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Colina SE, Serena MS, Echeverría MG, Metz GE. Clinical and molecular aspects of veterinary coronaviruses. Virus Res 2021; 297:198382. [PMID: 33705799 PMCID: PMC7938195 DOI: 10.1016/j.virusres.2021.198382] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/20/2020] [Accepted: 03/04/2021] [Indexed: 12/12/2022]
Abstract
Coronaviruses are a large group of RNA viruses that infect a wide range of animal species. The replication strategy of coronaviruses involves recombination and mutation events that lead to the possibility of cross-species transmission. The high plasticity of the viral receptor due to a continuous modification of the host species habitat may be the cause of cross-species transmission that can turn into a threat to other species including the human population. The successive emergence of highly pathogenic coronaviruses such as the Severe Acute Respiratory Syndrome (SARS) in 2003, the Middle East Respiratory Syndrome Coronavirus in 2012, and the recent SARS-CoV-2 has incentivized a number of studies on the molecular basis of the coronavirus and its pathogenesis. The high degree of interrelatedness between humans and wild and domestic animals and the modification of animal habitats by human urbanization, has favored new viral spreads. Hence, knowledge on the main clinical signs of coronavirus infection in the different hosts and the distinctive molecular characteristics of each coronavirus is essential to prevent the emergence of new coronavirus diseases. The coronavirus infections routinely studied in veterinary medicine must be properly recognized and diagnosed not only to prevent animal disease but also to promote public health.
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Affiliation(s)
- Santiago Emanuel Colina
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina
| | - María Soledad Serena
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina
| | - María Gabriela Echeverría
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina
| | - Germán Ernesto Metz
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina.
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102
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Zehra T, Siddique SK, Aamir R, Mahmood A, Kiani AH, Virk ST. Coronavirus Disease Clinical and Laboratory Parameters: Dismembering the Values Reveals Outcomes. Cureus 2021; 13:e13720. [PMID: 33833931 PMCID: PMC8018858 DOI: 10.7759/cureus.13720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background The medical community’s understanding of the novel coronavirus disease (COVID-19) was limited initially, and many laboratory investigations were performed to observe effects of the virus on the body, its complications, and outcomes. We observed that some laboratory investigations provided redundant information regarding outcomes, and, therefore, were not necessary. Therefore, the extent of laboratory investigations may need to be pared down to not only avoid issues related to repeated blood sampling but also to minimize the financial burdens in poor socioeconomic countries. Objective This study aimed to observe trends of clinical and laboratory values in COVID-19 patients and their relationship to outcomes, including disease severity, length of hospital stay, and mortality. Methods We conducted an observational cohort study of COVID-19 patients treated as inpatients at the Shifa International Hospital (SIH) in Islamabad in April 2020. Patients were included if they were nonsurgical, adult inpatients of SIH diagnosed with COVID-19 via positive polymerase chain reaction test. We monitored study participants' clinical and laboratory values (including hypoxia) on admission and throughout the study period. We used IBM SPSS Statistics for Windows, Version 23.0 (IBM Corp., Armonk, NY, USA) for data entry and analysis. Descriptive statistics were calculated for qualitative and quantitative data. We determined the effect of all variables on outcomes through chi-squared or Fisher's exact test, and p-values <0.05 with 95% confidence interval were considered statistically significant. Results A total of 51 patients with COVID-19 were enrolled. Most of the study participants were men older than age 50 with multiple comorbidities and resided in Khyber Pakhtunkhwa. Length of hospital stay ranged from eight to 14 days, and most patients had severe disease and survived. Factors such as patient age, gender, comorbid conditions, residence, and medication did not significantly affect outcomes. Hypotension during the height of symptoms and oxygen saturations <80% on admission was associated with prolonged hospital stays. Two complete blood count (CBC) parameters (platelet counts and mean corpuscular volume, MCV) were strongly associated with mortality and severity in our patients. Four non-CBC parameters (alanine transaminase, ALT; D-dimer; C-reactive protein, CRP; and lactate dehydrogenase, LDH) had strong statistical impact on disease severity, length of hospital stay, and mortality in our patients. Conclusion In a resource-limited country, laboratory testing must be chosen wisely and used appropriately. Patient age, gender, comorbid conditions, drugs, residence, and ferritin levels did not affect COVID-19 outcomes. Hemoglobin, platelet count, MCV, CRP, D-dimer, ALT, LDH, hypoxia, and hypotension were all correlated to disease outcomes. Therefore, these factors are useful laboratory examinations for COVID-19 patients, especially in poor countries.
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Affiliation(s)
- Tehzeeb Zehra
- Internal Medicine, Shifa Tameer-E-Millat University, Shifa College of Medicine, Islamabad, PAK
| | | | - Rahila Aamir
- Internal Medicine, Shifa Tameer-E-Millat University, Shifa College of Medicine, Islamabad, PAK
| | - Adil Mahmood
- Internal Medicine, Shifa International Hospital, Islamabad, PAK
| | | | - Sana T Virk
- Internal Medicine, Air University Islamabad, Islamabad, PAK
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103
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Dowlatshahi S, Shabani E, Abdekhodaie MJ. Serological assays and host antibody detection in coronavirus-related disease diagnosis. Arch Virol 2021; 166:715-731. [PMID: 33492524 PMCID: PMC7830048 DOI: 10.1007/s00705-020-04874-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/27/2020] [Indexed: 02/08/2023]
Abstract
Coronaviruses (CoV) are a family of viral pathogens that infect both birds and mammals, including humans. Seven human coronaviruses (HCoV) have been recognized so far. HCoV-229E, -OC43, -NL63, and -HKU1 account for one-third of common colds with mild symptoms. The other three members are severe acute respiratory syndrome (SARS)-CoV, Middle East respiratory syndrome (MERS)-CoV, and SARS-CoV-2. These viruses are responsible for SARS, MERS, and CoV disease 2019 (COVID-19), respectively. A variety of diagnostic techniques, including chest X-rays, computer tomography (CT) scans, analysis of viral nucleic acids, proteins, or whole virions, and host antibody detection using serological assays have been developed for the detection of these viruses. In this review, we discuss conventional serological tests, such as enzyme-linked immunosorbent assay (ELISA), western blot (WB), immunofluorescence assay (IFA), lateral flow immunoassay (LFIA), and chemiluminescence immunoassay (CLIA), as well as biosensor-based assays that have been developed for diagnosing HCoV-associated diseases since 2003, with an in-depth focus on COVID-19.
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Affiliation(s)
- Sayeh Dowlatshahi
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Ehsan Shabani
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Mohammad J Abdekhodaie
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran.
- Yeates School of Graduate Studies, Ryerson University, Toronto, ON, Canada.
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104
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White KM, Rosales R, Yildiz S, Kehrer T, Miorin L, Moreno E, Jangra S, Uccellini MB, Rathnasinghe R, Coughlan L, Martinez-Romero C, Batra J, Rojc A, Bouhaddou M, Fabius JM, Obernier K, Dejosez M, Guillén MJ, Losada A, Avilés P, Schotsaert M, Zwaka T, Vignuzzi M, Shokat KM, Krogan NJ, García-Sastre A. Plitidepsin has potent preclinical efficacy against SARS-CoV-2 by targeting the host protein eEF1A. Science 2021; 371:926-931. [PMID: 33495306 PMCID: PMC7963220 DOI: 10.1126/science.abf4058] [Citation(s) in RCA: 210] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/20/2021] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins interact with the eukaryotic translation machinery, and inhibitors of translation have potent antiviral effects. We found that the drug plitidepsin (aplidin), which has limited clinical approval, possesses antiviral activity (90% inhibitory concentration = 0.88 nM) that is more potent than remdesivir against SARS-CoV-2 in vitro by a factor of 27.5, with limited toxicity in cell culture. Through the use of a drug-resistant mutant, we show that the antiviral activity of plitidepsin against SARS-CoV-2 is mediated through inhibition of the known target eEF1A (eukaryotic translation elongation factor 1A). We demonstrate the in vivo efficacy of plitidepsin treatment in two mouse models of SARS-CoV-2 infection with a reduction of viral replication in the lungs by two orders of magnitude using prophylactic treatment. Our results indicate that plitidepsin is a promising therapeutic candidate for COVID-19.
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Affiliation(s)
- Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Soner Yildiz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa B Uccellini
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lynda Coughlan
- Department of Microbiology and Immunology and Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, MD, USA
| | - Carles Martinez-Romero
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jyoti Batra
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Ajda Rojc
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Marion Dejosez
- Huffington Foundation Center for Cell-Based Research in Parkinson's Disease, Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - María José Guillén
- Research and Development Department, PharmaMar, 28770 Colmenar Viejo, Madrid, Spain
| | - Alejandro Losada
- Research and Development Department, PharmaMar, 28770 Colmenar Viejo, Madrid, Spain
| | - Pablo Avilés
- Research and Development Department, PharmaMar, 28770 Colmenar Viejo, Madrid, Spain
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Zwaka
- Huffington Foundation Center for Cell-Based Research in Parkinson's Disease, Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Kevan M Shokat
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA
| | - Nevan J Krogan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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105
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Shahhosseini N, Wong G, Kobinger GP, Chinikar S. SARS-CoV-2 spillover transmission due to recombination event. GENE REPORTS 2021; 23:101045. [PMID: 33615041 PMCID: PMC7884226 DOI: 10.1016/j.genrep.2021.101045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/21/2021] [Accepted: 01/31/2021] [Indexed: 01/08/2023]
Abstract
In late 2019, a novel Coronavirus emerged in China. Perceiving the modulating factors of cross-species virus transmission is critical to elucidate the nature of virus emergence. Using bioinformatics tools, we analyzed the mapping of the SARS-CoV-2 genome, modeling of protein structure, and analyze the evolutionary origin of SARS-CoV-2, as well as potential recombination events. Phylogenetic tree analysis shows that SARS-CoV-2 has the closest evolutionary relationship with Bat-SL-CoV-2 (RaTG13) at the scale of the complete virus genome, and less similarity to Pangolin-CoV. However, the Receptor Binding Domain (RBD) of SARS-CoV-2 is almost identical to Pangolin-CoV at the aa level, suggesting that spillover transmission probably occurred directly from pangolins, but not bats. Further recombination analysis revealed the pathway for spillover transmission from Bat-SL-CoV-2 and Pangolin-CoV. Here, we provide evidence for recombination event between Bat-SL-CoV-2 and Pangolin-CoV that resulted in the emergence of SARS-CoV-2. Nevertheless, the role of mutations should be noted as another influencing factor in the continuing evolution and resurgence of novel SARS-CoV-2 variants.
