201
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Fielding BC. Editorial: Human coronavirus research: 20 years since the SARS-CoV outbreak. Front Microbiol 2022; 13:1035267. [PMID: 36212826 PMCID: PMC9540226 DOI: 10.3389/fmicb.2022.1035267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
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202
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In Vitro Evaluation of Leuconostoc mesenteroides Cell-Free-Supernatant GBUT-21 against SARS-CoV-2. Vaccines (Basel) 2022; 10:vaccines10101581. [PMID: 36298446 PMCID: PMC9612097 DOI: 10.3390/vaccines10101581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 01/08/2023] Open
Abstract
The unprecedented health catastrophe derived from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2 infection) met with a phenomenal scientific response across the globe. Worldwide, the scientific community was focused on finding a cure for the deadly disease. A wide range of research studies has consistently revealed the link between SARS-CoV-2 infection severity and abnormal gut microbiomes, suggesting its potential in developing novel therapeutic approaches. Probiotics have been extensively studied to promote health in human hosts and reestablish a balance in the dysbiotic gut microbiome; however, there is strong skepticism about their safety and efficacy. Consequently, the metabolic signatures of probiotics, often referred to as "postbiotics", could prove of paramount importance for adjuvant cures in patients with SARS-CoV-2. Postbiotics exhibit safety, enhanced shelf-life, and stability and, therefore, could be implemented in SARS-CoV-2 prophylactic strategies with no undue adverse side effects. The current study is a preliminary investigation of the antiviral properties of postbiotic metabolites derived from Leuconostoc mesenteroides GBUT-21. The study focuses on the potential biological role in inactivating SARS-CoV-2 and reducing related inflammatory pathways.
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203
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Kotani N, Nakano T, Kuwahara R. Host cell membrane proteins located near SARS-CoV-2 spike protein attachment sites are identified using proximity labeling and proteomic analysis. J Biol Chem 2022; 298:102500. [PMID: 36152751 PMCID: PMC9492400 DOI: 10.1016/j.jbc.2022.102500] [Citation(s) in RCA: 3] [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: 04/12/2022] [Revised: 08/31/2022] [Accepted: 09/08/2022] [Indexed: 11/19/2022] Open
Abstract
Coronavirus disease represents a real threat to the global population, and understanding the biological features of the causative virus, that is, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is imperative for mitigating this threat. Analyses of proteins such as primary receptors and coreceptors (cofactors), which are involved in the entry of SARS-CoV-2 into host cells, will provide important clues to help control the virus. Here, we identified host cell membrane protein candidates present in proximity to the attachment sites of SARS-CoV-2 spike proteins, using proximity labeling and proteomic analysis. The identified proteins represent key candidate factors that may be required for viral entry. We found SARS-CoV-2 host protein DPP4, cell adhesion protein Cadherin 17, and glycoprotein CD133 colocalized with cell membrane–bound SARS-CoV-2 spike proteins in Caco-2 cells and thus showed potential as candidate factors. Additionally, our analysis of the experimental infection of HEK293T cells with a SARS-CoV-2 pseudovirus indicated a 2-fold enhanced infectivity in the CD133-ACE2-coexpressing HEK293T cells compared to that in HEK293T cells expressing ACE-2 alone. The information and resources regarding these coreceptor labeling and analysis techniques could be utilized for the development of antiviral agents against SARS-CoV-2 and other emerging viruses.
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Affiliation(s)
- Norihiro Kotani
- Medical Research Center, Saitama Medical University, Moroyama-machi, Saitama, Japan; Department of Biochemistry, Saitama Medical University, Moroyama-machi, Saitama, Japan.
| | - Takanari Nakano
- Department of Biochemistry, Saitama Medical University, Moroyama-machi, Saitama, Japan
| | - Ryusuke Kuwahara
- Quantum Wave Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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204
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Hartley GE, Edwards ESJ, O’Hehir RE, van Zelm MC. New insights into human immune memory from SARS-CoV-2 infection and vaccination. Allergy 2022; 77:3553-3566. [PMID: 36048132 PMCID: PMC9538469 DOI: 10.1111/all.15502] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/13/2022] [Accepted: 08/29/2022] [Indexed: 01/28/2023]
Abstract
Since early 2020, the world has been embroiled in an ongoing viral pandemic with SARS-CoV-2 and emerging variants resulting in mass morbidity and an estimated 6 million deaths globally. The scientific community pivoted rapidly, providing unique and innovative means to identify infected individuals, technologies to evaluate immune responses to infection and vaccination, and new therapeutic strategies to treat infected individuals. Never before has immunology been so critically at the forefront of combatting a global pandemic. It has now become evident that not just antibody responses, but formation and durability of immune memory cells following vaccination are associated with protection against severe disease from SARS-CoV-2 infection. Furthermore, the emergence of variants of concern (VoC) highlight the need for immunological markers to quantify the protective capacity of Wuhan-based vaccines. Thus, harnessing and modulating the immune response is key to successful vaccination and treatment of disease. We here review the latest knowledge about immune memory generation and durability following natural infection and vaccination, and provide insights into the attributes of immune memory that may protect from emerging variants.
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Affiliation(s)
- Gemma E. Hartley
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Emily S. J. Edwards
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Robyn E. O’Hehir
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia,Allergy, Asthma and Clinical Immunology ServiceAlfred HospitalMelbourneVictoriaAustralia
| | - Menno C. van Zelm
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia,Allergy, Asthma and Clinical Immunology ServiceAlfred HospitalMelbourneVictoriaAustralia
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205
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Kalasariya HS, Patel NB, Gacem A, Alsufyani T, Reece LM, Yadav VK, Awwad NS, Ibrahium HA, Ahn Y, Yadav KK, Jeon BH. Marine Alga Ulva fasciata-Derived Molecules for the Potential Treatment of SARS-CoV-2: An In Silico Approach. Mar Drugs 2022; 20:md20090586. [PMID: 36135775 PMCID: PMC9506351 DOI: 10.3390/md20090586] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2 is the causative agent of the COVID-19 pandemic. This in silico study aimed to elucidate therapeutic efficacies against SARS-CoV-2 of phyco-compounds from the seaweed, Ulva fasciata. Twelve phyco-compounds were isolated and toxicity was analyzed by VEGA QSAR. Five compounds were found to be nonmutagenic, noncarcinogenic and nontoxic. Moreover, antiviral activity was evaluated by PASS. Binding affinities of five of these therapeutic compounds were predicted to possess probable biological activity. Fifteen SARS-CoV-2 target proteins were analyzed by the AutoDock Vina program for molecular docking binding energy analysis and the 6Y84 protein was determined to possess optimal binding affinities. The Desmond program from Schrödinger’s suite was used to study high performance molecular dynamic simulation properties for 3,7,11,15-Tetramethyl-2-hexadecen-1-ol—6Y84 for better drug evaluation. The ligand with 6Y84 had stronger binding affinities (−5.9 kcal/mol) over two standard drugs, Chloroquine (−5.6 kcal/mol) and Interferon α-2b (−3.8 kcal/mol). Swiss ADME calculated physicochemical/lipophilicity/water solubility/pharmacokinetic properties for 3,7,11,15-Tetramethyl-2-hexadecen-1-ol, showing that this therapeutic agent may be effective against SARS-CoV-2.
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Affiliation(s)
- Haresh S. Kalasariya
- Centre for Natural Products Discovery, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Nikunj B. Patel
- Microbiology Department, Sankalchand Patel University, Visnagar 384315, India
| | - Amel Gacem
- Department of Physics, Faculty of Sciences, University 20 Août 1955, Skikda 21000, Algeria
| | - Taghreed Alsufyani
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Lisa M. Reece
- Reece Life Science Consulting Agency, 819 N Amburn Rd, Texas City, TX 77591, USA
| | - Virendra Kumar Yadav
- Department of Biosciences, School of Liberal Arts & Sciences, Mody University of Science and Technology, Lakshmangarh, Sikar 332311, India
| | - Nasser S. Awwad
- Department of Chemistry, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Hala A. Ibrahium
- Biology Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Semi Pilot Plant, Nuclear Materials Authority, El Maadi, P.O. Box 530, Cairo 11381, Egypt
| | - Yongtae Ahn
- Department of Earth Resources & Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea
| | - Krishna Kumar Yadav
- Faculty of Science and Technology, Madhyanchal Professional University, Ratibad, Bhopal 462044, India
- Correspondence: (K.K.Y.); (B.-H.J.)
| | - Byong-Hun Jeon
- Department of Earth Resources & Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea
- Correspondence: (K.K.Y.); (B.-H.J.)
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206
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Zhai LY, Su AM, Liu JF, Zhao JJ, Xi XG, Hou XM. Recent advances in applying G-quadruplex for SARS-CoV-2 targeting and diagnosis: A review. Int J Biol Macromol 2022; 221:1476-1490. [PMID: 36130641 PMCID: PMC9482720 DOI: 10.1016/j.ijbiomac.2022.09.152] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/31/2022] [Accepted: 09/15/2022] [Indexed: 12/05/2022]
Abstract
The coronavirus SARS-CoV-2 has caused a health care crisis all over the world since the end of 2019. Although vaccines and neutralizing antibodies have been developed, rapidly emerging variants usually display stronger immune escape ability and can better surpass vaccine protection. Therefore, it is still vital to find proper treatment strategies. To date, antiviral drugs against SARS-CoV-2 have mainly focused on proteases or polymerases. Notably, noncanonical nucleic acid structures called G-quadruplexes (G4s) have been identified in many viruses in recent years, and numerous G4 ligands have been developed. During this pandemic, literature on SARS-CoV-2 G4s is rapidly accumulating. Here, we first summarize the recent progress in the identification of SARS-CoV-2 G4s and their intervention by ligands. We then introduce the potential interacting proteins of SARS-CoV-2 G4s from both the virus and the host that may regulate G4 functions. The innovative strategy to use G4s as a diagnostic tool in SARS-CoV-2 detection is also reviewed. Finally, we discuss some key questions to be addressed in the future.
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Affiliation(s)
- Li-Yan Zhai
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Ai-Min Su
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Jing-Fan Liu
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Jian-Jin Zhao
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; ENS Paris-Saclay, Université Paris-Saclay, CNRS UMR8113, IDA FR3242, Laboratory of Biology and Applied Pharmacology (LBPA), 91190 Gif-sur-Yvette, France
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling 712100, China.
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207
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Highly pathogenic coronavirus N protein aggravates inflammation by MASP-2-mediated lectin complement pathway overactivation. Signal Transduct Target Ther 2022; 7:318. [PMID: 36100602 PMCID: PMC9470675 DOI: 10.1038/s41392-022-01133-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/09/2022] [Accepted: 07/19/2022] [Indexed: 12/30/2022] Open
Abstract
Excessive inflammatory responses contribute to the pathogenesis and lethality of highly pathogenic human coronaviruses, but the underlying mechanism remains unclear. In this study, the N proteins of highly pathogenic human coronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV), middle east respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), were found to bind MASP-2, a key serine protease in the lectin pathway of complement activation, resulting in excessive complement activation by potentiating MBL-dependent MASP-2 activation, and the deposition of MASP-2, C4b, activated C3 and C5b-9. Aggravated inflammatory lung injury was observed in mice infected with adenovirus expressing the N protein. Complement hyperactivation was also observed in SARS-CoV-2-infected patients. Either blocking the N protein:MASP-2 interaction, MASP-2 depletion or suppressing complement activation can significantly alleviate N protein-induced complement hyperactivation and lung injury in vitro and in vivo. Altogether, these data suggested that complement suppression may represent a novel therapeutic approach for pneumonia induced by these highly pathogenic coronaviruses.
