their antiviral properties and the fact that the development of an effective coronavirus disease 2019 (COVID-19) treatment is an urgent public health priority, they and their derivatives are being explored as potential therapies against COVID-19. These explorations using various strategies, range from their direct interaction with the virus to using them as vaccine adjuvants. However, AMPs do not work in isolation, specifically in their role as potent immune modulators, where they interact with toll-like receptors (TLRs) and chemokine receptors. Both of these receptors have been shown to play roles in COVID-19 pathogenesis. In addition, it is known that a healthy lifestyle accompanied by controlled physical activity can represent a natural weapon against COVID-19. In competitive athletes, an increase in serum defensins has been shown to function as self-protection from the attack of microorganisms, consequently a controlled physical activity could act as a support to any therapies in fighting COVID-19. Therefore, including information on all these players' interactions would produce a complete picture of AMP-based therapies' response.
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Affiliation(s)
- Sonia Laneri
- Department of Pharmacy, University of Naples Federico II, Via Montesano, 80138 Naples, Italy; (S.L.); (M.G.D.B.)
| | - Mariarita Brancaccio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (M.B.); (C.M.)
| | - Cristina Mennitti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (M.B.); (C.M.)
| | - Margherita G. De Biasi
- Department of Pharmacy, University of Naples Federico II, Via Montesano, 80138 Naples, Italy; (S.L.); (M.G.D.B.)
| | - Maria Elena Pero
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Federico Delpino 1, 80137 Naples, Italy; (M.E.P.); (G.P.)
| | - Giuseppe Pisanelli
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Federico Delpino 1, 80137 Naples, Italy; (M.E.P.); (G.P.)
| | - Olga Scudiero
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (M.B.); (C.M.)
- Ceinge Biotecnologie Avanzate S.C.aR.L., 80131 Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
| | - Raffaela Pero
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (M.B.); (C.M.)
- Ceinge Biotecnologie Avanzate S.C.aR.L., 80131 Naples, Italy
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31
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Farkas C, Mella A, Turgeon M, Haigh JJ. A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity. Front Microbiol 2021; 12:665041. [PMID: 34234758 PMCID: PMC8256173 DOI: 10.3389/fmicb.2021.665041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 05/28/2021] [Indexed: 12/27/2022] Open
Abstract
An unprecedented amount of SARS-CoV-2 sequencing has been performed, however, novel bioinformatic tools to cope with and process these large datasets is needed. Here, we have devised a bioinformatic pipeline that inputs SARS-CoV-2 genome sequencing in FASTA/FASTQ format and outputs a single Variant Calling Format file that can be processed to obtain variant annotations and perform downstream population genetic testing. As proof of concept, we have analyzed over 229,000 SARS-CoV-2 viral sequences up until November 30, 2020. We have identified over 39,000 variants worldwide with increased polymorphisms, spanning the ORF3a gene as well as the 3' untranslated (UTR) regions, specifically in the conserved stem loop region of SARS-CoV-2 which is accumulating greater observed viral diversity relative to chance variation. Our analysis pipeline has also discovered the existence of SARS-CoV-2 hypermutation with low frequency (less than in 2% of genomes) likely arising through host immune responses and not due to sequencing errors. Among annotated non-sense variants with a population frequency over 1%, recurrent inactivation of the ORF8 gene was found. This was found to be present in the newly identified B.1.1.7 SARS-CoV-2 lineage that originated in the United Kingdom. Almost all VOC-containing genomes possess one stop codon in ORF8 gene (Q27∗), however, 13% of these genomes also contains another stop codon (K68∗), suggesting that ORF8 loss does not interfere with SARS-CoV-2 spread and may play a role in its increased virulence. We have developed this computational pipeline to assist researchers in the rapid analysis and characterization of SARS-CoV-2 variation.
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Affiliation(s)
- Carlos Farkas
- Research Institute in Oncology and Hematology (RIOH), CancerCare Manitoba, Winnipeg, MB, Canada
- Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Andy Mella
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
- Instituto de Ciencias Naturales, Universidad de las Américas, Santiago, Chile
| | - Maxime Turgeon
- Department of Statistics, University of Manitoba, Winnipeg, MB, Canada
- Department of Computer Science, University of Manitoba, Winnipeg, MB, Canada
| | - Jody J. Haigh
- Research Institute in Oncology and Hematology (RIOH), CancerCare Manitoba, Winnipeg, MB, Canada
- Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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32
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Chaqroun A, Hartard C, Schvoerer E. Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. Viruses 2021; 13:1171. [PMID: 34207378 PMCID: PMC8234553 DOI: 10.3390/v13061171] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is genetically variable, allowing it to adapt to various hosts including humans. Indeed, SARS-CoV-2 has accumulated around two mutations per genome each month. The first relevant event in this context was the occurrence of the mutant D614G in the Spike gene. Moreover, several variants have emerged, including the well-characterized 20I/501Y.V1, 20H/501Y.V2, and 20J/501Y.V3 strains, in addition to those that have been detected within clusters, such as 19B/501Y or 20C/655Y in France. Mutants have also emerged in animals, including a variant transmitted to humans, namely, the Mink variant detected in Denmark. The emergence of these variants has affected the transmissibility of the virus (for example, 20I/501Y.V1, which was up to 82% more transmissible than other preexisting variants), its severity, and its ability to escape natural, adaptive, vaccine, and therapeutic immunity. In this respect, we review the literature on variants that have currently emerged, and their effect on vaccines and therapies, and, in particular, monoclonal antibodies (mAbs). The emergence of SARS-CoV-2 variants must be examined to allow effective preventive and curative control strategies to be developed.
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Affiliation(s)
- Ahlam Chaqroun
- CNRS, LCPME, Université de Lorraine, 54100 Nancy, France; (A.C.); (C.H.)
| | - Cédric Hartard
- CNRS, LCPME, Université de Lorraine, 54100 Nancy, France; (A.C.); (C.H.)
- Laboratoire de Virologie, CHRU de Nancy Brabois, 54500 Vandoeuvre-lès-Nancy, France
| | - Evelyne Schvoerer
- CNRS, LCPME, Université de Lorraine, 54100 Nancy, France; (A.C.); (C.H.)
- Laboratoire de Virologie, CHRU de Nancy Brabois, 54500 Vandoeuvre-lès-Nancy, France
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33
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Clementi N, Ghosh S, De Santis M, Castelli M, Criscuolo E, Zanoni I, Clementi M, Mancini N. Viral Respiratory Pathogens and Lung Injury. Clin Microbiol Rev 2021; 34:e00103-20. [PMID: 33789928 PMCID: PMC8142519 DOI: 10.1128/cmr.00103-20] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Several viruses target the human respiratory tract, causing different clinical manifestations spanning from mild upper airway involvement to life-threatening acute respiratory distress syndrome (ARDS). As dramatically evident in the ongoing SARS-CoV-2 pandemic, the clinical picture is not always easily predictable due to the combined effect of direct viral and indirect patient-specific immune-mediated damage. In this review, we discuss the main RNA (orthomyxoviruses, paramyxoviruses, and coronaviruses) and DNA (adenoviruses, herpesviruses, and bocaviruses) viruses with respiratory tropism and their mechanisms of direct and indirect cell damage. We analyze the thin line existing between a protective immune response, capable of limiting viral replication, and an unbalanced, dysregulated immune activation often leading to the most severe complication. Our comprehension of the molecular mechanisms involved is increasing and this should pave the way for the development and clinical use of new tailored immune-based antiviral strategies.
