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Candido KL, Eich CR, de Fariña LO, Kadowaki MK, da Conceição Silva JL, Maller A, Simão RDCG. Spike protein of SARS-CoV-2 variants: a brief review and practical implications. Braz J Microbiol 2022; 53:1133-1157. [PMID: 35397075 PMCID: PMC8994061 DOI: 10.1007/s42770-022-00743-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022] Open
Abstract
The scientific community has been alarmed by the possible immunological evasion, higher infectivity, and severity of disease caused by the newest variants of SARS-CoV-2. The spike protein has an important role in the cellular invasion of viruses and is the target of several vaccines and therapeutic resources, such as monoclonal antibodies. In addition, some of the most relevant mutations in the different variants are on the spike (S) protein gene sequence that leads to structural alterations in the predicted protein, thus causing concern about the protection mediated by vaccines against these new strains. The present review highlights the most recent knowledge about COVID-19 and vaccines, emphasizing the different spike protein structures of SARS-CoV-2 and updating the reader about the emerging viral variants and their classifications, the more common viral mutations described and their distribution in Brazil. It also compiles a table with the most recent knowledge about all of the Omicron spike mutations.
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Affiliation(s)
- Kattlyn Laryssa Candido
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Caio Ricardo Eich
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Luciana Oliveira de Fariña
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Marina Kimiko Kadowaki
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - José Luis da Conceição Silva
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Alexandre Maller
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Rita de Cássia Garcia Simão
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
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2
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Ranjan P, Thomas V, Kumar P. 2D materials as a diagnostic platform for the detection and sensing of the SARS-CoV-2 virus: a bird's-eye view. J Mater Chem B 2021; 9:4608-4619. [PMID: 34013310 PMCID: PMC8559401 DOI: 10.1039/d1tb00071c] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Worldwide infections and fatalities caused by the SARS-CoV-2 virus and its variants responsible for COVID-19 have significantly impeded the economic growth of many nations. People in many nations have lost their livelihoods, it has severely impacted international relations and, most importantly, health infrastructures across the world have been tormented. This pandemic has already left footprints on human psychology, traits, and priorities and is certainly going to lead towards a new world order in the future. As always, science and technology have come to the rescue of the human race. The prevention of infection by instant and repeated cleaning of surfaces that are most likely to be touched in daily life and sanitization drives using medically prescribed sanitizers and UV irradiation of textiles are the first steps to breaking the chain of transmission. However, the real challenge is to develop and uplift medical infrastructure, such as diagnostic tools capable of prompt diagnosis and instant and economic medical treatment that is available to the masses. Two-dimensional (2D) materials, such as graphene, are atomic sheets that have been in the news for quite some time due to their unprecedented electronic mobilities, high thermal conductivity, appreciable thermal stability, excellent anchoring capabilities, optical transparency, mechanical flexibility, and a unique capability to integrate with arbitrary surfaces. These attributes of 2D materials make them lucrative for use as an active material platform for authentic and prompt (within minutes) disease diagnosis via electrical or optical diagnostic tools or via electrochemical diagnosis. We present the opportunities provided by 2D materials as a platform for SARS-CoV-2 diagnosis.
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Affiliation(s)
- Pranay Ranjan
- Department of Physics, UAE University, Al-Ain, Abu Dhabi 15551, United Arab Emirates
| | - Vinoy Thomas
- Department of Materials Science and Engineering, University of Alabama at Birmingham, USA.
| | - Prashant Kumar
- Department of Physics, Indian Institute of Technology Patna, India.
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3
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Sajid M, Moazzam M, Cho Y, Kato S, Xu A, Way JJ, Lohan S, Tiwari RK. siRNA Therapeutics for the Therapy of COVID-19 and Other Coronaviruses. Mol Pharm 2021; 18:2105-2121. [PMID: 33945284 PMCID: PMC9896947 DOI: 10.1021/acs.molpharmaceut.0c01239] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The ongoing pandemic of global concern has killed about three million humans and affected around 151 million people worldwide, as of April 30, 2021. Although recently approved vaccines for COVID-19 are engendering hope, finding new ways to cure the viral pandemic is still a quest for researchers worldwide. Major pandemics in history have been of viral origin, such as SARS, MERS, H1NI, Spanish flu, and so on. A larger emphasis has been on discovering potential vaccines, novel antiviral drugs, and agents that can mitigate the viral infection symptoms; however, a relatively new area, RNA interference (RNAi), has proven effective as an antiviral agent. The RNAi phenomenon has been largely exploited to cure cancer, neurodegenerative diseases, and some rare diseases. The U.S. Food and Drug Administration has recently approved three siRNA products for human use that garner significant hope in siRNA therapeutics for coronaviruses. There have been some commentaries and communications addressing this area. We have summarized and illustrated the significance and the potential of the siRNA therapeutics available as of April 30, 2021 to combat the ongoing viral pandemic and the emerging new variants such as B.1.1.7 and B.1.351. Numerous successful in vitro studies and several investigations to address the clinical application of siRNA therapeutics provide great hope in this field. This seminal Review describes the significance of siRNA-based therapy to treat diverse viral infections in addition to the current coronavirus challenge. In addition, we have thoroughly reviewed the patents approved for coronaviruses, the major challenges in siRNA therapy, and the potential approaches to address them, followed by innovation and prospects.