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208
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Lethal Swine Acute Diarrhea Syndrome Coronavirus Infection in Suckling Mice. J Virol 2022; 96:e0006522. [PMID: 35993737 PMCID: PMC9472626 DOI: 10.1128/jvi.00065-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a recently emerging bat-borne coronavirus responsible for high mortality rates in piglets. In vitro studies have indicated that SADS-CoV has a wide tissue tropism in different hosts, including humans. However, whether this virus potentially threatens other animals remains unclear. Here, we report the experimental infection of wild-type BALB/c and C57BL/6J suckling mice with SADS-CoV. We found that mice less than 7 days old are susceptible to the virus, which caused notable multitissue infections and damage. The mortality rate was the highest in 2-day-old mice and decreased in older mice. Moreover, a preliminary neuroinflammatory response was observed in 7-day-old SADS-CoV-infected mice. Thus, our results indicate that SADS-CoV has potential pathogenicity in young hosts. IMPORTANCE SADS-CoV, which likely has originated from bat coronaviruses, is highly pathogenic to piglets and poses a threat to the swine industry. Little is known about its potential to disseminate to other animals. No efficient treatment is available, and the quarantine strategy is the only preventive measure. In this study, we demonstrated that SADS-CoV can efficiently replicate in suckling mice younger than 7 days. In contrast to infected piglets, in which intestinal tropism is shown, SADS-CoV caused infection and damage in all murine tissues evaluated in this study. In addition, neuroinflammatory responses were detected in some of the infected mice. Our work provides a preliminary cost-effective model for the screening of antiviral drugs against SADS-CoV infection.
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209
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Lin CY, Su SB, Chen KT. An overview of gastrointestinal diseases in patients with COVID-19: A narrative review. Medicine (Baltimore) 2022; 101:e30297. [PMID: 36086768 PMCID: PMC10980500 DOI: 10.1097/md.0000000000030297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 06/01/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease-2019 (COVID-19), caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), has emerged as a global health concern. This study aimed to review the epidemiology and pathophysiology of COVID-19 and provide evidence for the implementation of control measures. We utilized several online databases, including MEDLINE (National Library of Medicine, Bethesda, Maryland, USA), PubMed, EMBASE, Web of Science, and Google Scholar, to collect relevant published papers using a combination of the following keywords: "COVID-19," "SARS-CoV-2," "novel coronavirus," "epidemiology," and "pathophysiology." The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were used in this study. Globally, approximately 3-46% of patients with SARS-CoV-2 infection experience gastrointestinal symptoms. The clinical spectrum of COVID-19 is wide, ranging from mild to severe, and even fatal. COVID-19 was initially reported as a respiratory tract disease; however, gastrointestinal symptoms have only recently been reported. COVID-19 Patients with gastrointestinal symptoms may have more severe clinical manifestations and poor prognosis. This study highlights the need to better understand the mechanisms involved in the development of gastrointestinal symptoms in patients with COVID-19 to prevent the further spread of this pathogen.
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Affiliation(s)
- Cheng-Yao Lin
- Division of Hematology-Oncology, Department of Internal Medicine, Chi-Mei Medical Center, Liouying, Taiwan
- Department of Senior Welfare and Services, Southern Taiwan University of Science and Technology, Tainan, Taiwan
- Department of Environmental and Occupational Health, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Bin Su
- Department of Occupational Medicine, Chi-Mei Medical Center, Tainan, Taiwan
| | - Kow-Tong Chen
- Department of Occupational Medicine, Tainan Municipal Hospital, Tainan, Taiwan
- Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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210
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da Silva SJR, do Nascimento JCF, Germano Mendes RP, Guarines KM, Targino Alves da Silva C, da Silva PG, de Magalhães JJF, Vigar JRJ, Silva-Júnior A, Kohl A, Pardee K, Pena L. Two Years into the COVID-19 Pandemic: Lessons Learned. ACS Infect Dis 2022; 8:1758-1814. [PMID: 35940589 PMCID: PMC9380879 DOI: 10.1021/acsinfecdis.2c00204] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19), which has massively impacted global public health and caused widespread disruption to daily life. The crisis caused by COVID-19 has mobilized scientists and public health authorities across the world to rapidly improve our knowledge about this devastating disease, shedding light on its management and control, and spawned the development of new countermeasures. Here we provide an overview of the state of the art of knowledge gained in the last 2 years about the virus and COVID-19, including its origin and natural reservoir hosts, viral etiology, epidemiology, modes of transmission, clinical manifestations, pathophysiology, diagnosis, treatment, prevention, emerging variants, and vaccines, highlighting important differences from previously known highly pathogenic coronaviruses. We also discuss selected key discoveries from each topic and underline the gaps of knowledge for future investigations.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Jessica Catarine Frutuoso do Nascimento
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Klarissa Miranda Guarines
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Poliana Gomes da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), 52171-011 Recife, Pernambuco, Brazil.,University of Pernambuco (UPE), Serra Talhada Campus, 56909-335 Serra Talhada, Pernambuco, Brazil.,Public Health Laboratory of the XI Regional Health, 56912-160 Serra Talhada, Pernambuco, Brazil
| | - Justin R J Vigar
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Abelardo Silva-Júnior
- Institute of Biological and Health Sciences, Federal University of Alagoas (UFAL), 57072-900 Maceió, Alagoas, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
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211
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Khemiri H, Ayouni K, Triki H, Haddad-Boubaker S. SARS-CoV-2 infection in pediatric population before and during the Delta (B.1.617.2) and Omicron (B.1.1.529) variants era. Virol J 2022; 19:144. [PMID: 36076271 PMCID: PMC9452867 DOI: 10.1186/s12985-022-01873-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/27/2022] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND COVID-19, the coronavirus disease that emerged in December 2019, caused drastic damage worldwide. At the beginning of the pandemic, available data suggested that the infection occurs more frequently in adults than in infants. In this review, we aim to provide an overview of SARS-CoV-2 infection in children before and after B.1.617.2 Delta and B.1.1.529 Omicron variants emergence in terms of prevalence, transmission dynamics, clinical manifestations, complications and risk factors. METHODS Our method is based on the literature search on PubMed, Science Direct and Google Scholar. From January 2020 to July 2022, a total of 229 references, relevant for the purpose of this review, were considered. RESULTS The incidence of SARS-CoV-2 infection in infants was underestimated. Up to the first half of May, most of the infected children presented asymptomatic or mild manifestations. The prevalence of COVID-19 varied from country to another: the highest was reported in the United States (22.5%). COVID-19 can progress and become more severe, especially with the presence of underlying health conditions. It can also progress into Kawasaki or Multisystem Inflammatory Syndrome (MIS) manifestations, as a consequence of exacerbating immune response. With the emergence of the B.1.617.2 Delta and B.1.1.529 Omicron variants, it seems that these variants affect a large proportion of the younger population with the appearance of clinical manifestations similar to those presented by adults with important hospitalization rates. CONCLUSION The pediatric population constitutes a vulnerable group that requires particular attention, especially with the emergence of more virulent variants. The increase of symptomatic SARS-CoV-2 infection and hospitalization rate among children highlights the need to extend vaccination to the pediatric population.
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Affiliation(s)
- Haifa Khemiri
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Kaouther Ayouni
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisia
| | - Sondes Haddad-Boubaker
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisia.
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.
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212
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Rizzi L, Sabbà C, Suppressa P. Sarcoidosis and autoimmunity: In the depth of a complex relationship. Front Med (Lausanne) 2022; 9:991394. [PMID: 36148452 PMCID: PMC9485866 DOI: 10.3389/fmed.2022.991394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/01/2022] [Indexed: 11/25/2022] Open
Abstract
Sarcoidosis is a chronic granulomatous disease that can virtually affect any organ. Its etiology is unknown, although it has been proposed that environmental or biological agents can act as triggers, ultimately leading to chronic inflammation in genetically predisposed individuals. The main component of sarcoid inflammation is represented by an exaggerated T- lymphocytic cellular response to a putative antigen that could not be efficiently cleared in the patient. However, several clinical and immunological observations, such as the association of sarcoidosis to autoimmune diseases or the presence of autoantibodies in the serum of patients with sarcoidosis, suggest that humoral-mediated immune response might also play a role in the pathogenesis of sarcoidosis. The aim of this review is to deepen the relationship between sarcoidosis and autoimmunity, by analyzing the most recent advances and proposing new fields of research.
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213
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Morales-Hernández S, Ugidos-Damboriena N, López-Sagaseta J. Self-Assembling Protein Nanoparticles in the Design of Vaccines: 2022 Update. Vaccines (Basel) 2022; 10:vaccines10091447. [PMID: 36146525 PMCID: PMC9505534 DOI: 10.3390/vaccines10091447] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Vaccines constitute a pillar in the prevention of infectious diseases. The unprecedented emergence of novel immunization strategies due to the COVID-19 pandemic has again positioned vaccination as a pivotal measure to protect humankind and reduce the clinical impact and socioeconomic burden worldwide. Vaccination pursues the ultimate goal of eliciting a protective response in immunized individuals. To achieve this, immunogens must be efficiently delivered to prime the immune system and produce robust protection. Given their safety, immunogenicity, and flexibility to display varied and native epitopes, self-assembling protein nanoparticles represent one of the most promising immunogen delivery platforms. Currently marketed vaccines against the human papillomavirus, for instance, illustrate the potential of these nanoassemblies. This review is intended to provide novelties, since 2015, on the ground of vaccine design and self-assembling protein nanoparticles, as well as a comparison with the current emergence of mRNA-based vaccines.
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Affiliation(s)
- Sergio Morales-Hernández
- Unit of Protein Crystallography and Structural Immunology, Navarrabiomed-Public University of Navarra (UPNA), 31008 Pamplona, Spain
- Navarra University Hospital, 31008 Pamplona, Spain
| | - Nerea Ugidos-Damboriena
- Unit of Protein Crystallography and Structural Immunology, Navarrabiomed-Public University of Navarra (UPNA), 31008 Pamplona, Spain
- Navarra University Hospital, 31008 Pamplona, Spain
| | - Jacinto López-Sagaseta
- Unit of Protein Crystallography and Structural Immunology, Navarrabiomed-Public University of Navarra (UPNA), 31008 Pamplona, Spain
- Navarra University Hospital, 31008 Pamplona, Spain
- Correspondence:
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Biswas A, Rajan C, Samajdar DP. A Novel HM-HD-RFET Biosensor for Label-Free Biomolecule Detection. JOURNAL OF ELECTRONIC MATERIALS 2022; 51:6388-6396. [PMID: 36092451 PMCID: PMC9439271 DOI: 10.1007/s11664-022-09872-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
The mortality of people worldwide caused by COVID-19 has enhanced the research interest to design and develop power-efficient, low-cost, and sensitive biosensors to detect a wide range of biomolecules or foreign particles that can cause severe negative impact on humans. A novel Bio-RFET biosensor with hetero-material (HM) for source/channel and drain regions and hetero-dielectric (HD) is proposed, which acts as an n-MOSFET or a p-MOSFET and n-TFET or p-TFET. This HM-HD-RFET biosensor senses the biomolecules by the label-free dielectric modulation (DM) technique. When the biomolecules are present in the nanocavity, the biosensor can detect the biomolecules without labeling costs. It also changes the dielectric polarization within the nanocavities, and causes a drain current variation in the presence of an electric field. In this research article, (SiO2 + TiO2) and an AlGaAs/Ge-based HD-HM-RFET have been analyzed for their use in biosensing. We found that the proposed device exhibits higher sensitivity as compared to a SiO2 + HfO2-HM-RFET and a Si-based SiO2 + TiO2-RFET for varying dielectric constants (K) from K = 20-80 and charge densities in the range - 5 × 1011 to 1 × 1013 C/cm2. Further, it can be noticed that n-SiO2 + TiO2-HM-TFET possesses the highest Id-Vgs sensitivity of 5.09 × 1013, ION/IOFF ratio of 1.23 × 109, lowest SS of 20.3 mV/dec, and Vth of 1.48 V.