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Affiliation(s)
- Nicola Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sreya Ghosh
- Harvard Medical School, Boston Children's Hospital, Division of Immunology, Boston, Massachusetts, USA
| | - Maria De Santis
- Department of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center-IRCCS, Rozzano, Italy
| | - Matteo Castelli
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
| | - Elena Criscuolo
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
| | - Ivan Zanoni
- Harvard Medical School, Boston Children's Hospital, Division of Immunology, Boston, Massachusetts, USA
- Harvard Medical School, Boston Children's Hospital, Division of Gastroenterology, Boston, Massachusetts, USA
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nicasio Mancini
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Timmers LFSM, Peixoto JV, Ducati RG, Bachega JFR, de Mattos Pereira L, Caceres RA, Majolo F, da Silva GL, Anton DB, Dellagostin OA, Henriques JAP, Xavier LL, Goettert MI, Laufer S. SARS-CoV-2 mutations in Brazil: from genomics to putative clinical conditions. Sci Rep 2021; 11:11998. [PMID: 34099808 PMCID: PMC8184806 DOI: 10.1038/s41598-021-91585-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/27/2021] [Indexed: 02/05/2023] Open
Abstract
Due to the high rate of transmissibility, Brazil became the new COVID-19 outbreak epicenter and, since then, is being monitored to understand how SARS-CoV-2 mutates and spreads. We combined genomic and structural analysis to evaluate genomes isolated from different regions of Brazil and show that the most prevalent mutations were located in the S, N, ORF3a and ORF6 genes, which are involved in different stages of viral life cycle and its interaction with the host cells. Structural analysis brought to light the positions of these mutations on protein structures, contributing towards studies of selective structure-based drug discovery and vaccine development.
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Affiliation(s)
- Luis Fernando Saraiva Macedo Timmers
- Graduate Program in Biotechnology, Universidade Do Vale Do Taquari - Univates, Lajeado, RS, Brazil.
- Graduate Program in Medical Sciences, Universidade Do Vale Do Taquari - Univates, Lajeado, RS, Brazil.
| | - Julia Vasconcellos Peixoto
- Graduate Program in Cellular and Molecular Biology, Federal University of Rio Grande Do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Rodrigo Gay Ducati
- Graduate Program in Biotechnology, Universidade Do Vale Do Taquari - Univates, Lajeado, RS, Brazil
| | - José Fernando Ruggiero Bachega
- Department of Pharmacosciences, Federal University of Health Sciences of Porto Alegre - UFCSPA, Porto Alegre, RS, Brazil
| | - Leandro de Mattos Pereira
- Laboratory of Molecular Microbial Ecology, Federal University of Rio de Janeiro - UFRJ, Rio de Janeiro, RJ, Brazil
| | - Rafael Andrade Caceres
- Department of Pharmacosciences, Federal University of Health Sciences of Porto Alegre - UFCSPA, Porto Alegre, RS, Brazil
- Graduate Program in Biosciences, Federal University of Health Sciences of Porto Alegre - UFCSPA, Porto Alegre, RS, Brazil
- Graduate Program in Health Sciences, Federal University of Health Sciences of Porto Alegre - UFCSPA, Porto Alegre, RS, Brazil
| | - Fernanda Majolo
- Graduate Program in Biotechnology, Universidade Do Vale Do Taquari - Univates, Lajeado, RS, Brazil
| | | | - Débora Bublitz Anton
- Graduate Program in Biotechnology, Universidade Do Vale Do Taquari - Univates, Lajeado, RS, Brazil
| | - Odir Antônio Dellagostin
- Graduate Program in Biotechnology, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas - UFPel, Pelotas, RS, Brazil
| | - João Antônio Pegas Henriques
- Graduate Program in Biotechnology, Universidade Do Vale Do Taquari - Univates, Lajeado, RS, Brazil
- Graduate Program in Medical Sciences, Universidade Do Vale Do Taquari - Univates, Lajeado, RS, Brazil
| | - Léder Leal Xavier
- Laboratory of Cell and Tissue Biology, Pontifical Catholic University of Rio Grande Do Sul - PUCRS, Porto Alegre, RS, Brazil
| | - Márcia Inês Goettert
- Graduate Program in Biotechnology, Universidade Do Vale Do Taquari - Univates, Lajeado, RS, Brazil
- Graduate Program in Medical Sciences, Universidade Do Vale Do Taquari - Univates, Lajeado, RS, Brazil
| | - Stefan Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Tübingen, Tübingen, Germany.
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35
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Das A, Ahmed R, Akhtar S, Begum K, Banu S. An overview of basic molecular biology of SARS-CoV-2 and current COVID-19 prevention strategies. GENE REPORTS 2021; 23:101122. [PMID: 33821222 PMCID: PMC8012276 DOI: 10.1016/j.genrep.2021.101122] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/08/2021] [Accepted: 03/24/2021] [Indexed: 01/18/2023]
Abstract
Coronavirus Disease 2019 (COVID-19) manifests as extreme acute respiratory conditions caused by a novel beta coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) which is reported to be the seventh coronavirus to infect humans. Like other SARS-CoVs it has a large positive-stranded RNA genome. But, specific furin site in the spike protein, mutation prone and phylogenetically mess open reading frame1ab (Orf1ab) separates SARS-CoV-2 from other RNA viruses. Since the outbreak (February-March 2020), researchers, scientists, and medical professionals are inspecting all possible facts and aspects including its replication, detection, and prevention strategies. This led to the prompt identification of its basic biology, genome characterization, structural and expression based functional information of proteins, and utilization of this information in optimizing strategies to prevent its spread. This review summarizes the recent updates on the basic molecular biology of SARS-CoV-2 and prevention strategies undertaken worldwide to tackle COVID-19. This recent information can be implemented for the development and designing of therapeutics against SARS-CoV-2.