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Affiliation(s)
- Nariman Shahhosseini
- Département de Microbiologie-Infectiologie et d'Immunologie, Université Laval, Québec City, Québec, Canada
| | - Gary Wong
- Département de Microbiologie-Infectiologie et d'Immunologie, Université Laval, Québec City, Québec, Canada.,Pasteur Institute of Shanghai, China
| | - Gary P Kobinger
- Département de Microbiologie-Infectiologie et d'Immunologie, Université Laval, Québec City, Québec, Canada.,Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Sadegh Chinikar
- Institute of Virology, University of Veterinary Medicine, Vienna, Austria.,Pasteur Institute of Tehran, Iran
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106
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Cruz-Pulido D, Boley PA, Ouma WZ, Alhamo MA, Saif LJ, Kenney SP. Comparative Transcriptome Profiling of Human and Pig Intestinal Epithelial Cells after Porcine Deltacoronavirus Infection. Viruses 2021; 13:v13020292. [PMID: 33668405 PMCID: PMC7918119 DOI: 10.3390/v13020292] [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: 12/31/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 01/16/2023] Open
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging infectious disease of swine with zoonotic potential. Phylogenetic analysis suggests that PDCoV originated recently from a host-switching event between birds and mammals. Little is known about how PDCoV interacts with its differing hosts. Human-derived cell lines are susceptible to PDCoV infection. Herein, we compare the gene expression profiles of an established host swine cells to potential emerging host human cells after infection with PDCoV. Cell lines derived from intestinal lineages were used to reproduce the primary sites of viral infection in the host. Porcine intestinal epithelial cells (IPEC-J2) and human intestinal epithelial cells (HIEC) were infected with PDCoV. RNA-sequencing was performed on total RNA extracted from infected cells. Human cells exhibited a more pronounced response to PDCoV infection in comparison to porcine cells with more differentially expressed genes (DEGs) in human, 7486, in comparison to pig cells, 1134. On the transcriptional level, the adoptive host human cells exhibited more DEGs in response to PDCoV infection in comparison to the primary pig host cells, where different types of cytokines can control PDCoV replication and virus production. Key immune-associated DEGs and signaling pathways are shared between human and pig cells during PDCoV infection. These included genes related to the NF-kappa-B transcription factor family, the interferon (IFN) family, the protein-kinase family, and signaling pathways such as the apoptosis signaling pathway, JAK-STAT signaling pathway, inflammation/cytokine–cytokine receptor signaling pathway. MAP4K4 was unique in up-regulated DEGs in humans in the apoptosis signaling pathway. While similarities exist between human and pig cells in many pathways, our research suggests that the adaptation of PDCoV to the porcine host required the ability to down-regulate many response pathways including the interferon pathway. Our findings provide an important foundation that contributes to an understanding of the mechanisms of PDCoV infection across different hosts. To our knowledge, this is the first report of transcriptome analysis of human cells infected by PDCoV.
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Affiliation(s)
- Diana Cruz-Pulido
- Department of Veterinary Preventive Medicine, Food Animal Health Research Program (FAHRP), Wooster, OH 44691, USA; (D.C.-P.); (P.A.B.); (M.A.A.); (L.J.S.)
| | - Patricia A. Boley
- Department of Veterinary Preventive Medicine, Food Animal Health Research Program (FAHRP), Wooster, OH 44691, USA; (D.C.-P.); (P.A.B.); (M.A.A.); (L.J.S.)
| | | | - Moyasar A. Alhamo
- Department of Veterinary Preventive Medicine, Food Animal Health Research Program (FAHRP), Wooster, OH 44691, USA; (D.C.-P.); (P.A.B.); (M.A.A.); (L.J.S.)
| | - Linda J. Saif
- Department of Veterinary Preventive Medicine, Food Animal Health Research Program (FAHRP), Wooster, OH 44691, USA; (D.C.-P.); (P.A.B.); (M.A.A.); (L.J.S.)
| | - Scott P. Kenney
- Department of Veterinary Preventive Medicine, Food Animal Health Research Program (FAHRP), Wooster, OH 44691, USA; (D.C.-P.); (P.A.B.); (M.A.A.); (L.J.S.)
- Correspondence: ; Tel.: +1-330-263-3747
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107
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Liu H, Yuan M, Huang D, Bangaru S, Lee CCD, Peng L, Zhu X, Nemazee D, van Gils MJ, Sanders RW, Kornau HC, Reincke SM, Prüss H, Kreye J, Wu NC, Ward AB, Wilson IA. A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.11.430866. [PMID: 33594361 PMCID: PMC7885913 DOI: 10.1101/2021.02.11.430866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Coronaviruses have caused several epidemics and pandemics including the ongoing coronavirus disease 2019 (COVID-19). Some prophylactic vaccines and therapeutic antibodies have already showed striking effectiveness against COVID-19. Nevertheless, concerns remain about antigenic drift in SARS-CoV-2 as well as threats from other sarbecoviruses. Cross-neutralizing antibodies to SARS-related viruses provide opportunities to address such concerns. Here, we report on crystal structures of a cross-neutralizing antibody CV38-142 in complex with the receptor binding domains from SARS-CoV-2 and SARS-CoV. Our structural findings provide mechanistic insights into how this antibody can accommodate antigenic variation in these viruses. CV38-142 synergizes with other cross-neutralizing antibodies, in particular COVA1-16, to enhance neutralization of SARS-CoV-2 and SARS-CoV. Overall, this study provides valuable information for vaccine and therapeutic design to address current and future antigenic drift in SARS-CoV-2 and to protect against zoonotic coronaviruses.
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Affiliation(s)
- Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology and Infection Prevention, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sandhya Bangaru
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D. Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology and Infection Prevention, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology and Infection Prevention, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Rogier W. Sanders
- Department of Medical Microbiology, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Hans-Christian Kornau
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Neuroscience Research Center (NWFZ), Cluster NeuroCure, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - S. Momsen Reincke
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jakob Kreye
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
- Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
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108
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Alipoor SD, Mortaz E, Jamaati H, Tabarsi P, Bayram H, Varahram M, Adcock IM. COVID-19: Molecular and Cellular Response. Front Cell Infect Microbiol 2021; 11:563085. [PMID: 33643932 PMCID: PMC7904902 DOI: 10.3389/fcimb.2021.563085] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 01/08/2021] [Indexed: 12/12/2022] Open
Abstract
In late December 2019, a vtiral pneumonia with an unknown agent was reported in Wuhan, China. A novel coronavirus was identified as the causative agent. Because of the human-to-human transmission and rapid spread; coronavirus disease 2019 (COVID-19) has rapidly increased to an epidemic scale and poses a severe threat to human health; it has been declared a public health emergency of international concern (PHEIC) by the World Health Organization (WHO). This review aims to summarize the recent research progress of COVID-19 molecular features and immunopathogenesis to provide a reference for further research in prevention and treatment of SARS coronavirus2 (SARS-CoV-2) infection based on the knowledge from researches on SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV).
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Affiliation(s)
- Shamila D. Alipoor
- Molecular Medicine Department, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Esmaeil Mortaz
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamidreza Jamaati
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Payam Tabarsi
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hasan Bayram
- Department of Pulmonary Medicine, Koc University School of Medicine, Koc University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Mohammad Varahram
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ian M. Adcock
- National Heart and Lung Institute, Imperial College London and the NIHR Imperial Biomedical Research Centre, London, United Kingdom
- Priority Research Centre for Asthma and Respiratory Disease, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
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109
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Devaux CA, Pinault L, Osman IO, Raoult D. Can ACE2 Receptor Polymorphism Predict Species Susceptibility to SARS-CoV-2? Front Public Health 2021; 8:608765. [PMID: 33643982 PMCID: PMC7902720 DOI: 10.3389/fpubh.2020.608765] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/23/2020] [Indexed: 12/16/2022] Open
Abstract
A novel severe acute respiratory syndrome coronavirus, SARS-CoV-2, emerged in China in December 2019 and spread worldwide, causing more than 1.3 million deaths in 11 months. Similar to the human SARS-CoV, SARS-CoV-2 shares strong sequence homologies with a sarbecovirus circulating in Rhinolophus affinis bats. Because bats are expected to be able to transmit their coronaviruses to intermediate animal hosts that in turn are a source of viruses able to cross species barriers and infect humans (so-called spillover model), the identification of an intermediate animal reservoir was the subject of intense researches. It was claimed that a reptile (Ophiophagus hannah) was the intermediate host. This hypothesis was quickly ruled out and replaced by the pangolin (Manis javanica) hypothesis. Yet, pangolin was also recently exonerated from SARS-CoV-2 transmission to humans, leaving other animal species as presumed guilty. Guided by the spillover model, several laboratories investigated in silico the species polymorphism of the angiotensin I converting enzyme 2 (ACE2) to find the best fits with the SARS-CoV-2 spike receptor-binding site. Following the same strategy, we used multi-sequence alignment, 3-D structure analysis, and electrostatic potential surface generation of ACE2 variants to predict their binding capacity to SARS-CoV-2. We report evidence that such simple in silico investigation is a powerful tool to quickly screen which species are potentially susceptible to SARS-CoV-2. However, possible receptor binding does not necessarily lead to successful replication in host. Therefore, we also discuss here the limitations of these in silico approaches in our quest on the origins of COVID-19 pandemic.
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Affiliation(s)
- Christian A. Devaux
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
- CNRS, Marseille, France
| | - Lucile Pinault
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
| | - Ikram Omar Osman
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
- Fondation IHU–Méditerranée Infection, Marseille, France
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110
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Comparison of Selected Characteristics of SARS-CoV-2, SARS-CoV, and HCoV-NL63. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The global pandemic known as coronavirus disease 2019 (COVID-19) was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This review article presents the taxonomy of SARS-CoV-2 coronaviruses, which have been classified as the seventh known human pathogenic coronavirus. The etiology of COVID-19 is also briefly discussed. Selected characteristics of SARS-CoV-2, SARS-CoV, and HCoV-NL63 are compared in the article. The angiotensin converting enzyme-2 (ACE-2) has been identified as the receptor for the SARS-CoV-2 viral entry. ACE2 is well-known as a counter-regulator of the renin-angiotensin system (RAAS) and plays a key role in the cardiovascular system. In the therapy of patients with COVID-19, there has been a concern about the use of RAAS inhibitors. As a result, it is hypothesized that ACE inhibitors do not directly affect ACE2 activity in clinical use. Coronaviruses are zoonotic RNA viruses. Identification of the primary causative agent of the SARS-CoV-2 is essential. Sequencing showed that the genome of the Bat CoVRaTG13 virus found in bats matches the genome of up to (96.2%) of SARS-CoV-2 virus. Sufficient knowledge of the molecular and biological mechanisms along with reliable information related to SARS-CoV-2 gives hope for a quick solution to epidemiological questions and therapeutic processes.
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111
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Narayanan S, Ritchey JC, Patil G, Narasaraju T, More S, Malayer J, Saliki J, Kaul A, Agarwal PK, Ramachandran A. SARS-CoV-2 Genomes From Oklahoma, United States. Front Genet 2021; 11:612571. [PMID: 33613621 PMCID: PMC7886813 DOI: 10.3389/fgene.2020.612571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/31/2020] [Indexed: 11/13/2022] Open
Abstract
Genomic sequencing has played a major role in understanding the pathogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the current pandemic, it is essential that SARS-CoV-2 viruses are sequenced regularly to determine mutations and genomic modifications in different geographical locations. In this study, we sequenced SARS-CoV-2 from five clinical samples obtained in Oklahoma, United States during different time points of pandemic presence in the state. One sample from the initial days of the pandemic in the state and four during the peak in Oklahoma were sequenced. Previously reported mutations including D614G in S gene, P4715L in ORF1ab, S194L, R203K, and G204R in N gene were identified in the genomes sequenced in this study. Possible novel mutations were also detected in the S gene (G1167V), ORF1ab (A6269S and P3371S), ORF7b (T28I), and ORF8 (G96R). Phylogenetic analysis of the genomes showed similarity to other SARS-CoV-2 viruses reported from across the globe. Structural characterization indicates that the mutations in S gene possibly influences conformational flexibility and motion of the spike protein, and the mutations in N gene are associated with disordered linker region within the nucleocapsid protein.