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Affiliation(s)
- Arpita Biswas
- Department of Electrical Engineering, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan India
| | - Chithraja Rajan
- Shri Ramdeobaba College of Engineering and Management, Nagpur, Maharashtra India
| | - Dip Prakash Samajdar
- PDPM Indian Institute of Information Technology, Design and Manufacturing, Jabalpur, Madhya Pradesh India
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215
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Beeraka NM, Sukocheva OA, Lukina E, Liu J, Fan R. Development of antibody resistance in emerging mutant strains of SARS CoV-2: Impediment for COVID-19 vaccines. Rev Med Virol 2022; 32:e2346. [PMID: 35416390 PMCID: PMC9111059 DOI: 10.1002/rmv.2346] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/28/2022] [Accepted: 03/06/2022] [Indexed: 02/05/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a highly infectious agent associated with unprecedented morbidity and mortality. A failure to stop growth of COVID-19-linked morbidity rates is caused by SARS-CoV-2 mutations and the emergence of new highly virulent SARS-CoV-2 strains. Several acquired SARS-CoV-2 mutations reflect viral adaptations to host immune defence. Mutations in the virus Spike-protein were associated with the lowered effectiveness of current preventive therapies, including vaccines. Recent in vitro studies detected diminished neutralisation capacity of vaccine-induced antibodies, which are targeted to bind Spike receptor-binding and N-terminal domains in the emerging strains. Lower than expected inhibitory activity of antibodies was reported against viruses with E484K Spike mutation, including B.1.1.7 (UK), P.1 (Brazil), B.1.351 (South African), and new Omicron variant (B.1.1.529) with E484A mutation. The vaccine effectiveness is yet to be examined against new mutant strains of SARS-CoV-2 originating in Europe, Nigeria, Brazil, South Africa, and India. To prevent the loss of anti-viral protection in vivo, often defined as antibody resistance, it is required to target highly conserved viral sequences (including Spike protein) and enhance the potency of antibody cocktails. In this review, we assess the reported mutation-acquiring potential of coronaviruses and compare efficacies of current COVID-19 vaccines against 'parent' and 'mutant' strains of SARS-CoV-2 (Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529)).
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Affiliation(s)
- Narasimha M. Beeraka
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
- Department of Human AnatomyI.M. Sechenov First Moscow State Medical University (Sechenov University)MoscowRussian Federation
| | - Olga A. Sukocheva
- Discipline of Health SciencesCollege of Nursing and Health SciencesFlinders University of South AustraliaBedford ParkAustralia
| | - Elena Lukina
- Discipline of BiologyCollege of SciencesFlinders University of South AustraliaBedford ParkAustralia
| | - Junqi Liu
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
| | - Ruitai Fan
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
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216
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Weidinger P, Kolodziejek J, Camp JV, Loney T, Kannan DO, Ramaswamy S, Tayoun AA, Corman VM, Nowotny N. MERS-CoV in sheep, goats, and cattle, United Arab Emirates, 2019: Virological and serological investigations reveal an accidental spillover from dromedaries. Transbound Emerg Dis 2022; 69:3066-3072. [PMID: 34463031 PMCID: PMC9786612 DOI: 10.1111/tbed.14306] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 04/14/2021] [Accepted: 08/29/2021] [Indexed: 12/30/2022]
Abstract
The recent COVID-19 pandemic has demonstrated again the global threat posed by emerging zoonotic coronaviruses. During the past two decades alone, humans have experienced the emergence of several coronaviruses, such as SARS-CoV in 2003, MERS-CoV in 2012, and SARS-CoV-2 in 2019. To date, MERS-CoV has been detected in 27 countries, with a case fatality ratio of approximately 34.5%. Similar to other coronaviruses, MERS-CoV presumably originated from bats; however, the main reservoir and primary source of human infections are dromedary camels. Other species within the Camelidae family, such as Bactrian camels, alpacas, and llamas, seem to be susceptible to the infection as well, although to a lesser extent. In contrast, susceptibility studies on sheep, goats, cattle, pigs, chickens, and horses obtained divergent results. In the present study, we tested nasal swabs and/or sera from 55 sheep, 45 goats, and 52 cattle, collected at the largest livestock market in the United Arab Emirates, where dromedaries are also traded, for the presence of MERS-CoV nucleic acid by RT-qPCR, and for specific antibodies by immunofluorescence assay. All sera were negative for MERS-CoV-reactive antibodies, but the nasal swab of one sheep (1.8%) repeatedly tested positive for MERS-CoV nucleic acid. Next generation sequencing (NGS) of the complete N gene of the sheep-derived MERS-CoV revealed >99% nucleotide identity to MERS-CoV sequences of five dromedaries in nearby pens and to three reference sequences. The NGS sequence of the sheep-derived MERS-CoV was confirmed by conventional RT-PCR of a part of the N gene and subsequent Sanger sequencing. All MERS-CoV sequences clustered within clade B, lineage 5. In conclusion, our study shows that noncamelid livestock, such as sheep, goats, and cattle do not play a major role in MERS-CoV epidemiology. The one sheep that tested positive most likely reflects an accidental viral spillover event from infected dromedaries in nearby pens.
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Affiliation(s)
- Pia Weidinger
- Viral ZoonosesEmerging and Vector‐Borne Infections GroupInstitute of VirologyUniversity of Veterinary MedicineViennaAustria
| | - Jolanta Kolodziejek
- Viral ZoonosesEmerging and Vector‐Borne Infections GroupInstitute of VirologyUniversity of Veterinary MedicineViennaAustria
| | - Jeremy V. Camp
- Viral ZoonosesEmerging and Vector‐Borne Infections GroupInstitute of VirologyUniversity of Veterinary MedicineViennaAustria,Center for VirologyMedical University of ViennaViennaAustria
| | - Tom Loney
- College of MedicineMohammed Bin Rashid University of Medicine and Health SciencesDubaiUnited Arab Emirates
| | | | - Sathishkumar Ramaswamy
- Al Jalila Genomics CenterAl Jalila Children's Specialty HospitalDubaiUnited Arab Emirates
| | - Ahmad Abou Tayoun
- College of MedicineMohammed Bin Rashid University of Medicine and Health SciencesDubaiUnited Arab Emirates,Al Jalila Genomics CenterAl Jalila Children's Specialty HospitalDubaiUnited Arab Emirates
| | - Victor M. Corman
- Institute of VirologyCharité‐Universitätsmedizin BerlinHumboldt‐Universität zu BerlinBerlin Institute of Healthand German Centre for Infection Research (DZIF)Partner Site CharitéBerlinGermany
| | - Norbert Nowotny
- Viral ZoonosesEmerging and Vector‐Borne Infections GroupInstitute of VirologyUniversity of Veterinary MedicineViennaAustria,College of MedicineMohammed Bin Rashid University of Medicine and Health SciencesDubaiUnited Arab Emirates
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217
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Sharma KS, Sharma R, Nehra S, Rajpurohit NA, Bhakar K, Kumar D. COVID-19: Consequences on pregnant women and neonates. HEALTH SCIENCES REVIEW 2022; 4:100044. [PMID: 35875514 PMCID: PMC9295334 DOI: 10.1016/j.hsr.2022.100044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 11/27/2022]
Abstract
Introduction Human species is confronting with a gigantic global COVID-19 pandemic. Initially, it was observed in Wuhan, China, and the COVID-19 cases spread across the globe with lightning speed and resulted in the 21st century pandemic. If scientific reports are taken care of, it is noteworthy that this virus possesses more specific characteristics due to its structure. The distinctive structure has a higher binding affinity with angiotensin-converting enzyme 2 (ACE2) protein, and this is used as an access point to gain access to hosts. Methods A complete literature search was conducted using PubMed, Google Scholar, SciFinder, and deep-diving Google Search using keywords such as "Pregnancy, COVID-19, Newborn, Fetus, Coronavirus 2019, Neonate, Pregnant women, and vertical transmission". Result and discussion The SARS-CoV-2 virus is unlike its former analogs: SARS-CoV, and MERS-CoV in 2002 and 2012, respectively, or anything mankind has faced earlier concerning viciousness, global spread, and gravity of a causative agent. The current review has delved into articles published in various journals worldwide including the latest studies on the impact of COVID-19 on pregnant women and neonates and has discussed complications and challenges, psychological health, immunological response, vertical transmission, concurrent disorders, vaccine debate, management recommendations, recent news of the approval of COVID-19 vaccine for 6 months and older babies, and future perspectives.
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218
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Ao Y, Xu J, Duan Z. A novel cardiovirus species identified in feces of wild Himalayan marmots. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105347. [PMID: 35932998 DOI: 10.1016/j.meegid.2022.105347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/17/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Recently a growing number of novel cardioviruses have been frequently discovered, which boosts interest in the search for the genetic diversity of cardioviruses. However, wild-marmot cardioviruses have been rarely reported. Here, a novel cardiovirus (tentatively named HHMCDV) was identified in fecal samples from wild Himalayan marmots in Qinghai Tibetan Plateau, China, by viral metagenomics analysis. 3 out of 99 fecal samples from Himalayan marmots were positive for HHMCDV, with the viral loads ranging from 2.7 × 105 to 1.3 × 107 gene copies/g. The complete genomic sequence of HHMCDV was 8108 nucleotides in length, with the typical cardiovirus genome organization and motifs. Coincidentally, while the data was analyzing, one marmot cardiovirus HT7 partial sequence was available in the Genbank, showing 95.1%, 95.6% and 96.0% amino acid (aa) identity in P1, P2 and P3, respectively. However, sequence analysis revealed that HHMCDV and HT7 are more closely related to species Cardiovirus F strain with 65.7%, 61.9-65.6%, 58.9-59.7%, 71.1-71.7%, 69.1-69.4% and 71.4-72.2% aa identity in polyprotein, P1, P2, P3, 2C and 3CD proteins, respectively. Phylogenetic analysis of P1, P2, P3 and 3CD aa sequences indicated that HHMCDV and HT7 clustered tightly and formed a distinct cluster in the Cardiovirus genus. Based on these data, we propose that HHMCDV and HT7 should be two different members of a potential novel species within the genus Cardiovirus. Further studies are needed to investigate the epidemiology and potential pathogenicity of the virus in Himalayan marmots.
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Affiliation(s)
- Yuanyun Ao
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jin Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China; Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 201102, China.
| | - Zhaojun Duan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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219
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Shi W, Wang L, Zhou T, Sastry M, Yang ES, Zhang Y, Chen M, Chen X, Choe M, Creanga A, Leung K, Olia AS, Pegu A, Rawi R, Schön A, Shen CH, Stancofski ESD, Talana CA, Teng IT, Wang S, Corbett KS, Tsybovsky Y, Mascola JR, Kwong PD. Vaccine-elicited murine antibody WS6 neutralizes diverse beta-coronaviruses by recognizing a helical stem supersite of vulnerability. Structure 2022; 30:1233-1244.e7. [PMID: 35841885 PMCID: PMC9284671 DOI: 10.1016/j.str.2022.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/06/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022]
Abstract
Immunization with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike elicits diverse antibodies, but it is unclear if any of the antibodies can neutralize broadly against other beta-coronaviruses. Here, we report antibody WS6 from a mouse immunized with mRNA encoding the SARS-CoV-2 spike. WS6 bound diverse beta-coronavirus spikes and neutralized SARS-CoV-2 variants, SARS-CoV, and related sarbecoviruses. Epitope mapping revealed WS6 to target a region in the S2 subunit, which was conserved among SARS-CoV-2, Middle East respiratory syndrome (MERS)-CoV, and hCoV-OC43. The crystal structure at 2 Å resolution of WS6 revealed recognition to center on a conserved S2 helix, which was occluded in both pre- and post-fusion spike conformations. Structural and neutralization analyses indicated WS6 to neutralize by inhibiting fusion and post-viral attachment. Comparison of WS6 with other recently identified antibodies that broadly neutralize beta-coronaviruses indicated a stem-helical supersite-centered on hydrophobic residues Phe1148, Leu1152, Tyr1155, and Phe1156-to be a promising target for vaccine design.