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Key Words
- AEC2, angiotensin-converting enzyme 2
- CD4 and CD8, cluster of differentiation
- CDC, Centers for Disease Control and Prevention
- COVID-19, Coronavirus Diseases 2019
- GM-CSF, macrophage colony-stimulating factor
- Genome organization and expression
- HCV, hepatitis C virus
- HIV, human immune deficiency virus
- LAMP, loop mediated isothermal amplification
- MARS-CoV, Middle East Respiratory Syndrome Coronavirus
- Prevention strategies
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- WHO, World Health Organization
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Affiliation(s)
- Ankur Das
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Raja Ahmed
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Suraiya Akhtar
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Khaleda Begum
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Sofia Banu
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014, India
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36
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Bickler SW, Cauvi DM, Fisch KM, Prieto JM, Sykes AG, Thangarajah H, Lazar DA, Ignacio RC, Gerstmann DR, Ryan AF, Bickler PE, De Maio A. Extremes of age are associated with differences in the expression of selected pattern recognition receptor genes and ACE2, the receptor for SARS-CoV-2: implications for the epidemiology of COVID-19 disease. BMC Med Genomics 2021; 14:138. [PMID: 34030677 PMCID: PMC8142073 DOI: 10.1186/s12920-021-00970-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Background Older aged adults and those with pre-existing conditions are at highest risk for severe COVID-19 associated outcomes. Methods Using a large dataset of genome-wide RNA-seq profiles derived from human dermal fibroblasts (GSE113957) we investigated whether age affects the expression of pattern recognition receptor (PRR) genes and ACE2, the receptor for SARS-CoV-2. Results Extremes of age are associated with increased expression of selected PRR genes, ACE2 and four genes that encode proteins that have been shown to interact with SAR2-CoV-2 proteins. Conclusions Assessment of PRR expression might provide a strategy for stratifying the risk of severe COVID-19 disease at both the individual and population levels. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-00970-7.
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Affiliation(s)
- Stephen W Bickler
- Rady Children's Hospital, Rady Children's Hospital, University of California San Diego, 3030 Children's Way, San Diego, CA, 92123, USA. .,Department of Surgery, University of California San Diego, La Jolla, CA, USA. .,Center for Investigations of Health and Education Disparities, University of California San Diego, La Jolla, CA, USA.
| | - David M Cauvi
- Department of Surgery, University of California San Diego, La Jolla, CA, USA.,Center for Investigations of Health and Education Disparities, University of California San Diego, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - James M Prieto
- Rady Children's Hospital, Rady Children's Hospital, University of California San Diego, 3030 Children's Way, San Diego, CA, 92123, USA.,Naval Medical Center San Diego, San Diego, CA, USA
| | - Alicia G Sykes
- Rady Children's Hospital, Rady Children's Hospital, University of California San Diego, 3030 Children's Way, San Diego, CA, 92123, USA.,Naval Medical Center San Diego, San Diego, CA, USA
| | - Hariharan Thangarajah
- Rady Children's Hospital, Rady Children's Hospital, University of California San Diego, 3030 Children's Way, San Diego, CA, 92123, USA.,Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | - David A Lazar
- Rady Children's Hospital, Rady Children's Hospital, University of California San Diego, 3030 Children's Way, San Diego, CA, 92123, USA.,Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | - Romeo C Ignacio
- Rady Children's Hospital, Rady Children's Hospital, University of California San Diego, 3030 Children's Way, San Diego, CA, 92123, USA.,Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | | | - Allen F Ryan
- Department of Surgery, University of California San Diego, La Jolla, CA, USA.,VA Medical Center, San Diego, CA, USA
| | - Philip E Bickler
- Department of Anesthesia, University of California San Francisco, San Francisco, CA, USA
| | - Antonio De Maio
- Department of Surgery, University of California San Diego, La Jolla, CA, USA.,Center for Investigations of Health and Education Disparities, University of California San Diego, La Jolla, CA, USA
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37
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Petrova NV, Ganina KK, Tarasov SA. [Susceptibility of animal species to experimental SARS-CoV-2 ( Coronaviridae: Coronavirinae: Betacoronavirus; Sarbecovirus) infection]. Vopr Virusol 2021; 66:103-111. [PMID: 33993680 DOI: 10.36233/0507-4088-47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 05/15/2021] [Indexed: 11/05/2022]
Abstract
Due to the new coronavirus infection pandemic, the global scientific community has been forced to change the direction of the most research, focusing on vaccine development as well as the search for new antiviral drugs to treat COVID-19. The choice of experimental models, timeframe and approaches for evaluating drugs and vaccines under development is crucial for the development of effective measures to prevent and control this disease.The purpose of this review was to summarize the relevant data concerning the susceptibility of laboratory animals to SARS-CoV-2. This paper describes the most virus-susceptible animal species that can be used to reproduce coronavirus infection, stressing the main advantages and disadvantages of each of them.According to the latest data, small rodents (Rodentia) and non-human primates (Strepsirrhini) are commonly used in the scientific community to model coronavirus infection. The viral load in the upper and lower parts of the respiratory system, clinical symptoms of infection (weight loss, body temperature and general health status), pathomorphological picture in target organs and the production of antibodies after infection are considered to the main markers of pathology. Despite the vast amount of data, none of the described models of SARS-CoV-2 infection may be considered a gold standard, since they do not reproduce all spectrum of morphological and pathogenetic mechanisms of infection, and do not fully reflect the clinical picture observed in patients in human population.Based on the analyzed literature data, we suppose that Syrian hamster (Mesocricetus auratus) and mice (Muridae) expressing the angiotensin converting enzyme receptor 2 (ACE2) are the most suitable animal species for their use in experiments with SARS-CoV-2 infection. The development of neutralizing antibodies makes it possible to evaluate the efficacy of vaccines, while the course and severity of symptoms infection makes the use of mice and hamsters especially popular for screening pharmacological substances with antiviral mechanism of action, when their administration can prevent or slow the disease progression.
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Affiliation(s)
- N V Petrova
- FSBRI «Institute of General Pathology and Pathophysiology»; LLC «NPF «Materia Medica Holding»
| | | | - S A Tarasov
- FSBRI «Institute of General Pathology and Pathophysiology»; LLC «NPF «Materia Medica Holding»
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Jungreis I, Sealfon R, Kellis M. SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Nat Commun 2021; 12:2642. [PMID: 33976134 PMCID: PMC8113528 DOI: 10.1038/s41467-021-22905-7] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 03/28/2021] [Indexed: 02/03/2023] Open
Abstract
Despite its clinical importance, the SARS-CoV-2 gene set remains unresolved, hindering dissection of COVID-19 biology. We use comparative genomics to provide a high-confidence protein-coding gene set, characterize evolutionary constraint, and prioritize functional mutations. We select 44 Sarbecovirus genomes at ideally-suited evolutionary distances, and quantify protein-coding evolutionary signatures and overlapping constraint. We find strong protein-coding signatures for ORFs 3a, 6, 7a, 7b, 8, 9b, and a novel alternate-frame gene, ORF3c, whereas ORFs 2b, 3d/3d-2, 3b, 9c, and 10 lack protein-coding signatures or convincing experimental evidence of protein-coding function. Furthermore, we show no other conserved protein-coding genes remain to be discovered. Mutation analysis suggests ORF8 contributes to within-individual fitness but not person-to-person transmission. Cross-strain and within-strain evolutionary pressures agree, except for fewer-than-expected within-strain mutations in nsp3 and S1, and more-than-expected in nucleocapsid, which shows a cluster of mutations in a predicted B-cell epitope, suggesting immune-avoidance selection. Evolutionary histories of residues disrupted by spike-protein substitutions D614G, N501Y, E484K, and K417N/T provide clues about their biology, and we catalog likely-functional co-inherited mutations. Previously reported RNA-modification sites show no enrichment for conservation. Here we report a high-confidence gene set and evolutionary-history annotations providing valuable resources and insights on SARS-CoV-2 biology, mutations, and evolution.