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Affiliation(s)
- Muhammad
Imran Sajid
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
- Faculty
of Pharmacy, University of Central Punjab, Lahore 54700, Pakistan
| | - Muhammad Moazzam
- Faculty
of Pharmacy, University of Central Punjab, Lahore 54700, Pakistan
| | - Yeseom Cho
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
- Department
of Biochemistry and Molecular Biology, Schmid College of Science and
Technology, Chapman University, Orange, California 92866, United States
| | - Shun Kato
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
- Department
of Biochemistry and Molecular Biology, Schmid College of Science and
Technology, Chapman University, Orange, California 92866, United States
| | - Ava Xu
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
| | - J. J. Way
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
| | - Sandeep Lohan
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
| | - Rakesh K. Tiwari
- Center
for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical
Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
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4
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Pilaquinga F, Morey J, Torres M, Seqqat R, Piña MDLN. Silver nanoparticles as a potential treatment against SARS-CoV-2: A review. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 13:e1707. [PMID: 33638618 PMCID: PMC7995207 DOI: 10.1002/wnan.1707] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/12/2022]
Abstract
Several human coronaviruses (HCoVs) are distinguished by the ability to generate epidemics or pandemics, with their corresponding diseases characterized by severe respiratory illness, such as that which occurs in severe acute respiratory syndrome (SARS-CoV), Middle East respiratory syndrome (MERS-CoV), and, today, in SARS-CoV-2, an outbreak that has struck explosively and uncontrollably beginning in December 2019 and has claimed the lives of more than 1.9 M people worldwide as of January 2021. The development of vaccines has taken one year, which is why it is necessary to investigate whether some already-existing alternatives that have been successfully developed in recent years can mitigate the pandemic's advance. Silver nanoparticles (AgNPs) have proved effective in antiviral action. Thus, in this review, several in vitro and in vivo studies of the effect of AgNPs on viruses that cause respiratory diseases are analyzed and discussed to promote an understanding of the possible interaction of AgNPs with SARS-CoV-2. The study focuses on several in vivo toxicological studies of AgNPs and a dose extrapolation to humans to determine the chief avenue of exposure. It can be concluded that the use of AgNPs as a possible treatment for SARS-CoV-2 could be viable, based on comparing the virus' behavior to that of similar viruses in in vivo studies, and that the suggested route of administration in terms of least degree of adverse effects is inhalation. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Nanomedicine for Respiratory Disease Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials.
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Affiliation(s)
- Fernanda Pilaquinga
- School of Chemistry Sciences, Pontificia Universidad Católica del Ecuador, Quito, Ecuador.,Department of Chemistry, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Jeroni Morey
- Department of Chemistry, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Marbel Torres
- Immunology and Virology Laboratory, Nanoscience and Nanotechnology Center, Universidad de las Fuerzas Armadas, ESPE, Sangolquí, Ecuador
| | - Rachid Seqqat
- Immunology and Virology Laboratory, Nanoscience and Nanotechnology Center, Universidad de las Fuerzas Armadas, ESPE, Sangolquí, Ecuador
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5
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Sirpilla O, Bauss J, Gupta R, Underwood A, Qutob D, Freeland T, Bupp C, Carcillo J, Hartog N, Rajasekaran S, Prokop JW. SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes. J Proteome Res 2020; 19:4275-4290. [PMID: 32686937 PMCID: PMC7418564 DOI: 10.1021/acs.jproteome.0c00421] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 (COVID-19) has infected millions of people worldwide, with lethality in hundreds of thousands. The rapid publication of information, both regarding the clinical course and the viral biology, has yielded incredible knowledge of the virus. In this review, we address the insights gained for the SARS-CoV-2 proteome, which we have integrated into the Viral Integrated Structural Evolution Dynamic Database, a publicly available resource. Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. This inhibition has the potential to not only regulate about 10% of all biological transcripts through altered ribosomal biology but also associate with viral-induced genetics, where suppressed human variants are activated to drive dominant, negative outcomes within cells. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics.
