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Shawky AM, Almalki FA, Alzahrani HA, Abdalla AN, Youssif BGM, Ibrahim NA, Gamal M, El-Sherief HAM, Abdel-Fattah MM, Hefny AA, Abdelazeem AH, Gouda AM. Covalent small-molecule inhibitors of SARS-CoV-2 Mpro: Insights into their design, classification, biological activity, and binding interactions. Eur J Med Chem 2024; 277:116704. [PMID: 39121741 DOI: 10.1016/j.ejmech.2024.116704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/10/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024]
Abstract
Since 2020, many compounds have been investigated for their potential use in the treatment of SARS-CoV-2 infection. Among these agents, a huge number of natural products and FDA-approved drugs have been evaluated as potential therapeutics for SARS-CoV-2 using virtual screening and docking studies. However, the identification of the molecular targets involved in viral replication led to the development of rationally designed anti-SARS-CoV-2 agents. Among these targets, the main protease (Mpro) is one of the key enzymes needed in the replication of the virus. The data gleaned from the crystal structures of SARS-CoV-2 Mpro complexes with small-molecule covalent inhibitors has been used in the design and discovery of many highly potent and broad-spectrum Mpro inhibitors. The current review focuses mainly on the covalent type of SARS-CoV-2 Mpro inhibitors. The design, chemistry, and classification of these inhibitors were also in focus. The biological activity of these inhibitors, including their inhibitory activities against Mpro, their antiviral activities, and the SAR studies, were discussed. The review also describes the potential mechanism of the interaction between these inhibitors and the catalytic Cys145 residue in Mpro. Moreover, the binding modes and key binding interactions of these covalent inhibitors were also illustrated. The covalent inhibitors discussed in this review were of diverse chemical nature and origin. Their antiviral activity was mediated mainly by the inhibition of SARS-CoV-2 Mpro, with IC50 values in the micromolar to the nanomolar range. Many of these inhibitors exhibited broad-spectrum inhibitory activity against the Mpro enzymes of other coronaviruses (SARS-CoV-1 and MERS-CoV). The dual inhibition of the Mpro and PLpro enzymes of SARS-CoV-2 could also provide higher therapeutic benefits than Mpro inhibition. Despite the approval of nirmatrelvir by the FDA, many mutations in the Mpro enzyme of SARS-CoV-2 have been reported. Although some of these mutations did not affect the potency of nirmatrelvir, there is an urgent need to develop a second generation of Mpro inhibitors. We hope that the data summarized in this review could help researchers in the design of a new potent generation of SARS-CoV-2 Mpro inhibitors.
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Affiliation(s)
- Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Faisal A Almalki
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Hayat Ali Alzahrani
- Applied Medical Science College, Medical Laboratory Technology Department, Northern Border University, Arar, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia; Department of Pharmacology and Toxicology, Medicinal And Aromatic Plants Research Institute, National Center for Research, Khartoum, 2404, Sudan
| | - Bahaa G M Youssif
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, 71526, Egypt.
| | - Nashwa A Ibrahim
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Mohammed Gamal
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Hany A M El-Sherief
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, Minia, Egypt
| | - Maha M Abdel-Fattah
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Ahmed A Hefny
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt; School of Pharmacy, University of Waterloo, Kitchener, Ontario, N2G 1C5, Canada
| | - Ahmed H Abdelazeem
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt; Pharmacy Department, College of Pharmacy, Nursing and Medical Sciences, Riyadh Elm University, Riyadh, 11681, Saudi Arabia
| | - Ahmed M Gouda
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt.
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2
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Frye C, Cunningham CL, Mihailescu MR. Characterization of the SARS-CoV-2 Genome 3'-Untranslated Region Interactions with Host MicroRNAs. ACS OMEGA 2024; 9:36148-36164. [PMID: 39220490 PMCID: PMC11360049 DOI: 10.1021/acsomega.4c01050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 07/23/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
The 2019 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has marked the spread of a novel human coronavirus. SARS-CoV-2 has exhibited increased disease severity and immune evasion across its variants, and the molecular mechanisms behind these phenomena remain largely unknown. Conserved elements of the viral genome, such as secondary structures within the 3'-untranslated region (UTR), could prove crucial in furthering our understanding of the host-virus interface. Analysis of the SARS-CoV-2 viral genome 3'-UTR revealed the potential for host microRNA (miR) binding sites, allowing for sequence-specific interactions. In this study, we demonstrate that the SARS-CoV-2 genome 3'-UTR binds the host cellular miRs miR-34a-5p, miR-34b-5p, and miR-760-3p in vitro. Native gel electrophoresis and steady-state fluorescence spectroscopy were utilized to biophysically characterize the binding of these miRs to their predicted sites within the SARS-CoV-2 genome 3'-UTR. Additionally, we investigated 2'-fluoro-d-arabinonucleic acid (FANA) analogs as competitive binding inhibitors for these interactions. These miRs modulate the translation of granulin (GRN), interleukin-6 (IL-6), and the IL-6 receptor (IL-6R), all of which are key modulators and activators of JAK/STAT3 signaling and are implicated in regulation of the immune response. Thus, we propose that hijacking of these miRs by SARS-CoV-2 could identify a mechanism of host immune modulation by the virus. The mechanisms detailed in this study have the potential to drive the development of antiviral treatments for SARS-CoV-2, through direct targeting of the virus-host interface.
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Affiliation(s)
- Caleb
J. Frye
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Caylee L. Cunningham
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Mihaela Rita Mihailescu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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3
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Nguyen HT, Falzarano D, Gerdts V, Liu Q. Construction and immunogenicity of SARS-CoV-2 virus-like particle expressed by recombinant baculovirus BacMam. Microbiol Spectr 2024; 12:e0095924. [PMID: 38916311 PMCID: PMC11302303 DOI: 10.1128/spectrum.00959-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/13/2024] [Indexed: 06/26/2024] Open
Abstract
The pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve to give rise to variants of concern that can escape vaccine-induced immunity. As such, more effective vaccines are urgently needed. In this study, we evaluated virus-like particle (VLP) as a vaccine platform for SARS-CoV-2. The spike, envelope, and membrane proteins of the SARS-CoV-2 Wuhan strain were expressed by a single recombinant baculovirus BacMam and assembled into VLPs in cell culture. The morphology and size of the SARS-CoV-2 VLP as shown by transmission electron microscopy were similar to the authentic SARS-CoV-2 virus particle. In a mouse trial, two intramuscular immunizations of the VLP BacMam with no adjuvant elicited spike-specific binding antibodies in both sera and bronchoalveolar lavage fluids. Importantly, BacMam VLP-vaccinated mouse sera showed neutralization activity against SARS-CoV-2 spike pseudotyped lentivirus. Our results indicated that the SARS-CoV-2 VLP BacMam stimulated spike-specific immune responses with neutralization activity. IMPORTANCE Although existing vaccines have significantly mitigated the impact of the COVID-19 pandemic, none of the vaccines can induce sterilizing immunity. The spike protein is the main component of all approved vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) due primarily to its ability to induce neutralizing antibodies. The conformation of the spike protein in the vaccine formulation should be critical for the efficacy of a vaccine. By way of closely resembling the authentic virions, virus-like particles (VLPs) should render the spike protein in its natural conformation. To this end, we utilized the baculovirus vector, BacMam, to express virus-like particles consisting of the spike, membrane, and envelope proteins of SARS-CoV-2. We demonstrated the immunogenicity of our VLP vaccine with neutralizing activity. Our data warrant further evaluation of the virus-like particles as a vaccine candidate in protecting against virus challenges.
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MESH Headings
- Animals
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- Vaccines, Virus-Like Particle/immunology
- Vaccines, Virus-Like Particle/genetics
- Vaccines, Virus-Like Particle/administration & dosage
- Baculoviridae/genetics
- Baculoviridae/immunology
- Mice
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- COVID-19 Vaccines/immunology
- COVID-19 Vaccines/administration & dosage
- COVID-19/prevention & control
- COVID-19/immunology
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- Humans
- Mice, Inbred BALB C
- Female
- Immunogenicity, Vaccine
- Coronavirus Envelope Proteins/immunology
- Coronavirus Envelope Proteins/genetics
- Coronavirus M Proteins
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Affiliation(s)
- Hai Trong Nguyen
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Qiang Liu
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Vaccinology and Immunotherapeutics, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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4
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Vidyasagar GVC, Reddy PVJ, Ghouse MM, Venkateswarulu TC, Kishor PBK, Suravajhala P, Polavarapu R. Designing and expression of novel recombinant fusion protein for efficient antigen screening of SARS-CoV-2. AMB Express 2024; 14:80. [PMID: 38990364 PMCID: PMC11239635 DOI: 10.1186/s13568-024-01719-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 05/08/2024] [Indexed: 07/12/2024] Open
Abstract
Corona virus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), claimed millions globally. After the report of the first incidence of the virus, variants emerged with each posing a unique threat than its predecessors. Though many advanced diagnostic assays like real-time PCR are available for screening of SARS-CoV-2, their applications are being hindered because of accessibility and cost. With the advent of rapid assays for antigenic screening of SARS-CoV-2 made diagnostics far easy as the assays are rapid, cost-effective and can be used at point-of-care settings. In the present study, a fusion construct was made utilising highly immunogenic B cell epitopes from the three important structural proteins of SARS-CoV-2. The protein was expressed; purified capture mAbs generated and rapid antigen assay was developed. Eight hundred and forty nasopharyngeal swab samples were screened for the evaluation of the developed assay which showed 37.14% positivity, 96.51% and 100% sensitivity and specificity respectively. The assay developed was supposed to identify SARS-CoV-2 wild-type as well as variants of concern and variants of importance in real-time conditions.
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Affiliation(s)
- G Vinaya Chandu Vidyasagar
- Genomix CARL Pvt. Ltd, YSR Kadapa, Pulivendula, 516 390, Andhra Pradesh, India
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, 522 213, India
| | - P V Janardhan Reddy
- Genomix CARL Pvt. Ltd, YSR Kadapa, Pulivendula, 516 390, Andhra Pradesh, India
| | - M Md Ghouse
- Genomix CARL Pvt. Ltd, YSR Kadapa, Pulivendula, 516 390, Andhra Pradesh, India
| | - T C Venkateswarulu
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, 522 213, India
| | - P B Kavi Kishor
- Genomix CARL Pvt. Ltd, YSR Kadapa, Pulivendula, 516 390, Andhra Pradesh, India
- Department of Genetics, Osmania University, Hyderabad, 500 007, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Viswa Vidyapeetham, Clappana, 690525, Kerala, India.
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5
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Islam S, Parves MR, Islam MJ, Ali MA, Efaz FM, Hossain MS, Ullah MO, Halim MA. Structural and functional effects of the L84S mutant in the SARS-COV-2 ORF8 dimer based on microsecond molecular dynamics study. J Biomol Struct Dyn 2024; 42:5770-5787. [PMID: 37403295 DOI: 10.1080/07391102.2023.2228919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/17/2023] [Indexed: 07/06/2023]
Abstract
The L84S mutation has been observed frequently in the ORF8 protein of SARS-CoV-2, which is an accessory protein involved in various important functions such as virus propagation, pathogenesis, and evading the immune response. However, the specific effects of this mutation on the dimeric structure of ORF8 and its impacts on interactions with host components and immune responses are not well understood. In this study, we performed one microsecond molecular dynamics (MD) simulation and analyzed the dimeric behavior of the L84S and L84A mutants in comparison to the native protein. The MD simulations revealed that both mutations caused changes in the conformation of the ORF8 dimer, influenced protein folding mechanisms, and affected the overall structural stability. In particular, the 73YIDI76 motif has found to be significantly affected by the L84S mutation, leading to structural flexibility in the region connecting the C-terminal β4 and β5 strands. This flexibility might be responsible for virus immune modulation. The free energy landscape (FEL) and principle component analysis (PCA) have also supported our investigation. Overall, the L84S and L84A mutations affect the ORF8 dimeric interfaces by reducing the frequency of protein-protein interacting residues (Arg52, Lys53, Arg98, Ile104, Arg115, Val117, Asp119, Phe120, and Ile121) in the ORF8 dimer. Our findings provide detail insights for further research in designing structure-based therapeutics against the SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shafiqul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Rimon Parves
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Jahirul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Faiyaz Md Efaz
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Shahadat Hossain
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
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6
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Bai H, Zhang X, Gong T, Ma J, Zhang P, Cai Z, Ren D, Zhang C. A systematic mutation analysis of 13 major SARS-CoV-2 variants. Virus Res 2024; 345:199392. [PMID: 38729218 PMCID: PMC11112362 DOI: 10.1016/j.virusres.2024.199392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 04/22/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
SARS-CoV-2 evolves constantly with various novel mutations. Due to their enhanced infectivity, transmissibility and immune evasion, a comprehensive understanding of the association between these mutations and the respective functional changes is crucial. However, previous mutation studies of major SARS-CoV-2 variants remain limited. Here, we performed systematic analyses of full-length amino acids mutation, phylogenetic features, protein physicochemical properties, molecular dynamics and immune escape as well as pseudotype virus infection assays among thirteen major SARS-CoV-2 variants. We found that Omicron exhibited the most abundant and complex mutation sites, higher indices of hydrophobicity and flexibility than other variants. The results of molecular dynamics simulation suggest that Omicron has the highest number of hydrogen bonds and strongest binding free energy between the S protein and ACE2 receptor. Furthermore, we revealed 10 immune escape sites in 13 major variants, some of them were reported previously, but four of which (i.e. 339/373/477/496) are first reported to be specific to Omicron, whereas 462 is specific to Epslion. The infectivity of these variants was confirmed by the pseudotype virus infection assays. Our findings may help us understand the functional consequences of the mutations within various variants and the underlying mechanisms of the immune escapes conferred by the S proteins.