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Affiliation(s)
- Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Rachel Sealfon
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Majumdar P, Niyogi S. SARS-CoV-2 mutations: the biological trackway towards viral fitness. Epidemiol Infect 2021; 149:e110. [PMID: 33928885 PMCID: PMC8134885 DOI: 10.1017/s0950268821001060] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/26/2021] [Accepted: 04/27/2021] [Indexed: 01/10/2023] Open
Abstract
The outbreak of pneumonia-like respiratory disorder at China and its rapid transmission world-wide resulted in public health emergency, which brought lineage B betacoronaviridae SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) into spotlight. The fairly high mutation rate, frequent recombination and interspecies transmission in betacoronaviridae are largely responsible for their temporal changes in infectivity and virulence. Investigation of global SARS-CoV-2 genotypes revealed considerable mutations in structural, non-structural, accessory proteins as well as untranslated regions. Among the various types of mutations, single-nucleotide substitutions are the predominant ones. In addition, insertion, deletion and frame-shift mutations are also reported, albeit at a lower frequency. Among the structural proteins, spike glycoprotein and nucleocapsid phosphoprotein accumulated a larger number of mutations whereas envelope and membrane proteins are mostly conserved. Spike protein and RNA-dependent RNA polymerase variants, D614G and P323L in combination became dominant world-wide. Divergent genetic variants created serious challenge towards the development of therapeutics and vaccines. This review will consolidate mutations in different SARS-CoV-2 proteins and their implications on viral fitness.
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Affiliation(s)
| | - Sougata Niyogi
- Dinabandhu Andrews Institute of Technology and Management, Block-S, 1/406A, Patuli, Kolkata, West Bengal700094, India
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Meinberger D, Koch M, Roth A, Hermes G, Stemler J, Cornely OA, Streichert T, Klatt AR. Analysis of IgM, IgA, and IgG isotype antibodies Directed against SARS-CoV-2 spike glycoprotein and ORF8 in the course of COVID-19. Sci Rep 2021; 11:8920. [PMID: 33903660 PMCID: PMC8076237 DOI: 10.1038/s41598-021-88356-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/08/2021] [Indexed: 12/24/2022] Open
Abstract
Immunoassays are a standard diagnostic tool that assesses immunity in severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection. However, immunoassays do not provide information about contaminating antigens or cross-reactions and might exhibit inaccurately high sensitivity and low specificity. We aimed to gain insight into the serological immune response of SARS-CoV-2 patients by immunoblot analysis. We analyzed serum immunoglobulins IgM, -A, and -G directed against SARS-CoV-2 proteins by immunoblot analysis from 12 infected patients. We determined IgG isotype antibodies by commercially available ELISA and assessed the clinical parameters of inflammation status and kidney and liver injury. Unexpectedly, we found no correlation between the presence of antibodies and the future course of the disease. However, attention should be paid to the parameters CRP, IL-6, and LDH. We found evidence of antibody cross-reactivity, which questions the reliability of results for serum samples that tested negative for anti-SARS-CoV-2 antibodies when assessed by immunoassays. Nevertheless, for the detection of IgG anti-SARS-CoV-2 antibodies, our data suggest that the use of the spike glycoprotein in immunoassays should be sufficient to identify positive patients. Using a combination of the spike glycoprotein and the open reading frame 8 protein could prove to be the best way of detecting anti-SARS-CoV-2 IgM antibodies.
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Affiliation(s)
- Denise Meinberger
- Institute for Clinical Chemistry, Medical Faculty, University of Cologne, 50937, Cologne, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Medical Faculty, University of Cologne, 50931, Cologne, Germany
- Center for Biochemistry II, Medical Faculty, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, 50931, Cologne, Germany
| | - Annika Roth
- Institute for Clinical Chemistry, Medical Faculty, University of Cologne, 50937, Cologne, Germany
| | - Gabriele Hermes
- Institute for Clinical Chemistry, Medical Faculty, University of Cologne, 50937, Cologne, Germany
| | - Jannik Stemler
- Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), Medical Faculty, University of Cologne, 50937, Cologne, Germany
- Chair Translational Research, Cologne Excellence Cluster On Cellular Stress Responses in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, 50931, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Medical Faculty, University of Cologne, 50937, Cologne, Germany
| | - Oliver A Cornely
- Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), Medical Faculty, University of Cologne, 50937, Cologne, Germany
- Chair Translational Research, Cologne Excellence Cluster On Cellular Stress Responses in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, 50931, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Medical Faculty, University of Cologne, 50937, Cologne, Germany
| | - Thomas Streichert
- Institute for Clinical Chemistry, Medical Faculty, University of Cologne, 50937, Cologne, Germany
| | - Andreas R Klatt
- Institute for Clinical Chemistry, Medical Faculty, University of Cologne, 50937, Cologne, Germany.
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Valdez-Cruz NA, García-Hernández E, Espitia C, Cobos-Marín L, Altamirano C, Bando-Campos CG, Cofas-Vargas LF, Coronado-Aceves EW, González-Hernández RA, Hernández-Peralta P, Juárez-López D, Ortega-Portilla PA, Restrepo-Pineda S, Zelada-Cordero P, Trujillo-Roldán MA. Integrative overview of antibodies against SARS-CoV-2 and their possible applications in COVID-19 prophylaxis and treatment. Microb Cell Fact 2021; 20:88. [PMID: 33888152 PMCID: PMC8061467 DOI: 10.1186/s12934-021-01576-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/03/2021] [Indexed: 02/06/2023] Open
Abstract
SARS-CoV-2 is a novel β-coronavirus that caused the COVID-19 pandemic disease, which spread rapidly, infecting more than 134 million people, and killing almost 2.9 million thus far. Based on the urgent need for therapeutic and prophylactic strategies, the identification and characterization of antibodies has been accelerated, since they have been fundamental in treating other viral diseases. Here, we summarized in an integrative manner the present understanding of the immune response and physiopathology caused by SARS-CoV-2, including the activation of the humoral immune response in SARS-CoV-2 infection and therefore, the synthesis of antibodies. Furthermore, we also discussed about the antibodies that can be generated in COVID-19 convalescent sera and their associated clinical studies, including a detailed characterization of a variety of human antibodies and identification of antibodies from other sources, which have powerful neutralizing capacities. Accordingly, the development of effective treatments to mitigate COVID-19 is expected. Finally, we reviewed the challenges faced in producing potential therapeutic antibodies and nanobodies by cell factories at an industrial level while ensuring their quality, efficacy, and safety.