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Affiliation(s)
- Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xuejun Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Misook Choe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwan Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Arne Schön
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erik-Stephane D Stancofski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chloe Adrienna Talana
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Yan Q, Wu K, Zeng W, Yu S, Li Y, Sun Y, Liu X, Ruan Y, Huang J, Ding H, Yi L, Zhao M, Chen J, Fan S. Historical Evolutionary Dynamics and Phylogeography Analysis of Transmissible Gastroenteritis Virus and Porcine Deltacoronavirus: Findings from 59 Suspected Swine Viral Samples from China. Int J Mol Sci 2022; 23:ijms23179786. [PMID: 36077190 PMCID: PMC9456201 DOI: 10.3390/ijms23179786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/14/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Since the beginning of the 21st century, humans have experienced three coronavirus pandemics, all of which were transmitted to humans via animals. Recent studies have found that porcine deltacoronavirus (PDCoV) can infect humans, so swine enteric coronavirus (SeCoV) may cause harm through cross-species transmission. Transmissible gastroenteritis virus (TGEV) and PDCoV have caused tremendous damage and loss to the pig industry around the world. Therefore, we analyzed the genome sequence data of these two SeCoVs by evolutionary dynamics and phylogeography, revealing the genetic diversity and spatiotemporal distribution characteristics. Maximum likelihood and Bayesian inference analysis showed that TGEV could be divided into two different genotypes, and PDCoV could be divided into four main lineages. Based on the analysis results inferred by phylogeography, we inferred that TGEV might originate from America, PDCoV might originate from Asia, and different migration events had different migration rates. In addition, we also identified positive selection sites of spike protein in TGEV and PDCoV, indicating that the above sites play an essential role in promoting membrane fusion to achieve adaptive evolution. In a word, TGEV and PDCoV are the past and future of SeCoV, and the relatively smooth transmission rate of TGEV and the increasing transmission events of PDCoV are their respective transmission characteristics. Our results provide new insights into the evolutionary characteristics and transmission diversity of these SeCoVs, highlighting the potential for cross-species transmission of SeCoV and the importance of enhanced surveillance and biosecurity measures for SeCoV in the context of the COVID-19 epidemic.
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Affiliation(s)
- Quanhui Yan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Keke Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Weijun Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Shu Yu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Yuwan Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Yawei Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Xiaodi Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Yang Ruan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Juncong Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Hongxing Ding
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Correspondence: (J.C.); (S.F.); Tel.: +86-20-8528-8017 (J.C.); +86-20-8528-8017 (S.F.)
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Correspondence: (J.C.); (S.F.); Tel.: +86-20-8528-8017 (J.C.); +86-20-8528-8017 (S.F.)
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Kiseleva I, Musaeva T, Ksenafontov A. SARS-CoV-2 Invasion: What Happens to Other Respiratory Viruses? Open Microbiol J 2022. [DOI: 10.2174/18742858-v16-e2206100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This letter briefly presents the relationships between respiratory viruses in the years prior to and during the COVID-19 pandemic. Viral common colds are self-limiting infections that typically resolve within a few days. However, when well-established epidemiological relationships are disrupted during a pandemic, they behave differently. For instance, during the 2009 influenza pandemic, while the majority of seasonal respiratory viruses lost ground under the pressure of a new pandemic strain, some others (for instance, human rhinoviruses) continued to circulate along with the pandemic pathogen and in some cases, even delayed its spread. With the arrival of the COVID-19 pandemic, the degree of circulation of many respiratory viruses has changed dramatically. Along with a significant reduction in the circulation of many seasonal respiratory pathogens, rhinoviruses, respiratory syncytial virus and non-COVID-19 coronaviruses—being the most frequently identified respiratory pathogens—have shown their unique capability to compete with SARS-CoV-2.
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Ullrich S, Nitsche C. SARS-CoV-2 Papain-Like Protease: Structure, Function and Inhibition. Chembiochem 2022; 23:e202200327. [PMID: 35993805 PMCID: PMC9538446 DOI: 10.1002/cbic.202200327] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/19/2022] [Indexed: 11/07/2022]
Abstract
Emerging variants of SARS-CoV-2 and potential novel epidemic coronaviruses underline the importance of investigating various viral proteins as potential drug targets. The papain-like protease of coronaviruses has been less explored than other viral proteins; however, its substantive role in viral replication and impact on the host immune response make it a suitable target to study. This review article focuses on the structure and function of the papain-like protease (PLpro) of SARS-CoV-2, including variants of concern, and compares it to those of other coronaviruses, such as SARS-CoV-1 and MERS-CoV. The protease's recognition motif is mirrored in ubiquitin and ISG15, which are important posttranslational modifiers of the antiviral immune response. Inhibitors, including GRL0617 derivatives, and their prospects as potential future antiviral agents are also discussed.
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Affiliation(s)
- Sven Ullrich
- Research School of ChemistryAustralian National UniversityCanberraACT 2601Australia
| | - Christoph Nitsche
- Research School of ChemistryAustralian National UniversityCanberraACT 2601Australia
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223
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Fengjiao S, Xiaodong L, Jian L, Hui L. Epidemiologic characteristics of SARS-CoV-2 in Wuhan, other regions of China, and globally based on data gathered from January 2020 to February 2021. Medicine (Baltimore) 2022; 101:e30019. [PMID: 35960106 PMCID: PMC9370246 DOI: 10.1097/md.0000000000030019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
This observation study examines coronavirus disease 2019 (COVID-19) data from outbreak and other sites in China and worldwide in order to examine the epidemiological pattern of COVID-19 before the acquisition of immunity through widespread vaccination and infection. COVID-19-related morbidity and mortality data for January 2020 to February 2021 were obtained from the Chinese Center for Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, and the World Health Organization. The number of cases was logarithmically transformed for comparison of the rate of increase or decrease with time across areas. From January to February 2020, the number of new confirmed cases in Wuhan grew substantially but returned to zero by May 2020. In other parts of China, the rate of decrease was lower than that in Wuhan, and the mortality rate was lower outside Wuhan (1.93%) than in Wuhan (7.68%). The influenza trends were similar to those of COVID-19, but the mortality rate of influenza was much lower (0.011%) than that of COVID-19. After the early stage, similar increase in the incidence rate with time was observed globally, although the total number of cases differed between regions. The outbreak severe acute respiratory syndrome coronavirus 2 strain in Wuhan had low epidemic intensity and high virulence, but the epidemiological characteristics of severe acute respiratory syndrome coronavirus 2 may not be associated with race, geography, or economic status. Importantly, more effective prevention and control measures and vaccines should be applied for controlling the variants.
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Affiliation(s)
- Song Fengjiao
- Department of Laboratory and Quarantine, Dalian Medical University, Dalian, China
| | - Li Xiaodong
- Department of Laboratory and Quarantine, Dalian Medical University, Dalian, China
| | - Li Jian
- Department of Laboratory and Quarantine, Dalian Medical University, Dalian, China
| | - Liu Hui
- Department of Laboratory and Quarantine, Dalian Medical University, Dalian, China
- *Correspondence: Liu Hui, Department of Laboratory and Quarantine, Dalian Medical University, No.9 of the west section of South Lvshun Road, 116044, Dalian, China (e-mail: )
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224
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Gutiérrez LJ, Tosso RD, Zarycz MNC, Enriz RD, Baldoni HA. Epitopes mapped onto SARS-CoV-2 receptor-binding motif by five distinct human neutralising antibodies. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2111421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Lucas J. Gutiérrez
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
| | - Rodrigo D. Tosso
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
| | - M. Natalia C. Zarycz
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
| | - Ricardo D. Enriz
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
| | - Héctor A. Baldoni
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
- Institute of Applied Mathematics of San Luis (IMASL. CONICET), San Luis, Argentina
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225
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Tiwari S, Adupa V, Das DS, Anki Reddy K, Bharat TV. Structural and Dynamic Insights into SARS-CoV-2 Spike-Protein-Montmorillonite Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:9186-9194. [PMID: 35855632 PMCID: PMC9344787 DOI: 10.1021/acs.langmuir.2c00837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/21/2022] [Indexed: 06/01/2023]
Abstract
The spike (S) protein of SARS-CoV-2 has been found to play a decisive role in the cell entry mechanism of the virus and has been the prime target of most vaccine development efforts. Although numerous vaccines are already in use and more than half of the world population has been fully vaccinated, the emergence of new variants of the virus poses a challenge to the existing vaccines. Hence, developing an effective drug therapy is a crucial step in ending the pandemic. Nanoparticles can play a crucial role as a drug or a drug carrier and help tackle the pandemic effectively. Here, we performed explicit all-atom molecular dynamics simulations to probe interactions between S protein and Montmorillonite (MMT) nano clay surface. We built two systems with different counterions (Na+ and Ca2+), namely Na-MMT and Ca-MMT, to investigate the effect of different ions on S protein-MMT interaction. Structural modification of S protein was observed in the presence of MMT surface, particularly the loss of helical content of S protein. We revealed that electrostatic and hydrophobic interactions synergistically govern the S protein-MMT interactions. However, hydrophobic interactions were more pronounced in the Na-MMT system than in Ca-MMT. We also revealed residues and glycans of S protein closely interacting with the MMT surface. Interestingly, N165 and N343, which we found to be closely interacting with MMT in our simulations, also have a critical role in cell entry and in thwarting the cell's immune response in recent studies. Overall, our work provides atomistic insights into S protein-MMT interaction and enriches our understanding of the nanoparticle-S protein interaction mechanism, which will help develop advanced therapeutic techniques in the future.
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Affiliation(s)
- Shivam Tiwari
- Department
of Chemical Engineering, Indian Institute
of Technology, Guwahati, Assam 781039, India
| | - Vasista Adupa
- Department
of Chemical Engineering, Indian Institute
of Technology, Guwahati, Assam 781039, India
| | - Dhanesh Sing Das
- Department
of Civil Engineering, Indian Institute of
Technology, Guwahati, Assam 781039, India
| | - K. Anki Reddy
- Department
of Chemical Engineering, Indian Institute
of Technology, Tirupati, Andhra Pradesh 517506, India
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226
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Ilyicheva TN, Netesov SV, Gureyev VN. COVID-19, Influenza, and Other Acute Respiratory Viral Infections: Etiology, Immunopathogenesis, Diagnosis, and Treatment. Part I. COVID-19 and Influenza. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY : MOLEKULYARNAYA GENETIKA, MIKROBIOLOGIYA I VIRUSOLOGIYA 2022; 37:1-9. [PMID: 35936505 PMCID: PMC9342941 DOI: 10.3103/s0891416822010025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/01/2021] [Accepted: 09/15/2021] [Indexed: 06/08/2023]
Abstract
The paper briefly reviews pathogens causing acute respiratory viral infections (ARVIs), including influenza viruses; coronaviruses, including SARS-CoV-2; parainfluenza viruses, adenoviruses, pneumoviruses, and specifically respiratory syncytial virus and metapneumoviruses, enteroviruses, rhinoviruses, and bocaviruses. This review presents modern data on the structure and replication of viruses, epidemiology, and immunopathogenesis of diseases and on diagnostics, preventive vaccination, and antiviral drugs for the treatment of ARVIs. Special attention is paid to the SARS-CoV-2 virus caused COVID-19 pandemic with analyses of similarities and differences between COVID-19 and other ARVIs, first of all, influenza virus. Topical issues regarding ARVI vaccination and the search for new broad-spectrum antiviral drugs are discussed.
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Affiliation(s)
- T. N. Ilyicheva
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Vector State Research Center of Virology and Biotechnology, 630559 Koltsovo, Russia
| | - S. V. Netesov
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - V. N. Gureyev
- Vector State Research Center of Virology and Biotechnology, 630559 Koltsovo, Russia
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227
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Wu Y, Shi Z, Chen J, Zhang H, Li M, Zhao Y, Shi H, Shi D, Guo L, Feng L. Porcine deltacoronavirus E protein induces interleukin-8 production via NF-κB and AP-1 activation. Vet Microbiol 2022; 274:109553. [PMID: 36181744 PMCID: PMC9428115 DOI: 10.1016/j.vetmic.2022.109553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/22/2022] [Accepted: 08/27/2022] [Indexed: 11/23/2022]
Abstract
Infection induces the production of proinflammatory cytokines and chemokines such as interleukin-8 (IL-8) and interleukin-6 (IL-6). Although they facilitate local antiviral immunity, their excessive release leads to life-threatening cytokine release syndrome, exemplified by the severe cases of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In the present study, we found that interleukin-8 (IL-8) was upregulated by PDCoV infection. We then demonstrated that PDCoV E protein induced IL-8 production and that the TM domain and the C-terminal domain of the E protein were important for IL-8 production. Subsequently, we showed here that deleting the AP-1 and NF-κB binding motif in porcine IL-8 promoter abrogated its activation, suggesting that IL-8 expression was dependent on AP-1 and NF-κB. Furthermore, PDCoV E induced IL-8 production, which was also dependent on the NF-κB pathway through activating nuclear factor p65 phosphorylation and NF-κB inhibitor alpha (IκBα) protein phosphorylation, as well as inducing the nuclear translocation of p65, eventually resulting in the promotion of IL-8 production. PDCoV E also activated c-fos and c-jun, both of which are members of the AP-1 family. These findings provide new insights into the molecular mechanisms of PDCoV-induced IL-8 production and help us further understand the pathogenesis of PDCoV infection.