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Affiliation(s)
- Han Bai
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China
| | - Xuan Zhang
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Tian Gong
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Junpeng Ma
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Peng Zhang
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Zeqiong Cai
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China
| | - Doudou Ren
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China
| | - Chengsheng Zhang
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China; Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China.
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7
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Herrmann L, Breuer J, Duc TN, Thomé N, Ghazaani F, Kamhieh-Milz S, Kamhieh-Milz J, Pfützner A. Comparison of the diagnostic accuracy of the Pluslife Mini Dock RHAM technology with Abbott ID Now and Cepheid GenXpert: A retrospective evaluation study. Sci Rep 2024; 14:13978. [PMID: 38886535 PMCID: PMC11183097 DOI: 10.1038/s41598-024-64406-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
Rapid and sensitive detection of pathogens is critical in interrupting the transmission chain of infectious diseases. Currently, real-time (RT-)PCR represents the gold standard for the detection of SARS-CoV-2. RNase HII-assisted amplification (RHAM) is a promising technology, enabling reliable point-of-care (PoC) testing; however, its diagnostic accuracy has not yet been investigated. The present study compared the Pluslife Mini Dock (RHAM technology), with Abbott ID Now and Cepheid GeneXpert IV. The positive percent agreement (PPA) and negative percent agreement (NPA) were determined in 100 SARS-CoV-2 positive and 210 SARS-CoV-2 negative samples. Further, the reliability of the Pluslife Mini Dock was investigated in different SARS-CoV-2 variants (Delta and Omicron subvariants). The PPA was 99.00% for Pluslife, 100.00% for Abbott ID Now, and 99.00% for Cepheid GeneXpert, with an NPA of 100.00%, 98.90%, and 93.72%, respectively. Abbott ID Now demonstrated the highest rate of invalid results. All SARS-CoV-2 analysed variants were detected by the Pluslife device. Altogether, the Pluslife Mini Dock demonstrated a PPA of 99.16% (235/237) for CT < 36 and an NPA of 100.00% (313/313), respectively. In conclusion, the Pluslife Mini Dock demonstrated better analytical performance than Abbott ID Now and Cepheid GeneXpert IV, representing a highly accurate and rapid PoC alternative to RT-PCR.
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Affiliation(s)
| | - Juliana Breuer
- Lifecare Laboratories, Mainz, Germany
- Pfützner Science and Health Institute, Mainz, Germany
| | - Tuan Ngo Duc
- DHS - Diagnostic HealthCare Solutions, Berlin, Germany
| | - Nicole Thomé
- Lifecare Laboratories, Mainz, Germany
- Pfützner Science and Health Institute, Mainz, Germany
| | | | | | - Julian Kamhieh-Milz
- DHS - Diagnostic HealthCare Solutions, Berlin, Germany.
- Institute of Transfusion Medicine, Charité - Universitätsmedizin Berlin, Robert-Koch Platz 4, 10117, Berlin, Germany.
| | - Andreas Pfützner
- Pfützner Science and Health Institute, Mainz, Germany
- Institute for Internal Medicine and Laboratory Medicine, University for Digital Technologies in Medicine and Dentistry, Wiltz, Luxembourg
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8
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Liu X, Wang Y, Sun L, Xiao G, Hou N, Chen J, Wang W, Xu X, Gu Y. Screening and optimization of shark nanobodies against SARS-CoV-2 spike RBD. Antiviral Res 2024; 226:105898. [PMID: 38692413 DOI: 10.1016/j.antiviral.2024.105898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 03/28/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
SARS-CoV-2 continues to threaten human health, antibody therapy is one way to control the infection. Because new SARS-CoV-2 mutations are constantly emerging, there is an urgent need to develop broadly neutralizing antibodies to block the viral entry into host cells. VNAR from sharks is the smallest natural antigen binding domain, with the advantages of small size, flexible paratopes, good stability, and low manufacturing cost. Here, we used recombinant SARS-CoV-2 Spike-RBD to immunize sharks and constructed a VNAR phage display library. VNAR R1C2, selected from the library, efficiently binds to the RBD domain and blocks the infection of ACE2-positive cells by pseudovirus. Next, homologous bivalent VNARs were constructed through the tandem fusion of two R1C2 units, which enhanced both the affinity and neutralizing activity of R1C2. R1C2 was predicted to bind to a relatively conserved region within the RBD. By introducing mutations at four key binding sites within the CDR3 and HV2 regions of R1C2, the affinity and neutralizing activity of R1C2 were significantly improved. Furthermore, R1C2 also exhibits an effective capacity of binding to the Omicron variants (BA.2 and XBB.1). Together, these results suggest that R1C2 could serve as a valuable candidate for preventing and treating SARS-CoV-2 infections.
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Affiliation(s)
- Xiaochun Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Marine Biomedical Research Institute of Qingdao, Qingdao, 266071, China
| | - Yanqing Wang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Lishan Sun
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Guokai Xiao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Ning Hou
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Jin Chen
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Wei Wang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Ximing Xu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Marine Biomedical Research Institute of Qingdao, Qingdao, 266071, China.
| | - Yuchao Gu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
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9
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Karpuj MV, Shaytov DR, Shemer-Avni Y, Gideon M, Frenkel ZM, Sivan S. Comparative Bioinformatic Analysis Reveals Conserved Regions in SARS-CoV-2 Genome for RAPID Pandemic Response. Int J Mol Sci 2024; 25:5764. [PMID: 38891951 PMCID: PMC11172030 DOI: 10.3390/ijms25115764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 06/21/2024] Open
Abstract
In the face of the SARS-CoV-2 pandemic, characterized by the virus's rapid mutation rates, developing timely and targeted therapeutic and diagnostic interventions presents a significant challenge. This study utilizes bioinformatic analyses to pinpoint conserved genomic regions within SARS-CoV-2, offering a strategic advantage in the fight against this and future pathogens. Our approach has enabled the creation of a diagnostic assay that is not only rapid, reliable, and cost-effective but also possesses a remarkable capacity to detect a wide array of current and prospective variants with unmatched precision. The significance of our findings lies in the demonstration that focusing on these conserved genomic sequences can significantly enhance our preparedness for and response to emerging infectious diseases. By providing a blueprint for the development of versatile diagnostic tools and therapeutics, this research paves the way for a more effective global pandemic response strategy.
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Affiliation(s)
- Marcela Viviana Karpuj
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel 2161002, Israel
| | - D. R. Shaytov
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel 2161002, Israel
| | - Yonat Shemer-Avni
- Laboratory of Clinical Virology, Soroka University Medical Center, Beer-Sheva 84101, Israel
| | - Michael Gideon
- Department of Neurosurgery, Soroka Medical Center, Beer-Sheva 84101, Israel
| | - Zakharia M. Frenkel
- Department of Software Engineering, Braude College of Engineering, Karmiel 2161002, Israel
| | - Sarit Sivan
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel 2161002, Israel
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10
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Zhao Z, Bashiri S, Ziora ZM, Toth I, Skwarczynski M. COVID-19 Variants and Vaccine Development. Viruses 2024; 16:757. [PMID: 38793638 PMCID: PMC11125726 DOI: 10.3390/v16050757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), the global pandemic caused by severe acute respiratory syndrome 2 virus (SARS-CoV-2) infection, has caused millions of infections and fatalities worldwide. Extensive SARS-CoV-2 research has been conducted to develop therapeutic drugs and prophylactic vaccines, and even though some drugs have been approved to treat SARS-CoV-2 infection, treatment efficacy remains limited. Therefore, preventive vaccination has been implemented on a global scale and represents the primary approach to combat the COVID-19 pandemic. Approved vaccines vary in composition, although vaccine design has been based on either the key viral structural (spike) protein or viral components carrying this protein. Therefore, mutations of the virus, particularly mutations in the S protein, severely compromise the effectiveness of current vaccines and the ability to control COVID-19 infection. This review begins by describing the SARS-CoV-2 viral composition, the mechanism of infection, the role of angiotensin-converting enzyme 2, the host defence responses against infection and the most common vaccine designs. Next, this review summarizes the common mutations of SARS-CoV-2 and how these mutations change viral properties, confer immune escape and influence vaccine efficacy. Finally, this review discusses global strategies that have been employed to mitigate the decreases in vaccine efficacy encountered against new variants.
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Affiliation(s)
- Ziyao Zhao
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Sahra Bashiri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
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11
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M L SP, Kumari S, Martinek TA, M ES. De novo design of potential peptide analogs against the main protease of Omicron variant using in silico studies. Phys Chem Chem Phys 2024; 26:14006-14017. [PMID: 38683190 DOI: 10.1039/d4cp01199f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
SARS-CoV-2 and its variants are crossing the immunity barrier induced through vaccination. Recent Omicron sub-variants are highly transmissible and have a low mortality rate. Despite the low severity of Omicron variants, these new variants are known to cause acute post-infectious syndromes. Nowadays, novel strategies to develop new potential inhibitors for SARS-CoV-2 and other Omicron variants have gained prominence. For viral replication and survival the main protease of SARS-CoV-2 plays a vital role. Peptide-like inhibitors that mimic the substrate peptide have already proved to be effective in inhibiting the Mpro of SARS-CoV-2 variants. Our systematic canonical amino acid point mutation analysis on the native peptide has revealed various ways to improve the native peptide of the main protease. Multi mutation analysis has led us to identify and design potent peptide-analog inhibitors that act against the Mpro of the Omicron sub-variants. Our in-depth analysis of all-atom molecular dynamics studies has paved the way to characterize the atomistic behavior of Mpro in Omicron variants. Our goal is to develop potent peptide-analogs that could be therapeutically effective against Omicron and its sub-variants.
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Affiliation(s)
- Stanly Paul M L
- Institute of Pharmaceutical Analysis, University of Szeged, Eotvos u. 6, G-6720 Szeged, Hungary.
| | - Sonia Kumari
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67, S.A.S. Nagar, Mohali 160062, India.
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary.
| | - Elizabeth Sobhia M
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67, S.A.S. Nagar, Mohali 160062, India.
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12
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Kumar DS, Prasanth K, Bhandari A, Kumar Jha V, Naveen A, Prasanna M. Innovations and Challenges in the Development of COVID-19 Vaccines for a Safer Tomorrow. Cureus 2024; 16:e60015. [PMID: 38854201 PMCID: PMC11162516 DOI: 10.7759/cureus.60015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2024] [Indexed: 06/11/2024] Open
Abstract
Vaccination, a historically effective public health intervention, has shielded millions from various diseases. Lessons from severe acute respiratory syndrome coronavirus (SARS-CoV) have improved COVID-19 vaccine development. Despite mRNA vaccines' efficacy, emerging variants pose challenges, exhibiting increased transmissibility, infectivity, and severity. Developing COVID-19 vaccines has faced hurdles due to urgency, limited virus understanding, and the need for safe solutions. Genetic variability necessitates continuous vaccine adjustments and production challenges demand scaling up manufacturing with stringent quality control. This review explores SARS-CoV-2's evolution, upcoming mutations that challenge vaccines, and strategies such as structure-based, T cell-based, respiratory mucosal-based, and nanotechnology approaches for vaccine development. This review insight provides a roadmap for navigating virus evolution and improving vaccine development.
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Affiliation(s)
- Devika S Kumar
- Research, Panimalar Medical College Hospital and Research Institute, Chennai, IND
| | - Krishna Prasanth
- Department of Community Medicine, Sree Balaji Medical College and Hospital, Chennai, IND
| | - Ashni Bhandari
- Department of Community Medicine, Sree Balaji Medical College and Hospital, Chennai, IND
| | - Vivek Kumar Jha
- Department of Audiology and Speech Language Pathology, Shree Guru Gobind Singh Tricentenary (SGT) University, Haryana, IND
| | - Avula Naveen
- Pharmacology and Therapeutics, All India Institute Of Medical Science Bilaspur, Bilaspur, IND
| | - Muthu Prasanna
- Pharmaceutics, Pharmaceutical Biotechnology, Surya School of Pharmacy, Surya Group of Institutions, Villupuram, IND
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13
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Chinnamadhu A, Ramakrishnan J, Suresh S, Poomani K. Binding properties of selective inhibitors of P323L mutated RdRp of SARS-CoV-2: a combined molecular screening, docking and dynamics simulation study. J Biomol Struct Dyn 2024; 42:4283-4296. [PMID: 37301607 DOI: 10.1080/07391102.2023.2219762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
Since 2019 the SARS-CoV-2 and its variants caused COVID-19, such incidents brought the world in pandemic situation. This happened due to furious mutations in SARS-CoV-2, in which some variants had high transmissibility and infective, this led the virus emerged as virulent and worsened the COVID-19 situation. Among the variants, P323L is one of the important mutants of RdRp in SARS-CoV-2. To inhibit the erroneous function of this mutated RdRp, we have screened 943 molecules against the P323L mutated RdRp with the criteria that the molecules with 90% similar to the structure of remdesivir (control drug) resulted nine molecules. Further, these molecules were evaluated by induced fit docking (IFD) identified two molecules (M2 & M4) which are forming strong intermolecular interactions with the key residues of mutated RdRp and has high binding affinity. Docking score of the M2 and M4 molecules with mutated RdRp are -9.24 and -11.87 kcal/mol, respectively. Further, to understand the intermolecular interactions, conformational stability, the molecular dynamics simulation and binding free energy calculations were performed. The binding free energy values of M2 and M4 molecules with the P323L mutated RdRp complexes are -81.60 and -83.07 kcal/mol, respectively. The results of this in silico study confirm that M4 is a potential molecule; hence, it may be considered as the potential inhibitor of P323L mutated RdRp to treat COVID-19 after clinical investigation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Archana Chinnamadhu
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Jaganathan Ramakrishnan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Suganya Suresh
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
| | - Kumaradhas Poomani
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, India
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14
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Zheng Z, Sun H, Hu X, Xuan Z, Fu M, Bai Y, Du Y, Liu B, Sui X, Zheng J, Shao C. Prevention and treatment strategies for kidney transplant recipients in the context of long-term existence of COVID-19. Front Med (Lausanne) 2024; 11:1287836. [PMID: 38633308 PMCID: PMC11021598 DOI: 10.3389/fmed.2024.1287836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
The sudden outbreak of coronavirus disease 2019 (COVID-19) in early 2020 posed a massive threat to human life and caused an economic upheaval worldwide. Kidney transplant recipients (KTRs) became susceptible to infection during the COVID-19 pandemic owing to their use of immunosuppressants, resulting in increased hospitalization and mortality rates. Although the current epidemic situation is alleviated, the long-term existence of COVID-19 still seriously threatens the life and health of KTRs with low immunity. The Omicron variant, a highly infectious but less-pathogenic strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has raised concerns among transplant physicians regarding managing KTRs diagnosed with this variant. However, currently, there are no clear and unified guidelines for caring for KTRs infected with this variant. Therefore, we aimed to summarize the ongoing research on drugs that can treat Omicron variant infections in KTRs and explore the potential of adjusting immunotherapy strategies to enhance their responsiveness to vaccines. Herein, we discuss the situation of KTRs since the emergence of COVID-19 and focus on various prevention and treatment strategies for KTRs since the Omicron variant outbreak. We hope to assist physicians in managing KTRs in the presence of long-term COVID-19 variants.