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Affiliation(s)
- Sai Narayanan
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - John C. Ritchey
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Girish Patil
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Teluguakula Narasaraju
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Sunil More
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Jerry Malayer
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Jeremiah Saliki
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
| | - Anil Kaul
- Center for Health Sciences, Oklahoma State University, Tulsa, OK, United States
| | - Pratul K. Agarwal
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
- High-Performance Computing Center, Oklahoma State University, Stillwater, OK, United States
| | - Akhilesh Ramachandran
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
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112
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Biodiversity loss and COVID-19 pandemic: The role of bats in the origin and the spreading of the disease. Biochem Biophys Res Commun 2021; 538:2-13. [PMID: 33092787 PMCID: PMC7566801 DOI: 10.1016/j.bbrc.2020.10.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022]
Abstract
The loss of biodiversity in the ecosystems has created the general conditions that have favored and, in fact, made possible, the insurgence of the COVID-19 pandemic. A lot of factors have contributed to it: deforestation, changes in forest habitats, poorly regulated agricultural surfaces, mismanaged urban growth. They have altered the composition of wildlife communities, greatly increased the contacts of humans with wildlife, and altered niches that harbor pathogens, increasing their chances to come in contact with humans. Among the wildlife, bats have adapted easily to anthropized environments such as houses, barns, cultivated fields, orchards, where they found the suitable ecosystem to prosper. Bats are major hosts for αCoV and βCoV: evolution has shaped their peculiar physiology and their immune system in a way that makes them resistant to viral pathogens that would instead successfully attack other species, including humans. In time, the coronaviruses that bats host as reservoirs have undergone recombination and other modifications that have increased their ability for inter-species transmission: one modification of particular importance has been the development of the ability to use ACE2 as a receptor in host cells. This particular development in CoVs has been responsible for the serious outbreaks in the last two decades, and for the present COVID-19 pandemic.
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113
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Anjorin AA, Ashaka OS, Tijani SO, Openibo JO, Odetokun IA. Zoonotic and reverse zoonotic transmission of severe acute respiratory syndrome coronavirus 2: a review and implications for Africa. Pan Afr Med J 2021; 38:39. [PMID: 33777307 PMCID: PMC7955601 DOI: 10.11604/pamj.2021.38.39.24170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 01/08/2021] [Indexed: 01/10/2023] Open
Abstract
There is an urgent need to properly understand the transmission dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the event of continuous rise in morbidity in both humans and animals as well as an increase in the mortality rate in man. Since the novel SARS-CoV-2 emerged in Wuhan, China with its global spread in over 200 countries, several studies have been published on the epidemiology of the virus in man with limited information on the roles of animals and the possibility of reverse zoonosis. We therefore collected published research literature on COVID-19 from public search engines for information on SARS-CoV-2 in animals and reverse zoonosis from man. A critical and thorough study appraisal/evaluation was performed to include recent quality publications that focus on the scope of this write-up including zoonosis and reverse zoonosis of SARS-CoV-2. We highlighted what is known about SARS-CoV-2 in animals, identify gaps for future research, summarized possible reverse zoonotic transmission of SARS-CoV-2 from man to animals and included the likely implications of our summary for Africa, despite the dearth of information in Africa on the key concepts of this study.
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Affiliation(s)
| | - Oluwaseyi Sedowhe Ashaka
- Department of Medical Microbiology and Parasitology, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Sodiq Olawale Tijani
- Department of Medical Microbiology and Parasitology, College of Medicine, University of Lagos, Idi-Araba, Nigeria
| | - John Oluwayomi Openibo
- Department of Biological Sciences, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
| | - Ismail Ayoade Odetokun
- Department of Veterinary Public Health and Preventive Medicine, University of Ilorin, Ilorin, Kwara State, Nigeria
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114
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Ellis P, Somogyvári F, Virok DP, Noseda M, McLean GR. Decoding Covid-19 with the SARS-CoV-2 Genome. CURRENT GENETIC MEDICINE REPORTS 2021; 9:1-12. [PMID: 33457109 PMCID: PMC7794078 DOI: 10.1007/s40142-020-00197-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2020] [Indexed: 02/06/2023]
Abstract
Purpose of Review SARS-CoV-2, the recently emerged coronavirus (CoV) that is responsible for the current global pandemic Covid-19, first appeared in late 2019 in Wuhan, China. Here, we summarise details of the SARS-CoV-2 genome to assist understanding of the emergence, evolution and diagnosis of this deadly new virus. Recent Findings Based on high similarities in the genome sequences, the virus is thought to have arisen from SARS-like CoVs in bats but the lack of an intermediate species containing a CoV with even greater similarity has so far eluded discovery. The critical determinant of the SARS-CoV-2 genome is the spike (S) gene encoding the viral structural protein that interacts with the host cell entry receptor ACE2. The S protein is sufficiently adapted to bind human ACE2 much more readily than SARS-CoV, the most closely related human CoV. Summary Although the SARS-CoV-2 genome is undergoing subtle evolution in humans through mutation that may enhance transmission, there is limited evidence for attenuation that might weaken the virus. It is also still unclear as to the events that led to the virus’ emergence from bats. Importantly, current diagnosis requires specific recognition and amplification of the SARS-CoV-2 RNA genome by qPCR, despite these ongoing viral genome changes. Alternative diagnostic procedures relying on immunoassay are becoming more prevalent.
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Affiliation(s)
- Phoebe Ellis
- School of Human Sciences, London Metropolitan University, London, UK
| | - Ferenc Somogyvári
- Department of Medical Microbiology and Immunobiology, University of Szeged, Szeged, Hungary
| | - Dezső P Virok
- Department of Medical Microbiology and Immunobiology, University of Szeged, Szeged, Hungary
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Gary R McLean
- School of Human Sciences, London Metropolitan University, London, UK.,National Heart and Lung Institute, Imperial College London, London, UK.,Cellular and Molecular Immunology Research Centre, London Metropolitan University, London, UK
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115
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Mykytyn AZ, Breugem TI, Riesebosch S, Schipper D, van den Doel PB, Rottier RJ, Lamers MM, Haagmans BL. SARS-CoV-2 entry into human airway organoids is serine protease-mediated and facilitated by the multibasic cleavage site. eLife 2021; 10:e64508. [PMID: 33393462 PMCID: PMC7806259 DOI: 10.7554/elife.64508] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/31/2020] [Indexed: 01/19/2023] Open
Abstract
Coronavirus entry is mediated by the spike protein that binds the receptor and mediates fusion after cleavage by host proteases. The proteases that mediate entry differ between cell lines, and it is currently unclear which proteases are relevant in vivo. A remarkable feature of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the presence of a multibasic cleavage site (MBCS), which is absent in the SARS-CoV spike. Here, we report that the SARS-CoV-2 spike MBCS increases infectivity on human airway organoids (hAOs). Compared with SARS-CoV, SARS-CoV-2 entered faster into Calu-3 cells and, more frequently, formed syncytia in hAOs. Moreover, the MBCS increased entry speed and plasma membrane serine protease usage relative to cathepsin-mediated endosomal entry. Blocking serine proteases, but not cathepsins, effectively inhibited SARS-CoV-2 entry and replication in hAOs. Our findings demonstrate that SARS-CoV-2 enters relevant airway cells using serine proteases, and suggest that the MBCS is an adaptation to this viral entry strategy.
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Affiliation(s)
- Anna Z Mykytyn
- Viroscience Department, Erasmus University Medical CenterRotterdamNetherlands
| | - Tim I Breugem
- Viroscience Department, Erasmus University Medical CenterRotterdamNetherlands
| | - Samra Riesebosch
- Viroscience Department, Erasmus University Medical CenterRotterdamNetherlands
| | - Debby Schipper
- Viroscience Department, Erasmus University Medical CenterRotterdamNetherlands
| | | | - Robbert J Rottier
- Department of Pediatric Surgery, Erasmus University Medical Center - Sophia Children's HospitalRotterdamNetherlands
| | - Mart M Lamers
- Viroscience Department, Erasmus University Medical CenterRotterdamNetherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus University Medical CenterRotterdamNetherlands
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116
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Bonilla-Aldana DK, Jimenez-Diaz SD, Arango-Duque JS, Aguirre-Florez M, Balbin-Ramon GJ, Paniz-Mondolfi A, Suárez JA, Pachar MR, Perez-Garcia LA, Delgado-Noguera LA, Sierra MA, Muñoz-Lara F, Zambrano LI, Rodriguez-Morales AJ. Bats in ecosystems and their Wide spectrum of viral infectious potential threats: SARS-CoV-2 and other emerging viruses. Int J Infect Dis 2021; 102:87-96. [PMID: 32829048 PMCID: PMC7440229 DOI: 10.1016/j.ijid.2020.08.050] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/08/2020] [Accepted: 08/16/2020] [Indexed: 12/15/2022] Open
Abstract
Bats have populated earth for approximately 52 million years, serving as natural reservoirs for a variety of viruses through the course of evolution. Transmission of highly pathogenic viruses from bats has been suspected or linked to a spectrum of potential emerging infectious diseases in humans and animals worldwide. Examples of such viruses include Marburg, Ebolavirus, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Herein, we provide a narrative review focused in selected emerging viral infectious diseases that have been reported from bats.
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Affiliation(s)
- D Katterine Bonilla-Aldana
- Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda, Colombia; Public Health and Infection Research Group and Incubator, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Risaralda, Colombia
| | - S Daniela Jimenez-Diaz
- Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda, Colombia
| | | | - Mateo Aguirre-Florez
- Public Health and Infection Research Group and Incubator, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Risaralda, Colombia
| | - Graciela J Balbin-Ramon
- Master in Clinical Epidemiology and Biostatistics, Universidad Cientifica del Sur, Lima, Peru; Hospital de Emergencias Jose Casimiro Ulloa, Lima, Peru
| | - Alberto Paniz-Mondolfi
- Laboratory of Medical Microbiology, Department of Pathology, Molecular and Cell-based Medicine, The Mount Sinai Hospital-Icahn School of Medicine at Mount Sinai, New York, USA; Laboratorio de Señalización Celular y Bioquímica de Parásitos, Instituto de Estudios Avanzados (IDEA), Caracas, Caracas, Venezuela; Academia Nacional de Medicina, Caracas, Venezuela
| | - Jose Antonio Suárez
- Investigador SNI Senacyt Panamá, Clinical Research Deparment, Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | - Monica R Pachar
- Medicine Department-Infectious Diseases Service, Hospital Santo Tomas, Panama City, Panama
| | - Luis A Perez-Garcia
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Cabudare, Edo. Lara, Venezuela
| | - Lourdes A Delgado-Noguera
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Cabudare, Edo. Lara, Venezuela
| | - Manuel Antonio Sierra
- Facultad de Ciencias Médicas, UNAH, Tegucigalpa, Honduras; Facultad de Ciencias de la Salud, Universidad Tecnológica Centroamericana, Tegucigalpa, Honduras
| | - Fausto Muñoz-Lara
- Departamento de Medicina Interna, Hospital Escuela, Tegucigalpa, Honduras; Departamento de Medicina Interna, Facultad de Ciencias Médicas, UNAH, Tegucigalpa, Honduras
| | - Lysien I Zambrano
- Departments of Physiological and Morphological Sciences, School of Medical Sciences, Universidad Nacional Autónoma de Honduras (UNAH), Tegucigalpa, Honduras
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group and Incubator, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Risaralda, Colombia; Master in Clinical Epidemiology and Biostatistics, Universidad Cientifica del Sur, Lima, Peru; Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda, Colombia.
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117
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Kumar A, Manikandan R, Magesh S, Patan R, Ramesh S, Gupta D. Image analysis and data processing for COVID-19. DATA SCIENCE FOR COVID-19 2021. [PMCID: PMC8138042 DOI: 10.1016/b978-0-12-824536-1.00035-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
COVID-19 is a deadly disease caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2). It was first discovered by variations in the respirational and immune systems of a patient who died of a severe acute respiratory syndrome. The first country heavily affected by coronavirus was China. The first case was detected in Wuhan city, China. This virus spreads rapidly from person to person. Based on laboratory tests for coronavirus disease in humans, it is suspected that bats are the natural source of spread of large varieties of virus. The two major viruses, SARS-CoV and Middle East respiratory syndrome coronavirus, originated from the bat; it caused an unexpected disease outbreak in the 21st century throughout the world. Researchers and doctors have investigated COVID in cadavers. The virus was detected in lung, trachea/bronchus, stomach, small intestine, distal convoluted renal tubule, sweat gland, pancreas, adrenal gland, parathyroid, pituitary, cerebrum, and liver. However, it was not noted in bone marrow, heart, aorta, cerebellum, thyroid, testis, esophagus, spleen, lymph node, ovary, muscle, or uterus. This chapter briefly discusses image analysis and data processing used to accelerate COVID-19 detection and support the efforts of researchers and physician to help infected people and break the chain of disease from person to person.