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228
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Lan J, Chen P, Liu W, Ren W, Zhang L, Ding Q, Zhang Q, Wang X, Ge J. Structural insights into the binding of SARS-CoV-2, SARS-CoV, and hCoV-NL63 spike receptor-binding domain to horse ACE2. Structure 2022; 30:1432-1442.e4. [PMID: 35917815 PMCID: PMC9341007 DOI: 10.1016/j.str.2022.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 06/06/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, and human coronavirus (hCoV)-NL63 utilize ACE2 as the functional receptor for cell entry, which leads to zoonotic infection. Horses (Equus caballus) attracted our attention because the spike protein receptor-binding domains (RBDs) of SARS-CoV-2 and SARS-CoV-2-related coronaviruses bind equine ACE2 (eACE2) with high affinity. Here we show that eACE2 binds the RBDs of these three coronaviruses and also SARS-CoV-2 variants but with lower affinities compared with human ACE2 (hACE2). Structural analysis and mutation assays indicated that eACE2-H41 accounts for the lower binding affinity of eACE2 to the RBDs of SARS-CoV-2 variants (Alpha, Beta, and Gamma), SARS-CoV, and hCoV-NL63. Pseudovirus infection assays showed that the SARS-CoV-2 Delta strain (B.1.617.2) displayed a significantly increased infection efficiency in eACE2-expressing HeLa cells. Our results reveal the molecular basis of eACE2 binding to the RBDs of SARS-CoV, SARS-CoV-2, and hCoV-NL63, which provides insights into the potential animal transmission of these ACE2-dependent coronaviruses.
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Affiliation(s)
- Jun Lan
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Peng Chen
- Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine and Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Weiming Liu
- Department of Critical Care Medicine, Beijing Boai Hospital, China Rehabilitation Research Centre, No. 10 Jiaomen Beilu, Fengtai District, Beijing 100068, China
| | - Wenlin Ren
- Center for Infectious Disease Research, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Linqi Zhang
- Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine and Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Qiang Ding
- Center for Infectious Disease Research, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Qi Zhang
- Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine and Vanke School of Public Health, Tsinghua University, Beijing, China.
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Jiwan Ge
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing, China.
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229
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Zamani Rarani F, Zamani Rarani M, Hamblin MR, Rashidi B, Hashemian SMR, Mirzaei H. Comprehensive overview of COVID-19-related respiratory failure: focus on cellular interactions. Cell Mol Biol Lett 2022; 27:63. [PMID: 35907817 PMCID: PMC9338538 DOI: 10.1186/s11658-022-00363-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/06/2022] [Indexed: 01/08/2023] Open
Abstract
The pandemic outbreak of coronavirus disease 2019 (COVID-19) has created health challenges in all parts of the world. Understanding the entry mechanism of this virus into host cells is essential for effective treatment of COVID-19 disease. This virus can bind to various cell surface molecules or receptors, such as angiotensin-converting enzyme 2 (ACE2), to gain cell entry. Respiratory failure and pulmonary edema are the most important causes of mortality from COVID-19 infections. Cytokines, especially proinflammatory cytokines, are the main mediators of these complications. For normal respiratory function, a healthy air-blood barrier and sufficient blood flow to the lungs are required. In this review, we first discuss airway epithelial cells, airway stem cells, and the expression of COVID-19 receptors in the airway epithelium. Then, we discuss the suggested molecular mechanisms of endothelial dysfunction and blood vessel damage in COVID-19. Coagulopathy can be caused by platelet activation leading to clots, which restrict blood flow to the lungs and lead to respiratory failure. Finally, we present an overview of the effects of immune and non-immune cells and cytokines in COVID-19-related respiratory failure.
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Affiliation(s)
- Fahimeh Zamani Rarani
- Department of Anatomical Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Zamani Rarani
- Department of Anatomical Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028 South Africa
| | - Bahman Rashidi
- Department of Anatomical Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Mohammad Reza Hashemian
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamed Mirzaei
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, IR Iran
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230
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Chen MX, Zhu XD, Zhang H, Liu Z, Liu YN. SMRI: A New Method for siRNA Design for COVID-19 Therapy. JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY 2022; 37:991-1002. [PMID: 35992496 PMCID: PMC9374573 DOI: 10.1007/s11390-021-0826-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/31/2021] [Indexed: 06/15/2023]
Abstract
UNLABELLED First discovered in Wuhan, China, SARS-CoV-2 is a highly pathogenic novel coronavirus, which rapidly spread globally and became a pandemic with no vaccine and limited distinctive clinical drugs available till March 13th, 2020. Ribonucleic Acid interference (RNAi) technology, a gene-silencing technology that targets mRNA, can cause damage to RNA viruses effectively. Here, we report a new efficient small interfering RNA (siRNA) design method named Simple Multiple Rules Intelligent Method (SMRI) to propose a new solution of the treatment of COVID-19. To be specific, this study proposes a new model named Base Preference and Thermodynamic Characteristic model (BPTC model) indicating the siRNA silencing efficiency and a new index named siRNA Extended Rules index (SER index) based on the BPTC model to screen high-efficiency siRNAs and filter out the siRNAs that are difficult to take effect or synthesize as a part of the SMRI method, which is more robust and efficient than the traditional statistical indicators under the same circumstances. Besides, to silence the spike protein of SARS-CoV-2 to invade cells, this study further puts forward the SMRI method to search candidate high-efficiency siRNAs on SARS-CoV-2's S gene. This study is one of the early studies applying RNAi therapy to the COVID-19 treatment. According to the analysis, the average value of predicted interference efficiency of the candidate siRNAs designed by the SMRI method is comparable to that of the mainstream siRNA design algorithms. Moreover, the SMRI method ensures that the designed siRNAs have more than three base mismatches with human genes, thus avoiding silencing normal human genes. This is not considered by other mainstream methods, thereby the five candidate high-efficiency siRNAs which are easy to take effect or synthesize and much safer for human body are obtained by our SMRI method, which provide a new safer, small dosage and long efficacy solution for the treatment of COVID-19. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11390-021-0826-x.
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Affiliation(s)
- Meng-Xin Chen
- College of Software, Jilin University, Changchun, 130012 China
| | - Xiao-Dong Zhu
- Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, 130012 China
| | - Hao Zhang
- College of Computer Science and Technology, Jilin University, Changchun, 130012 China
| | - Zhen Liu
- College of Computer Science and Technology, Jilin University, Changchun, 130012 China
- Graduate School of Engineering, Nagasaki Institute of Applied Science, Nagasaki, 851-0193 Japan
| | - Yuan-Ning Liu
- College of Computer Science and Technology, Jilin University, Changchun, 130012 China
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231
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Li Y, Zheng P, Liu T, Shi C, Wang B, Xu Y, Jin T. Structural Requirements and Plasticity of Receptor-Binding Domain in Human Coronavirus Spike. Front Mol Biosci 2022; 9:930931. [PMID: 35903152 PMCID: PMC9315343 DOI: 10.3389/fmolb.2022.930931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 11/22/2022] Open
Abstract
The most recent human coronaviruses including severe acute respiratory syndrome coronavirus-2 causing severe respiratory tract infection and high pathogenicity bring significant global public health concerns. Infections are initiated by recognizing host cell receptors by coronavirus spike protein S1 subunit, and then S2 mediates membrane fusion. However, human coronavirus spikes undergo frequent mutation, which may result in diverse pathogenesis and infectivity. In this review, we summarize some of these recent structural and mutational characteristics of RBD of human coronavirus spike protein and their interaction with specific human cell receptors and analyze the structural requirements and plasticity of RBD. Stability of spike protein, affinity toward receptor, virus fitness, and infectivity are the factors controlling the viral tropisms. Thus, understanding the molecular details of RBDs and their mutations is critical in deciphering virus evolution. Structural information of spike and receptors of human coronaviruses not only reveals the molecular mechanism of host–microbe interaction and pathogenesis but also helps develop effective drug to control these infectious pathogens and cope with the future emerging coronavirus outbreaks.
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Affiliation(s)
- Yajuan Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Peiyi Zheng
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Tingting Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Cuixiao Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Bo Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Tengchuan Jin
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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232
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Dutta S, Panthi B, Chandra A. All-Atom Simulations of Human ACE2-Spike Protein RBD Complexes for SARS-CoV-2 and Some of its Variants: Nature of Interactions and Free Energy Diagrams for Dissociation of the Protein Complexes. J Phys Chem B 2022; 126:5375-5389. [PMID: 35833966 PMCID: PMC9328126 DOI: 10.1021/acs.jpcb.2c00833] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/25/2022] [Indexed: 12/18/2022]
Abstract
The spike protein of SARS-CoV-2 is known to interact with the human ACE2 protein via its receptor binding domain (RBD). We have investigated the molecular nature of this interprotein interaction and the associated free energy diagrams for the unbinding of the two proteins for SARS-CoV-2 and some of its known variants through all-atom simulations. The present work involves generation and analysis of 2.5 μs of unbiased and 4.2 μs of biased molecular dynamics trajectories in total for five explicitly solvated RBD-ACE2 systems at full atomic level. First, we have made a comparative analysis of the details of residue-wise specific interactions of the spike protein with ACE2 for SARS-CoV-1 and SARS-CoV-2. It is found that the average numbers of both direct interprotein and water-bridged hydrogen bonds between the RBD and ACE2 are higher for SARS-CoV-2 than SARS-CoV-1. These higher hydrogen bonded interactions are further aided by enhanced nonspecific electrostatic attractions between the two protein surfaces for SARS-CoV-2. The free energy calculations reveal that there is an increase in the free energy barrier by ∼1.5 kcal/mol for the unbinding of RBD from ACE2 for SARS-CoV-2 compared to that for SARS-CoV-1. Subsequently, we considered the RBDs of three variants of SARS-CoV-2, namely N501Y, E484Q/L452R, and N440K. The free energy barrier of protein unbinding for the N501Y variant is found to be ∼4 kcal/mol higher than the wild type SARS-CoV-2 which can be attributed to additional specific interactions involving Tyr501 of RBD and Lys353 and Tyr42 of ACE2 and also enhanced nonspecific electrostatic interaction between the protein surfaces. For the other two mutant variants of E484Q/L452R and N440K, the free energy barrier for protein unbinding increases by ∼2 and ∼1 kcal/mol, respectively, compared with the wild type SARS-CoV-2, which can be attributed to an increase in the number of interprotein hydrogen bonds for the former and also to enhanced positive electrostatic potential on the RBD surfaces for both of the variants. The successive breaking of interprotein hydrogen bonds along the free energy pathway of the unbinding process is also found out for all five systems studied here.
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Affiliation(s)
- Saheb Dutta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Bhavana Panthi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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233
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Kabi AK, Pal M, Gujjarappa R, Malakar CC, Roy M. Overview of Hydroxychloroquine and Remdesivir on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). J Heterocycl Chem 2022; 60:JHET4541. [PMID: 35942205 PMCID: PMC9349740 DOI: 10.1002/jhet.4541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/08/2022]
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the ongoing pandemic named COVID-19 which causes a serious emergency on public health hazards of international concern. In the face of a critical medical emergency, repositioning of drugs is one of the most authentic options to design an adequate treatment for infected patients immediately. In this strategy, Remdesivir (Veklury), Hydroxychloroquine appears to be the drug of choice and garnered unprecedented attention as potential therapeutic agents against the pandemic realized worldwide due to SARS-CoV-2 infection. These are the breathtaking instances of possible repositioning of drugs, whose pharmacokinetics and optimal dosage are familiar. In this review, we provide an overview of these medications, their synthesis, and the possible mechanism of action against SARS-CoV-2.