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Affiliation(s)
- Zeyuan Zheng
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Huimin Sun
- Central Laboratory, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Xiaoyan Hu
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Zuodong Xuan
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Meiling Fu
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yang Bai
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yifan Du
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Bin Liu
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Xiuyuan Sui
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jianzhong Zheng
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Chen Shao
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
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15
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Khalid K, Lim HX, Anwar A, Tan SH, Hwang JS, Ong SK, Poh CL. Preclinical Development of a Novel Epitope-based DNA Vaccine Candidate against SARS-CoV-2 and Evaluation of Immunogenicity in BALB/c Mice. AAPS PharmSciTech 2024; 25:60. [PMID: 38472523 DOI: 10.1208/s12249-024-02778-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
The protective efficacies of current licensed vaccines against COVID-19 have significantly reduced as a result of SARS-CoV-2 variants of concern (VOCs) which carried multiple mutations in the Spike (S) protein. Considering that these vaccines were developed based on the S protein of the original SARS-CoV-2 Wuhan strain, we designed a recombinant plasmid DNA vaccine based on highly conserved and immunogenic B and T cell epitopes against SARS-CoV-2 Wuhan strain and the Omicron VOC. Literature mining and bioinformatics were used to identify 6 immunogenic peptides from conserved regions of the SARS-CoV-2 S and membrane (M) proteins. Nucleotide sequences encoding these peptides representing highly conserved B and T cell epitopes were cloned into a pVAX1 vector to form the pVAX1/S2-6EHGFP recombinant DNA plasmid vaccine. The DNA vaccine was intranasally or intramuscularly administered to BALB/c mice and evaluations of humoral and cellular immune responses were performed. The intramuscular administration of pVAX1/S2-6EHGFP was associated with a significantly higher percentage of CD8+ T cells expressing IFN-γ when compared with the empty vector and PBS controls. Intramuscular or intranasal administrations of pVAX1/S2-6EHGFP resulted in robust IgG antibody responses. Sera from mice intramuscularly immunized with pVAX1/S2-6EHGFP were found to elicit neutralizing antibodies capable of SARS-CoV-2 Omicron variant with the ACE2 cell surface receptor. This study demonstrated that the DNA vaccine construct encoding highly conserved immunogenic B and T cell epitopes was capable of eliciting potent humoral and cellular immune responses in mice.
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Affiliation(s)
- Kanwal Khalid
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Hui Xuan Lim
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
- Sunway Microbiome Centre, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Ayaz Anwar
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Soon Hao Tan
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Jung Shan Hwang
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Seng-Kai Ong
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia.
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16
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Han G, Deng W, Lyu Q, Ma Q, Qiao L. Multiplexed discrimination of SARS-CoV-2 variants via duplex-specific nuclease combined MALDI-TOF MS. Anal Bioanal Chem 2024; 416:1833-1842. [PMID: 38367041 DOI: 10.1007/s00216-024-05202-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/19/2024]
Abstract
The frequent mutations in SARS-CoV-2 significantly increase the virus's pathogenicity and transmissibility while also diminishing the effectiveness of vaccines. Consequently, assays capable of rapidly and simultaneously identifying multiple SARS-CoV-2 variants are essential for large-scale applications that aim to monitor the evolution of the virus. In this work, we propose a method combining duplex-specific nuclease (DSN)-assisted cyclic amplification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) detection, enabling the simultaneous identification of multiple SARS-CoV-2 variants at high-throughput. Due to the high specificity of DSN, single-base mutations can be resolved by the method. With ultra-sensitive detection by MALDI-TOF MS, a limit of detection of 100 pM viral RNA fragment was demonstrated. The assay was used for simultaneous identification and typing of SARS-CoV-2 Alpha, Beta, and Delta variants. The whole assay can be accomplished within 3 h, and the amplification is performed under constant temperature, making the technique simple in operation and efficient. It is also feasible to extend the technique to the detection of many other variants of the virus. We expect that the method can add value to the rapid screening of viral variants and can play an important role in pandemic control.
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Affiliation(s)
- Guobin Han
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China
| | - Wenchan Deng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Qian Lyu
- Bioyong Technologics Inc, Beijing, 100176, China
| | - Qingwei Ma
- Bioyong Technologics Inc, Beijing, 100176, China
| | - Liang Qiao
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China.
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17
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Seo SE, Kim KH, Ha S, Oh H, Kim J, Kim S, Kim L, Seo M, An JE, Park YM, Lee KG, Kim YK, Kim WK, Hong JJ, Song HS, Kwon OS. Synchronous Diagnosis of Respiratory Viruses Variants via Receptonics Based on Modeling Receptor-Ligand Dynamics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2303079. [PMID: 37487578 DOI: 10.1002/adma.202303079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/19/2023] [Indexed: 07/26/2023]
Abstract
The transmission and pathogenesis of highly contagious fatal respiratory viruses are increasing, and the need for an on-site diagnostic platform has arisen as an issue worldwide. Furthermore, as the spread of respiratory viruses continues, different variants have become the dominant circulating strains. To prevent virus transmission, the development of highly sensitive and accurate on-site diagnostic assays is urgently needed. Herein, a facile diagnostic device is presented for multi-detection based on the results of detailed receptor-ligand dynamics simulations for the screening of various viral strains. The novel bioreceptor-treated electronics (receptonics) device consists of a multichannel graphene transistor and cell-entry receptors conjugated to N-heterocyclic carbene (NHC). An ultrasensitive multi-detection performance is achieved without the need for sample pretreatment, which will enable rapid diagnosis and prevent the spread of pathogens. This platform can be applied for the diagnosis of variants of concern in clinical respiratory virus samples and primate models. This multi-screening platform can be used to enhance surveillance and discriminate emerging virus variants before they become a severe threat to public health.
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Affiliation(s)
- Sung Eun Seo
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Kyung Ho Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Siyoung Ha
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, MD, 21853, USA
| | - Hanseul Oh
- College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Jinyeong Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Soomin Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Lina Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Minah Seo
- Sensor System Research Center, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Republic of Korea
| | - Jai Eun An
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yoo Min Park
- Center for NanoBio Development, National NanoFab Center, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Kyoung G Lee
- Center for NanoBio Development, National NanoFab Center, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yu Kyung Kim
- Department of Clinical Pathology, School of Medicine, Kyungpook National University, Daegu, 41944, Republic of Korea
| | - Woo-Keun Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Jung Joo Hong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34141, Republic of Korea
| | - Hyun Seok Song
- Sensor System Research Center, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Oh Seok Kwon
- SKKU Advanced Institute of Nanotechnology (SAINT), Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- Department of Nano Science and Technology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
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18
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Nurrohman DT, Chiu NF. Unraveling the Dynamics of SARS-CoV-2 Mutations: Insights from Surface Plasmon Resonance Biosensor Kinetics. BIOSENSORS 2024; 14:99. [PMID: 38392018 PMCID: PMC10887047 DOI: 10.3390/bios14020099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/08/2024] [Accepted: 02/11/2024] [Indexed: 02/24/2024]
Abstract
Surface Plasmon Resonance (SPR) technology is known to be a powerful tool for studying biomolecular interactions because it offers real-time and label-free multiparameter analysis with high sensitivity. This article summarizes the results that have been obtained from the use of SPR technology in studying the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations. This paper will begin by introducing the working principle of SPR and the kinetic parameters of the sensorgram, which include the association rate constant (ka), dissociation rate constant (kd), equilibrium association constant (KA), and equilibrium dissociation constant (KD). At the end of the paper, we will summarize the kinetic data on the interaction between angiotensin-converting enzyme 2 (ACE2) and SARS-CoV-2 obtained from the results of SPR signal analysis. ACE2 is a material that mediates virus entry. Therefore, understanding the kinetic changes between ACE2 and SARS-CoV-2 caused by the mutation will provide beneficial information for drug discovery, vaccine development, and other therapeutic purposes.
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Affiliation(s)
- Devi Taufiq Nurrohman
- Laboratory of Nano-Photonics and Biosensors, Institute of Electro-Optical Engineering, National Taiwan Normal University, Taipei 11677, Taiwan;
| | - Nan-Fu Chiu
- Laboratory of Nano-Photonics and Biosensors, Institute of Electro-Optical Engineering, National Taiwan Normal University, Taipei 11677, Taiwan;
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
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19
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You C, Jiang S, Ding Y, Ye S, Zou X, Zhang H, Li Z, Chen F, Li Y, Ge X, Guo X. RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages. Virol Sin 2024; 39:156-168. [PMID: 38253258 PMCID: PMC10877444 DOI: 10.1016/j.virs.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for coronavirus disease 2019 (COVID-19), continues to evolve, giving rise to more variants and global reinfections. Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations. In this study, we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples, including human coronaviruses (HCoVs) and SARSr-CoV-2 lineages. Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets, encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages. Through genetic-level species testing, we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2. Subsequently, 75 main and subordinate species-specific barcode segments for SARS-CoV-2, located in ORF1ab, S, E, ORF7a, and N coding sequences, were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores. Post-testing, these segments exhibited high recall rates (nearly 100%), specificity (almost 30% at the nucleotide level), and precision (100%) performance on identification. They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database (http://virusbarcodedatabase.top/). The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis. Moreover, this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.
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Affiliation(s)
- Changqiao You
- College of Biology, Hunan University, Changsha, 410082, China
| | - Shuai Jiang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Yunyun Ding
- College of Biology, Hunan University, Changsha, 410082, China
| | - Shunxing Ye
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Xiaoxiao Zou
- College of Biology, Hunan University, Changsha, 410082, China
| | - Hongming Zhang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Zeqi Li
- College of Biology, Hunan University, Changsha, 410082, China
| | - Fenglin Chen
- College of Biology, Hunan University, Changsha, 410082, China
| | - Yongliang Li
- College of Biology, Hunan University, Changsha, 410082, China.
| | - Xingyi Ge
- College of Biology, Hunan University, Changsha, 410082, China.
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha, 410082, China.
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20
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Zech F, Jung C, Jacob T, Kirchhoff F. Causes and Consequences of Coronavirus Spike Protein Variability. Viruses 2024; 16:177. [PMID: 38399953 PMCID: PMC10892391 DOI: 10.3390/v16020177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Coronaviruses are a large family of enveloped RNA viruses found in numerous animal species. They are well known for their ability to cross species barriers and have been transmitted from bats or intermediate hosts to humans on several occasions. Four of the seven human coronaviruses (hCoVs) are responsible for approximately 20% of common colds (hCoV-229E, -NL63, -OC43, -HKU1). Two others (SARS-CoV-1 and MERS-CoV) cause severe and frequently lethal respiratory syndromes but have only spread to very limited extents in the human population. In contrast the most recent human hCoV, SARS-CoV-2, while exhibiting intermediate pathogenicity, has a profound impact on public health due to its enormous spread. In this review, we discuss which initial features of the SARS-CoV-2 Spike protein and subsequent adaptations to the new human host may have helped this pathogen to cause the COVID-19 pandemic. Our focus is on host forces driving changes in the Spike protein and their consequences for virus infectivity, pathogenicity, immune evasion and resistance to preventive or therapeutic agents. In addition, we briefly address the significance and perspectives of broad-spectrum therapeutics and vaccines.
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Affiliation(s)
- Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Christoph Jung
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; (C.J.); (T.J.)
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; (C.J.); (T.J.)