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Affiliation(s)
- Norma A Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México.
| | - Enrique García-Hernández
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Clara Espitia
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Laura Cobos-Marín
- Facultad de Medicina Veterinaria Y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Claudia Altamirano
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil N° 2950, Valparaíso, Chile
| | - Carlos G Bando-Campos
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Luis F Cofas-Vargas
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Enrique W Coronado-Aceves
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Ricardo A González-Hernández
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Pablo Hernández-Peralta
- Facultad de Medicina Veterinaria Y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Daniel Juárez-López
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Paola A Ortega-Portilla
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Sara Restrepo-Pineda
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Patricio Zelada-Cordero
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Mauricio A Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México.
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Yadav R, Chaudhary JK, Jain N, Chaudhary PK, Khanra S, Dhamija P, Sharma A, Kumar A, Handu S. Role of Structural and Non-Structural Proteins and Therapeutic Targets of SARS-CoV-2 for COVID-19. Cells 2021; 10:cells10040821. [PMID: 33917481 PMCID: PMC8067447 DOI: 10.3390/cells10040821] [Citation(s) in RCA: 241] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus belongs to the family of Coronaviridae, comprising single-stranded, positive-sense RNA genome (+ ssRNA) of around 26 to 32 kilobases, and has been known to cause infection to a myriad of mammalian hosts, such as humans, cats, bats, civets, dogs, and camels with varied consequences in terms of death and debilitation. Strikingly, novel coronavirus (2019-nCoV), later renamed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), and found to be the causative agent of coronavirus disease-19 (COVID-19), shows 88% of sequence identity with bat-SL-CoVZC45 and bat-SL-CoVZXC21, 79% with SARS-CoV and 50% with MERS-CoV, respectively. Despite key amino acid residual variability, there is an incredible structural similarity between the receptor binding domain (RBD) of spike protein (S) of SARS-CoV-2 and SARS-CoV. During infection, spike protein of SARS-CoV-2 compared to SARS-CoV displays 10-20 times greater affinity for its cognate host cell receptor, angiotensin-converting enzyme 2 (ACE2), leading proteolytic cleavage of S protein by transmembrane protease serine 2 (TMPRSS2). Following cellular entry, the ORF-1a and ORF-1ab, located downstream to 5' end of + ssRNA genome, undergo translation, thereby forming two large polyproteins, pp1a and pp1ab. These polyproteins, following protease-induced cleavage and molecular assembly, form functional viral RNA polymerase, also referred to as replicase. Thereafter, uninterrupted orchestrated replication-transcription molecular events lead to the synthesis of multiple nested sets of subgenomic mRNAs (sgRNAs), which are finally translated to several structural and accessory proteins participating in structure formation and various molecular functions of virus, respectively. These multiple structural proteins assemble and encapsulate genomic RNA (gRNA), resulting in numerous viral progenies, which eventually exit the host cell, and spread infection to rest of the body. In this review, we primarily focus on genomic organization, structural and non-structural protein components, and potential prospective molecular targets for development of therapeutic drugs, convalescent plasm therapy, and a myriad of potential vaccines to tackle SARS-CoV-2 infection.
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Affiliation(s)
- Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India; (P.D.); (S.H.)
- Correspondence: ; Tel.: +91-94-1415-3849
| | | | - Neeraj Jain
- Department of Medical Oncology & Hematology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India;
| | - Pankaj Kumar Chaudhary
- Molecular Biology & Proteomics Laboratory, Department of Biotechnology, Indian Institute of Technology (IIT), Roorkee 247667, India;
| | - Supriya Khanra
- Uttaranchal Institute of Pharmaceutical Sciences, Dehradun 248007, India;
| | - Puneet Dhamija
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India; (P.D.); (S.H.)
| | - Ambika Sharma
- Department of Biochemistry, U.P. Pt. Deen Dayal Upadhyaya Veterinary Science University, Mathura 281001, India;
| | - Ashish Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh 249203, India;
| | - Shailendra Handu
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India; (P.D.); (S.H.)
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Zhang Y, Hu H, Liu W, Yan SM, Li Y, Tan L, Chen Y, Liu J, Peng Z, Yuan Y, Huang W, Yu F, He X, Li B, Zhang H. Amino acids and RagD potentiate mTORC1 activation in CD8 + T cells to confer antitumor immunity. J Immunother Cancer 2021; 9:e002137. [PMID: 33883257 PMCID: PMC8061841 DOI: 10.1136/jitc-2020-002137] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND In the tumor microenvironment, tumor cells are able to suppress antitumor immunity by competing for essential nutrients, including amino acids. However, whether amino acid depletion modulates the activity of CD8+ tumor-infiltrating lymphocytes (TILs) is unclear. METHOD In this study, we evaluated the roles of amino acids and the Rag complex in regulating mammalian target of rapamycin complex 1 (mTORC1) signaling in CD8+ TILs. RESULTS We discovered that the Rag complex, particularly RagD, was crucial for CD8+ T-cell antitumor immunity. RagD expression was positively correlated with the antitumor response of CD8+ TILs in both murine syngeneic tumor xenografts and clinical human colon cancer samples. On RagD deficiency, CD8+ T cells were rendered more dysfunctional, as demonstrated by attenuation of mTORC1 signaling and reductions in proliferation and cytokine secretion. Amino acids maintained RagD-mediated mTORC1 translocation to the lysosome, thereby achieving maximal mTORC1 activity in CD8+ T cells. Moreover, the limited T-cell access to leucine (LEU), overshadowed by tumor cell amino acid consumption, led to impaired RagD-dependent mTORC1 activity. Finally, combined with antiprogrammed cell death protein 1 antibody, LEU supplementation improved T-cell immunity in MC38 tumor-bearing mice in vivo. CONCLUSION Our results revealed that robust signaling of amino acids by RagD and downstream mTORC1 signaling were crucial for T-cell receptor-initiated antitumor immunity. The characterization the role of RagD and LEU in nutrient mTORC1 signaling in TILs might suggest potential therapeutic strategies based on the manipulation of RagD and its upstream pathway.