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Affiliation(s)
- Olivia Sirpilla
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Department of Pharmacology and
Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
- Walsh
University, North Canton, Ohio 44720,
United States
| | - Jacob Bauss
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
| | - Ruchir Gupta
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Department of Pharmacology and
Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Adam Underwood
- Walsh
University, North Canton, Ohio 44720,
United States
| | - Dinah Qutob
- Walsh
University, North Canton, Ohio 44720,
United States
| | - Tom Freeland
- Walsh
University, North Canton, Ohio 44720,
United States
| | - Caleb Bupp
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Spectrum Health Medical
Genetics, Grand Rapids, Michigan 49503,
United States
| | - Joseph Carcillo
- Department of Critical Care Medicine
and Pediatrics, Children’s Hospital of Pittsburgh,
University of Pittsburgh School of
Medicine, Pittsburgh, Pennsylvania 15421,
United States
| | - Nicholas Hartog
- Allergy & Immunology,
Spectrum Health, Grand Rapids, Michigan 49503,
United States
| | - Surender Rajasekaran
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Pediatric Intensive Care
Unit, Helen DeVos Children’s Hospital,
Grand Rapids, Michigan 49503, United States
- Office of Research,
Spectrum Health, Grand Rapids, Michigan 49503,
United States
| | - Jeremy W. Prokop
- Department of Pediatrics and Human
Development, College of Human Medicine, Michigan State
University, Grand Rapids, Michigan 49503,
United States
- Department of Pharmacology and
Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
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6
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Paul AS, Islam R, Parves MR, Mamun AA, Shahriar I, Hossain MI, Hossain MN, Ali MA, Halim MA. Cysteine focused covalent inhibitors against the main protease of SARS-CoV-2. J Biomol Struct Dyn 2020; 40:1639-1658. [PMID: 33047658 DOI: 10.1080/07391102.2020.1831610] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In viral replication and transcription, the main protease (Mpro) of SARS-CoV-2 plays an important role and appears to be a vital target for drug design. In Mpro, there is a Cys-His catalytic dyad, and ligands that interact with the Cys145 assumed to be an effective approach to inhibit the Mpro. In this study, approximately 1400 cysteine-focused ligands were screened to identify the best candidates that can act as potent inhibitors against Mpro. Our results show that the selected ligands strongly interact with the key Cys145 and His41 residues. Covalent docking was performed for the selected candidates containing the acrylonitrile group, which can form a covalent bond with Cys145. All atoms molecular dynamics (MD) simulation was performed on the selected four inhibitors including L1, L2, L3 and L4 to validate the docking interactions. Our results were also compared with a control ligand, α-ketoamide (11r). Principal component analysis on structural and energy data obtained from the MD trajectories shows that L1, L3, L4 and α-ketoamide (11r) have structural similarity with the apo-form of the Mpro. Quantitative structure-activity relationship method was employed for pattern recognition of the best ligands, which discloses that ligands containing acrylonitrile and amide warheads can show better performance. ADMET analysis displays that our selected candidates appear to be safer inhibitors. Our combined studies suggest that the best cysteine focused ligands can help to design an effective lead drug for COVID-19 treatment. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Archi Sundar Paul
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Rajib Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Rimon Parves
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Abdulla Al Mamun
- Key Laboratory of Soft Chemistry and Functional Materials of MOE, School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Imrul Shahriar
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Md Imran Hossain
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Nayeem Hossain
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mohammad A Halim
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh.,Department of Physical Sciences, University of Arkansas-Fort Smith, Fort Smith, AR, USA
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7
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Ansari MA, Almatroudi A, Alzohairy MA, AlYahya S, Alomary MN, Al-Dossary HA, Alghamdi S. Lipid-based nano delivery of Tat-peptide conjugated drug or vaccine-promising therapeutic strategy for SARS-CoV-2 treatment. Expert Opin Drug Deliv 2020; 17:1671-1674. [PMID: 32820694 PMCID: PMC7484566 DOI: 10.1080/17425247.2020.1813712] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institute for Research & Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University , Dammam, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University , Qassim, Saudi Arabia
| | - Mohammad A Alzohairy
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University , Qassim, Saudi Arabia
| | - Sami AlYahya
- National Center for Biotechnology, King Abdulaziz City for Science and Technology , Riyadh, Saudi Arabia