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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21
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Wang C, Han J, Xue D, Gu C, Zeng S, Jiang J, Jiang T, Li X, Wu K. SERS-active immunoassay kit for SARS-CoV‑2 mediated by the cooperative chemical and electromagnetic effects of MXene modified with gold nanowires. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123445. [PMID: 37757541 DOI: 10.1016/j.saa.2023.123445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/16/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023]
Abstract
Surface-enhanced Raman scattering (SERS) technique with high sensitivity, reliable specificity, and rapid recognition ability exhibits attractive promise for the effective fast-monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein, a novel SERS-active immunoassay kit for SARS-CoV-2 nucleocapsid (N) protein was prepared by in-situ growing gold (Au) nanowire forests (NFs) onto Ti3C2Tx, which was then modified onto polymethyl methacrylate (PMMA) matrix and encapsulated into kit. It was noted that the Au nanowires with fibrous structures which vertically anchored on Ti3C2Tx served as perfect channels to promote photo-induced charge transfer. The synergistic action of electromagnetic and chemical effects resulted in an enhancement factor (EF) of 1.27 × 107. Furthermore, the unreliable fluctuation of the enhanced signal was eliminated by using the intrinsic Raman signal of the flexible PMMA platform, achieving an improved correlation coefficient (R2) value from 0.950 to 0.990. Moreover, the as-designed immunoassay kit with both high sensitivity and remedied quantitative ability rendered by the Ti3C2Tx@Au NFs-PMMA composite exhibited a powerful performance in the practical detection of N-protein with concentration low to 5.0 × 10-8 mg/mL.
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Affiliation(s)
- Chucheng Wang
- School of Materials Science and Chemical Engineering, School of Physical Science and Technology, The Research Institute of Advanced Technology, Ningbo University, Ningbo 315211, Zhejiang, PR China
| | - Junshan Han
- School of Materials Science and Chemical Engineering, School of Physical Science and Technology, The Research Institute of Advanced Technology, Ningbo University, Ningbo 315211, Zhejiang, PR China
| | - Danni Xue
- School of Materials Science and Chemical Engineering, School of Physical Science and Technology, The Research Institute of Advanced Technology, Ningbo University, Ningbo 315211, Zhejiang, PR China
| | - Chenjie Gu
- School of Materials Science and Chemical Engineering, School of Physical Science and Technology, The Research Institute of Advanced Technology, Ningbo University, Ningbo 315211, Zhejiang, PR China
| | - Shuwen Zeng
- XLIM Research Institute, UMR 7252 CNRS/University of Limoges, 87060 Limoges, France
| | - Junhui Jiang
- Translational Research Laboratory for Urology, Department of Urology, The First Affiliated Hospital of Ningbo University, Ningbo University, Ningbo 315010, Zhejiang, PR China
| | - Tao Jiang
- School of Materials Science and Chemical Engineering, School of Physical Science and Technology, The Research Institute of Advanced Technology, Ningbo University, Ningbo 315211, Zhejiang, PR China.
| | - Xing Li
- School of Materials Science and Chemical Engineering, School of Physical Science and Technology, The Research Institute of Advanced Technology, Ningbo University, Ningbo 315211, Zhejiang, PR China.
| | - Kerong Wu
- Translational Research Laboratory for Urology, Department of Urology, The First Affiliated Hospital of Ningbo University, Ningbo University, Ningbo 315010, Zhejiang, PR China.
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22
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Liu Y, Hu B, Li J, Pei X, Hu X. Perspectives and Prospects on the Application of DNA Aptamer in SARS-CoV-2. Curr Med Chem 2024; 31:273-279. [PMID: 37031389 DOI: 10.2174/0929867330666230408193030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/06/2023] [Accepted: 02/22/2023] [Indexed: 04/10/2023]
Affiliation(s)
- Yunyi Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Bei Hu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Juan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Xiaming Pei
- Department of Urology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine. Changsha, Hunan, 410013, China
| | - Xiaoxiao Hu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Molecular Science and Biomedicine Laboratory and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Research Institute of Hunan University in Chongqing, Chongqing, 401120, China
- Shenzhen Research Institute, Hunan University, Shenzhen, 518000, China
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23
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Bateyi Mustafa SH, Kabamba M, Onyango RO. Determinants of parents' intention to vaccinate their children aged 12-17 years against COVID-19 in North Kivu (Democratic Republic of Congo). Hum Vaccin Immunother 2023; 19:2179788. [PMID: 36864602 PMCID: PMC10026875 DOI: 10.1080/21645515.2023.2179788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Abstract
Parents are facing tremendous stress in relation to the COVID-19 pandemic and the effectiveness of the COVID-19 vaccination program for children. We aimed to investigate parents' willingness to vaccinate their children against COVID-19 in North Kivu province, (Democratic Republic of Congo). A cross-sectional survey between 1 December 2021 to 20 January 2022 in six health zones (Goma, Karisimbi, Butembo, Beni, Kamango, and Katwa) was conducted in the province of North Kivu. In each health zone, we selected five clusters (Health area) using the method of probabilistic selection proportional to population size. In total, 522 parents participated in our study. Results: Overall, 32.8% of parents intended to vaccinate their children. In the multivariate analysis, a younger age of parents (aOR: 2.40, CI: [1.50-3.83]), a higher level of fear that "a member of my family" could contract COVID-19 (aOR: 2.35, CI: [1.38-4.02]), a higher level of perceived vulnerability to COVID-19 within the family (aOR: 1.70, CI: [1.005-2.2881]), a higher level of perceived susceptibility to COVID-19 within the family (aOR: 3.07, CI: [1.80-5.23]), and a history of vaccination against COVID-19 among parents (aOR: 16.47, CI: [8.39-32.33]), were all significantly associated with the intention of parents to have their children or adolescents vaccinated. According to the different explanatory factors of the will to have their children vaccinated, an emphasis on the health education of parents who are prone to refusal or hesitation of the vaccine, by addressing the common reasons for the refusal of the vaccine and highlight the vaccine's benefits.
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Affiliation(s)
- Stephane Hans Bateyi Mustafa
- Expanded Program on Immunization, Goma, Democratic Republic of the Congo
- Department of Public Health, Faculty of Health and Community Development, Great Lacs University of Kisumu, Kisumu, Kenya
| | - Michel Kabamba
- Expanded Program on Immunization, Kinshasa, Democratic Republic of the Congo
- Department of Public Health, Faculty of Medicine, University of Kamina, Kamina, Democratic Republic of Congo
| | - Rosebella O Onyango
- Department of Public Health, Faculty of Health and Community Development, Great Lacs University of Kisumu, Kisumu, Kenya
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24
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Liu J, Jaijyan DK, Chen Y, Feng C, Yang S, Xu Z, Zhan N, Hong C, Li S, Cheng T, Zhu H. Cytomegalovirus-vectored COVID-19 vaccines elicit neutralizing antibodies against the SARS-CoV-2 Omicron variant (BA.2) in mice. Microbiol Spectr 2023; 11:e0246323. [PMID: 37971259 PMCID: PMC10883801 DOI: 10.1128/spectrum.02463-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Cytomegalovirus (CMV) has been used as a novel viral vector for vaccine development and gene therapy. Coronavirus disease 2019 is an infectious disease caused by the SARS-CoV-2 virus, which is highly mutable and is still circulating globally. The study showed that the CMV viral vector caused transient systemic infection and induced robust transgene expression in vivo. CMV vectors expressing different SARS-CoV-2 proteins were immunogenic and could elicit neutralizing antibodies against a highly mutated Omicron variant (BA.2). The expression level of receptor-binding domain (RBD) protein was higher than that of full-length S protein using CMV as a vaccine vector, and CMV vector expression RBD protein elicited higher RBD-binding and neutralizing antibodies. Moreover, the study showed that CMV-vectored vaccines would not cause unexpected viral transmission, and pre-existing immunity might impair the immunogenicity of subsequent CMV-vectored vaccines. These works provide meaningful insights for the development of a CMV-based vector vaccine platform and the prevention and control strategies for SARS-CoV-2 infection.
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Affiliation(s)
- Jian Liu
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Dabbu Kumar Jaijyan
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School , Newark, New Jersey, USA
| | - Yanling Chen
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Changcan Feng
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Shaomin Yang
- Shenzhen Municipal Key Laboratory for Pain Medicine, Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital , Shenzhen, Guangdong, China
| | - Zhenglong Xu
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Nichun Zhan
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Congming Hong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University , Xiamen, Fujian, China
| | - Shuxuan Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University , Xiamen, Fujian, China
| | - Tong Cheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University , Xiamen, Fujian, China
| | - Hua Zhu
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School , Newark, New Jersey, USA
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25
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Liu Y, Yang Y, Wang G, Wang D, Shao PL, Tang J, He T, Zheng J, Hu R, Liu Y, Xu Z, Niu D, Lv J, Yang J, Xiao H, Wu S, He S, Tang Z, Liu Y, Tang M, Jiang X, Yuan J, Dai H, Zhang B. Multiplexed discrimination of SARS-CoV-2 variants via plasmonic-enhanced fluorescence in a portable and automated device. Nat Biomed Eng 2023; 7:1636-1648. [PMID: 37735541 DOI: 10.1038/s41551-023-01092-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 08/17/2023] [Indexed: 09/23/2023]
Abstract
Portable assays for the rapid identification of lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to aid large-scale efforts in monitoring the evolution of the virus. Here we report a multiplexed assay in a microarray format for the detection, via isothermal amplification and plasmonic-gold-enhanced near-infrared fluorescence, of variants of SARS-CoV-2. The assay, which has single-nucleotide specificity for variant discrimination, single-RNA-copy sensitivity and does not require RNA extraction, discriminated 12 lineages of SARS-CoV-2 (in three mutational hotspots of the Spike protein) and detected the virus in nasopharyngeal swabs from 1,034 individuals at 98.8% sensitivity and 100% specificity, with 97.6% concordance with genome sequencing in variant discrimination. We also report a compact, portable and fully automated device integrating the entire swab-to-result workflow and amenable to the point-of-care detection of SARS-CoV-2 variants. Portable, rapid, accurate and multiplexed assays for the detection of SARS-CoV-2 variants and lineages may facilitate variant-surveillance efforts.
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Affiliation(s)
- Ying Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Guanghui Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dou Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Pan-Lin Shao
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target and Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiahu Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Tingzhen He
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jintao Zheng
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Ruibin Hu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yiyi Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Ziyi Xu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dan Niu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jiahui Lv
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jingkai Yang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Hongjun Xiao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Shuai Wu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Shuang He
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Zhongrong Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yan Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | | | - Xingyu Jiang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
| | - Jing Yuan
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China.
| | - Hongjie Dai
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Bo Zhang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
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26
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Singh M, Lo SH, Dubey R, Kumar S, Chaubey KK, Kumar S. Plant-Derived Natural Compounds as an Emerging Antiviral in Combating COVID-19. Indian J Microbiol 2023; 63:429-446. [PMID: 38031604 PMCID: PMC10682353 DOI: 10.1007/s12088-023-01121-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a human virus that burst at Wuhan in China and spread quickly over the world, leading to millions of deaths globally. The journey of this deadly virus to different mutant strains is still ongoing. The plethora of drugs and vaccines have been tested to cope up this pandemic. The herbal plants and different spices have received great attention during pandemic, because of their anti-inflammatory, and immunomodulatory properties in treating viruses and their symptoms. Also, it has been shown that nano-formulation of phytochemicals has potential therapeutic effect against COVID-19. Furthermore, the plant derived compound nano-formulation specifically increases its antiviral property by enhancing its bioavailability, solubility, and target-specific delivery system. This review highlights the potentiality of herbal plants and their phytochemical against SARS-CoV-2 utilizing different mechanisms such as blocking the ACE-2 receptors, inhibiting the main proteases, binding spike proteins and reducing the cytokine storms.
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Affiliation(s)
- Mansi Singh
- Department of Pharmacy, Institute of Pharmaceutical Research, GLA University, Mathura, UP 281406 India
| | - Shih-Hsiu Lo
- Department of Urology, Taipei Medical University Hospital, Taipei, Taiwan
| | - Rajni Dubey
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, No. 252, Wuxing Street, Taipei, 11031 Taiwan
| | - Sudhashekhar Kumar
- Department of Physiology, School of Medical Sciences and Research, Sharda University, Greater Noida, UP 201310 India
| | - Kundan Kumar Chaubey
- Division of Research and Innovation, School of Applied and Life Sciences, Uttaranchal University, Arcadia Grant, P.O. Chandanwari, Premnagar, Dehradun, Uttarakhand 248007 India
- School of Basic and Applied Sciences, Sanskriti University, Mathura, UP 281401 India
| | - Sanjay Kumar
- Biological and Bio-Computational Lab, Department of Life Science, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, UP 201310 India
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27
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Zhao JH, Wang YW, Yang J, Tong ZJ, Wu JZ, Wang YB, Wang QX, Li QQ, Yu YC, Leng XJ, Chang L, Xue X, Sun SL, Li HM, Ding N, Duan JA, Li NG, Shi ZH. Natural products as potential lead compounds to develop new antiviral drugs over the past decade. Eur J Med Chem 2023; 260:115726. [PMID: 37597436 DOI: 10.1016/j.ejmech.2023.115726] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/22/2023] [Accepted: 08/13/2023] [Indexed: 08/21/2023]
Abstract
Virus infection has been one of the main causes of human death since the ancient times. Even though more and more antiviral drugs have been approved in clinic, long-term use can easily lead to the emergence of drug resistance and side effects. Fortunately, there are many kinds of metabolites which were produced by plants, marine organisms and microorganisms in nature with rich structural skeletons, and they are natural treasure house for people to find antiviral active substances. Aiming at many types of viruses that had caused serious harm to human health in recent years, this review summarizes the natural products with antiviral activity that had been reported for the first time in the past ten years, we also sort out the source, chemical structure and safety indicators in order to provide potential lead compounds for the research and development of new antiviral drugs.