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118
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Layman NC, Tuschhoff BM, Nuismer SL. Designing transmissible viral vaccines for evolutionary robustness and maximum efficiency. Virus Evol 2021; 7:veab002. [PMID: 33680502 PMCID: PMC7920745 DOI: 10.1093/ve/veab002] [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] [Indexed: 11/25/2022] Open
Abstract
The danger posed by emerging infectious diseases necessitates the development of new tools that can mitigate the risk of animal pathogens spilling over into the human population. One promising approach is the development of recombinant viral vaccines that are transmissible, and thus capable of self-dissemination through hard to reach populations of wild animals. Indeed, mathematical models demonstrate that transmissible vaccines can greatly reduce the effort required to control the spread of zoonotic pathogens in their animal reservoirs, thereby limiting the chances of human infection. A key challenge facing these new vaccines, however, is the inevitability of evolutionary change resulting from their ability to self-replicate and generate extended chains of transmission. Further, carrying immunogenic transgenes is often costly, in terms of metabolic burden, increased competition with the pathogen, or due to unintended interactions with the viral host regulatory network. As a result, natural selection is expected to favor vaccine strains that down-regulate or delete these transgenes resulting in increased rates of transmission and reduced efficacy against the target pathogen. In addition, efficacy and evolutionary stability will often be at odds; as when longer, more efficacious antigens experience faster rates of evolutionary decay. Here, we ask how such trade-offs influence the overall performance of transmissible vaccines. We find that evolutionary instability can substantially reduce performance, even for vaccine candidates with the ideal combination of efficacy and transmission. However, we find that, at least in some cases, vaccine stability and overall performance can be improved by the inclusion of a second, redundant antigen. Overall, our results suggest that the successful application of recombinant transmissible vaccines will require consideration of evolutionary dynamics and epistatic effects, as well as basic measurements of epidemiological features.
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Affiliation(s)
| | - Beth M Tuschhoff
- Department of Mathematics, University of Idaho, 875 Perimeter Drive, Moscow, ID 83844, USA
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119
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Rehman MFU, Fariha C, Anwar A, Shahzad N, Ahmad M, Mukhtar S, Farhan Ul Haque M. Novel coronavirus disease (COVID-19) pandemic: A recent mini review. Comput Struct Biotechnol J 2020; 19:612-623. [PMID: 33398233 PMCID: PMC7773542 DOI: 10.1016/j.csbj.2020.12.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 02/06/2023] Open
Abstract
The COVID-19, caused by a novel coronavirus, was declared as a global pandemic by WHO more than five months ago, and we are still experiencing a state of global emergency. More than 74.30 million confirmed cases of the COVID-19 have been reported globally so far, with an average fatality rate of almost 3.0%. Seven different types of coronaviruses had been detected from humans; three of them have resulted in severe outbreaks, i.e., MERS-CoV, SARS-CoV, and SARS-CoV-2. Phylogenetic analysis of the genomes suggests that the possible occurrence of recombination between SARS-like-CoVs from pangolin and bat might have led to the origin of SARS-CoV-2 and the COVID-19 outbreak. Coronaviruses are positive-sense, single-stranded RNA viruses and harbour a genome (30 kb) consisting of two terminal untranslated regions and twelve putative functional open reading frames (ORFs), encoding for non-structural and structural proteins. There are sixteen putative non-structural proteins, including proteases, RNA-dependent RNA polymerase, helicase, other proteins involved in the transcription and replication of SARS-CoV-2, and four structural proteins, including spike protein (S), envelope (E), membrane (M), and nucleocapsid (N). SARS-CoV-2 infection, with a heavy viral load in the body, destroys the human lungs through cytokine storm, especially in elderly persons and people with immunosuppressed disorders. A number of drugs have been repurposed and employed, but still, no specific antiviral medicine has been approved by the FDA to treat this disease. This review provides a current status of the COVID-19, epidemiology, an overview of phylogeny, mode of action, diagnosis, and possible treatment methods and vaccines.
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Affiliation(s)
| | - Chaudhary Fariha
- School of Biological Sciences, University of the Punjab, Lahore 54000, Pakistan
| | - Aqsa Anwar
- School of Biological Sciences, University of the Punjab, Lahore 54000, Pakistan
| | - Naveed Shahzad
- School of Biological Sciences, University of the Punjab, Lahore 54000, Pakistan
| | - Munir Ahmad
- School of Biological Sciences, University of the Punjab, Lahore 54000, Pakistan
| | - Salma Mukhtar
- School of Biological Sciences, University of the Punjab, Lahore 54000, Pakistan
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120
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Affiliation(s)
- Eun-Joong Kim
- Department of Clinical Laboratory Science, Chungbuk Health & Science University, Cheongju, Korea
| | - Dongsup Lee
- Department of Clinical Laboratory Science, Hyejeon College, Hongseong, Korea
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Li C, Chu H, Liu X, Chiu MC, Zhao X, Wang D, Wei Y, Hou Y, Shuai H, Cai J, Chan JFW, Zhou J, Yuen KY. Human coronavirus dependency on host heat shock protein 90 reveals an antiviral target. Emerg Microbes Infect 2020; 9:2663-2672. [PMID: 33179566 PMCID: PMC7751432 DOI: 10.1080/22221751.2020.1850183] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rapid accumulation of viral proteins in host cells render viruses highly dependent on cellular chaperones including heat shock protein 90 (Hsp90). Three highly pathogenic human coronaviruses, including MERS-CoV, SARS-CoV and SARS-CoV-2, have emerged in the past 2 decades. However, there is no approved antiviral agent against these coronaviruses. We inspected the role of Hsp90 for coronavirus propagation. First, an Hsp90 inhibitor, 17-AAG, significantly suppressed MERS-CoV propagation in cell lines and physiological-relevant human intestinal organoids. Second, siRNA depletion of Hsp90β, but not Hsp90α, significantly restricted MERS-CoV replication and abolished virus spread. Third, Hsp90β interaction with MERS-CoV nucleoprotein (NP) was revealed in a co-immunoprecipitation assay. Hsp90β is required to maintain NP stability. Fourth, 17-AAG substantially inhibited the propagation of SARS-CoV and SARS-CoV-2. Collectively, Hsp90 is a host dependency factor for human coronavirus MERS-CoV, SARS-CoV and SARS-COV-2. Hsp90 inhibitors can be repurposed as a potent and broad-spectrum antiviral against human coronaviruses.
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Affiliation(s)
- Cun Li
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, People's Republic of China.,Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, People's Republic of China.,Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Xiaojuan Liu
- Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Man Chun Chiu
- Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Xiaoyu Zhao
- Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Dong Wang
- Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Yuxuan Wei
- Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Yuxin Hou
- Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Huiping Shuai
- Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Jianpiao Cai
- Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, People's Republic of China.,Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, People's Republic of China.,Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Kwok Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, People's Republic of China.,Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, People's Republic of China
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122
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AL-Mutar HAH. The evolution of Genetic Molecular Map and phylogenetic tree of Coronavirus (COVID-19). THE IRAQI JOURNAL OF VETERINARY MEDICINE 2020. [DOI: 10.30539/ijvm.v44i2.977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Coronavirus (COVID-19) is suspected to originate from an animal host (zoonotic) followed by a human to human transmission, The purpose of the present study is to determine the genetic affinity of a phylogenetic tree and conformation of protein between human and bat. Through study of genetic sequencing, as shown in the tree design of strains and genetic variants, the main cause of COVID-19 is the Bat Coronavirus RaTG13 (SARS) virus in ID: MN996532.1 and ID: MG772933.1 (24-Jul-2013 and Feb-2017) shows that the evolution of the Corona virus from 2003, 2013 to 2020 which has become the most deadly peak in humans, the virus evolved from the bat effect on Humans. Protein analysis show 98 change of amino acid form RaTG13 (SARS) virus to COVID-19 Homo sapiens. Consequently, this study increased our understanding of the genetic variety of the COVID-19 carried by bats. So we conclude that a protein conformation drawing shows high identity compatibility between a bat and a human
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Zhu Z, Meng K, Meng G. Genomic recombination events may reveal the evolution of coronavirus and the origin of SARS-CoV-2. Sci Rep 2020; 10:21617. [PMID: 33303849 PMCID: PMC7728743 DOI: 10.1038/s41598-020-78703-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
To trace the evolution of coronaviruses and reveal the possible origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), we collected and thoroughly analyzed 29,452 publicly available coronavirus genomes, including 26,312 genomes of SARS-CoV-2 strains. We observed coronavirus recombination events among different hosts including 3 independent recombination events with statistical significance between some isolates from humans, bats and pangolins. Consistent with previous records, we also detected putative recombination between strains similar or related to Bat-CoV-RaTG13 and Pangolin-CoV-2019. The putative recombination region is located inside the receptor-binding domain (RBD) of the spike glycoprotein (S protein), which may represent the origin of SARS-CoV-2. Population genetic analyses provide estimates suggesting that the putative introduced DNA within the RBD is undergoing directional evolution. This may result in the adaptation of the virus to hosts. Unsurprisingly, we found that the putative recombination region in S protein was highly diverse among strains from bats. Bats harbor numerous coronavirus subclades that frequently participate in recombination events with human coronavirus. Therefore, bats may provide a pool of genetic diversity for the origin of SARS-CoV-2.
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Affiliation(s)
- Zhenglin Zhu
- School of Life Sciences, Chongqing University, No. 55 Daxuecheng South Road, Shapingba, Chongqing, 401331, China.
| | - Kaiwen Meng
- College of Veterinary Medicine, China Agricultural University, Beijing, 100094, China
| | - Geng Meng
- College of Veterinary Medicine, China Agricultural University, Beijing, 100094, China.
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124
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Alexandrova R, Beykov P, Vassilev D, Jukić M, Podlipnik Č. The virus that shook the world: questions and answers about SARS-CoV-2 and COVID-19. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1847683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Radostina Alexandrova
- Department of Pathology Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Pencho Beykov
- Department of Pathology Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kliment Ohridski”, Sofa, Bulgaria
| | - Dobrin Vassilev
- “Alexandrovska” University Hospital, Medical University of Sofia, Sofia, Bulgaria
| | - Marko Jukić
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor, Maribor, Slovenia
- Natural Sciences and Information Technologies, Faculty of Mathematics, University of Primorska, Koper, Slovenia
| | - Črtomir Podlipnik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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125
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Krishnamoorthy S, Swain B, Verma RS, Gunthe SS. SARS-CoV, MERS-CoV, and 2019-nCoV viruses: an overview of origin, evolution, and genetic variations. Virusdisease 2020; 31:411-423. [PMID: 33102628 PMCID: PMC7567416 DOI: 10.1007/s13337-020-00632-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
Coronaviruses are single stranded RNA viruses usually present in bats (reservoir hosts), and are generally lethal, highly transmissible, and pathogenic viruses causing sever morbidity and mortality rates in human. Several animals including civets, camels, etc. have been identified as intermediate hosts enabling effective recombination of these viruses to emerge as new virulent and pathogenic strains. Among the seven known human coronaviruses SARS-CoV, MERS-CoV, and SARS-CoV-2 (2019-nCoV) have evolved as severe pathogenic forms infecting the human respiratory tract. About 8096 cases and 774 deaths were reported worldwide with the SARS-CoV infection during year 2002; 2229 cases and 791 deaths were reported for the MERS-CoV that emerged during 2012. Recently ~ 33,849,737 cases and 1,012,742 deaths (data as on 30 Sep 2020) were reported from the recent evolver SARS-CoV-2 infection. Studies on epidemiology and pathogenicity have shown that the viral spread was potentially caused by the contact route especially through the droplets, aerosols, and contaminated fomites. Genomic studies have confirmed the role of the viral spike protein in virulence and pathogenicity. They target the respiratory tract of the human causing severe progressive pneumonia affecting other organs like central nervous system in case of SARS-CoV, severe renal failure in MERS-CoV, and multi-organ failure in SARS-CoV-2. Herein, with respect to current awareness and role of coronaviruses in global public health, we review the various factors involving the origin, evolution, and transmission including the genetic variations observed, epidemiology, and pathogenicity of the three potential coronaviruses variants SARS-CoV, MERS-CoV, and 2019-nCoV.