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Affiliation(s)
- Arup K. Kabi
- Department of ChemistryNational Institute of Technology ManipurImphalManipurIndia
| | - Maynak Pal
- Department of ChemistryNational Institute of Technology ManipurImphalManipurIndia
| | - Raghuram Gujjarappa
- Department of ChemistryNational Institute of Technology ManipurImphalManipurIndia
| | - Chandi C. Malakar
- Department of ChemistryNational Institute of Technology ManipurImphalManipurIndia
| | - Mithun Roy
- Department of ChemistryNational Institute of Technology ManipurImphalManipurIndia
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Rebendenne A, Roy P, Bonaventure B, Chaves Valadão AL, Desmarets L, Arnaud-Arnould M, Rouillé Y, Tauziet M, Giovannini D, Touhami J, Lee Y, DeWeirdt P, Hegde M, Urbach S, Koulali KE, de Gracia FG, McKellar J, Dubuisson J, Wencker M, Belouzard S, Moncorgé O, Doench JG, Goujon C. Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs. Nat Genet 2022; 54:1090-1102. [PMID: 35879413 DOI: 10.1038/s41588-022-01110-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 05/26/2022] [Indexed: 12/23/2022]
Abstract
CRISPR knockout (KO) screens have identified host factors regulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. Here, we conducted a meta-analysis of these screens, which showed a high level of cell-type specificity of the identified hits, highlighting the necessity of additional models to uncover the full landscape of host factors. Thus, we performed genome-wide KO and activation screens in Calu-3 lung cells and KO screens in Caco-2 colorectal cells, followed by secondary screens in four human cell lines. This revealed host-dependency factors, including AP1G1 adaptin and ATP8B1 flippase, as well as inhibitors, including mucins. Interestingly, some of the identified genes also modulate Middle East respiratory syndrome coronavirus (MERS-CoV) and seasonal human coronavirus (HCoV) (HCoV-NL63 and HCoV-229E) replication. Moreover, most genes had an impact on viral entry, with AP1G1 likely regulating TMPRSS2 activity at the plasma membrane. These results demonstrate the value of multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential targets for therapeutic interventions.
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Affiliation(s)
| | - Priyanka Roy
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Lowiese Desmarets
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - Yves Rouillé
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - Donatella Giovannini
- IGMM, CNRS, Montpellier University, Montpellier, France.,Metafora Biosystems, Paris, France
| | - Jawida Touhami
- IGMM, CNRS, Montpellier University, Montpellier, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Yenarae Lee
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mudra Hegde
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Serge Urbach
- IGF, Montpellier University, CNRS, INSERM, Montpellier, France
| | | | | | - Joe McKellar
- IRIM, CNRS, Montpellier University, Montpellier, France
| | - Jean Dubuisson
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - Sandrine Belouzard
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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235
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Li H, Hong X, Ding L, Meng S, Liao R, Jiang Z, Liu D. Sequence similarity of SARS-CoV-2 and humans: Implications for SARS-CoV-2 detection. Front Genet 2022; 13:946359. [PMID: 35937998 PMCID: PMC9355506 DOI: 10.3389/fgene.2022.946359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
Detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) needs human samples, which inevitably contain trace human DNA and RNA. Sequence similarity may cause invalid detection results; however, there is still a lack of gene similarity analysis of SARS-CoV-2 and humans. All publicly reported complete genome assemblies in the Entrez genome database were collected for multiple sequence alignment, similarity and phylogenetic analysis. The complete genomes showed high similarity (>99.88% sequence identity). Phylogenetic analysis divided these viruses into three major clades with significant geographic group effects. Viruses from the United States showed considerable variability. Sequence similarity analysis revealed that SARS-CoV-2 has 612 similar sequences with the human genome and 100 similar sequences with the human transcriptome. The sequence characteristics and genome distribution of these similar sequences were confirmed. The sequence similarity and evolutionary mutations provide indispensable references for dynamic updates of SARS-CoV-2 detection primers and methods.
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Affiliation(s)
- Heng Li
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | - Xiaoping Hong
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Liping Ding
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Shuhui Meng
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Rui Liao
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Zhenyou Jiang
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, China
- *Correspondence: Zhenyou Jiang, ; Dongzhou Liu,
| | - Dongzhou Liu
- Department of Rheumatology and Immunology, Shenzhen People’s Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, China
- *Correspondence: Zhenyou Jiang, ; Dongzhou Liu,
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236
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Loibner M, Barach P, Wolfgruber S, Langner C, Stangl V, Rieger J, Föderl-Höbenreich E, Hardt M, Kicker E, Groiss S, Zacharias M, Wurm P, Gorkiewicz G, Regitnig P, Zatloukal K. Resilience and Protection of Health Care and Research Laboratory Workers During the SARS-CoV-2 Pandemic: Analysis and Case Study From an Austrian High Security Laboratory. Front Psychol 2022; 13:901244. [PMID: 35936273 PMCID: PMC9353000 DOI: 10.3389/fpsyg.2022.901244] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/10/2022] [Indexed: 11/25/2022] Open
Abstract
The SARS-CoV-2 pandemic has highlighted the interdependency of healthcare systems and research organizations on manufacturers and suppliers of personnel protective equipment (PPE) and the need for well-trained personnel who can react quickly to changing working conditions. Reports on challenges faced by research laboratory workers (RLWs) are rare in contrast to the lived experience of hospital health care workers. We report on experiences gained by RLWs (e.g., molecular scientists, pathologists, autopsy assistants) who significantly contributed to combating the pandemic under particularly challenging conditions due to increased workload, sickness and interrupted PPE supply chains. RLWs perform a broad spectrum of work with SARS-CoV-2 such as autopsies, establishment of virus cultures and infection models, development and verification of diagnostics, performance of virus inactivation assays to investigate various antiviral agents including vaccines and evaluation of decontamination technologies in high containment biological laboratories (HCBL). Performance of autopsies and laboratory work increased substantially during the pandemic and thus led to highly demanding working conditions with working shifts of more than eight hours working in PPE that stressed individual limits and also the ergonomic and safety limits of PPE. We provide detailed insights into the challenges of the stressful daily laboratory routine since the pandemic began, lessons learned, and suggest solutions for better safety based on a case study of a newly established HCBL (i.e., BSL-3 laboratory) designed for autopsies and research laboratory work. Reduced personal risk, increased resilience, and stress resistance can be achieved by improved PPE components, better training, redundant safety measures, inculcating a culture of safety, and excellent teamwork.
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Affiliation(s)
- Martina Loibner
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Paul Barach
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
- College of Population Health, Thomas Jefferson University, Philadelphia, PA, United States
- School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Stella Wolfgruber
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Christine Langner
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Verena Stangl
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Julia Rieger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | | | - Melina Hardt
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Eva Kicker
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Silvia Groiss
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Martin Zacharias
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Philipp Wurm
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Gregor Gorkiewicz
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Peter Regitnig
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Kurt Zatloukal
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
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237
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Imbert F, Leavitt G, Langford D. SUMOylation and Viral Infections of the Brain. Pathogens 2022; 11:818. [PMID: 35890062 PMCID: PMC9324588 DOI: 10.3390/pathogens11070818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/12/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
The small ubiquitin-like modifier (SUMO) system regulates numerous biological processes, including protein localization, stability and/or activity, transcription, and DNA repair. SUMO also plays critical roles in innate immunity and antiviral defense by mediating interferon (IFN) synthesis and signaling, as well as the expression and function of IFN-stimulated gene products. Viruses including human immunodeficiency virus-1, Zika virus, herpesviruses, and coronaviruses have evolved to exploit the host SUMOylation system to counteract the antiviral activities of SUMO proteins and to modify their own proteins for viral persistence and pathogenesis. Understanding the exploitation of SUMO is necessary for the development of effective antiviral therapies. This review summarizes the interplay between viruses and the host SUMOylation system, with a special emphasis on viruses with neuro-invasive properties that have pathogenic consequences on the central nervous system.
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Affiliation(s)
| | | | - Dianne Langford
- Department of Neural Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (F.I.); (G.L.)
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238
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Infection Rate of Respiratory Viruses in the Pandemic SARS-CoV-2 Period Considering Symptomatic Patients: Two Years of Ongoing Observations. Biomolecules 2022; 12:biom12070987. [PMID: 35883543 PMCID: PMC9313449 DOI: 10.3390/biom12070987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In the last two years, the SARS-CoV-2 pandemic has determined radical changes in human behaviors and lifestyles, with a drastic reduction in socialization due to physical distancing and self-isolation. These changes have also been reflected in the epidemiological patterns of common respiratory viruses. For this reason, early discrimination of respiratory viruses is important as new variants emerge. METHODS Nasopharyngeal swabs of 2554 patients, with clinically suspected Acute Respiratory Infections (ARIs) from October 2019 to November 2021, were collected to detect 1 or more of the 23 common respiratory pathogens, especially viruses, via BioFilmArray RP2.1plus, including SARS-CoV-2. Demographical characteristics and epidemiological analyses were performed as well as a laboratory features profile of positive patients. RESULTS An observational study on 2300 patients (254 patients were excluded because of missing data) including 1560 men and 760 women, median age of 64.5 years, was carried out. Considering the respiratory virus research request, most of the patients were admitted to the Emergency Medicine Department (41.2%, of patients), whereas 29.5% were admitted to the Infectious Diseases Department. The most frequently detected pathogens included SARS-CoV-2 (31.06%, 707/2300, from March 2020 to November 2021), InfA-B (1.86%, 43/2300), HCoV (2.17% 50/2300), and HSRV (1.65%, 38/2300). Interestingly, coinfection rates decreased dramatically in the SARS-CoV-2 pandemic period. The significative decrease in positive rate of SARS-CoV-2 was associated with the massive vaccination. CONCLUSION This study represents a dynamic picture of the epidemiological curve of common respiratory viruses during the two years of pandemic, with a disregarded trend for additional viruses. Our results showed that SARS-CoV-2 had a preferential tropism for the respiratory tract without co-existing with other viruses. The possible causes were attributable either to the use of masks, social isolation, or to specific respiratory receptors mostly available for this virus, external and internal lifestyle factors, vaccination campaigns, and emergence of new SARS-CoV-2 variants.
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239
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Otieno JR, Cherry JL, Spiro DJ, Nelson MI, Trovão NS. Origins and Evolution of Seasonal Human Coronaviruses. Viruses 2022; 14:1551. [PMID: 35891531 PMCID: PMC9320361 DOI: 10.3390/v14071551] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Four seasonal human coronaviruses (sHCoVs) are endemic globally (229E, NL63, OC43, and HKU1), accounting for 5-30% of human respiratory infections. However, the epidemiology and evolution of these CoVs remain understudied due to their association with mild symptomatology. Using a multigene and complete genome analysis approach, we find the evolutionary histories of sHCoVs to be highly complex, owing to frequent recombination of CoVs including within and between sHCoVs, and uncertain, due to the under sampling of non-human viruses. The recombination rate was highest for 229E and OC43 whereas substitutions per recombination event were highest in NL63 and HKU1. Depending on the gene studied, OC43 may have ungulate, canine, or rabbit CoV ancestors. 229E may have origins in a bat, camel, or an unsampled intermediate host. HKU1 had the earliest common ancestor (1809-1899) but fell into two distinct clades (genotypes A and B), possibly representing two independent transmission events from murine-origin CoVs that appear to be a single introduction due to large gaps in the sampling of CoVs in animals. In fact, genotype B was genetically more diverse than all the other sHCoVs. Finally, we found shared amino acid substitutions in multiple proteins along the non-human to sHCoV host-jump branches. The complex evolution of CoVs and their frequent host switches could benefit from continued surveillance of CoVs across non-human hosts.
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Affiliation(s)
- James R. Otieno
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Joshua L. Cherry
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - David J. Spiro
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Martha I. Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
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Mas M, García-Vicente JA, Estrada-Gelonch A, Pérez-Mañá C, Papaseit E, Torrens M, Farré M. Antidepressant Drugs and COVID-19: A Review of Basic and Clinical Evidence. J Clin Med 2022; 11:jcm11144038. [PMID: 35887802 PMCID: PMC9319396 DOI: 10.3390/jcm11144038] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 01/27/2023] Open
Abstract
The COVID-19 pandemic has encouraged the repurposing of existing drugs as a shorter development strategy in order to support clinicians with this difficult therapeutic dilemma. There is evidence to support the theory that some antidepressants can reduce concentrations of different cytokines in humans and animals and, recently, the antiviral activity of some antidepressants against SARS-CoV-2 has been reported. The aims of this narrative review are to evaluate the possible role of antidepressants in the treatment of COVID-19 infection and the possible benefits and risks of patients taking antidepressants for mental disorders and COVID-19 infection. A review was performed to analyse the current literature to identify the role of antidepressant medication in the treatment of COVID-19 patients. The electronic search was completed in MEDLINE and MedRxiv/BioRxiv for published literature and in ClinicalTrials.gov for ongoing clinical trials. The results show some evidence from preclinical data and observational studies about the possible efficacy of some specific antidepressants for treating COVID-19 infection. In addition, two published phase II studies testing fluvoxamine showed positive results for clinical deterioration and hospitalization rate versus a placebo. Seven ongoing clinical trials testing fluvoxamine, fluoxetine, and tramadol (as per its anti-inflammatory and antidepressant effect) are still in the early phases. Although the available evidence is limited, the sum of the antiviral and anti-inflammatory preclinical studies and the results from several observational studies and two phase II clinical trials provide the basis for ongoing clinical trials evaluating the possible use of antidepressants for COVID-19 infection in humans. Further investigations will be needed to support the possible use of antidepressants for this application.