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Affiliation(s)
- Jing-Han Zhao
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Yue-Wei Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Jin Yang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Zhen-Jiang Tong
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Jia-Zhen Wu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Yi-Bo Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Qing-Xin Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Qing-Qing Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Yan-Cheng Yu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Xue-Jiao Leng
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Liang Chang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Xin Xue
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Shan-Liang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - He-Min Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Ning Ding
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China.
| | - Jin-Ao Duan
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China.
| | - Nian-Guang Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China.
| | - Zhi-Hao Shi
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
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Yánez Arcos DL, Thirumuruganandham SP. Structural and pKa Estimation of the Amphipathic HR1 in SARS-CoV-2: Insights from Constant pH MD, Linear vs. Nonlinear Normal Mode Analysis. Int J Mol Sci 2023; 24:16190. [PMID: 38003380 PMCID: PMC10671649 DOI: 10.3390/ijms242216190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
A comprehensive understanding of molecular interactions and functions is imperative for unraveling the intricacies of viral protein behavior and conformational dynamics during cellular entry. Focusing on the SARS-CoV-2 spike protein (SARS-CoV-2 sp), a Principal Component Analysis (PCA) on a subset comprising 131 A-chain structures in presence of various inhibitors was conducted. Our analyses unveiled a compelling correlation between PCA modes and Anisotropic Network Model (ANM) modes, underscoring the reliability and functional significance of low-frequency modes in adapting to diverse inhibitor binding scenarios. The role of HR1 in viral processing, both linear Normal Mode Analysis (NMA) and Nonlinear NMA were implemented. Linear NMA exhibited substantial inter-structure variability, as evident from a higher Root Mean Square Deviation (RMSD) range (7.30 Å), nonlinear NMA show stability throughout the simulations (RMSD 4.85 Å). Frequency analysis further emphasized that the energy requirements for conformational changes in nonlinear modes are notably lower compared to their linear counterparts. Using simulations of molecular dynamics at constant pH (cpH-MD), we successfully predicted the pKa order of the interconnected residues within the HR1 mutations at lower pH values, suggesting a transition to a post-fusion structure. The pKa determination study illustrates the profound effects of pH variations on protein structure. Key results include pKa values of 9.5179 for lys-921 in the D936H mutant, 9.50 for the D950N mutant, and a slightly higher value of 10.49 for the D936Y variant. To further understand the behavior and physicochemical characteristics of the protein in a biologically relevant setting, we also examine hydrophobic regions in the prefused states of the HR1 protein mutants D950N, D936Y, and D936H in our study. This analysis was conducted to ascertain the hydrophobic moment of the protein within a lipid environment, shedding light on its behavior and physicochemical properties in a biologically relevant context.
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29
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Allahverdiyeva A, Ağaçfidan A, Dogan L, Önel M, Uysal HK, Medetalibeyoğlu A, Şenkal N, Alaskarov E, Meşe S. Evaluation of SARS-CoV-2-Positive Patients with Suspected Reinfection. Viruses 2023; 15:2222. [PMID: 38005899 PMCID: PMC10675471 DOI: 10.3390/v15112222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
The aim of this study was to investigate the reinfection rates and characteristics of SARS-CoV-2 in individuals with SARS-CoV-2 RNA present in their clinical specimens for COVID-19. Our data from the COVID-19 Laboratory of Istanbul University were analyzed for 27,240 cases between 27 March 2020 to 8 February 2022. Demographic characteristics, vaccination statuses, comorbidities, and laboratory findings were evaluated in cases with suspected reinfection, as determined by the presence of SARS-CoV-2 RNA at a rate of 0.3% in clinical specimens. When comparing laboratory values, leukocyte counts were lower in the second and third infections compared with the first infection (p = 0.035), and neutrophil counts were lower in the second infection (p = 0.009). Symptoms varied, with coughing being common in the first infection and malaise being common in subsequent infections. These results suggest that it is important to continue to monitor reinfection rates and develop strategies to prevent reinfection. Our results also suggest that clinicians should be aware of the possibility of reinfection and monitor patients for recurrent symptoms.
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Affiliation(s)
- Aytaj Allahverdiyeva
- Institute of Health Sciences, Istanbul University, Istanbul 34126, Turkey;
- Department of Medical Microbiology, Azerbaijan Medical University, Baku 370022, Azerbaijan
| | - Ali Ağaçfidan
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul 34093, Turkey; (A.A.); (M.Ö.); (H.K.U.)
| | - Lerzan Dogan
- Institute of Health Sciences, Istanbul University, Istanbul 34126, Turkey;
| | - Mustafa Önel
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul 34093, Turkey; (A.A.); (M.Ö.); (H.K.U.)
| | - Hayriye Kırkoyun Uysal
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul 34093, Turkey; (A.A.); (M.Ö.); (H.K.U.)
| | - Alpay Medetalibeyoğlu
- Department of Internal Medicine, Istanbul Faculty of Medicine, Istanbul University, Istanbul 34093, Turkey; (A.M.); (N.Ş.)
| | - Naci Şenkal
- Department of Internal Medicine, Istanbul Faculty of Medicine, Istanbul University, Istanbul 34093, Turkey; (A.M.); (N.Ş.)
| | - Elvin Alaskarov
- Department of Otorhinolaryngology, Istanbul Medipol University, Istanbul 34230, Turkey
| | - Sevim Meşe
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul 34093, Turkey; (A.A.); (M.Ö.); (H.K.U.)
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30
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Treeza M M, Augustine S, Mathew AA, Kanthlal S, Panonummal R. Targeting Viral ORF3a Protein: A New Approach to Mitigate COVID-19 Induced Immune Cell Apoptosis and Associated Respiratory Complications. Adv Pharm Bull 2023; 13:678-687. [PMID: 38022818 PMCID: PMC10676557 DOI: 10.34172/apb.2023.069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/15/2022] [Accepted: 01/20/2023] [Indexed: 12/01/2023] Open
Abstract
Infection with SARS-CoV-2 is a growing concern to the global well-being of the public at present. Different amino acid mutations alter the biological and epidemiological characteristics, as well as immune resistance of SARS-CoV-2. The virus-induced pulmonary impairment and inflammatory cytokine storm are directly related to its clinical manifestations. But, the fundamental mechanisms of inflammatory responses are found to be the reason for the death of immune cells which render the host immune system failure. Apoptosis of immune cells is one of the most common forms of programmed cell death induced by the virus for its survival and virulence property. ORF3a, a SARS-CoV-2 accessory viral protein, induces apoptosis in host cells and suppress the defense mechanism. This suggests, inhibiting SARS-CoV-2 ORF3a protein is a good therapeutic strategy for the treatment in COVID-19 infection by promoting the host immune defense mechanism.
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Affiliation(s)
- Minu Treeza M
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
| | - Sanu Augustine
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
| | | | - S.K. Kanthlal
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
| | - Rajitha Panonummal
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
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31
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Sanchez Jimenez B, Sterling T, Brown A, Modica B, Gibson K, Collins H, Koch C, Schwarz T, Dye KN. Wastewater surveillance in the COVID-19 post-emergency pandemic period: A promising approach to monitor and predict SARS-CoV-2 surges and evolution. Heliyon 2023; 9:e22356. [PMID: 38045160 PMCID: PMC10689941 DOI: 10.1016/j.heliyon.2023.e22356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/17/2023] [Accepted: 11/10/2023] [Indexed: 12/05/2023] Open
Abstract
On May 24, 2023, approximately 3.5 years into the pandemic, the World Health Organization (WHO) declared the end of the COVID-19 global health emergency. However, as there are still ∼3000 COVID-19 deaths per day in May 2023, robust surveillance systems are still warranted to return to normalcy in times of low risk and respond appropriately in times of high risk. The different phases of the pandemic have been defined by infection numbers and variants, both of which have been determined through clinical tests that are subject to many biases. Unfortunately, the end of the COVID-19 emergency threatens to exasperate these biases, thereby warranting alternative tracking methods. We hypothesized that wastewater surveillance could be used as a more accurate and comprehensive method to track SARS-CoV-2 in the post-emergency pandemic period (PEPP). SARS-CoV-2 was quantified and sequenced from wastewater between June 2022 and March 2023 to research the anticipated 2022/23 winter surge. However, in the 2022/23 winter, there was lower-than-expected SARS-CoV-2 circulation, which was hypothesized to be due to diagnostic testing biases but was confirmed by our wastewater analysis, thereby emphasizing the unpredictable nature of SARS-CoV-2 surges while also questioning its winter seasonality. Even in times of low baseline circulation, we found wastewater surveillance to be sensitive enough to detect minor changes in circulation levels ∼30-46 days prior to diagnostic tests, suggesting that wastewater surveillance may be a more appropriate early warning system to prepare for unpredictable surges in the PEPP. Furthermore, sequencing of wastewater detected variants of concern that were positively correlated with clinical samples and also provided a method to identify mutations with a high likelihood of appearing in future variants, necessary for updating vaccines and therapeutics prior to novel variant circulation. Together, these data highlight the effectiveness of wastewater surveillance in the PEPP to limit the global health burden of SARS-CoV-2 due to increases in circulation and/or viral evolution.
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Affiliation(s)
| | - Trinity Sterling
- Department of Health Sciences, Stetson University, DeLand, FL, 32723, USA
| | - Austin Brown
- Department of Health Sciences, Stetson University, DeLand, FL, 32723, USA
| | - Brian Modica
- Department of Health Sciences, Stetson University, DeLand, FL, 32723, USA
| | - Kaylee Gibson
- Department of Health Sciences, Stetson University, DeLand, FL, 32723, USA
| | - Hannah Collins
- Department of Health Sciences, Stetson University, DeLand, FL, 32723, USA
| | - Carolyn Koch
- Department of Health Sciences, Stetson University, DeLand, FL, 32723, USA
| | - Tyler Schwarz
- Department of Health Sciences, Stetson University, DeLand, FL, 32723, USA
| | - Kristine N. Dye
- Department of Health Sciences, Stetson University, DeLand, FL, 32723, USA
- Department of Biology, Stetson University, DeLand, FL, 32723, USA
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32
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Pan B, Fang S, Wang L, Pan Z, Li M, Liu L. Quercetin: A promising drug candidate against the potential SARS-CoV-2-Spike mutants with high viral infectivity. Comput Struct Biotechnol J 2023; 21:5092-5098. [PMID: 37881508 PMCID: PMC10597750 DOI: 10.1016/j.csbj.2023.10.029] [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: 07/06/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023] Open
Abstract
The emergence of SARS-CoV-2-Spike mutants not only enhances viral infectivity but also lead to treatment failure. Gaining a comprehensive understanding of the molecular binding mode between the mutant SARS-CoV-2-Spike and human ACE2 receptor is crucial for therapeutic development against this virus. Building upon our previous predictions and verifications regarding heightened viral infectivity of six potential SARS-CoV-2-Spike mutants, this study aims to further investigate the potential disruption of the interaction between these mutants and ACE2 by quercetin, a Chinese herbal compound. Molecular docking and dynamics simulations results reveal that the binding sites of quercetin particularly enriched around a specific "cavity" at the interface of Spike/ACE2 complex, indicating a favorable region for quercetin to interfere with Spike/ACE2 interaction. Virus infection assay confirms that quercetin not only attenuates wild-type virus infectivity but also suppresses the infectivity of all six tested SARS-CoV-2-Spike mutants. Therefore, quercetin represents a promising therapeutic candidate against both wild-type and potential future variants of SARS-CoV-2 exhibiting high viral infectivity.
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Affiliation(s)
- Boyu Pan
- Department of Molecular Pharmacology, Tianjin Medical University Cancer Institute & Hospital; National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Senbiao Fang
- School of Computer Science and Engineering; Central South University, Changsha 410006, Hunan, China
| | - Liangjiao Wang
- Department of Molecular Pharmacology, Tianjin Medical University Cancer Institute & Hospital; National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Zhanyu Pan
- Department of Integrative Oncology; Tianjin Medical University Cancer Institute and Hospital; Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Min Li
- School of Computer Science and Engineering; Central South University, Changsha 410006, Hunan, China
| | - Liren Liu
- Department of Molecular Pharmacology, Tianjin Medical University Cancer Institute & Hospital; National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
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33
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Jones RP, Ponomarenko A. COVID-19-Related Age Profiles for SARS-CoV-2 Variants in England and Wales and States of the USA (2020 to 2022): Impact on All-Cause Mortality. Infect Dis Rep 2023; 15:600-634. [PMID: 37888139 PMCID: PMC10606787 DOI: 10.3390/idr15050058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 10/28/2023] Open
Abstract
Since 2020, COVID-19 has caused serious mortality around the world. Given the ambiguity in establishing COVID-19 as the direct cause of death, we first investigate the effects of age and sex on all-cause mortality during 2020 and 2021 in England and Wales. Since infectious agents have their own unique age profile for death, we use a 9-year time series and several different methods to adjust single-year-of-age deaths in England and Wales during 2019 (the pre-COVID-19 base year) to a pathogen-neutral single-year-of-age baseline. This adjusted base year is then used to confirm the widely reported higher deaths in males for most ages above 43 in both 2020 and 2021. During 2020 (+COVID-19 but no vaccination), both male and female population-adjusted deaths significantly increased above age 35. A significant reduction in all-cause mortality among both males and females aged 75+ could be demonstrated in 2021 during the widespread COVID-19 vaccination period; however, deaths below age 75 progressively increased. This finding arises from a mix of vaccination coverage and year-of-age profiles of deaths for the different SARS-CoV-2 variants. In addition, specific effects of age around puberty were demonstrated, where females had higher deaths than males. There is evidence that year-of-birth cohorts may also be involved, indicating that immune priming to specific pathogen outbreaks in the past may have led to lower deaths for some birth cohorts. To specifically identify the age profile for the COVID-19 variants from 2020 to 2023, we employ the proportion of total deaths at each age that are potentially due to or 'with' COVID-19. The original Wuhan strain and the Alpha variant show somewhat limited divergence in the age profile, with the Alpha variant shifting to a moderately higher proportion of deaths below age 84. The Delta variant specifically targeted individuals below age 65. The Omicron variants showed a significantly lower proportion of overall mortality, with a markedly higher relative proportion of deaths above age 65, steeply increasing with age to a maximum around 100 years of age. A similar age profile for the variants can be seen in the age-banded deaths in US states, although they are slightly obscured by using age bands rather than single years of age. However, the US data shows that higher male deaths are greatly dependent on age and the COVID variant. Deaths assessed to be 'due to' COVID-19 (as opposed to 'involving' COVID-19) in England and Wales were especially overestimated in 2021 relative to the change in all-cause mortality. This arose as a by-product of an increase in COVID-19 testing capacity in late 2020. Potential structure-function mechanisms for the age-specificity of SARS-CoV-2 variants are discussed, along with potential roles for small noncoding RNAs (miRNAs). Using data from England, it is possible to show that the unvaccinated do indeed have a unique age profile for death from each variant and that vaccination alters the shape of the age profile in a manner dependent on age, sex, and the variant. The question is posed as to whether vaccines based on different variants carry a specific age profile.