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Affiliation(s)
- Yiwen Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hongrong Hu
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Weiwei Liu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shu-Mei Yan
- Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuzhuang Li
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Likai Tan
- Institute of Immunology, Hannover Medical School, Hannover, Niedersachsen, Germany
| | - Yingshi Chen
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jun Liu
- School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Zhilin Peng
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yaochang Yuan
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenjing Huang
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Fei Yu
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xin He
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Bo Li
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hui Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
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Structural insights into SARS-CoV-2 infection and therapeutics development. Stem Cell Res 2021; 52:102219. [PMID: 33550140 PMCID: PMC7985237 DOI: 10.1016/j.scr.2021.102219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 01/18/2023] Open
Abstract
The current COVID-19 pandemic is caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). By late October 2020, more than 43 million cases of infections, including over 1.15 million deaths, have been confirmed worldwide. This review focuses on our current understanding of SARS-CoV-2 from the perspective of the three-dimensional (3D) structures of SARS-CoV-2 viral proteins and their implications on therapeutics development against COVID-19.
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Surleac M, Casangiu C, Banica L, Milu P, Florea D, Sandulescu O, Streinu-Cercel A, Vlaicu O, Tudor A, Hohan R, Paraschiv S, Otelea D. Short Communication:Evidence of Novel SARS-CoV-2 Variants Circulation in Romania. AIDS Res Hum Retroviruses 2021; 37:329-332. [PMID: 33544010 DOI: 10.1089/aid.2021.0009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
New SARS-CoV-2 variants are constantly emerging and putting a strain on public health systems by spreading faster and potentially evading immune protection through vaccination. One of these strains is the B.1.1.7 variant that has initially been described in the United Kingdom and has subsequently spread to several countries. Monitoring the amplification of the S gene-a major hotspot for molecular evolution-by reverse transcription polymerase chain reaction (RT-PCR) allows rapidly screening for such variants. This report describes the detection of sequence variants in Romania by using this strategy followed by next-generation sequencing of the entire genome for confirmation and further characterization. One B.1.1.7 and three B.1.258 sequences were confirmed. Each of these strains presented additional mutations with possible impact on the replicative capacity. Public health strategies should be devised to ensure molecular monitoring of SARS-CoV-2 evolution during the pandemic and allow adequate and rapid reaction.
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Affiliation(s)
- Marius Surleac
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, Bucharest, Romania
- Research Institute of the University of Bucharest, Bucharest, Romania
| | - Corina Casangiu
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, Bucharest, Romania
- “Marie Curie” Emergency Clinical Hospital, Bucharest, Romania
| | - Leontina Banica
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, Bucharest, Romania
| | - Petre Milu
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, Bucharest, Romania
- “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania
| | - Dragos Florea
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, Bucharest, Romania
- “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania
| | - Oana Sandulescu
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, Bucharest, Romania
- “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania
| | - Anca Streinu-Cercel
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, Bucharest, Romania
- “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania
| | - Ovidiu Vlaicu
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, Bucharest, Romania
| | - Andreea Tudor
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, Bucharest, Romania
| | - Robert Hohan
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, Bucharest, Romania
| | - Simona Paraschiv
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, Bucharest, Romania
- “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania
| | - Dan Otelea
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, Bucharest, Romania
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Evans N, Martinez E, Petrosillo N, Nichols J, Islam E, Pruitt K, Almodovar S. SARS-CoV-2 and Human Immunodeficiency Virus: Pathogen Pincer Attack. HIV AIDS (Auckl) 2021; 13:361-375. [PMID: 33833585 PMCID: PMC8020331 DOI: 10.2147/hiv.s300055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
Paramount efforts worldwide are seeking to increase understanding of the basic virology of SARS-CoV-2, characterize the spectrum of complications associated with COVID-19, and develop vaccines that can protect from new and recurrent infections with SARS-CoV-2. While we continue learning about this new virus, it is clear that 1) the virus is spread via the respiratory route, primarily by droplets and contact with contaminated surfaces and fomites, as well as by aerosol formation during invasive respiratory procedures; 2) the airborne route is still controversial; and 3) that those infected can spread the virus without necessarily developing COVID-19 (ie, asymptomatic). With the number of SARS-CoV-2 infections increasing globally, the possibility of co-infections and/or co-morbidities is becoming more concerning. Co-infection with Human Immunodeficiency Virus (HIV) is one such example of polyparasitism of interest. This military-themed comparative review of SARS-CoV-2 and HIV details their virology and describes them figuratively as separate enemy armies. HIV, an old enemy dug into trenches in individuals already infected, and SARS-CoV-2 the new army, attempting to attack and capture territories, tissues and organs, in order to provide resources for their expansion. This analogy serves to aid in discussion of three main areas of focus and draw attention to how these viruses may cooperate to gain the upper hand in securing a host. Here we compare their target, the key receptors found on those tissues, viral lifecycles and tactics for immune response surveillance. The last focus is on the immune response to infection, addressing similarities in cytokines released. While the majority of HIV cases can be successfully managed with antiretroviral therapy nowadays, treatments for SARS-CoV-2 are still undergoing research given the novelty of this army.
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Affiliation(s)
- Nicholas Evans
- Texas Tech University Health Sciences Center, Department of Immunology & Molecular Microbiology, Lubbock, TX, USA
| | - Edgar Martinez
- Texas Tech University Health Sciences Center, Department of Immunology & Molecular Microbiology, Lubbock, TX, USA
| | - Nicola Petrosillo
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Jacob Nichols
- Texas Tech University Health Sciences Center, Department of Internal Medicine, Lubbock, TX, USA
| | - Ebtesam Islam
- Texas Tech University Health Sciences Center, Department of Internal Medicine, Lubbock, TX, USA
| | - Kevin Pruitt
- Texas Tech University Health Sciences Center, Department of Immunology & Molecular Microbiology, Lubbock, TX, USA
| | - Sharilyn Almodovar
- Texas Tech University Health Sciences Center, Department of Immunology & Molecular Microbiology, Lubbock, TX, USA
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47
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Zhang Y, Gargan S, Lu Y, Stevenson NJ. An Overview of Current Knowledge of Deadly CoVs and Their Interface with Innate Immunity. Viruses 2021; 13:560. [PMID: 33810391 PMCID: PMC8066579 DOI: 10.3390/v13040560] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Coronaviruses are a large family of zoonotic RNA viruses, whose infection can lead to mild or lethal respiratory tract disease. Severe Acute Respiratory Syndrome-Coronavirus-1 (SARS-CoV-1) first emerged in Guangdong, China in 2002 and spread to 29 countries, infecting 8089 individuals and causing 774 deaths. In 2012, Middle East Respiratory Syndrome-Coronavirus (MERS-CoV) emerged in Saudi Arabia and has spread to 27 countries, with a mortality rate of ~34%. In 2019, SARS-CoV-2 emerged and has spread to 220 countries, infecting over 100,000,000 people and causing more than 2,000,000 deaths to date. These three human coronaviruses cause diseases of varying severity. Most people develop mild, common cold-like symptoms, while some develop acute respiratory distress syndrome (ARDS). The success of all viruses, including coronaviruses, relies on their evolved abilities to evade and modulate the host anti-viral and pro-inflammatory immune responses. However, we still do not fully understand the transmission, phylogeny, epidemiology, and pathogenesis of MERS-CoV and SARS-CoV-1 and -2. Despite the rapid application of a range of therapies for SARS-CoV-2, such as convalescent plasma, remdesivir, hydroxychloroquine and type I interferon, no fully effective treatment has been determined. Remarkably, COVID-19 vaccine research and development have produced several offerings that are now been administered worldwide. Here, we summarise an up-to-date understanding of epidemiology, immunomodulation and ongoing anti-viral and immunosuppressive treatment strategies. Indeed, understanding the interplay between coronaviruses and the anti-viral immune response is crucial to identifying novel targets for therapeutic intervention, which may even prove invaluable for the control of future emerging coronavirus.