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Affiliation(s)
- Marta Mas
- Medical Writing Department, TFS Healthcare, 08007 Barcelona, Spain; (M.M.); (A.E.-G.)
- Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Juan Antonio García-Vicente
- Department of Pharmacology, Therapeutics and Toxicology, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08290 Barcelona, Spain; (C.P.-M.); (E.P.); (M.T.)
- Pharmacy Unit, Northern Metropolitan Primary Care Directorate, Catalan Institute of Health, 08911 Barcelona, Spain
- Correspondence: (J.A.G.-V.); (M.F.)
| | - Anaïs Estrada-Gelonch
- Medical Writing Department, TFS Healthcare, 08007 Barcelona, Spain; (M.M.); (A.E.-G.)
| | - Clara Pérez-Mañá
- Department of Pharmacology, Therapeutics and Toxicology, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08290 Barcelona, Spain; (C.P.-M.); (E.P.); (M.T.)
- Clinical Pharmacology Unit, Hospital Universitari Germans Trias i Pujol and Institut de Recerca Germans Trias i Pujol (HUGTP-IGTP), 08916 Barcelona, Spain
| | - Esther Papaseit
- Department of Pharmacology, Therapeutics and Toxicology, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08290 Barcelona, Spain; (C.P.-M.); (E.P.); (M.T.)
- Clinical Pharmacology Unit, Hospital Universitari Germans Trias i Pujol and Institut de Recerca Germans Trias i Pujol (HUGTP-IGTP), 08916 Barcelona, Spain
| | - Marta Torrens
- Department of Pharmacology, Therapeutics and Toxicology, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08290 Barcelona, Spain; (C.P.-M.); (E.P.); (M.T.)
- Addiction Unit, Hospital del Mar Medical Research Institute (IMIM), Institut de Neuropsiquiatria i Addiccions, Parc de Salut Mar, 08003 Barcelona, Spain
| | - Magí Farré
- Department of Pharmacology, Therapeutics and Toxicology, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08290 Barcelona, Spain; (C.P.-M.); (E.P.); (M.T.)
- Clinical Pharmacology Unit, Hospital Universitari Germans Trias i Pujol and Institut de Recerca Germans Trias i Pujol (HUGTP-IGTP), 08916 Barcelona, Spain
- Correspondence: (J.A.G.-V.); (M.F.)
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241
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Imboumy-Limoukou RK, Ngoubangoye B, Dibakou SE, Oyegue-Liabagui SL, Mounioko F, Kouna LC, Matangoye WR, Ontoua SS, Mbani Mpega NC, Lekana-Douki JB. Knowledge, Attitude and Practice during the COVID-19 Pandemic in South-East Gabon. Behav Sci (Basel) 2022; 12:bs12070226. [PMID: 35877296 PMCID: PMC9312151 DOI: 10.3390/bs12070226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/16/2022] Open
Abstract
COVID-19 is an emerging respiratory disease; it was declared a global pandemic by the World Health Organization. This survey aimed to describe the knowledge, attitudes, perception and practices of the Gabonese public towards COVID-19. This study was performed on 1016 participants. All participants filled in the questionnaire voluntarily, reporting demographic characteristics and answering questions assessing their level of knowledge, attitudes, perceptions and practice towards COVID-19. Among participants, there were 535 men and 476 women. The mean age of the participants was 33.2 ± 16.7 years old. Almost all participants (98.1%) said that they had heard about COVID-19 but only 2.8% knew the pathogenic agent responsible for COVID-19. More than 80% knew that the disease could be transmitted by greeting infected people (87.3%), kissing an infected person (90.0%), touching an infected doorknob (83.5%) and attending meetings (83.9%). The mean knowledge score was higher among younger than older participants, higher among participants living in urban areas than those living in rural areas and higher among participants with higher levels of education than those with lower levels of education. In general, respondents had good knowledge of COVID-19 and a positive attitude towards using protective measures; however, there were differences according to gender, age group, place of residence, professional group and level of education.
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Affiliation(s)
- Roméo Karl Imboumy-Limoukou
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; (S.E.D.); (S.L.O.-L.); (F.M.); (L.C.K.); (W.R.M.); (S.S.O.); (N.C.M.M.); (J.-B.L.-D.)
- Correspondence: (R.K.I.-L.); (B.N.); Tel.: +241-66072638 (R.K.I.-L.); +241-62521239 (B.N.)
| | - Barthélemy Ngoubangoye
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; (S.E.D.); (S.L.O.-L.); (F.M.); (L.C.K.); (W.R.M.); (S.S.O.); (N.C.M.M.); (J.-B.L.-D.)
- Correspondence: (R.K.I.-L.); (B.N.); Tel.: +241-66072638 (R.K.I.-L.); +241-62521239 (B.N.)
| | - Serge Ely Dibakou
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; (S.E.D.); (S.L.O.-L.); (F.M.); (L.C.K.); (W.R.M.); (S.S.O.); (N.C.M.M.); (J.-B.L.-D.)
| | - Sandrine Lydie Oyegue-Liabagui
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; (S.E.D.); (S.L.O.-L.); (F.M.); (L.C.K.); (W.R.M.); (S.S.O.); (N.C.M.M.); (J.-B.L.-D.)
- Laboratoire de Recherches en Immunologie, Parasitologie et Microbiologie, Ecole Doctorale Régionale d’Afrique Centrale en Infectiologie Tropicale (ECODRAC), Université des Sciences et Techniques de Masuku, BP 876 Franceville, Gabon
| | - Franck Mounioko
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; (S.E.D.); (S.L.O.-L.); (F.M.); (L.C.K.); (W.R.M.); (S.S.O.); (N.C.M.M.); (J.-B.L.-D.)
| | - Lady Charlene Kouna
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; (S.E.D.); (S.L.O.-L.); (F.M.); (L.C.K.); (W.R.M.); (S.S.O.); (N.C.M.M.); (J.-B.L.-D.)
| | - Walter Roddy Matangoye
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; (S.E.D.); (S.L.O.-L.); (F.M.); (L.C.K.); (W.R.M.); (S.S.O.); (N.C.M.M.); (J.-B.L.-D.)
| | - Steede Seinnat Ontoua
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; (S.E.D.); (S.L.O.-L.); (F.M.); (L.C.K.); (W.R.M.); (S.S.O.); (N.C.M.M.); (J.-B.L.-D.)
| | - Nancy Cheronne Mbani Mpega
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; (S.E.D.); (S.L.O.-L.); (F.M.); (L.C.K.); (W.R.M.); (S.S.O.); (N.C.M.M.); (J.-B.L.-D.)
| | - Jean-Bernard Lekana-Douki
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; (S.E.D.); (S.L.O.-L.); (F.M.); (L.C.K.); (W.R.M.); (S.S.O.); (N.C.M.M.); (J.-B.L.-D.)
- Département de Parasitologie-Mycologie, Université des Sciences de la Santé, BP 4009 Libreville, Gabon
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Sanghani H, Bansal S, Parmar V, Shah R. Study of Arterial Blood Gas Analysis in Moderate-to-Severe COVID-19 Patients. Cureus 2022; 14:e26715. [PMID: 35967170 PMCID: PMC9362693 DOI: 10.7759/cureus.26715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2022] [Indexed: 01/08/2023] Open
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243
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Andola P, Pagag J, Laxman D, Guruprasad L. Fragment-based inhibitor design for SARS-CoV2 main protease. Struct Chem 2022; 33:1467-1487. [PMID: 35811782 PMCID: PMC9251026 DOI: 10.1007/s11224-022-01995-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/14/2022] [Indexed: 11/28/2022]
Abstract
COVID-19 disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) has resulted in tremendous loss of lives across the world and is continuing to do so. Extensive work is under progress to develop inhibitors which can prevent the disease by arresting the virus in its life cycle. One such way is by targeting the main protease of the virus which is crucial for the cleavage and conversion of polyproteins into functional units of polypeptides. In this endeavor, our effort was to identify hit molecule inhibitors for SARS-CoV2 main protease using fragment-based drug discovery (FBDD), based on the available crystal structure of chromene-based inhibitor (PDB_ID: 6M2N). The designed molecules were validated by molecular docking and molecular dynamics simulations. The stability of the complexes was further assessed by calculating their binding free energies, normal mode analysis, mechanical stiffness, and principal component analysis.
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Affiliation(s)
- Priyanka Andola
- School of Chemistry, University of Hyderabad, Hyderabad, 500046 India
| | - Jishu Pagag
- School of Chemistry, University of Hyderabad, Hyderabad, 500046 India
| | - Durgam Laxman
- School of Chemistry, University of Hyderabad, Hyderabad, 500046 India
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Rai H, Saad T, Rawat S, Mishra N, Mishra S. IS COVID 19 PANDEMIC ADDING MORE OF DIABETIC POPULATION: A STUDY IN CENTRAL INDIA. INDIAN JOURNAL OF APPLIED RESEARCH 2022:63-65. [DOI: 10.36106/ijar/4002154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Background– COVID 19 is associated with high prevalence of diabetes along with other comorbidities which also
increase the severity and mortality risk in COVID 19 disease. Recently many studies have shown the association between
COVID 19 and new onset diabetes. This study was done with objectives1.To nd out the incidence of new onset of hyperglycemia/diabetes in
COVID 19 patients and 2.To develop screening policy for detection of new onset hyperglycemia in COVID-19 patients. Materials And
Methods- This study is a hospital based observational cross sectional and prospective, cohort study conducted in the COVID ICU of Dedicated
COVID Hospital, Bundelkhand Government Medical College, Sagar (M.P.) India, a teaching tertiary care centre. Out of 1562 COVID 19
positive patients admitted with moderate to severe pneumonia from JULY 2020 to JANUARY 2021, 487 patients were hyperglycemic at the time
of admission. Patients were categorized into two subgroups: 1.Patients with previously conrmed diabetes or Prediabetes and 2.Hyperglycemia
with no existing diabetes. Patients in this later subgroup were our follow up subjects for this study; their blood sugar level was monitored
regularly during their stay in hospital & a correlation of COVID 19 and hyperglycemia was observed. In present study Incidence of newResults-
onset hyperglycemia was 16.8%; 262 out of 1562. Of all 1562 patients admitted in hospital, 660 (44.7%) were found to be hyperglycemic.
Among 660 patients, 436 (66.06%) patients were already known diabetic or pre-diabetic and 262 (16.8) were with newly onset hyperglycemia.
15 out of 262 (5.7%) patients were expired during their disease course, 157(60%) remained hyperglycemic while 90 (34.3) had attained
normoglycemia without anti-diabetic drugs. COVID 19 disease is causative factor for new onset hyperglycemia /new onsetConclusion-
diabetes.