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Affiliation(s)
| | - Andrey Ponomarenko
- Department of Biophysics, Informatics and Medical Instrumentation, Odessa National Medical University, Valikhovsky Lane 2, 65082 Odessa, Ukraine
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34
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Tewari D, Miller R, Livengood J, Wang L, Killian ML, Bustamante F, Kessler C, Thirumalapura N, Terio K, Torchetti M, Lantz K, Rosenberg J. SARS-CoV-2 Infection Dynamics in the Pittsburgh Zoo Wild Felids with Two Viral Variants (Delta and Alpha) during the 2021-2022 Pandemic in the United States. Animals (Basel) 2023; 13:3094. [PMID: 37835700 PMCID: PMC10571823 DOI: 10.3390/ani13193094] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/17/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been reported in multiple animal species besides humans. The goal of this study was to report clinical signs, infection progression, virus detection and antibody response in a group of wild felids housed in adjacent but neighboring areas at the Pittsburgh Zoo. Initially, five African lions (Panthera leo krugeri) housed together exhibited respiratory clinical signs with viral shedding in their feces in March of 2021 coinciding with infection of an animal keeper. During the second infection wave in December 2021, four Amur tigers (Panthera tigris altaica) and a Canadian lynx (Lynx canadensis) showed clinical signs and tested positive for viral RNA in feces. In infected animals, viral shedding in feces was variable lasting up to 5 weeks and clinical signs were observed for up to 4 weeks. Despite mounting an antibody response to initial exposure, lions exhibited respiratory clinical signs during the second infection wave, but none shed the virus in their feces. The lions were positive for alpha variant (B.1.1.7 lineage) during the first wave and the tiger and lynx were positive for delta variant (AY.25.1. lineage) during the second wave. The viruses recovered from felids were closely related to variants circulating in human populations at the time of the infection. Cheetahs (Acinonyx jubatus) in the park did not show either the clinical signs or the antibody response.
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Affiliation(s)
- Deepanker Tewari
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Ryan Miller
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Julia Livengood
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Leyi Wang
- Illinois Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA;
| | - Mary Lea Killian
- National Veterinary Services Laboratory, United States Department of Agriculture, Ames, IA 50010, USA; (M.L.K.); (M.T.); (K.L.)
| | - Felipe Bustamante
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Candy Kessler
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Nagaraja Thirumalapura
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA (J.L.); (F.B.); (N.T.)
| | - Karen Terio
- Zoological Pathology Program, University of Illinois, Brookfield, IL 60513, USA;
| | - Mia Torchetti
- National Veterinary Services Laboratory, United States Department of Agriculture, Ames, IA 50010, USA; (M.L.K.); (M.T.); (K.L.)
| | - Kristina Lantz
- National Veterinary Services Laboratory, United States Department of Agriculture, Ames, IA 50010, USA; (M.L.K.); (M.T.); (K.L.)
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Valipour M, Irannejad H, Keyvani H. An Overview on Anti-COVID-19 Drug Achievements and Challenges Ahead. ACS Pharmacol Transl Sci 2023; 6:1248-1265. [PMID: 37705590 PMCID: PMC10496143 DOI: 10.1021/acsptsci.3c00121] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Indexed: 09/15/2023]
Abstract
The appearance of several coronavirus pandemics/epidemics during the last two decades (SARS-CoV-1 in 2002, MERS-CoV in 2012, and SARS-CoV-2 in 2019) indicates that humanity will face increasing challenges from coronaviruses in the future. The emergence of new strains with similar transmission characteristics as SARS-CoV-2 and mortality rates similar to SARS-CoV-1 (∼10% mortality) or MERS-CoV (∼35% mortality) in the future is a terrifying possibility. Therefore, getting enough preparations to face such risks is an inevitable necessity. The present study aims to review the drug achievements and challenges in the fight against SARS-CoV-2 with a combined perspective derived from pharmacology, pharmacotherapy, and medicinal chemistry insights. Appreciating all the efforts made during the past few years, there is strong evidence that the desired results have not yet been achieved and research in this area should still be pursued seriously. By expressing some pessimistic possibilities and concluding that the drug discovery and pharmacotherapy of COVID-19 have not been successful so far, this short essay tries to draw the attention of responsible authorities to be more prepared against future coronavirus epidemics/pandemics.
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Affiliation(s)
- Mehdi Valipour
- Razi
Drug Research Center, Iran University of
Medical Sciences, Tehran 1134845764, Iran
| | - Hamid Irannejad
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari 48157-33971, Iran
| | - Hossein Keyvani
- Department
of Virology, School of Medicine, Iran University
of Medical Sciences, Tehran 1134845764, Iran
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36
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Yu MZ, Wang NN, Zhu JQ, Lin YX. The clinical progress and challenges of mRNA vaccines. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2023; 15:e1894. [PMID: 37096256 DOI: 10.1002/wnan.1894] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 04/26/2023]
Abstract
Owing to the breakthroughs in the prevention and control of the COVID-19 pandemic, messenger RNA (mRNA)-based vaccines have emerged as promising alternatives to conventional vaccine approaches for infectious disease prevention and anticancer treatments. Advantages of mRNA vaccines include flexibility in designing and manipulating antigens of interest, scalability in rapid response to new variants, ability to induce both humoral and cell-mediated immune responses, and ease of industrialization. This review article presents the latest advances and innovations in mRNA-based vaccines and their clinical translations in the prevention and treatment of infectious diseases or cancers. We also highlight various nanoparticle delivery platforms that contribute to their success in clinical translation. Current challenges related to mRNA immunogenicity, stability, and in vivo delivery and the strategies for addressing them are also discussed. Finally, we provide our perspectives on future considerations and opportunities for applying mRNA vaccines to fight against major infectious diseases and cancers. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Biology-Inspired Nanomaterials > Lipid-Based Structures.
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Affiliation(s)
- Meng-Zhen Yu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing, People's Republic of China
- University of Chinese Academy of Sciences (UCAS), Beijing, People's Republic of China
| | - Nan-Nan Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing, People's Republic of China
- University of Chinese Academy of Sciences (UCAS), Beijing, People's Republic of China
| | - Jia-Qing Zhu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing, People's Republic of China
| | - Yao-Xin Lin
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing, People's Republic of China
- University of Chinese Academy of Sciences (UCAS), Beijing, People's Republic of China
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37
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Sun Z, Wang L, Li L, Sun Y, Zhang D, Zhou S, Li Y, Li X, Qiao H, Cui Q, Lan Z, Meng X, Xu J, Geng Y, Dai Y. Structure basis of two nanobodies neutralizing SARS-CoV-2 Omicron variant by targeting ultra-conservative epitopes. J Struct Biol 2023; 215:107996. [PMID: 37419228 DOI: 10.1016/j.jsb.2023.107996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/25/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
The evolving SARS-CoV-2 Omicron strain has repeatedly caused widespread disease epidemics, and effective antibody drugs continue to be in short supply. Here, we identified a batch of nanobodies with high affinity for receptor binding domain (RBD) of SARS-CoV-2 spike protein, separated them into three classes using high performance liquid chromatography (HPLC), and then resolved the crystal structure of the ternary complexes of two non-competing nanobodies (NB1C6 and NB1B5) with RBD using X-ray crystallography. The structures showed that NB1B5 and NB1C6 bind to the left and right flank of the RBD, respectively, and that the binding epitopes are highly conserved cryptic sites in all SARS-CoV-2 mutant strains, as well as that NB1B5 can effectively block the ACE2. These two nanobodies were covalently linked into multivalent and bi-paratopic formats, and have a high affinity and neutralization potency for omicron, potentially inhibiting viral escape. The binding sites of these two nanobodies are relatively conserved, which help guide the structural design of antibodies targeting future variants of SARS-CoV-2 to combat COVID-19 epidemics and pandemics.
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Affiliation(s)
- Zengchao Sun
- Department of Biopharmaceutics, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lu Wang
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lingyun Li
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yili Sun
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
| | - Daizhou Zhang
- Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China
| | - Siyu Zhou
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuying Li
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiyang Li
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Huarui Qiao
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qianqian Cui
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhongyun Lan
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiangjing Meng
- Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China.
| | - Jianfeng Xu
- Department of Biopharmaceutics, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
| | - Yong Geng
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yuanyuan Dai
- Department of Pharmacy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital of Chinese Academy of Medical Sciences Langfang Campus, Langfang, 065001, China.
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Zeng Z, Geng X, Wen X, Chen Y, Zhu Y, Dong Z, Hao L, Wang T, Yang J, Zhang R, Zheng K, Sun Z, Zhang Y. Novel receptor, mutation, vaccine, and establishment of coping mode for SARS-CoV-2: current status and future. Front Microbiol 2023; 14:1232453. [PMID: 37645223 PMCID: PMC10461067 DOI: 10.3389/fmicb.2023.1232453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023] Open
Abstract
Since the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its resultant pneumonia in December 2019, the cumulative number of infected people worldwide has exceeded 670 million, with over 6.8 million deaths. Despite the marketing of multiple series of vaccines and the implementation of strict prevention and control measures in many countries, the spread and prevalence of SARS-CoV-2 have not been completely and effectively controlled. The latest research shows that in addition to angiotensin converting enzyme II (ACE2), dozens of protein molecules, including AXL, can act as host receptors for SARS-CoV-2 infecting human cells, and virus mutation and immune evasion never seem to stop. To sum up, this review summarizes and organizes the latest relevant literature, comprehensively reviews the genome characteristics of SARS-CoV-2 as well as receptor-based pathogenesis (including ACE2 and other new receptors), mutation and immune evasion, vaccine development and other aspects, and proposes a series of prevention and treatment opinions. It is expected to provide a theoretical basis for an in-depth understanding of the pathogenic mechanism of SARS-CoV-2 along with a research basis and new ideas for the diagnosis and classification, of COVID-19-related disease and for drug and vaccine research and development.
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Affiliation(s)
- Zhaomu Zeng
- Department of Neurosurgery, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
- Department of Neurosurgery, Xiangya Hospital Jiangxi Hospital of Central South University, National Regional Medical Center for Nervous System Diseases, Nanchang, China
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Xiuchao Geng
- Department of Nursing, School of Medicine, Taizhou University, Taizhou, China
| | - Xichao Wen
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Yueyue Chen
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
| | - Yixi Zhu
- Department of Pharmacy, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zishu Dong
- Department of Zoology, Advanced Research Institute, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Liangchao Hao
- Department of Plastic Surgery, Shaoxing People’s Hospital, Shaoxing, China
| | - Tingting Wang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Jifeng Yang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Ruobing Zhang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Kebin Zheng
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
| | - Yuhao Zhang
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, China
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Zhu J, Yan H, Shi M, Zhang M, Lu J, Wang J, Chen L, Wang Y, Li L, Miao L, Zhang H. Luteolin inhibits spike protein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) binding to angiotensin-converting enzyme 2. Phytother Res 2023; 37:3508-3521. [PMID: 37166054 DOI: 10.1002/ptr.7826] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a respiratory illness that poses a serious threat to global public health. In an essential step during infection, SARS-CoV-2 uses the receptor-binding domain (RBD) of the spike (S) protein to engage with angiotensin-converting enzyme 2 (ACE2) in host cells. Chinese herbal medicines and their active components exhibit antiviral activity, with luteolin being a flavonoid that can significantly inhibit SARS-CoV infection. However, whether it can block the interaction between the S-protein RBD of SARS-CoV-2 and ACE2 has not yet been elucidated. Here, we investigated the effects of luteolin on the binding of the S-protein RBD to ACE2. By employing a competitive binding assay in vitro, we found that luteolin significantly blocked the binding of S-protein RBD to ACE2 with IC50 values of 0.61 mM, which was confirmed by the neutralized infection with SARS-CoV-2 pseudovirus in vivo. A surface plasmon resonance-based competition assay revealed that luteolin significantly affects the binding of the S-protein RBD to the ACE2 receptor. Molecular docking was performed to predict the binding sites of luteolin to the S-protein RBD-ACE2 complex. The active binding sites were defined based on published literature, and we found that luteolin might interfere with the mixture at residues including LYS353, ASP30, and TYR83 in the cellular ACE2 receptor and GLY496, GLN498, TYR505, LEU455, GLN493, and GLU484 in the S-protein RBD. These residues may together form attractive charges and destroy the stable interaction of S-protein RBD-ACE2. Luteolin also inhibits SARS-CoV-2 spike protein-induced platelet spreading, thereby inhibiting the binding of the spike protein to ACE2. Our results are the first to provide evidence that luteolin is an anti-SARS-CoV-2 agent associated with interference between viral S-protein RBD-ACE2 interactions.