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Affiliation(s)
- Sarayu Krishnamoorthy
- EWRE Division, Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, 600 036 India
| | - Basudev Swain
- EWRE Division, Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, 600 036 India
| | - R. S. Verma
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600 036 India
| | - Sachin S. Gunthe
- EWRE Division, Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, 600 036 India
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126
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Tiwari R, Dhama K, Sharun K, Iqbal Yatoo M, Malik YS, Singh R, Michalak I, Sah R, Bonilla-Aldana DK, Rodriguez-Morales AJ. COVID-19: animals, veterinary and zoonotic links. Vet Q 2020; 40:169-182. [PMID: 32393111 PMCID: PMC7755411 DOI: 10.1080/01652176.2020.1766725] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/05/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), has spread over 210 countries and territories beyond China shortly. On February 29, 2020, the World Health Organization (WHO) denoted it in a high-risk category, and on March 11, 2020, this virus was designated pandemic, after its declaration being a Public Health International Emergency on January 30, 2020. World over high efforts are being made to counter and contain this virus. The COVID-19 outbreak once again proves the potential of the animal-human interface to act as the primary source of emerging zoonotic diseases. Even though the circumstantial evidence suggests the possibility of an initial zoonotic emergence, it is too early to confirm the role of intermediate hosts such as snakes, pangolins, turtles, and other wild animals in the origin of SARS-CoV-2, in addition to bats, the natural hosts of multiple coronaviruses such as SARS-CoV and MERS-CoV. The lessons learned from past episodes of MERS-CoV and SARS-CoV are being exploited to retort this virus. Best efforts are being taken up by worldwide nations to implement effective diagnosis, strict vigilance, heightened surveillance, and monitoring, along with adopting appropriate preventive and control strategies. Identifying the possible zoonotic emergence and the exact mechanism responsible for its initial transmission will help us to design and implement appropriate preventive barriers against the further transmission of SARS-CoV-2. This review discusses in brief about the COVID-19/SARS-CoV-2 with a particular focus on the role of animals, the veterinary and associated zoonotic links along with prevention and control strategies based on One-health approaches.
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Affiliation(s)
- Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pt. Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Mohd. Iqbal Yatoo
- Sher-E, Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Rajendra Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Izabela Michalak
- Faculty of Chemistry, Department of Advanced Material Technologies, Wrocław University of Science and Technology, Wrocław, Poland
| | - Ranjit Sah
- Department of Microbiology, Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal
| | - D. Katterine Bonilla-Aldana
- Semillero de Zoonosis, Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda, Colombia
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnologica de Pereira, Pereira, Colombia
- Grupo de Investigacion Biomedicina, Faculty of Medicine, Fundacion Universitaria Autonoma de las Americas, Pereira, Risaralda, Colombia
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127
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Zhao X, Ding Y, Du J, Fan Y. 2020 update on human coronaviruses: One health, one world. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2020; 8:100043. [PMID: 33521622 PMCID: PMC7836940 DOI: 10.1016/j.medntd.2020.100043] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/04/2020] [Accepted: 08/19/2020] [Indexed: 01/18/2023] Open
Abstract
Since human coronavirus (HCoVs) was first described in the 1960s, seven strains of respiratory human coronaviruses have emerged and caused human infections. After the emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), a pneumonia outbreak of coronavirus disease 2019 (COVID-19) caused by a novel coronavirus (SARS-CoV-2) has represented a pandemic threat to global public health in the 21st century. Without effectively prophylactic and therapeutic strategies including vaccines and antiviral drugs, these three coronaviruses have caused severe respiratory syndrome and high case-fatality rates around the world. In this review, we detail the emergence event, origin and reservoirs of all HCoVs, compare the differences with regard to structure and receptor usage, and summarize therapeutic strategies for COVID-19 that cause severe pneumonia and global pandemic.
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Affiliation(s)
- Xinbin Zhao
- Key Laboratory for Biomechanics and Mechanobiology of Chinese Education Ministry, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Yuecheng Ding
- School of Public Health, Peking University, Beijing, 100871, China
| | - Jing Du
- Key Laboratory for Biomechanics and Mechanobiology of Chinese Education Ministry, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, 100191, China
| | - Yubo Fan
- Key Laboratory for Biomechanics and Mechanobiology of Chinese Education Ministry, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, 100191, China
- Key Laboratory of Human Motion Analysis and Rehabilitation Technology of the Ministry of Civil Affairs, National Research Center for Rehabilitation Technical Aids, Beijing, 100176, China
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128
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Nazeam J, Mohammed EZ, Raafat M, Houssein M, Elkafoury A, Hamdy D, Jamil L. Based on Principles and Insights of COVID-19 Epidemiology, Genome Sequencing, and Pathogenesis: Retrospective Analysis of Sinigrin and Prolixin RX (Fluphenazine) Provides Off-Label Drug Candidates. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:1123-1140. [PMID: 32804597 PMCID: PMC8960168 DOI: 10.1177/2472555220950236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 12/21/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative pathogen of pandemic coronavirus disease 2019 (COVID-19). So far, no approved therapy has been developed to halt the spread of the pathogen, and unfortunately, the strategies for developing a new therapy will require a long time and very extensive resources. Therefore, drug repurposing has emerged as an ideal strategy toward a smart, versatile, quick way to confine the lethal disease. In this endeavor, natural products have been an untapped source for new drugs. This review represents the confederated experience of multidisciplinary researchers of 99 articles using several databases: Google Scholar, Science Direct, MEDLINE, Web of Science, Scopus, and PubMed. To establish the hypothesis, a Bayesian perspective of a systematic review was used to outline evidence synthesis. Our docking documentation of 69 compounds and future research agenda assumptions were directed toward finding an effective and economic anti-COVID-19 treatment from natural products. Glucosinolate, flavones, and sulfated nitrogenous compounds demonstrate direct anti-SARS-CoV-2 activity through inhibition protease enzymes and may be considered potential candidates against coronavirus. These findings could be a starting point to initiate an integrative study that may encompass interested scientists and research institutes to test the hypothesis in vitro, in vivo, and in clinics after satisfying all ethical requirements.
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Affiliation(s)
- Jilan Nazeam
- Center of Excellence, Natural Products Unit, Pharmacognosy Department, Faculty of Pharmacy, October 6 University, Cairo, Egypt
| | - Esraa Z. Mohammed
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, October 6 University, Cairo, Egypt
| | - Mariam Raafat
- Center of Excellence, Natural Products Unit, Pharmacognosy Department, Faculty of Pharmacy, October 6 University, Cairo, Egypt
| | - Mariam Houssein
- Center of Excellence, Natural Products Unit, Pharmacognosy Department, Faculty of Pharmacy, October 6 University, Cairo, Egypt
| | - Asmaa Elkafoury
- Center of Excellence, Natural Products Unit, Pharmacognosy Department, Faculty of Pharmacy, October 6 University, Cairo, Egypt
| | - Dina Hamdy
- Center of Excellence, Natural Products Unit, Pharmacognosy Department, Faculty of Pharmacy, October 6 University, Cairo, Egypt
| | - Lina Jamil
- Microbiology Department, Faculty of Pharmacy, October 6 University, Cairo, Egypt
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129
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Ali M, Imran M, Khan A. Analysis and prediction of the COVID-19 outbreak in Pakistan. JOURNAL OF BIOLOGICAL DYNAMICS 2020; 14:730-747. [PMID: 32875961 DOI: 10.1080/17513758.2020.1814883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/08/2020] [Indexed: 06/11/2023]
Abstract
In this study, we estimate the severity of the COVID-19 outbreak in Pakistan prior to and after lockdown restrictions were eased. We also project the epidemic curve considering realistic quarantine, social distancing and possible medication scenarios. The pre-lock down value of R0 is estimated to be 1.07 and the post lock down value is estimated to be 1.86. Using this analysis, we project the epidemic curve. We note that if no substantial efforts are made to contain the epidemic, it will peak in mid-September, 2020, with the maximum projected active cases being close to 700, 000. In a realistic, best case scenario, we project that the epidemic peaks in early to mid-July, 2020, with the maximum active cases being around 120, 000. We note that social distancing measures and medication will help flatten the curve; however, without the reintroduction of further lock down, it would be very difficult to make R0<1 .
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Affiliation(s)
- Mohsin Ali
- Department of Mathematics, Lahore University of Management Sciences, Lahore, Pakistan
| | - Mudassar Imran
- Department of Mathematics and Natural Sciences, Gulf University for Science & Technology, Mishref, Kuwait
| | - Adnan Khan
- Department of Mathematics, Lahore University of Management Sciences, Lahore, Pakistan
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130
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Ali M, Shah STH, Imran M, Khan A. The role of asymptomatic class, quarantine and isolation in the transmission of COVID-19. JOURNAL OF BIOLOGICAL DYNAMICS 2020; 14:389-408. [PMID: 32498655 DOI: 10.1080/17513758.2020.1773000] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We formulate a deterministic epidemic model for the spread of Corona Virus Disease (COVID-19). We have included asymptomatic, quarantine and isolation compartments in the model, as studies have stressed upon the importance of these population groups on the transmission of the disease. We calculate the basic reproduction number [Formula: see text] and show that for [Formula: see text] the disease dies out and for [Formula: see text] the disease is endemic. Using sensitivity analysis we establish that [Formula: see text] is most sensitive to the rate of quarantine and isolation and that a high level of quarantine needs to be maintained as well as isolation to control the disease. Based on this we devise optimal quarantine and isolation strategies, noting that high levels need to be maintained during the early stages of the outbreak. Using data from the Wuhan outbreak, which has nearly run its course we estimate that [Formula: see text] which while in agreement with other estimates in the literature is on the lower side.