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Affiliation(s)
- Yamei Zhang
- Viral Immunology Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland; (Y.Z.); (S.G.)
| | - Siobhan Gargan
- Viral Immunology Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland; (Y.Z.); (S.G.)
| | - Yongxu Lu
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK;
| | - Nigel J. Stevenson
- Viral Immunology Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland; (Y.Z.); (S.G.)
- Viral Immunology Group, Royal College of Surgeons in Ireland—Medical University of Bahrain, Adliya 15503, Bahrain
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48
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Goncalves Cabecinhas AR, Roloff T, Stange M, Bertelli C, Huber M, Ramette A, Chen C, Nadeau S, Gerth Y, Yerly S, Opota O, Pillonel T, Schuster T, Metzger CMJA, Sieber J, Bel M, Wohlwend N, Baumann C, Koch MC, Bittel P, Leuzinger K, Brunner M, Suter-Riniker F, Berlinger L, Søgaard KK, Beckmann C, Noppen C, Redondo M, Steffen I, Seth-Smith HMB, Mari A, Lienhard R, Risch M, Nolte O, Eckerle I, Martinetti Lucchini G, Hodcroft EB, Neher RA, Stadler T, Hirsch HH, Leib SL, Risch L, Kaiser L, Trkola A, Greub G, Egli A. SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Microorganisms 2021; 9:677. [PMID: 33806013 PMCID: PMC8064472 DOI: 10.3390/microorganisms9040677] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/10/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological and microbiological definitions. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 13,387 VoCs have been identified since the detection of the first Swiss case in October 2020, with 4194 being B.1.1.7, 172 B.1.351, and 7 P.1. The remaining 9014 cases of VoCs have been described without further lineage specification. Overall, all diagnostic centers reported a rapid increase of the percentage of detected VOCs, with a range of 6 to 46% between 25 to 31 of January 2021 increasing towards 41 to 82% between 22 to 28 of February. A total of 739 N501Y positive genomes were analysed and show a broad range of introduction events to Switzerland. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs.
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Affiliation(s)
- Ana Rita Goncalves Cabecinhas
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland; (A.R.G.C.); (S.Y.); (I.E.); (L.K.)
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Clinical Bacteriology and Mycology, University Hospital Basel & University of Basel, 4031 Basel, Switzerland
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
| | - Madlen Stange
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Clinical Bacteriology and Mycology, University Hospital Basel & University of Basel, 4031 Basel, Switzerland
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (C.B.); (O.O.); (T.P.); (G.G.)
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (M.H.); (A.T.)
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; (C.C.); (S.N.)
| | - Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; (C.C.); (S.N.)
| | - Yannick Gerth
- Center for Laboratory Medicine, 9001 Saint Gall, Switzerland; (Y.G.); (O.N.)
| | - Sabine Yerly
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland; (A.R.G.C.); (S.Y.); (I.E.); (L.K.)
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
| | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (C.B.); (O.O.); (T.P.); (G.G.)
| | - Trestan Pillonel
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (C.B.); (O.O.); (T.P.); (G.G.)
| | - Tobias Schuster
- Federal Office of Public Health FOPH, 3097 Berne, Switzerland; (T.S.); (M.B.)
| | - Cesar M. J. A. Metzger
- Spiez Laboratory, Federal Office for Civil Protection FOCP, 3700 Spiez, Switzerland; (C.M.J.A.M.); (J.S.)
| | - Jonas Sieber
- Spiez Laboratory, Federal Office for Civil Protection FOCP, 3700 Spiez, Switzerland; (C.M.J.A.M.); (J.S.)
| | - Michael Bel
- Federal Office of Public Health FOPH, 3097 Berne, Switzerland; (T.S.); (M.B.)
| | - Nadia Wohlwend
- Clinical Microbiology, Labormedizinisches Zentrum Dr. Risch, 9470 Buchs SG, Switzerland; (N.W.); (M.R.); (L.R.)
| | - Christian Baumann
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Michel C. Koch
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Pascal Bittel
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Karoline Leuzinger
- Clinical Virology, University Hospital Basel, 4031 Basel, Switzerland; (K.L.); (H.H.H.)
- Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Myrta Brunner
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
| | - Franziska Suter-Riniker
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | | | - Kirstine K. Søgaard
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Clinical Bacteriology and Mycology, University Hospital Basel & University of Basel, 4031 Basel, Switzerland
| | | | - Christoph Noppen
- Viollier AG, 4123 Allschwil, Switzerland; (C.B.); (C.N.); (M.R.)
| | - Maurice Redondo
- Viollier AG, 4123 Allschwil, Switzerland; (C.B.); (C.N.); (M.R.)
| | | | - Helena M. B. Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Clinical Bacteriology and Mycology, University Hospital Basel & University of Basel, 4031 Basel, Switzerland
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
| | - Alfredo Mari
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
| | - Reto Lienhard
- ADMED Microbiology, 2300 La Chaux-de-Fonds, Switzerland;
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland;
| | - Martin Risch
- Clinical Microbiology, Labormedizinisches Zentrum Dr. Risch, 9470 Buchs SG, Switzerland; (N.W.); (M.R.); (L.R.)
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland;
| | - Oliver Nolte
- Center for Laboratory Medicine, 9001 Saint Gall, Switzerland; (Y.G.); (O.N.)
| | - Isabella Eckerle
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland; (A.R.G.C.); (S.Y.); (I.E.); (L.K.)
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
| | - Gladys Martinetti Lucchini
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland;
- EOC Microbiological Laboratory, 6500 Bellinzona, Switzerland
| | - Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland;
| | - Richard A. Neher
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Tanja Stadler
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; (C.C.); (S.N.)
| | - Hans H. Hirsch
- Clinical Virology, University Hospital Basel, 4031 Basel, Switzerland; (K.L.); (H.H.H.)
- Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4031 Basel, Switzerland
| | - Stephen L. Leib
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Lorenz Risch
- Clinical Microbiology, Labormedizinisches Zentrum Dr. Risch, 9470 Buchs SG, Switzerland; (N.W.); (M.R.); (L.R.)
- Faculty of Medical Sciences, Private University of the Principality of Liechtenstein, 9495 Triesen, Liechtenstein
- Centre of Laboratory Medicine, University Institute of Clinical Chemistry, University of Bern, 3010 Bern, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland; (A.R.G.C.); (S.Y.); (I.E.); (L.K.)