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Affiliation(s)
- Junjie Zhu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Huimin Yan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Mengyao Shi
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Min Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jia Lu
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jiabao Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lu Chen
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yu Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lin Li
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lin Miao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Han Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Kuang Y, Shen W, Ma X, Wang Z, Xu R, Rao Q, Yang S. In silico identification of natural compounds against SARS-CoV-2 main protease from Chinese herbal medicines. Future Sci OA 2023; 9:FSO873. [PMID: 37485448 PMCID: PMC10357396 DOI: 10.2144/fsoa-2023-0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/30/2023] [Indexed: 07/25/2023] Open
Abstract
Aims To determine natural compounds with inhibitory effects toward SARS-CoV-2 Mpro from Chinese herbal medicines. Materials & methods ∼1200 natural compounds from 19 Chinese herbal medicines were collected. Computational methods including molecular docking, drug-likeness assessment, molecular dynamics simulation and molecular mechanics Poisson-Boltzmann surface area analysis were combined to obtain potent inhibitors against SARS-CoV-2 Mpro. Results Top 20 compounds mainly originated from Ranunculus ternatus and Picrasma quassioides exhibited low binding free energies which below -9.0 kcal/mol. Compounds Japonicone G and Picrasidine T were obtained with favorable drug-likeness. Moreover, the complex of Japonicone G and Mpro had prominent stability. Conclusion Natural compound Japonicone G is highly promising as a potent inhibitor against SARS-CoV-2 for further study.
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Affiliation(s)
- Yi Kuang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China
| | - Wenjing Shen
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China
| | - Xiaodong Ma
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China
| | - Ziwei Wang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China
| | - Rui Xu
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China
| | - Qingqing Rao
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China
| | - Shengxiang Yang
- College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China
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Yan L, Wu J, Fan X, Liu J, Zhang L, Hu J, Li X, Su Y, Zhang F, Xu X, Chen X, Yang H. Analysis of risk factors and short-term prognostic factors of arrhythmia in patients infected with mild/moderate SARS-CoV-2 Omicron variant. Front Med (Lausanne) 2023; 10:1186200. [PMID: 37575983 PMCID: PMC10413106 DOI: 10.3389/fmed.2023.1186200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/11/2023] [Indexed: 08/15/2023] Open
Abstract
Background Complications, including arrhythmia, following severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection continue to be of concern. Omicron is the mainstream SARS-CoV-2 mutant circulating in mainland China. At present, there are few epidemiological studies concerning the relationship between arrhythmia and Omicron variant infection in mainland China. Objectives To investigate the risk factors of arrhythmia in patients infected with the SARS-CoV-2 Omicron variant and the factors influencing prognosis. Methods Data from 192 Omicron infected patients with symptoms of arrhythmia (AH group) and 100 Omicron infected patients without arrhythmia (Control group) were collected. Patients in the AH group were divided into the good and poor prognosis groups, according to the follow-up results 4-6 weeks after infection. The general and clinical data between the AH and Control groups, and between the good and poor prognosis groups were compared. The variables with differences between the groups were included in the multivariate logistic regression analysis, and the quantitative variables were analyzed by receiver operating characteristic curve to obtain their cut-off values. Results Compared with the control group, the body mass index (BMI), proportion of patients with a history of arrhythmia, proportion of antibiotics taken, heart rate, moderate disease severity, white blood cell (WBC) count, and the aspartate aminotransferase, creatine kinase (CK), CK isoenzyme (CK-MB), myoglobin (Mb), high-sensitive troponin I (hs-cTnI), lymphocyte ratio and high sensitivity C-reactive protein (hs-CRP) levels in the AH group were significantly higher (p < 0.05). In addition, obesity (BMI ≥24 kg/m2), fast heart rate (≥100 times/min), moderate disease severity, and WBC, CK-MB and hs-cTnI levels were independent risk factors of arrhythmia for patients with Omicron infection (p < 0.05), and hs-CRP was a protective factor (p < 0.05). Compared with the good prognosis group, the age, proportion of patients with a history of arrhythmia, heart rate, proportion of moderate disease severity, and hs-CRP, CK, Mb and hs-cTnI levels were significantly higher in the poor prognosis group, while the proportion of vaccination was lower in the poor prognosis group (p < 0.05). Advanced age (≥65 years old), proportion of history of arrhythmia, moderate disease severity, vaccination, and hs-CRP, Mb and cTnI levels were independent factors for poor prognosis of patients with arrhythmia (p < 0.05). Conclusion The factors that affect arrhythmia and the prognosis of patients infected with Omicron include obesity, high heart rate, severity of the disease, age. history of arrhythmia, WBC, hs-CRP, and myocardial injury indexes, which could be used to evaluate and prevent arrhythmia complications in patients in the future.
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Affiliation(s)
- Lijie Yan
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Fuwai Central China Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jintao Wu
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Fuwai Central China Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xianwei Fan
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Fuwai Central China Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jingjing Liu
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Fuwai Central China Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Leiming Zhang
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Fuwai Central China Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Juan Hu
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Fuwai Central China Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xuejie Li
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Fuwai Central China Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yandong Su
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Fuwai Central China Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Futao Zhang
- Department of Cardiology, Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China
| | - Xizheng Xu
- Department of Cardiology, Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China
| | - Xiaosheng Chen
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Fuwai Central China Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haitao Yang
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Fuwai Central China Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Gul S, Ali A, Sheikh NA, Gul I, Sheikh TS, Prajjwal P. Comparative assessment of SARS CoV2-associated mortalities in 3 COVID waves and related risk factors: The South Kashmir's experience. J Family Med Prim Care 2023; 12:1430-1434. [PMID: 37649761 PMCID: PMC10465047 DOI: 10.4103/jfmpc.jfmpc_2318_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] [Received: 11/27/2022] [Revised: 04/24/2023] [Accepted: 05/25/2023] [Indexed: 09/01/2023] Open
Abstract
Introduction Severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019 (COVID-19) pandemic have spurted in three major waves in India at different times and had different levels of severity in different waves. The objective of our study was to determine the comparative mortality rate in three COVID-19 waves and determine the factors associated with mortality. Methods We identified a cohort of 1,132 COVID-19 patients who were admitted between April 14, 2020 and February 08, 2022 at our center. All the admitted patients with positive COVID-polymerase chain reaction were included in the study. Sample characteristics were determined by screening age, sex, socio-economic status, occupation, symptomatology of COVID, patient status on admission, baseline investigations, comorbidities, medical history, oxygen dosage needed during admission, the span of hospital stay, diagnosis, and vitals such as blood pressure, pulse, and oxygen saturation. All the data were procured from an institutional database. Results In total, 1,132 patients included in the study, the mean age was 65.08 ± 12.29 and 56% were males. The affliction rate was 42.13% in >60 years, 29.5% in 46-60 years, 20.8% in 31-45 years, and 7.4% in 30 years' group. In the first, second, and third waves of COVID-19, the mortality rates were 13.21%, 23.53%, and 11.39%, respectively. Among the comorbidities, mortality rates were proportionately higher in those with hypertension (6.7%), and diabetes (5.5%), than those with chronic obstructive pulmonary disease (3.3%), chronic kidney disease (CKD) (1.5%), heart disease (1.6%), and malignancy (0.2%). Conclusion We identify the peaked mortalities in the second encounter which was predicted by age, comorbidities such as hypertension, and diabetes.
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Affiliation(s)
- Shujat Gul
- Department of Internal Medicine, Maharishi Markandeshwar Institute of Medical Sciences and Research, Mullana, Ambala, Haryana, India
| | - Asifa Ali
- Department of Gynaecology and Obstetrics, Government Medical College, Srinagar, Jammu and Kashmir, India
| | - Nawaz Ahmad Sheikh
- Department of Internal Medicine, Government Medical College, Anantnag, Jammu and Kashmir, India
| | - Irfan Gul
- Department of Internal Medicine, Government Medical College, Anantnag, Jammu and Kashmir, India
| | - Tariq Sultan Sheikh
- Department of Respiratory Medicine, Government Medical College, Anantnag, Jammu and Kashmir, India
| | - Priyadarshi Prajjwal
- Department of Internal Medicine, Bharati Vidyapeeth University Medical College, Pune, Maharashtra, India
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Hammad LF, Almutairi AN, Aldahlawi RH. Effect of infection with severe acute respiratory syndrome coronavirus 2 on the fetus in pregnant women who recovered from infection. Ann Saudi Med 2023; 43:213-218. [PMID: 37554020 DOI: 10.5144/0256-4947.2023.213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND The effect of maternal infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the fetus is unclear, and there is no data from Saudi Arabia. OBJECTIVE Assess the effect of maternal SARS-CoV-2 infection on fetal growth. DESIGN Retrospective case-control SETTING: Tertiary care hospital, Riyadh, Saudi Arabia PATIENTS AND METHODS: We selected pregnant women who underwent an obstetric growth scan and umbilical artery Doppler ultra-sound examination between 28 and 41 weeks of pregnancy. Women with multiple pregnancy, fetal abnormalities, maternal body mass index >30, maternal hypertension, any other chronic diseases that might affect fetal growth or pregnant women suffering from cancer were excluded. Fetal growth parameters assessed included fetal biometry (biparietal diameter, head circumference, abdominal circumference and femur length). We also did an umbilical artery Doppler assessment, which includes the umbilical artery pulsatility index, resistive index and the systolic/diastolic ratio. MAIN OUTCOME MEASURE Fetal biometry and biophysical profile SAMPLE SIZE: 48 SARS-CoV-2; 98 non-SARS-CoV-2 RESULTS: More women who had recovered from SARS-CoV-2 infection had small for gestational age fetuses compared with the control group (P=.001). CONCLUSION Maternal SARS-CoV-2 infection during pregnancy was associated with a higher prevalence of small for gestational age (SGA) fetuses. LIMITATIONS Retrospective, middle cerebral artery and uterine artery Doppler data were not included nor were the effect of tobacco use and socioeconomic status, the relationship between the date of infection with the date of conceiving or the relationship between the severity of infection in the mother and fetal biometry and growth. CONFLICT OF INTEREST None.
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Affiliation(s)
- Lina Fahmi Hammad
- From the Department of Radiological Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ahad Naif Almutairi
- From the Department of Radiological Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Rana Hussain Aldahlawi
- From the Department of Radiological Sciences, King Saud University, Riyadh, Saudi Arabia
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Ksouri A, Klouz A, Bouhaouala-Zahar B, Moussa F, Bezzarga M. Docking-Based Evidence for the Potential of ImmunoDefender: A Novel Formulated Essential Oil Blend Incorporating Synergistic Antiviral Bioactive Compounds as Promising Mpro Inhibitors against SARS-CoV-2. Molecules 2023; 28:molecules28114296. [PMID: 37298772 DOI: 10.3390/molecules28114296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023] Open
Abstract
Essential oils (Eos) have demonstrated antiviral activity, but their toxicity can hinder their use as therapeutic agents. Recently, some essential oil components have been used within safe levels of acceptable daily intake limits without causing toxicity. The "ImmunoDefender," a novel antiviral compound made from a well-known mixture of essential oils, is considered highly effective in treating SARS-CoV-2 infections. The components and doses were chosen based on existing information about their structure and toxicity. Blocking the main protease (Mpro) of SARS-CoV-2 with high affinity and capacity is critical for inhibiting the virus's pathogenesis and transmission. In silico studies were conducted to examine the molecular interactions between the main essential oil components in "ImmunoDefender" and SARS-CoV-2 Mpro. The screening results showed that six key components of ImmunoDefender formed stable complexes with Mpro via its active catalytic site with binding energies ranging from -8.75 to -10.30 kcal/mol, respectively for Cinnamtannin B1, Cinnamtannin B2, Pavetannin C1, Syzyginin B, Procyanidin C1, and Tenuifolin. Furthermore, three essential oil bioactive inhibitors, Cinnamtannin B1, Cinnamtannin B2, and Pavetannin C, had significant ability to bind to the allosteric site of the main protease with binding energies of -11.12, -10.74, and -10.79 kcal/mol; these results suggest that these essential oil bioactive compounds may play a role in preventing the attachment of the translated polyprotein to Mpro, inhibiting the virus's pathogenesis and transmission. These components also had drug-like characteristics similar to approved and effective drugs, suggesting that further pre-clinical and clinical studies are needed to confirm the generated in silico outcomes.
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Affiliation(s)
- Ayoub Ksouri
- Laboratoire des Biomolécules, Venins et Applications Théranostiques, Institut Pasteur de Tunis, Université Tunis El Manar, 13 Place Pasteur, BP74, Tunis 1002, Tunisia
| | - Anis Klouz
- Faculté de Médecine de Tunis, Université Tunis El Manar, 15 Rue Djebel Lakhdhar, La Rabta, Tunis 1007, Tunisia
| | - Balkiss Bouhaouala-Zahar
- Laboratoire des Biomolécules, Venins et Applications Théranostiques, Institut Pasteur de Tunis, Université Tunis El Manar, 13 Place Pasteur, BP74, Tunis 1002, Tunisia
- Faculté de Médecine de Tunis, Université Tunis El Manar, 15 Rue Djebel Lakhdhar, La Rabta, Tunis 1007, Tunisia
| | - Fathi Moussa
- Institute of Physical Chemistry, CNRS-UMR 8000, University Paris-Saclay, Rue Noetzlin, 91190 Gif-sur-Yvette, France
| | - Mounir Bezzarga
- Laboratoire de Modélisation Mathématique, Faculté des Sciences de Tunis, Université Tunis El Manar, Analyse Harmonique et Théorie du Potentiel, Campus Universitaire, Tunis 1068, Tunisia
- Institut Préparatoire aux Etudes d'Ingénieurs de Tunis, Université de Tunis, Tunis 1068, Tunisia
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Sun J, Li Y, Xiao LF, Shao NY, Liu M. Flattening the Curve after the Initial Outbreak of Coronavirus Disease 2019: A Data-Driven Modeling Analysis for the Omicron Pandemic in China. Vaccines (Basel) 2023; 11:vaccines11051009. [PMID: 37243113 DOI: 10.3390/vaccines11051009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/20/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
China is relaxing COVID-19 measures from the "dynamic zero tolerance" (DZT) level. The "flatten-the-curve" (FTC) strategy, which decreases and maintains the low rate of infection to avoid overwhelming the healthcare system by adopting relaxed nonpharmaceutical interventions (NPIs) after the outbreak, has been perceived as the most appropriate and effective method in preventing the spread of the Omicron variant. Hence, we established an improved data-driven model of Omicron transmission based on the age-structured stochastic compartmental susceptible-latent-infectious-removed-susceptible model constructed by Cai to deduce the overall prevention effect throughout China. At the current level of immunity without the application of any NPIs, more than 1.27 billion (including asymptomatic individuals) were infected within 90 days. Moreover, the Omicron outbreak would result in 1.49 million deaths within 180 days. The application of FTC could decrease the number of deaths by 36.91% within 360 days. The strict implementation of FTC policy combined with completed vaccination and drug use, which only resulted in 0.19 million deaths in an age-stratified model, will help end the pandemic within about 240 days. The pandemic would be successfully controlled within a shorter period of time without a high fatality rate; therefore, the FTC policy could be strictly implemented through enhancement of immunity and drug use.