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Affiliation(s)
- Mohsin Ali
- Department of Mathematics, Lahore University of Management Sciences, DHA Lahore, Pakistan
| | - Syed Touqeer H Shah
- Department of Mathematics, Lahore University of Management Sciences, DHA Lahore, Pakistan
| | - Mudassar Imran
- Department of Mathematics and Natural Sciences, Gulf University for Science & Technology, Mishref, Kuwait
| | - Adnan Khan
- Department of Mathematics, Lahore University of Management Sciences, DHA Lahore, Pakistan
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131
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Jakhmola S, Indari O, Kashyap D, Varshney N, Rani A, Sonkar C, Baral B, Chatterjee S, Das A, Kumar R, Jha HC. Recent updates on COVID-19: A holistic review. Heliyon 2020; 6:e05706. [PMID: 33324769 PMCID: PMC7729279 DOI: 10.1016/j.heliyon.2020.e05706] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/21/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023] Open
Abstract
Coronaviruses are large positive-sense RNA viruses with spike-like peplomers on their surface. The Coronaviridae family's strains infect different animals and are popularly associated with several outbreaks, namely SARS and MERS epidemic. COVID-19 is one such recent outbreak caused by SARS-CoV-2 identified first in Wuhan, China. COVID-19 was declared a pandemic by WHO on 11th March 2020. Our review provides information covering various facets of the disease starting from its origin, transmission, mutations in the virus to pathophysiological changes in the host upon infection followed by diagnostics and possible therapeutics available to tackle the situation. We have highlighted the zoonotic origin of SARS-CoV-2, known to share 96.2% nucleotide similarity with bat coronavirus. Notably, several mutations in SARS-CoV-2 spike protein, nucleocapsid protein, PLpro, and ORF3a are reported across the globe. These mutations could alter the usual receptor binding function, fusion process with the host cell, virus replication, and the virus's assembly. Therefore, studying these mutations could help understand the virus's virulence properties and design suitable therapeutics. Moreover, the aggravated immune response to COVID-19 can be fatal. Hypertension, diabetes, and cardiovascular diseases are comorbidities substantially associated with SARS-CoV-2 infection. The review article discusses these aspects, stating the importance of various comorbidities in disease outcomes. Furthermore, medications' unavailability compels the clinicians to opt for atypical drugs like remdesivir, chloroquine, etc. The current diagnostics of COVID-19 include qRT-PCR, CT scan, serological tests, etc. We have described these aspects to expose the information to the scientific community and to accelerate the research.
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Affiliation(s)
- Shweta Jakhmola
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Omkar Indari
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Dharmendra Kashyap
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Nidhi Varshney
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Annu Rani
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Charu Sonkar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Budhadev Baral
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Sayantani Chatterjee
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Ayan Das
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Rajesh Kumar
- Discipline of Physics, Indian Institute of Technology, Indore, India
| | - Hem Chandra Jha
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
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132
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Taha BA, Al Mashhadany Y, Hafiz Mokhtar MH, Dzulkefly Bin Zan MS, Arsad N. An Analysis Review of Detection Coronavirus Disease 2019 (COVID-19) Based on Biosensor Application. SENSORS (BASEL, SWITZERLAND) 2020; 20:E6764. [PMID: 33256085 PMCID: PMC7729752 DOI: 10.3390/s20236764] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/17/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023]
Abstract
Timely detection and diagnosis are essentially needed to guide outbreak measures and infection control. It is vital to improve healthcare quality in public places, markets, schools and airports and provide useful insights into the technological environment and help researchers acknowledge the choices and gaps available in this field. In this narrative review, the detection of coronavirus disease 2019 (COVID-19) technologies is summarized and discussed with a comparison between them from several aspects to arrive at an accurate decision on the feasibility of applying the best of these techniques in the biosensors that operate using laser detection technology. The collection of data in this analysis was done by using six reliable academic databases, namely, Science Direct, IEEE Xplore, Scopus, Web of Science, Google Scholar and PubMed. This review includes an analysis review of three highlights: evaluating the hazard of pandemic COVID-19 transmission styles and comparing them with Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) to identify the main causes of the virus spreading, a critical analysis to diagnose coronavirus disease 2019 (COVID-19) based on artificial intelligence using CT scans and CXR images and types of biosensors. Finally, we select the best methods that can potentially stop the propagation of the coronavirus pandemic.
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Affiliation(s)
- Bakr Ahmed Taha
- UKM—Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (B.A.T.); (M.H.H.M.); (M.S.D.B.Z.)
| | - Yousif Al Mashhadany
- Department of Electrical Engineering, College of Engineering, University of Anbar, Anbar 00964, Iraq;
| | - Mohd Hadri Hafiz Mokhtar
- UKM—Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (B.A.T.); (M.H.H.M.); (M.S.D.B.Z.)
| | - Mohd Saiful Dzulkefly Bin Zan
- UKM—Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (B.A.T.); (M.H.H.M.); (M.S.D.B.Z.)
| | - Norhana Arsad
- UKM—Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (B.A.T.); (M.H.H.M.); (M.S.D.B.Z.)
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Shaikh SS, Jose AP, Nerkar DA, Vijaykumar KV M, Shaikh SK. COVID-19 pandemic crisis-a complete outline of SARS-CoV-2. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2020; 6:116. [PMID: 33224993 PMCID: PMC7670985 DOI: 10.1186/s43094-020-00133-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/26/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Coronavirus (SARS-CoV-2), the cause of COVID-19, a fatal disease emerged from Wuhan, a large city in the Chinese province of Hubei in December 2019. MAIN BODY OF ABSTRACT The World Health Organization declared COVID-19 as a pandemic due to its spread to other countries inside and outside Asia. Initial confirmation of the pandemic shows patient exposure to the Huanan seafood market. Bats might be a significant host for the spread of coronaviruses via an unknown intermediate host. The human-to-human transfer has become a significant concern due to one of the significant reasons that is asymptomatic carriers or silent spreaders. No data is obtained regarding prophylactic treatment for COVID-19, although many clinical trials are underway. CONCLUSION The most effective weapon is prevention and precaution to avoid the spread of the pandemic. In this current review, we outline pathogenesis, diagnosis, treatment, ongoing clinical trials, prevention, and precautions. We have also highlighted the impact of pandemic worldwide and challenges that can help to overcome the fatal disease in the future.
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Affiliation(s)
| | - Anooja P. Jose
- Government College of Pharmacy, Aurangabad, 431001 India
| | | | | | - Saquib Khaleel Shaikh
- Y. B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Aurangabad, 431001 India
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134
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Sreekanth Reddy O, Lai WF. Tackling COVID-19 Using Remdesivir and Favipiravir as Therapeutic Options. Chembiochem 2020; 22:939-948. [PMID: 33031623 PMCID: PMC7675336 DOI: 10.1002/cbic.202000595] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/08/2020] [Indexed: 12/11/2022]
Abstract
The human world is currently influenced largely by the outbreak of pandemic COVID‐19. At this moment, most researchers focus on developing treatment strategies and measures to work against COVID‐19. Treatment strategies specific for COVID‐19 are lacking. This article provides an overview of the life cycle and routes of transmission of SARS‐CoV‐2. The therapeutic effects of two drugs [i. e., remdesivir (RDV) and favipiravir (FPV)] which can potentially tackle COVID‐19 are discussed based on current published data. This review can serve as a reference for future studies.
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Affiliation(s)
| | - Wing-Fu Lai
- Ciechanover Institute of Precision and Regenerative Medicine, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, 518172, P. R. China.,Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, P. R. China
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135
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Antiochia R. Nanobiosensors as new diagnostic tools for SARS, MERS and COVID-19: from past to perspectives. Mikrochim Acta 2020; 187:639. [PMID: 33151419 PMCID: PMC7642243 DOI: 10.1007/s00604-020-04615-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/21/2020] [Indexed: 12/23/2022]
Abstract
The severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) and novel coronavirus 19 (COVID-19) epidemics represent the biggest global health threats in the last two decades. These infections manifest as bronchitis, pneumonia or severe, sometimes fatal, respiratory illness. The novel coronavirus seems to be associated with milder infections but it has spread globally more rapidly becoming a pandemic. This review summarises the state of the art of nanotechnology-based affinity biosensors for SARS, MERS and COVID-19 detection. The nanobiosensors are antibody- or DNA-based biosensors with electrochemical, optical or FET-based transduction. Various kinds of nanomaterials, such as metal nanoparticles, nanowires and graphene, have been merged to the affinity biosensors to enhance their analytical performances. The advantages of the use of the nanomaterials are highlighted, and the results compared with those obtained using non-nanostructured biosensors. A critical comparison with conventional methods, such as RT-PCR and ELISA, is also reported. It is hoped that this review will provide interesting information for the future development of new reliable nano-based platforms for point-of-care diagnostic devices for COVID-19 prevention and control.
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Affiliation(s)
- Riccarda Antiochia
- Department of Chemistry and Drug Technologies, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy.
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136
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Duda-Chodak A, Lukasiewicz M, Zięć G, Florkiewicz A, Filipiak-Florkiewicz A. Covid-19 pandemic and food: Present knowledge, risks, consumers fears and safety. Trends Food Sci Technol 2020; 105:145-160. [PMID: 32921922 PMCID: PMC7480472 DOI: 10.1016/j.tifs.2020.08.020] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/04/2020] [Accepted: 08/29/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND COVID-19 is a pandemic disease that has paralyzed social life and the economy around the world since the end of 2019, and which has so far killed nearly 600,000 people. The rapidity of its spread and the lack of detailed research on the course and methods of transmission significantly impede both its eradication and prevention. SCOPE AND APPROACH Due to the high transmission rate and fatality resulting from COVID-19 disease, the paper focuses on analyzing the current state of knowledge about SARS-CoV-2 as well as its potential connection with food as a source of pathogen and infection. KEY FINDINGS AND CONCLUSIONS There is currently no evidence (scientific publications, WHO, EFSA etc.) that COVID-19 disease can spread directly through food and the human digestive system. However, according to the hypothesis regarding the primary transmission of the virus, the source of which was food of animal origin (meat of wild animals), as well as the fact that food is a basic necessity for humans, it is worth emphasizing that food can, if not directly, be a carrier of the virus. Particular attention should be paid to this indirect pathway when considering the potential for the spread of an epidemic and the development of prevention principles.
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137
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Farah S, Atkulwar A, Praharaj MR, Khan R, Gandham R, Baig M. Phylogenomics and phylodynamics of SARS-CoV-2 genomes retrieved from India. Future Virol 2020. [PMCID: PMC7720652 DOI: 10.2217/fvl-2020-0243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background: This is the first phylodynamic study attempted on SARS-CoV-2 genomes from India to infer the current state of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution using phylogenetic network and growth trends. Materials & Methods: Out of 286 retrieved whole genomes from India, 138 haplotypes were used to build a phylogenetic network. The birth–death serial model (BDSIR) package of BEAST2 was used to calculate the reproduction number of SARS-CoV-2. Population dynamics were investigated using the stamp date method as implemented in BEAST2 and BEAST 1.10.4. Results: A median-joining network revealed two ancestral clusters. A high basic reproduction number of SARS-CoV-2 was found. An exponential rise in the effective population size of Indian isolates was detected. Conclusion: The phylogenetic network reveals dual ancestry and possibility of community transmission of SARS-CoV-2 in India.
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Affiliation(s)
- Sameera Farah
- Department of Zoology, Laboratory of Molecular & Conservation Genetics, Govt. Vidarbha Institute of Science & Humanities, VMV, Road, Amravati 444604, India
- Department of Integrative Biology, University of Guelph, Guelph, 50 Stone Road, East, N1G 2W1, ON, Canada
| | - Ashwin Atkulwar
- Department of Zoology, Laboratory of Molecular & Conservation Genetics, Govt. Vidarbha Institute of Science & Humanities, VMV, Road, Amravati 444604, India
- Department of Zoology, Amolakchand Mahavidyalaya, Godhani Road, Yavatmal 445001, India
| | - Manas Ranjan Praharaj
- National Institutes of Animal Biotechnology, Gowlidoddy, Hyderabad, Telangana 500032, India
| | - Raja Khan
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, India
| | - Ravikumar Gandham
- National Institutes of Animal Biotechnology, Gowlidoddy, Hyderabad, Telangana 500032, India
| | - Mumtaz Baig
- Department of Zoology, Laboratory of Molecular & Conservation Genetics, Govt. Vidarbha Institute of Science & Humanities, VMV, Road, Amravati 444604, India
- Department of Integrative Biology, University of Guelph, Guelph, 50 Stone Road, East, N1G 2W1, ON, Canada
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Kumar D, Chauhan G, Kalra S, Kumar B, Gill MS. A perspective on potential target proteins of COVID-19: Comparison with SARS-CoV for designing new small molecules. Bioorg Chem 2020; 104:104326. [PMID: 33142431 PMCID: PMC7524440 DOI: 10.1016/j.bioorg.2020.104326] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2 (COVID-19) epidemic has created an unprecedented medical and economic crisis all over the world. SARS-CoV-2 is found to have more contagious character as compared to MERS-CoV and is spreading in a very fast manner all around the globe. It has affected over 31 million people all over the world till date. This virus shares around 80% of genome similarity with SARS-CoV. In this perspective, we have explored three major targets namely; SARS-CoV-2 spike (S) protein, RNA dependent RNA polymerase, and 3CL or Mpro Protease for the inhibition of SARS-CoV-2. These targets have attracted attention of the medicinal chemists working on computer-aided drug design in developing new small molecules that might inhibit these targets for combating COVID-19 disease. Moreover, we have compared the similarity of these target proteins with earlier reported coronavirus (SARS-CoV). We have observed that both the coronaviruses share around 80% similarity in their amino acid sequence. The key amino acid interactions which can play a crucial role in designing new small molecule inhibitors against COVID-19 have been reported in this perspective. Authors believe that this study will help the medicinal chemists to understand the key amino acids essential for interactions at the active site of target proteins in SARS-CoV-2, based on their similarity with earlier reported viruses. In this review, we have also described the lead molecules under various clinical trials for their efficacy against COVID-19.
