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Olorunfemi AB, Suliman SA, Tran TT, Ayorinde B, Fowora MA, Iwalokun BA, Olowe OA, Opaleye OO, Osman M, Salako BL, Adegbola R, Thomas BN, Pallerla SR, Velavan TP, Ojurongbe O. Whole genome sequencing and phylogenetic analysis of SARS-CoV-2 strains isolated during the COVID-19 pandemic in Nigeria. IJID REGIONS 2024; 10:174-178. [PMID: 38322246 PMCID: PMC10845906 DOI: 10.1016/j.ijregi.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
Objectives The emergence and spread of SARS-CoV-2 have stimulated ongoing research into the virus transmission dynamics, circulating variants, and potential mutations. This study was conducted to understand the genomic dynamics of the epidemic in Nigeria. Design Whole genome sequencing was conducted on SARS-CoV-2 samples collected during the first and second outbreaks using the Oxford Nanopore MinION sequencing platform. Phylogenetic analysis was conducted, and genomes were grouped into different pangolin lineages. Results The study revealed four circulating SARS-CoV-2 variants. The Alpha (B.1.1.7) variant was the most prevalent (32.7%), followed by Beta (B.1 B.1.1, L.3, and B.1.1.318) (30.8%), Eta (B.1.525) (28.9%), and Delta (B.1.617, AY.1, AY.109, and AY.36) (7.7%). Phylogenetic analysis revealed three clusters with four Nextstrain clades (20I, 20B, 21D, and 21J). The Alpha lineages (B.1.1.7) clustered with references from Italy. The Beta lineages (Clade 20B) (B.11, B.11318, and L3) and sub-lineage B.11 were distinct. Sub-lineage B.11318 is clustered with references from the USA, whereas sub-lineage L3 is clustered with references from Russia, the Philippines, Australia, and Japan. The 21D and 21J, belonging to two Pango lineages, Eta (B.1525) and Delta (B.1.617 and AY.109), showed high genetic similarity. Conclusion The phylogenetic relatedness of the lineages suggests multiple virus introduction, which could be a source of more virulent, locally adapted variants.
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Affiliation(s)
- Adedolapo B. Olorunfemi
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | | | - Tung T. Tran
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
| | - Babatunde Ayorinde
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Muinah A. Fowora
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Bamidele A. Iwalokun
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Olugbenga A. Olowe
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Oluyinka O. Opaleye
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Mohamed Osman
- Institute of Endemic Diseases, University of Khartoum, Sudan
- York Biomedical Research Institute, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Babatunde L. Salako
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Richard Adegbola
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Bolaji N. Thomas
- Department of Biomedical Sciences, College of Health Sciences and Technology, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Srinivas Reddy Pallerla
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Universität Tübingen, Germany
| | - Thirumalaisamy P. Velavan
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Universität Tübingen, Germany
| | - Olusola Ojurongbe
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
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Lin J, Anjum Huma F, Irfan A, Ali SS, Waheed Y, Mohammad A, Munir M, Khan A, Wei DQ. Structural plasticity of omicron BA.5 and BA.2.75 for enhanced ACE-dependent entry into cells. J Biomol Struct Dyn 2023; 41:10762-10773. [PMID: 36541923 DOI: 10.1080/07391102.2022.2158944] [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: 10/31/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
The current study investigated the binding variations among the wilt type, Omicron sub-variants BA.2.75 and BA.5, using protein-protein docking, protein structural graphs (P SG), and molecular simulation methods. HADDOCK predicted docking scores and dissociation constant (KD) revealed tighter binding of these sub-variants in contrast to the WT. Further investigation revealed variations in the hub residues, protein sub-networks, and GlobalMetapath in these variants as compared to the WT. A very unusual dynamic for BA.2.75 and BA.5 was observed, and secondary structure transition can also be witnessed in the loops (44-505). The results show that the flexibility of these three loops is increased by the mutations as an allosteric effect and thus enhances the chances of bonding with the nearby residues to connect and form a stable connection. Furthermore, the additional hydrogen bonding contacts steer the robust binding of these variants in contrast to the wild type. The total binding free energy for the wild type was calculated to be -61.38 kcal/mol, while for BA.2.75 and BA.5 variants the T BE was calculated to be -70.42 kcal/mol and 69.78 kcal/mol, respectively. We observed that the binding of BA.2.75 is steered by the electrostatic interactions while the BA.5 additional contacts are due to the vdW (Van der Waal) energy. From these findings, it can be observed the Spike (S) protein is undergoing structural adjustments to bind efficiently to the hACE2 (human angiotensin-converting enzyme 2) receptor and, in turn, increase entry to the host cells. The current study will aid the development of structure-based drugs against these variants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Junqi Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | | | - Aiza Irfan