| | - Mohammad N Alomary
- National Center for Biotechnology, Life Science and Environmental Research Institute, King Abdulaziz City for Science and Technology , Riyadh, Saudi Arabia
| | - Hanan A Al-Dossary
- Department of Epidemic Disease Research, Institute for Research & Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University , Dammam, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University , Makkah, Saudi Arabia
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8
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Colunga-Salas P, Hernández-Canchola G. Bats and humans during the SARS-CoV-2 outbreak: The case of bat-coronaviruses from Mexico. Transbound Emerg Dis 2020; 68:987-992. [PMID: 32725795 DOI: 10.1111/tbed.13751] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/30/2020] [Accepted: 07/18/2020] [Indexed: 12/28/2022]
Abstract
The novel SARS-CoV-2 coronavirus has attracted attention due to the high number of human cases around the world. It has been proposed that this virus originated in bats, possibly transmitted to humans by an intermediate host, making bats a group of great interest during this outbreak. Almost 10% of the world's bat species inhabit Mexico, and 14 previous novel CoVs have been recorded in Mexican bats. However, the phylogenetic relationships between these viruses and the novel coronavirus are unknown. The aim of this communication was therefore to describe the phylogenetic relationships between Mexican bat-CoVs and SARS-CoV-2. We showed that Mexican bat-CoVs sequences are grouped into two genera, Alphacoronavirus and Betacoronavirus, and the new coronavirus is an independent clade within Betacoronavirus. Due to the diversity of CoVs in Mexican bats, the propensity of CoVs to shift hosts, the invasion mechanisms described for this new virus, and previous reports of animals infected by SARS-CoV-2, the risk of possible infection from humans to Mexican bats should not be discarded and warrants further analyses. To avoid future zoonotic infectious diseases and to limit persecution of bats, we urge researchers and the general population to take extreme precautions and avoid manipulation of bats during the current and future similar outbreaks.
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Affiliation(s)
- Pablo Colunga-Salas
- Centro de Medicina Tropical, División de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México.,Posgrado en Ciencias Biomédicas, Unidad de Posgrado, Universidad Nacional Autónoma de México, Ciudad de México, México
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9
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Kİ̇Lİ̇ÇASLAN Ö, SAV N, ERİŞEN KARACA S, KOCABAY K. COVID-19 Disease in Children: Clinical Course, Diagnosis and Treatment Overview and Literature Data Compilation. KONURALP TIP DERGISI 2020. [DOI: 10.18521/ktd.722266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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10
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Gupta R, Charron J, Stenger CL, Painter J, Steward H, Cook TW, Faber W, Frisch A, Lind E, Bauss J, Li X, Sirpilla O, Soehnlen X, Underwood A, Hinds D, Morris M, Lamb N, Carcillo JA, Bupp C, Uhal BD, Rajasekaran S, Prokop JW. SARS-CoV2 (COVID-19) Structural/Evolution Dynamicome: Insights into functional evolution and human genomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32511397 DOI: 10.1101/2020.05.15.098616] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The SARS-CoV-2 pandemic, starting in 2019, has challenged the speed at which labs perform science, ranging from discoveries of the viral composition to handling health outcomes in humans. The small ~30kb single-stranded RNA genome of Coronaviruses makes them adept at cross species spread and drift, increasing their probability to cause pandemics. However, this small genome also allows for a robust understanding of all proteins coded by the virus. We employed protein modeling, molecular dynamic simulations, evolutionary mapping, and 3D printing to gain a full proteome and dynamicome understanding of SARS-CoV-2. The Viral Integrated Structural Evolution Dynamic Database (VIStEDD) has been established (prokoplab.com/vistedd), opening future discoveries and educational usage. In this paper, we highlight VIStEDD usage for nsp6, Nucleocapsid (N), and Spike (S) surface glycoprotein. For both nsp6 and N we reveal highly conserved surface amino acids that likely drive protein-protein interactions. In characterizing viral S protein, we have developed a quantitative dynamics cross correlation matrix insight into interaction with the ACE2/SLC6A19 dimer complex. From this quantitative matrix, we elucidated 47 potential functional missense variants from population genomic databases within ACE2/SLC6A19/TMPRSS2, warranting genomic enrichment analyses in SARS-CoV-2 patients. Moreover, these variants have ultralow frequency, but can exist as hemizygous in males for ACE2, which falls on the X-chromosome. Two noncoding variants (rs4646118 and rs143185769) found in ~9% of African descent individuals for ACE2 may regulate expression and be related to increased susceptibility of African Americans to SARS-CoV-2. This powerful database of SARS-CoV-2 can aid in research progress in the ongoing pandemic.
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