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Affiliation(s)
- Jiaqi Sun
- Department of Mathematics, Faculty of Science and Technology, University of Macau, Taipa, Macau, China
| | - Yusi Li
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Lin-Fan Xiao
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Ning-Yi Shao
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
| | - Miao Liu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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46
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Frye CJ, Cunningham CL, Mihailescu MR. Host microRNA interactions with the SARS-CoV-2 viral genome 3'-untranslated region. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541401. [PMID: 37292986 PMCID: PMC10245713 DOI: 10.1101/2023.05.18.541401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The 2019 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has marked the spread of a novel human coronavirus. While the viral life cycle is well understood, most of the interactions at the virus-host interface remain elusive. Furthermore, the molecular mechanisms behind disease severity and immune evasion are still largely unknown. Conserved elements of the viral genome such as secondary structures within the 5'- and 3'-untranslated regions (UTRs) serve as attractive targets of interest and could prove crucial in furthering our understanding of virus-host interactions. It has been proposed that microRNA (miR) interactions with viral components could be used by both the virus and host for their own benefit. Analysis of the SARS-CoV-2 viral genome 3'-UTR has revealed the potential for host cellular miR binding sites, providing sites for specific interactions with the virus. In this study, we demonstrate that the SARS-CoV-2 genome 3'-UTR binds the host cellular miRNAs miR-760-3p, miR-34a-5p, and miR-34b-5p, which have been shown to influence translation of interleukin-6 (IL-6), the IL-6 receptor (IL-6R), as well as progranulin (PGRN), respectively, proteins that have roles in the host immune response and inflammatory pathways. Furthermore, recent work suggests the potential of miR-34a-5p and miR-34b-5p to target and inhibit translation of viral proteins. Native gel electrophoresis and steady-state fluorescence spectroscopy were utilized to characterize the binding of these miRs to their predicted sites within the SARS-CoV-2 genome 3'-UTR. Additionally, we investigated 2'-fluoro-D-arabinonucleic acid (FANA) analogs of these miRNAs as competitive binding inhibitors for these miR binding interactions. The mechanisms detailed in this study have the potential to drive the development of antiviral treatments for SARS-CoV-2 infection, and provide a potential molecular basis for cytokine release syndrome and immune evasion which could implicate the host-virus interface.
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Affiliation(s)
- Caleb J Frye
- Department of Chemistry & Biochemistry, Duquesne University, Pittsburgh, PA 15282, USA
| | - Caylee L Cunningham
- Department of Chemistry & Biochemistry, Duquesne University, Pittsburgh, PA 15282, USA
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Alsuwairi FA, Alsaleh AN, Alsanea MS, Al-Qahtani AA, Obeid D, Almaghrabi RS, Alahideb BM, AlAbdulkareem MA, Mutabagani MS, Althawadi SI, Altamimi SA, Alshukairi AN, Alhamlan FS. Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves. Microorganisms 2023; 11:1288. [PMID: 37317262 PMCID: PMC10224071 DOI: 10.3390/microorganisms11051288] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/22/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
SARS-CoV-2 genomic mutations outside the spike protein that may increase transmissibility and disease severity have not been well characterized. This study identified mutations in the nucleocapsid protein and their possible association with patient characteristics. We analyzed 695 samples from patients with confirmed COVID-19 in Saudi Arabia between 1 April 2021, and 30 April 2022. Nucleocapsid protein mutations were identified through whole genome sequencing. 𝜒2 tests and t tests assessed associations between mutations and patient characteristics. Logistic regression estimated the risk of intensive care unit (ICU) admission or death. Of the 60 mutations identified, R203K was the most common, followed by G204R, P13L, E31del, R32del, and S33del. These mutations were associated with reduced risk of ICU admission. P13L, E31del, R32del, and S33del were also associated with reduced risk of death. By contrast, D63G, R203M, and D377Y were associated with increased risk of ICU admission. Most mutations were detected in the SR-rich region, which was associated with low risk of death. The C-tail and central linker regions were associated with increased risk of ICU admission, whereas the N-arm region was associated with reduced ICU admission risk. Consequently, mutations in the N protein must be observed, as they may exacerbate viral infection and disease severity. Additional research is needed to validate the mutations' associations with clinical outcomes.
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Affiliation(s)
- Feda A. Alsuwairi
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Asma N. Alsaleh
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Madain S. Alsanea
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Ahmed A. Al-Qahtani
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Dalia Obeid
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- Public Health Laboratories, Public Health Authority, Riyadh 13351, Saudi Arabia
| | - Reem S. Almaghrabi
- Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Basma M. Alahideb
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Maha A. AlAbdulkareem
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Maysoon S. Mutabagani
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Sahar I. Althawadi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Sara A. Altamimi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Abeer N. Alshukairi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah 23433, Saudi Arabia
| | - Fatimah S. Alhamlan
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
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Costanzo M, De Giglio MAR, Roviello GN. Deciphering the Relationship between SARS-CoV-2 and Cancer. Int J Mol Sci 2023; 24:ijms24097803. [PMID: 37175509 PMCID: PMC10178366 DOI: 10.3390/ijms24097803] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Some viruses are known to be associated with the onset of specific cancers. These microorganisms, oncogenic viruses or oncoviruses, can convert normal cells into cancer cells by modulating the central metabolic pathways or hampering genomic integrity mechanisms, consequently inhibiting the apoptotic machinery and/or enhancing cell proliferation. Seven oncogenic viruses are known to promote tumorigenesis in humans: human papillomavirus (HPV), hepatitis B and C viruses (HBV, HCV), Epstein-Barr virus (EBV), human T-cell leukemia virus 1 (HTLV-1), Kaposi sarcoma-associated herpesvirus (KSHV), and Merkel cell polyomavirus (MCPyV). Recent research indicates that SARS-CoV-2 infection and COVID-19 progression may predispose recovered patients to cancer onset and accelerate cancer development. This hypothesis is based on the growing evidence regarding the ability of SARS-CoV-2 to modulate oncogenic pathways, promoting chronic low-grade inflammation and causing tissue damage. Herein, we summarize the main relationships known to date between virus infection and cancer, providing a summary of the proposed biochemical mechanisms behind the cellular transformation. Mechanistically, DNA viruses (such as HPV, HBV, EBV, and MCPyV) encode their virus oncogenes. In contrast, RNA viruses (like HCV, HTLV-1) may encode oncogenes or trigger host oncogenes through cis-/-trans activation leading to different types of cancer. As for SARS-CoV-2, its role as an oncogenic virus seems to occur through the inhibition of oncosuppressors or controlling the metabolic and autophagy pathways in the infected cells. However, these effects could be significant in particular scenarios like those linked to severe COVID-19 or long COVID. On the other hand, looking at the SARS-CoV-2─cancer relationship from an opposite perspective, oncolytic effects and anti-tumor immune response were triggered by SARS-CoV-2 infection in some cases. In summary, our work aims to recall comprehensive attention from the scientific community to elucidate the effects of SARS-CoV-2 and, more in general, β-coronavirus infection on cancer susceptibility for cancer prevention or supporting therapeutic approaches.
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Affiliation(s)
- Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore s.c.ar.l., Via G. Salvatore 486, 80145 Naples, Italy
| | | | - Giovanni Nicola Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Via P. Castellino 111, 80131 Naples, Italy
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Tworek A, Jaroń K, Cicha M, Rydzewski A, Wierzba W, Zaczyński A, Król Z, Rydzewska G. The persistence of SARS-CoV-2 neutralizing antibodies after COVID-19: A one-year observation. Is a SARS-CoV-2 vaccination booster dose necessary? Cent Eur J Immunol 2023; 48:92-96. [PMID: 37692027 PMCID: PMC10485689 DOI: 10.5114/ceji.2023.126206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 02/27/2023] [Indexed: 09/12/2023] Open
Abstract
Introduction The aim of this study was to investigate the persistence of SARS-CoV-2 neutralizing antibodies (NAbs) one year after contracting COVID-19. Material and methods The study included 38 patients - 34 men and 4 women - suffering from COVID-19 between March 15 and May 26, 2020. The median age in the group was 31 years, ranging from 22 to 67 years. The levels of neutralizing antibodies were measured at three time-points - baseline, 6 months, and 12 months. The primary endpoint was a post-infection positive result for NAbs (> 15 AU/ml; Liaison SARS-CoV-2 S1/S2 IgG quantitative test) 12 months after infection. Results The median level of NAbs after 12 months was 26.5 AU/ml. At the end of observation (12 months), 21 of the 38 patients had a NAb level of >15 AU/ml (positive). The median antibody half-life was 5.8 months. Conclusions A high percentage of the patients maintained positive levels of antibodies 6 and 12 months after COVID-19 infection. The dynamics of the antibody level decline suggests the need for booster vaccination at least once a year.
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Affiliation(s)
- Adam Tworek
- Clinical Department of Internal Medicine and Gastroenterology with Inflammatory Bowel Disease Unit, Central Clinical Hospital of the Ministry of the Interior and Administration, Warsaw, Poland
| | - Krzysztof Jaroń
- Clinical Department of Internal Medicine and Gastroenterology with Inflammatory Bowel Disease Unit, Central Clinical Hospital of the Ministry of the Interior and Administration, Warsaw, Poland
| | - Małgorzata Cicha
- Diagnostic Laboratory of Central Clinical Hospital of the Ministry of the Interior and Administration, Warsaw, Poland
| | - Andrzej Rydzewski
- Department of Internal Medicine, Nephrology and Transplantation Medicine, Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
- Department of Internal Medicine, Nephrology and Transplantation Medicine, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Waldemar Wierzba
- Central Clinical Hospital of the Ministry of the Interior and Administration, Warsaw, Poland
- University of Humanities and Economics in Łódz, Satellite Campus in Warsaw, Warsaw, Poland
| | - Artur Zaczyński
- Central Clinical Hospital of the Ministry of the Interior and Administration, Warsaw, Poland
| | - Zbigniew Król
- Central Clinical Hospital of the Ministry of the Interior and Administration, Warsaw, Poland
| | - Grażyna Rydzewska
- Clinical Department of Internal Medicine and Gastroenterology with Inflammatory Bowel Disease Unit, Central Clinical Hospital of the Ministry of the Interior and Administration, Warsaw, Poland
- Collegium Medicum, Jan Kochanowski University, Kielce, Poland
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50
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Broni E, Miller WA. Computational Analysis Predicts Correlations among Amino Acids in SARS-CoV-2 Proteomes. Biomedicines 2023; 11:512. [PMID: 36831052 PMCID: PMC9953644 DOI: 10.3390/biomedicines11020512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious global challenge requiring urgent and permanent therapeutic solutions. These solutions can only be engineered if the patterns and rate of mutations of the virus can be elucidated. Predicting mutations and the structure of proteins based on these mutations have become necessary for early drug and vaccine design purposes in anticipation of future viral mutations. The amino acid composition (AAC) of proteomes and individual viral proteins provide avenues for exploitation since AACs have been previously used to predict structure, shape and evolutionary rates. Herein, the frequency of amino acid residues found in 1637 complete proteomes belonging to 11 SARS-CoV-2 variants/lineages were analyzed. Leucine is the most abundant amino acid residue in the SARS-CoV-2 with an average AAC of 9.658% while tryptophan had the least abundance of 1.11%. The AAC and ranking of lysine and glycine varied in the proteome. For some variants, glycine had higher frequency and AAC than lysine and vice versa in other variants. Tryptophan was also observed to be the most intolerant to mutation in the various proteomes for the variants used. A correlogram revealed a very strong correlation of 0.999992 between B.1.525 (Eta) and B.1.526 (Iota) variants. Furthermore, isoleucine and threonine were observed to have a very strong negative correlation of -0.912, while cysteine and isoleucine had a very strong positive correlation of 0.835 at p < 0.001. Shapiro-Wilk normality test revealed that AAC values for all the amino acid residues except methionine showed no evidence of non-normality at p < 0.05. Thus, AACs of SARS-CoV-2 variants can be predicted using probability and z-scores. AACs may be beneficial in classifying viral strains, predicting viral disease types, members of protein families, protein interactions and for diagnostic purposes. They may also be used as a feature along with other crucial factors in machine-learning based algorithms to predict viral mutations. These mutation-predicting algorithms may help in developing effective therapeutics and vaccines for SARS-CoV-2.
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Affiliation(s)
- Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
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