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Affiliation(s)
- Devendra Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Ghal Kalan, G.T Road, Moga, Punjab 142001, India
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, Nuevo León, Mexico
| | - Sourav Kalra
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research, SAS Nagar, Sector 67, Mohali, Punjab 160062, India
| | - Bhupinder Kumar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Ghal Kalan, G.T Road, Moga, Punjab 142001, India.
| | - Manjinder Singh Gill
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research, SAS Nagar, Sector 67, Mohali, Punjab 160062, India.
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139
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Guruprasad L. Human coronavirus spike protein-host receptor recognition. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 161:39-53. [PMID: 33137344 PMCID: PMC7604128 DOI: 10.1016/j.pbiomolbio.2020.10.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/12/2020] [Accepted: 10/23/2020] [Indexed: 01/06/2023]
Abstract
A variety of coronaviruses (CoVs) have infected humans and caused mild to severe respiratory diseases that could result in mortality. The human CoVs (HCoVs) belong to the genera of α- and β-CoVs that originate in rodents and bats and are transmitted to humans via zoonotic contacts. The binding of viral spike proteins to the host cell receptors is essential for mediating fusion of viral and host cell membranes to cause infection. The SARS-CoV-2 originated in bats (RaTG13 SARS-CoV) and is transmitted to humans via pangolins. The presence of 'PRRA' sequence motif in SARS-CoV-2 spike proteins from human, dog, cat, mink, tiger and lion suggests a common viral entry mechanism into host cells. In this review, we discuss structural features of HCoV spike proteins and recognition of host protein and carbohydrate receptors.
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Jaiswal S, Kumar M, Mandeep, Sunita, Singh Y, Shukla P. Systems Biology Approaches for Therapeutics Development Against COVID-19. Front Cell Infect Microbiol 2020; 10:560240. [PMID: 33194800 PMCID: PMC7655984 DOI: 10.3389/fcimb.2020.560240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding the systems biology approaches for promoting the development of new therapeutic drugs is attaining importance nowadays. The threat of COVID-19 outbreak needs to be vanished for global welfare, and every section of research is focusing on it. There is an opportunity for finding new, quick, and accurate tools for developing treatment options, including the vaccine against COVID-19. The review at this moment covers various aspects of pathogenesis and host factors for exploring the virus target and developing suitable therapeutic solutions through systems biology tools. Furthermore, this review also covers the extensive details of multiomics tools i.e., transcriptomics, proteomics, genomics, lipidomics, immunomics, and in silico computational modeling aiming towards the study of host-virus interactions in search of therapeutic targets against the COVID-19.
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Affiliation(s)
- Shweta Jaiswal
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Mohit Kumar
- Soil Microbial Ecology and Environmental Toxicology Laboratory, Department of Zoology, University of Delhi, Delhi, India
- Department of Zoology, Hindu College, University of Delhi, Delhi, India
| | - Mandeep
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Sunita
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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141
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Antiochia R. Developments in biosensors for CoV detection and future trends. Biosens Bioelectron 2020; 173:112777. [PMID: 33189015 PMCID: PMC7591947 DOI: 10.1016/j.bios.2020.112777] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 12/24/2022]
Abstract
This review summarizes the state of art of biosensor technology for Coronavirus (CoV) detection, the current challenges and the future perspectives. Three categories of affinity-based biosensors (ABBs) have been developed, depending on their transduction mechanism, namely electrochemical, optical and piezoelectric biosensors. The biorecognition elements include antibodies and DNA, which undergo important non-covalent binding interactions, with the formation of antigen-antibody and ssDNA/oligonucleotide-complementary strand complexes in immuno- and DNA-sensors, respectively. The analytical performances, the advantages and drawbacks of each type of biosensor are highlighted, discussed, and compared to traditional methods. It is hoped that this review will encourage scientists and academics to design and develop new biosensing platforms for point-of-care (POC) diagnostics to manage the coronavirus disease 2019 (COVID-19) pandemic, providing interesting reference for future studies.
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Affiliation(s)
- Riccarda Antiochia
- Department of Chemistry and Drug Technologies, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy.
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142
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Edwards CE, Yount BL, Graham RL, Leist SR, Hou YJ, Dinnon KH, Sims AC, Swanstrom J, Gully K, Scobey TD, Cooley MR, Currie CG, Randell SH, Baric RS. Swine acute diarrhea syndrome coronavirus replication in primary human cells reveals potential susceptibility to infection. Proc Natl Acad Sci U S A 2020; 117:26915-26925. [PMID: 33046644 PMCID: PMC7604506 DOI: 10.1073/pnas.2001046117] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Zoonotic coronaviruses represent an ongoing threat, yet the myriads of circulating animal viruses complicate the identification of higher-risk isolates that threaten human health. Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a newly discovered, highly pathogenic virus that likely evolved from closely related HKU2 bat coronaviruses, circulating in Rhinolophus spp. bats in China and elsewhere. As coronaviruses cause severe economic losses in the pork industry and swine are key intermediate hosts of human disease outbreaks, we synthetically resurrected a recombinant virus (rSADS-CoV) as well as a derivative encoding tomato red fluorescent protein (tRFP) in place of ORF3. rSADS-CoV replicated efficiently in a variety of continuous animal and primate cell lines, including human liver and rectal carcinoma cell lines. Of concern, rSADS-CoV also replicated efficiently in several different primary human lung cell types, as well as primary human intestinal cells. rSADS-CoV did not use human coronavirus ACE-2, DPP4, or CD13 receptors for docking and entry. Contemporary human donor sera neutralized the group I human coronavirus NL63, but not rSADS-CoV, suggesting limited human group I coronavirus cross protective herd immunity. Importantly, remdesivir, a broad-spectrum nucleoside analog that is effective against other group 1 and 2 coronaviruses, efficiently blocked rSADS-CoV replication in vitro. rSADS-CoV demonstrated little, if any, replicative capacity in either immune-competent or immunodeficient mice, indicating a critical need for improved animal models. Efficient growth in primary human lung and intestinal cells implicate SADS-CoV as a potential higher-risk emerging coronavirus pathogen that could negatively impact the global economy and human health.
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Affiliation(s)
- Caitlin E Edwards
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Boyd L Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Rachel L Graham
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Kenneth H Dinnon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Amy C Sims
- Chemical and Biological Signatures Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Jesica Swanstrom
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Kendra Gully
- Department of Comparative Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Trevor D Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Michelle R Cooley
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Caroline G Currie
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Scott H Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill, NC 27599
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143
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Silva TF, Tomiotto-Pellissier F, Sanfelice RA, Gonçalves MD, da Silva Bortoleti BT, Detoni MB, Rodrigues ACJ, Carloto ACM, Concato VM, Siqueira EDS, Costa IN, Pavanelli WR, Conchon-Costa I, Miranda-Sapla MM. A 21st Century Evil: Immunopathology and New Therapies of COVID-19. Front Immunol 2020; 11:562264. [PMID: 33193331 PMCID: PMC7652766 DOI: 10.3389/fimmu.2020.562264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/05/2020] [Indexed: 01/08/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19) has been classified as a global threat, affecting millions of people and killing thousands. It is caused by the SARS-CoV-2 virus, which emerged at the end of 2019 in Wuhan, China, quickly spreading worldwide. COVID-19 is a disease with symptoms that range from fever and breathing difficulty to acute respiratory distress and death, critically affecting older patients and people with previous comorbidities. SARS-CoV-2 uses the angiotensin-converting enzyme 2 (ACE2) receptor and mainly spreads through the respiratory tract, which it then uses to reach several organs. The immune system of infected patients has been demonstrated to suffer important alterations, such as lymphopenia, exhausted lymphocytes, excessive amounts of inflammatory monocytes and macrophages, especially in the lungs, and cytokine storms, which may contribute to its severity and difficulty of establishing an effective treatment. Even though no specific treatment is currently available, several studies have been investigating potential therapeutic strategies, including the use of previously approved drugs and immunotherapy. In this context, this review addresses the interaction between SARS-CoV-2 and the patient's host immune system during infection, in addition to discussing the main immunopathological mechanisms involved in the development of the disease and potential new therapeutic approaches.
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Affiliation(s)
- Taylon Felipe Silva
- Laboratory of Immunoparasitology of Neglected Diseases and Cancer—LIDNC, Department of Pathological Sciences, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | | | - Raquel Arruda Sanfelice
- Laboratory of Immunoparasitology of Neglected Diseases and Cancer—LIDNC, Department of Pathological Sciences, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Manoela Daiele Gonçalves
- Laboratory of Biotransformation and Phytochemistry, Department of Chemistry, Center of Exact Sciences, State University of Londrina, Londrina, Brazil
| | | | - Mariana Barbosa Detoni
- Laboratory of Immunoparasitology of Neglected Diseases and Cancer—LIDNC, Department of Pathological Sciences, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Ana Carolina Jacob Rodrigues
- Laboratory of Immunoparasitology of Neglected Diseases and Cancer—LIDNC, Department of Pathological Sciences, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Amanda Cristina Machado Carloto
- Laboratory of Immunoparasitology of Neglected Diseases and Cancer—LIDNC, Department of Pathological Sciences, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Virgínia Márcia Concato
- Laboratory of Immunoparasitology of Neglected Diseases and Cancer—LIDNC, Department of Pathological Sciences, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Elaine da Silva Siqueira
- Laboratory of Immunoparasitology of Neglected Diseases and Cancer—LIDNC, Department of Pathological Sciences, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Idessania Nazareth Costa
- Laboratory of Immunoparasitology of Neglected Diseases and Cancer—LIDNC, Department of Pathological Sciences, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Wander Rogério Pavanelli
- Laboratory of Immunoparasitology of Neglected Diseases and Cancer—LIDNC, Department of Pathological Sciences, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Ivete Conchon-Costa
- Laboratory of Immunoparasitology of Neglected Diseases and Cancer—LIDNC, Department of Pathological Sciences, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Milena Menegazzo Miranda-Sapla
- Laboratory of Immunoparasitology of Neglected Diseases and Cancer—LIDNC, Department of Pathological Sciences, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
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Talwar S, Sood S, Kumar J, Chauhan R, Sharma M, Tuli HS. Ayurveda and Allopathic Therapeutic Strategies in Coronavirus Pandemic Treatment 2020. ACTA ACUST UNITED AC 2020; 6:354-363. [PMID: 33106765 PMCID: PMC7577842 DOI: 10.1007/s40495-020-00245-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2020] [Indexed: 12/20/2022]
Abstract
Purpose of Review In the last month of 2019, i.e., December, COVID-19 hit Wuhan city in China. Since then, it has infected more than 210 countries and nearly about 33.4 million people with one million deaths globally. It is a viral disease with flu-like symptoms; hence, prevention and management is the best option to be adopted for its cure. Recent Findings Many healthcare systems, scientists, and researchers are fighting for the cure of this pandemic. Ayurvedic and allopathic treatments have been studied extensively and approached for the cure of COVID-19. In addition to ayurvedic treatments, the Ministry of Ayush, India, has also recommended many remedies to boost up immunity. Allopathic studies involved several antiviral drugs which were used in different combinations for the treatment of COVID-19. Summary Comparative analysis of Ayurveda and allopathic treatment strategies were carried out in the present study. Depending upon the patient’s conditions and symptoms, Ayurveda is useful for the treatment of COVID-19. Allopathic treatments inhibit viral infection by targeting majorly endocytosis, and angiotensin-converting enzyme (Ace) receptor signaling. In this article, we summarize different ayurvedic and allopathic medicines and treatment strategies which have been used for the treatment of COVID-19, a global pandemic.