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (M.H.); (A.T.)
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (C.B.); (O.O.); (T.P.); (G.G.)
| | - Adrian Egli
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland;
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49
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Khan MT, Ali S, Khan AS, Muhammad N, Khalil F, Ishfaq M, Irfan M, Al-Sehemi AG, Muhammad S, Malik A, Khan TA, Wei DQ. SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. ACS OMEGA 2021; 6:6588-6599. [PMID: 33748571 PMCID: PMC7944396 DOI: 10.1021/acsomega.0c05163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/05/2021] [Indexed: 05/08/2023]
Abstract
Among viral outbreaks, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the deadliest ones, and it has triggered the global COVID-19 pandemic. In Pakistan, until 5th September 2020, a total of 6342 deaths have been reported, of which 1255 were from the Khyber Pakhtunkhwa (KPK) province. To understand the disease progression and control and also to produce vaccines and therapeutic efforts, whole genome sequence analysis is important. In the current investigation, we sequenced a single sample of SARS-CoV-2 genomes (accession no. MT879619) from a male suspect from Peshawar, the KPK capital city, during the first wave of infection. The local SARS-CoV-2 strain shows some unique characteristics compared to neighboring Iranian and Chinese isolates in phylogenetic tree and mutations. The circulating strains of SARS-CoV-2 represent an intermediate evolution from China and Iran. Furthermore, eight complete whole genome sequences, including the current Pakistani isolates which have been submitted to Global Initiative on Sharing All Influenza Data (GSAID), were also investigated for specific mutations and characters. Some novel mutations [NSP2 (D268del), NSP5 (N228K), and NS3 (F105S)] and specific characters have been detected in the coding regions, which may affect viral transmission, epidemiology, and disease severity. The computational modeling revealed that a majority of these mutations may have a stabilizing effect on the viral protein structure. In conclusion, the genome sequencing of local strains is important for better understanding the pathogenicity, immunogenicity, and epidemiology of causative agents.
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Affiliation(s)
- Muhammad Tahir Khan
- Institute of Molecular
Biology and Biotechnology (IMBB), The University
of Lahore, KM Defence Road, Lahore 58810, Pakistan
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
| | - Sajid Ali
- Department of Microbiology, Quaid-i-Azam University Islamabad, Islamabad 45320, Pakistan
| | - Anwar Sheed Khan
- Department of Microbiology, Kohat University of Science and Technology, Bannu Road, Near Jarma Bridge, Kohat 26000, Pakistan
| | - Noor Muhammad
- Department of Microbiology, Kohat University of Science and Technology, Bannu Road, Near Jarma Bridge, Kohat 26000, Pakistan
| | - Faiza Khalil
- Department of Biochemistry, Khyber Medical
College, Peshawar 25160, Pakistan
- University
of Peshawar, Road No.
2, Rahat Abad, Peshawar 25120, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ishfaq
- Centre for Omic Sciences, Islamia
College Peshawar. Grand Trunk Road, Rahat Abad, Peshawar 25120, Pakistan
| | - Muhammad Irfan
- Department
of Oral Biology, College of Dentistry, University
of Florida, Gainesville, Florida 32611, United States
| | - Abdullah G. Al-Sehemi
- Research Center for Advanced Materials
Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Shabbir Muhammad
- Research Center for Advanced Materials
Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
| | - Arif Malik
- Institute of Molecular
Biology and Biotechnology (IMBB), The University
of Lahore, KM Defence Road, Lahore 58810, Pakistan
| | - Taj Ali Khan
- Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Phase V, Hayatabad, Peshawar, Khyber Pakhtunkhwa 25000, Pakistan
| | - Dong Qing Wei
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
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50
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Agerer B, Koblischke M, Gudipati V, Montaño-Gutierrez LF, Smyth M, Popa A, Genger JW, Endler L, Florian DM, Mühlgrabner V, Graninger M, Aberle SW, Husa AM, Shaw LE, Lercher A, Gattinger P, Torralba-Gombau R, Trapin D, Penz T, Barreca D, Fae I, Wenda S, Traugott M, Walder G, Pickl WF, Thiel V, Allerberger F, Stockinger H, Puchhammer-Stöckl E, Weninger W, Fischer G, Hoepler W, Pawelka E, Zoufaly A, Valenta R, Bock C, Paster W, Geyeregger R, Farlik M, Halbritter F, Huppa JB, Aberle JH, Bergthaler A. SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8 + T cell responses. Sci Immunol 2021; 6:6/57/eabg6461. [PMID: 33664060 PMCID: PMC8224398 DOI: 10.1126/sciimmunol.abg6461] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/27/2021] [Indexed: 12/26/2022]
Abstract
CD8+ T cell immunity to SARS-CoV-2 has been implicated in COVID-19 severity and virus control. Here, we identified nonsynonymous mutations in MHC-I-restricted CD8+ T cell epitopes after deep sequencing of 747 SARS-CoV-2 virus isolates. Mutant peptides exhibited diminished or abrogated MHC-I binding in a cell-free in vitro assay. Reduced MHC-I binding of mutant peptides was associated with decreased proliferation, IFN-γ production and cytotoxic activity of CD8+ T cells isolated from HLA-matched COVID-19 patients. Single cell RNA sequencing of ex vivo expanded, tetramer-sorted CD8+ T cells from COVID-19 patients further revealed qualitative differences in the transcriptional response to mutant peptides. Our findings highlight the capacity of SARS-CoV-2 to subvert CD8+ T cell surveillance through point mutations in MHC-I-restricted viral epitopes.
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Affiliation(s)
- Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Venugopal Gudipati
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Mark Smyth
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexandra Popa
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jakob-Wendelin Genger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lukas Endler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - David M Florian
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Vanessa Mühlgrabner
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Anna-Maria Husa
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Lisa Ellen Shaw
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Alexander Lercher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Pia Gattinger
- Department of Pathophysiology and Allergy Research, Division of Immunopathology, Medical University of Vienna, Vienna, Austria
| | - Ricard Torralba-Gombau
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Doris Trapin
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniele Barreca
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ingrid Fae
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Sabine Wenda
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Gernot Walder
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Winfried F Pickl
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.,Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Hannes Stockinger
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Gottfried Fischer
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Erich Pawelka
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Alexander Zoufaly
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Rudolf Valenta
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.,Department of Pathophysiology and Allergy Research, Division of Immunopathology, Medical University of Vienna, Vienna, Austria.,Karl Landsteiner University of Health Sciences, Krems, Austria.,Laboratory for Immunopathology, Department of Clinical Immunology and Allergy, First Moscow State Medical University Sechenov, Moscow, Russia.,NRC Institute of Immunology FMBA of Russia, Moscow, Russia
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Paster
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - René Geyeregger
- St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | | | - Johannes B Huppa
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Judith H Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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