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Affiliation(s)
- Hindeshwari Rai
- Assistant professor, General Medicine, Bundelkhand Medical College, Sagar (MP) India
| | - Talha Saad
- Associate professor, Pulmonary Medicine, Bundelkhand Medical College, Sagar (MP) India
| | | | - Nitu Mishra
- Research Scientist, Microbiology, Bundelkhand Medical College, Sagar (MP) India
| | - Shraddha Mishra
- Associate professor, Community Medicine, Bundelkhand Medical College, Sagar (MP) India
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Held A, Dellweg D, Köhler D, Pfaender S, Scheuch G, Schumacher S, Steinmann E, Weingartner E, Weinzierl B, Asbach C. [Interdisciplinary Perspectives on the Role of Aerosol Transmission in SARS-CoV-2 Infections]. DAS GESUNDHEITSWESEN 2022; 84:566-574. [PMID: 35835094 DOI: 10.1055/a-1808-0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The relevance of aerosols for the transmission of the Severe Acute Respiratory Syndrome Coronavirus Type 2 (SARS-CoV-2) is still debated. However, over time, in addition to distancing and hygiene rules, aerosol physics-based measures such as wearing face masks and ventilating indoor spaces were found to be efficient in reducing infections. In an interdisciplinary workshop "Aerosol & SARS-CoV-2" of the Association for Aerosol Research (GAeF) in cooperation with the German Society for Pneumology and Respiratory Medicine (DGP), the Professional Association of General Air Technology of the VDMA, the German Society for Virology (GfV), the Health Technology Society (GG) and the International Society for Aerosols in Medicine (ISAM) under the auspices of the Robert Koch Institute (RKI) in March 2021, the need for research and coordination on this topic was addressed. Fundamental findings from the various disciplines as well as interdisciplinary perspectives on aerosol transmission of SARS-CoV-2 and infection mitigation measures are summarized here. Finally, open research questions and needs are presented.
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Affiliation(s)
- Andreas Held
- FG Umweltchemie und Luftreinhaltung, Technische Universität Berlin, Berlin, Germany
| | - Dominic Dellweg
- Pneumologie, Fachkrankenhaus Kloster Grafschaft GmbH, Schmallenberg, Germany
| | | | - Stephanie Pfaender
- Abteilung für Molekulare und Medizinische Virologie, Ruhr-Universität Bochum, Bochum, Germany
| | | | - Stefan Schumacher
- Bereich Luftreinhaltung und Filtration, Institut für Energie- und Umwelttechnik e.V. (IUTA), Duisburg, Germany
| | - Eike Steinmann
- Abteilung für Molekulare und Medizinische Virologie, Ruhr-Universität Bochum, Bochum, Germany
| | - Ernest Weingartner
- Fachgruppe Aerosolmesstechnik, Fachhochschule Nordwestschweiz FHNW, Windisch, Switzerland
| | | | - Christof Asbach
- Bereich Luftreinhaltung und Filtration, Institut für Energie- und Umwelttechnik e.V. (IUTA), Duisburg, Germany
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246
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Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2. Nat Microbiol 2022; 7:1063-1074. [PMID: 35773398 DOI: 10.1038/s41564-022-01155-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 05/20/2022] [Indexed: 12/23/2022]
Abstract
Frequent outbreaks of coronaviruses underscore the need for antivirals and vaccines that can counter a broad range of coronavirus types. We isolated a human antibody named 76E1 from a COVID-19 convalescent patient, and report that it has broad-range neutralizing activity against multiple α- and β-coronaviruses, including the SARS-CoV-2 variants. 76E1 also binds its epitope in peptides from γ- and δ-coronaviruses. 76E1 cross-protects against SARS-CoV-2 and HCoV-OC43 infection in both prophylactic and therapeutic murine animal models. Structural and functional studies revealed that 76E1 targets a unique epitope within the spike protein that comprises the highly conserved S2' site and the fusion peptide. The epitope that 76E1 binds is partially buried in the structure of the SARS-CoV-2 spike trimer in the prefusion state, but is exposed when the spike protein binds to ACE2. This observation suggests that 76E1 binds to the epitope at an intermediate state of the spike trimer during the transition from the prefusion to the postfusion state, thereby blocking membrane fusion and viral entry. We hope that the identification of this crucial epitope, which can be recognized by 76E1, will guide epitope-based design of next-generation pan-coronavirus vaccines and antivirals.
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247
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Frutos MC, Origlia J, Gallo Vaulet ML, Venuta ME, García MG, Armitano R, Cipolla L, Madariaga MJ, Cuffini C, Cadario ME. SARS-CoV-2 and Chlamydia pneumoniae co-infection: A review of the literature. Rev Argent Microbiol 2022; 54:247-257. [PMID: 35931565 PMCID: PMC9189145 DOI: 10.1016/j.ram.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/10/2022] [Accepted: 05/02/2022] [Indexed: 01/08/2023] Open
Abstract
Bacterial co-pathogens are commonly identified in viral respiratory infections and are important causes of morbid-mortality. The prevalence of Chlamydia (C.) pneumoniae infection in patients infected with SARS-CoV-2 has not been sufficiently studied. The objective of the present review was to describe the prevalence of C. pneumoniae in patients with coronavirus disease 2019 (COVID-19). A search in MEDLINE and Google Scholar databases for English language literature published between January 2020 and August 2021 was performed. Studies evaluating patients with confirmed COVID-19 and reporting the simultaneous detection of C. pneumoniae were included. Eleven articles were included in the systematic review (5 case cross-sectional studies and 6 retrospective studies). A total of 18 450 patients were included in the eleven studies. The detection of laboratory-confirmed C. pneumoniae infection varied between 1.78 and 71.4% of the total number of co-infections. The median age of patients ranged from 35 to 71 years old and 65% were male. Most of the studies reported one or more pre-existing comorbidities and the majority of the patients presented with fever, cough and dyspnea. Lymphopenia and eosinopenia were described in COVID-19 co-infected patients. The main chest CT scan showed a ground glass density shadow, consolidation and bilateral pneumonia. Most patients received empirical antibiotics. Bacterial co-infection was not associated with increased ICU admission and mortality. Despite frequent prescription of broad-spectrum empirical antimicrobials in patients with coronavirus 2-associated respiratory infections, there is a paucity of data to support the association with respiratory bacterial co-infection. Prospective evidence generation to support the development of an antimicrobial policy and appropriate stewardship interventions specific for the COVID-19 pandemic are urgently required.
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Affiliation(s)
- María Celia Frutos
- Instituto de Virología, Dr. J.M. Vanella, Facultad de Ciencias Médicas - Universidad Nacional de Córdoba, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| | - Javier Origlia
- Cátedra de Patología de Aves y Pilíferos, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Lucia Gallo Vaulet
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Inmunología y Virología Clínica, Argentina
| | - María Elena Venuta
- Servicio de Microbiología, Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Miriam Gabriela García
- Laboratorio de Virología y Biología Molecular, Hospital Interzonal General Agudos Pedro Fiorito, Buenos Aires, Argentina
| | - Rita Armitano
- Departamento de Bacteriología, INEI-ANLIS Dr. Carlos G Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Lucía Cipolla
- Departamento de Bacteriología, INEI-ANLIS Dr. Carlos G Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Julia Madariaga
- Sección Serología y Pruebas Biológicas, Instituto de Zoonosis Luis Pasteur, Ciudad Autónoma de Buenos Aires, Argentina
| | - Cecilia Cuffini
- Instituto de Virología, Dr. J.M. Vanella, Facultad de Ciencias Médicas - Universidad Nacional de Córdoba, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - María Estela Cadario
- Departamento de Bacteriología, INEI-ANLIS Dr. Carlos G Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
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In silico exploration of disulfide derivatives of Ferula foetida oleo-gum (Covexir®) as promising therapeutics against SARS-CoV-2. Comput Biol Med 2022; 146:105566. [PMID: 35598351 PMCID: PMC9112615 DOI: 10.1016/j.compbiomed.2022.105566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 01/17/2023]
Abstract
Although vaccines have been significantly successful against coronavirus, due to the high rate of the Omicron variant spread many researchers are trying to find efficient drugs against COVID-19. Herein, we conducted a computational study to investigate the binding mechanism of four potential inhibitors (including disulfide derivatives isolated from Ferula foetida) to SARS-CoV-2 main protease. Our findings revealed that the disulfides mainly interacted with HIS41, MET49, CYS145, HIS64, MET165, and GLN189 residues of SARS-CoV-2 main protease. The binding free energy decomposition results also showed that the van der Waals (vdW) energy plays the main role in the interaction of HIS41, MET49, CYS145, HIS64, MET165, and GLN189 residues with the inhibitors. Furthermore, it is found that the Z-isomer derivatives have a stronger interaction with SARS-CoV-2, and the strongest interaction belongs to the (Z)-1-(1-(methylthio)propyl)-2-(prop-1-enyl)disulfane (ΔG = -18.672 kcal/mol). The quantum mechanical calculations demonstrated that the second-order perturbation stabilization energy and the electron density values for MET49-ligand interactions are higher than the other residue-ligand complexes. This finding confirms the stronger interaction of this residue with the ligands.
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249
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Pan J, Yan H, Li Z, Lou X, Mao H, Shi W, Yao W, Zhang Y. An external quality assessment for the molecular testing of the SARS-CoV-2 virus genome in Zhejiang Province, China. Diagn Microbiol Infect Dis 2022; 104:115766. [PMID: 36084422 PMCID: PMC9297680 DOI: 10.1016/j.diagmicrobio.2022.115766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/22/2022]
Abstract
The COVID-19 pandemic has necessitated the rapid expansion of laboratories that conduct SARS-CoV-2 tests. A provincial external quality assessment (EQA) scheme on SARS-CoV-2 tests was organized by Zhejiang Provincial CDC to assess the accuracy of the tests in individual CDC municipal and county laboratories in Zhejiang Province, China. Three positive samples in high, medium, and low concentrations, respectively, were prepared using the serial dilutions from the culture with the viral titer concentration of 1×106.3 TCID50/mL, and one negative sample were included. A total of 93 laboratories participated, contributing results from 36 distinct combinations of nucleic acid extraction methods and PCR reagents. There was 100% concordance among all laboratories for all EQA samples, and no false-positive or false-negative results were observed. The EQA survey provides confidence in the identification of infected individuals or asymptomatic populations and assurance for clinical and public health decision-making based on test results.
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250
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Kabay G, DeCastro J, Altay A, Smith K, Lu HW, Capossela AM, Moarefian M, Aran K, Dincer C. Emerging Biosensing Technologies for the Diagnostics of Viral Infectious Diseases. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2201085. [PMID: 35288985 DOI: 10.1002/adma.202201085] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Several viral infectious diseases appear limitless since the beginning of the 21st century, expanding into pandemic lengths. Thus, there are extensive efforts to provide more efficient means of diagnosis, a better understanding of acquired immunity, and improved monitoring of inflammatory biomarkers, as these are all crucial for controlling the spread of infection while aiding in vaccine development and improving patient outcomes. In this regard, various biosensors have been developed recently to streamline pathogen and immune response detection by addressing the limitations of traditional methods, including isothermal amplification-based systems and lateral flow assays. This review explores state-of-the-art biosensors for detecting viral pathogens, serological assays, and inflammatory biomarkers from the material perspective, by discussing their advantages, limitations, and further potential regarding their analytical performance, clinical utility, and point-of-care adaptability. Additionally, next-generation biosensing technologies that offer better sensitivity and selectivity, and easy handling for end-users are highlighted. An emerging example of these next-generation biosensors are those powered by novel synthetic biology tools, such as clustered regularly interspaced short palindromic repeats (CRISPR) with CRISPR-associated proteins (Cas), in combination with integrated point-of-care devices. Lastly, the current challenges are discussed and a roadmap for furthering these advanced biosensing technologies to manage future pandemics is provided.
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Affiliation(s)
- Gözde Kabay
- FIT Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, 79110, Freiburg, Germany
- Department of Microsystems Engineering - IMTEK, University of Freiburg, 79110, Freiburg, Germany
- Institute of Functional Interfaces - IFG, Karlsruhe Institute of Technology, 76344, Karlsruhe, Germany
| | - Jonalyn DeCastro
- The Claremont Colleges, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Alara Altay
- FIT Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, 79110, Freiburg, Germany
- Department of Microsystems Engineering - IMTEK, University of Freiburg, 79110, Freiburg, Germany
| | - Kasey Smith
- The Claremont Colleges, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Hsiang-Wei Lu
- The Claremont Colleges, Keck Graduate Institute, Claremont, CA, 91711, USA
| | | | - Maryam Moarefian
- The Claremont Colleges, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Kiana Aran
- The Claremont Colleges, Keck Graduate Institute, Claremont, CA, 91711, USA
- Cardea Bio Inc., San Diego, CA, 92121, USA
| | - Can Dincer
- FIT Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, 79110, Freiburg, Germany
- Department of Microsystems Engineering - IMTEK, University of Freiburg, 79110, Freiburg, Germany
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