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Affiliation(s)
- Shivangi Talwar
- Amity Institute of Biotechnology, Amity University, Noida, Noida, India
| | - Shivani Sood
- Department of Biotechnology, Mukand Lal National College, Yamuna Nagar, India
| | - Jayant Kumar
- Department of Biotechnology, Mukand Lal National College, Yamuna Nagar, India
| | - Ritu Chauhan
- Amity Institute of Biotechnology, Amity University, Noida, Noida, India
| | - Mamta Sharma
- School of Law, Justice and Governance, Gautam Buddha University, Greater Noida, India
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, 133207 India
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Choudhary S, Sreenivasulu K, Mitra P, Misra S, Sharma P. Role of Genetic Variants and Gene Expression in the Susceptibility and Severity of COVID-19. Ann Lab Med 2020; 41:129-138. [PMID: 33063674 PMCID: PMC7591285 DOI: 10.3343/alm.2021.41.2.129] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/20/2020] [Accepted: 09/22/2020] [Indexed: 01/08/2023] Open
Abstract
Since its first report in December 2019, coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly emerged as a pandemic affecting nearly all countries worldwide. As the COVID-19 pandemic progresses, the need to identify genetic risk factors for susceptibility to this serious illness has emerged. Host genetic factors, along with other risk factors may help determine susceptibility to respiratory tract infections. It is hypothesized that the ACE2 gene, encoding angiotensin-converting enzyme 2 (ACE2), is a genetic risk factor for SARS-CoV-2 infection and is required by the virus to enter cells. Together with ACE2, transmembrane protease serine 2 (TMPRSS2) and dipeptidyl peptidase-4 (DPP4) also play an important role in disease severity. Evaluating the role of genetic variants in determining the direction of respiratory infections will help identify potential drug target candidates for further study in COVID-19 patients. We have summarized the latest reports demonstrating that ACE2 variants, their expression, and epigenetic factors may influence an individual’s susceptibility to SARS-CoV-2 infection and disease outcome.
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Affiliation(s)
- Sarita Choudhary
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, India
| | - Karli Sreenivasulu
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, India
| | - Prasenjit Mitra
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, India
| | - Sanjeev Misra
- Department of Surgical Oncology, All India Institute of Medical Sciences, Jodhpur, India
| | - Praveen Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, India
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146
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Baruah C, Devi P, Sharma DK. Sequence Analysis and Structure Prediction of SARS-CoV-2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7234961. [PMID: 33102591 PMCID: PMC7576348 DOI: 10.1155/2020/7234961] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/12/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a single-stranded RNA genome that encodes 14 open reading frames (ORFs), eight of which encode accessory proteins that allow the virus to infect the host and promote virulence. The genome expresses around 29 structural and nonstructural protein products. The accessory proteins of SARS-CoV-2 are not essential for virus replication but do affect viral release, stability, and pathogenesis and finally contribute to virulence. This paper has attempted the structure prediction and functional analysis of two such accessory proteins, 9b and ORF14, in the absence of experimental structures. Sequence analysis, structure prediction, functional characterization, and evolutionary analysis based on the UniProtKB reviewed the amino acid sequences of SARS-CoV-2 9b (P0DTD2) and ORF14 (P0DTD3) proteins. Modeling has been presented with the introduction of hybrid comparative and ab initio modeling. QMEANDisCo 4.0.0 and ProQ3 for global and local (per residue) quality estimates verified the structures as high quality, which may be attributed to structure-based drug design targets. Tunnel analysis revealed the presence of 1-2 highly active tunneling sites, perhaps which will able to provide certain inputs for advanced structure-based drug design or to formulate potential vaccines in the absence of a complete experimental structure. The evolutionary analysis of both proteins of human SARS-CoV-2 indicates close relatedness to the bat coronavirus. The whole-genome phylogeny indicates that only the new bat coronavirus followed by pangolin coronaviruses has a close evolutionary relationship with the novel SARS-CoV-2.
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Affiliation(s)
- Chittaranjan Baruah
- Bioinformatics Laboratory (DBT-Star College), P.G. Department of Zoology, Darrang College, Tezpur, 784 001 Assam, India
| | | | - Dhirendra K. Sharma
- School of Biological Sciences, University of Science and Technology, Meghalaya, Baridua-793101, India
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147
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Coronaviruses: Innate Immunity, Inflammasome Activation, Inflammatory Cell Death, and Cytokines. Trends Immunol 2020; 41:1083-1099. [PMID: 33153908 PMCID: PMC7561287 DOI: 10.1016/j.it.2020.10.005] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022]
Abstract
The innate immune system acts as the first line of defense against pathogens, including coronaviruses (CoVs). Severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV are epidemic zoonotic CoVs that emerged at the beginning of the 21st century. The recently emerged virus SARS-CoV-2 is a novel strain of CoV that has caused the coronavirus 2019 (COVID-19) pandemic. Scientific advancements made by studying the SARS-CoV and MERS-CoV outbreaks have provided a foundation for understanding pathogenesis and innate immunity against SARS-CoV-2. In this review, we focus on our present understanding of innate immune responses, inflammasome activation, inflammatory cell death pathways, and cytokine secretion during SARS-CoV, MERS-CoV, and SARS-CoV-2 infection. We also discuss how the pathogenesis of these viruses influences these biological processes.
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148
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Dousset B, Mothe J. Getting Insights from a Large Corpus of Scientific Papers on Specialisted Comprehensive Topics - the Case of COVID-19. ACTA ACUST UNITED AC 2020; 176:2287-2296. [PMID: 33042309 PMCID: PMC7531911 DOI: 10.1016/j.procs.2020.09.287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
COVID-19 is one of the most important topics these days, specifically on search engines and news. While fake news is easily shared, scientific papers are reliable sources where information can be extracted. With about 24,000 scientific publications on COVID-19 and related research on PubMed, automatic computer-assisted analysis is required. In this paper, we develop two methodologies to get insights on specific sub-topics of interest and latest research sub-topics. These rely on natural language processing and graph-based visualizations. We run these methodologies on two cases: the virus origin and the uses of existing drugs.
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Affiliation(s)
| | - Josiane Mothe
- IRIT, UMR5505, CNRS & INSPEE UT2J, Univ. Toulouse, France
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149
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Abstract
Since the WHO declared coronavirus disease 2019 (COVID-19) as a pandemic, huge efforts were made to understand the disease, its pathogenesis, and treatment. COVID-19 is caused by severe acute respiratory syndrome (SARS) coronavirus-2 (SARS-CoV2), which is closely related to SARS-associated coronavirus (SARS-CoV). This article attempts to provide a timely and comprehensive review of the coronaviruses over the years, and the epidemics they caused in this century with a focus on the current pandemic COVID-19. It also covers the basics about the disease immunopathogenesis, diagnosis, prognosis, and treatment options. Although almost every single week new clinical findings are published, which change our understanding of COVID-19, this review explores and explains the disease and the treatment options available so far. In summary, many therapeutic options are being investigated to treat and/or ameliorate the symptoms of COVID-19, but none is registered and no sufficient data to support immune-based therapy beyond the context of clinical trials. For that, strengthening our immune system is the best defense at this time.
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Affiliation(s)
- Areej M Assaf
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Randa N Haddadin
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Amal A Akour
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, The University of Jordan, Amman, Jordan
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Sumarmi S. Kerja Harmoni Zat Gizi dalam Meningkatkan Imunitas Tubuh Terhadap Covid-19: Mini Review. AMERTA NUTRITION 2020. [DOI: 10.20473/amnt.v4i3.2020.250-256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
ABSTRACTBackground: The Covid-19 pandemic in Indonesia has been running since March 2020. Efforts to break the chain of transmission of the disease caused by the new SARS-CoV 2 coronavirus are by avoiding contact by practicing social & physical distancing and improving personal hygiene, and increase immunity or body defense against the corona virus.Purpose: This article discusses the role of macro nutrients and micronutrients that have the potential to increase immunity such as omega-3 fatty acids, several water soluble vitamins such as vitamin B6, vitamin C, as well as fat soluble vitamins such as vitamin A, vitamin D and vitamin E. as well as several minerals such as Fe, Zn, Se. The mechanisms of innate immunity and adaptive immunity that involve these nutrients will be discussed in depth, as well as how the cellular mechanism fights the corona virus.Discussion: The mechanism for the entry of the corona virus into the cell is through a mechanism called endocytosis, in which the virus is captured by the receptors on the surface of the cell, then drawn into the cell. Spike protein (protein S) facilitates the entry of viruses into target cells, especially lung cells.Conclusion The body's defense mechanisms against the corona virus are: 1) strengthening the body's frontline defenses or innate immunity; 2) stimulates the production of IgM and IgG immunoglobulins in the circulation; 3) blocking the virus from binding to the ACE-2 receptor; 4) reduce the intensity of cytokine storms; 5) reduce the speed of virus replication. ABSTRAKLatar Belakang: Pandemi Covid-19 di Indonesia telah berjalan sejak bulan Maret 2020. Upaya untuk memutus rantai penularan penyakit yang disebabkan oleh virus corona jenis baru SARS-CoV 2 adalah dengan menghidari kontak dengan cara mempraktekkan social & physical distancing dan meningkatkan kebersihan diri, serta meningkatkan imunitas atau pertahanan tubuh terhadap virus corona. Tujuan: Artikel ini membahas peran zat gizi makro dan zat gizi mikro yang berpotensi untuk meningkatkan imunitas seperti asam lemak omega-3, beberapa vitamin larut air seperti vitamin B6, vitamin C, juga vitamin larut lemak seperti vitamin A, vitamin D dan vitamin E, serta beberapa mineral seperti Fe, Zn, Se. Mekanisme innate immunity dan adaptive immunity yang melibatkan zat gizi tersebut akan dibahas secara mendalam, serta bagaimana mekanisme selular melawan virus corona. Ulasan: Mekanisme masuknya virus corona ke dalam sel adalah melalui mekanisme yang disebut endositosis, yaitu virus ditangkap oleh reseptor yang terdapat di permukaan sel, kemudian ditarik masuk ke dalam sel. Spike protein (protein S) bertugas memfasilitasi masuknya virus ke dalam sel target, terutama sel paru.Kesimpulan Mekanisme pertahanan tubuh melawan virus corona adalah: 1) menguatkan pertahanan tubuh garis depan atau innate immunity; 2) menstimulasi produksi immunoglobulin IgM dan IgG di dalam sirkulasi; 3) memblokir agar virus tidak terikat oleh receptor ACE-2; 4) menurunkan intensitas badai sitokin; 5) menurunkan kecepatan replikasi virus.
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