- Rawalpindi Medical University, Punjab, Pakistan
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Yasir Waheed
- Office of Research, Innovation & Commercialization, Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, Pakistan
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, P.R. China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, P.R. China
- Peng Cheng Laboratory, Nashan District, Shenzhen, Guangdong, P.R China
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3
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Karkashan A, Attar R. Computational screening of natural products to identify potential inhibitors for human neuropilin-1 (NRP1) receptor to abrogate the binding of SARS-CoV-2 and host cell. J Biomol Struct Dyn 2023; 41:9987-9996. [PMID: 36437796 DOI: 10.1080/07391102.2022.2150685] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/17/2022] [Indexed: 11/29/2022]
Abstract
Recently, a new variant B.1.1.529 or Omicron variant and its sub-variants (BA2.75, BA.5) of SARS-CoV-2 (Severe acute respiratory virus 2) have been reported with a larger number of mutations in the spike protein and particularly in the RBD (receptor-binding domain). The omicron (B.1.1.529) variant has aggravated the pandemic situation further and needs more analysis for therapeutic development. Keeping in view the urgency of the required data, the current study used molecular modeling and simulation-based methods to target the NRP1 (Neuropilin 1) protein to halt the entry into the host cell. Employing a molecular screening approach to screen the North-East African natural compounds database (NEANCDB) revealed Subereamine B with a docking score of -8.44 kcal/mol, Zinolol with the docking score of -8.05 while Subereamine A with a docking score of -7.88 kcal/mol as the best hits against NRP1. Molecular simulation-based further validation revealed stable dynamics, good structural packing, and dynamic residues flexibility index. Moreover, hydrogen bonding fraction analysis demonstrated the interactions remained sustained during the simulation. Furthermore, the total binding free energy for Subereamine B was -44.24 ±0.91 kcal/mol, for Zinolol -34.32 ±0.40 kcal/mol while for Subereamine A the TBE was calculated to be -41.78 ± 0.36 kcal/mol respectively. This shows that the two arginine-based alkaloids, i.e. Subereamine B and Subereamine A could inhibit the NRP1 more strongly than Zinolol. In conclusion, this study provides a basis for the development of novel drugs against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alaa Karkashan
- Department of Biology, College of Sciences, University of Jeddah, Jeddah, Saudi Arabia
| | - Roba Attar
- Department of Biology, College of Sciences, University of Jeddah, Jeddah, Saudi Arabia
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Mathenge V, Onuekwe C, Nass S, Akim C, Msunyaro E, Mfinanga E, Mambo WP, Mwabulambo SG, Manozas S, Kayera D, Tinuga F, Tegegne S, Mwengee W, Atuhebwe P, Zabulon Y. Strategies to improve COVID-19 vaccination coverage in Manyara region, Tanzania, July to September 2022: best practices and lessons learned. Pan Afr Med J 2023; 45:3. [PMID: 37538365 PMCID: PMC10395112 DOI: 10.11604/pamj.supp.2023.45.1.39608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/24/2023] [Indexed: 08/05/2023] Open
Affiliation(s)
- Violet Mathenge
- World Health Organization, Tanzania Country Office, Dar es Salaam, Tanzania
| | - Chima Onuekwe
- World Health Organization, Tanzania Country Office, Dar es Salaam, Tanzania
- World Health Organization, Inter-Country Support Team - East and Southern Africa, Harare, Zimbabwe
| | - Shafique Nass
- World Health Organization, Inter-Country Support Team - East and Southern Africa, Harare, Zimbabwe
| | - Caroline Akim
- World Health Organization, Tanzania Country Office, Dar es Salaam, Tanzania
| | - Erick Msunyaro
- Health Promotion Section, Ministry of Health, Dodoma, Tanzania
| | | | | | | | - Suleiman Manozas
- Office of the Regional Commissioner, Manyara Region, Babati, Tanzania
| | - Damas Kayera
- Office of the Regional Commissioner, Manyara Region, Babati, Tanzania
| | - Florian Tinuga
- World Health Organization, Regional Office for Africa, Brazzaville, Congo
| | - Sisay Tegegne
- World Health Organization, Tanzania Country Office, Dar es Salaam, Tanzania
| | - William Mwengee
- World Health Organization, Tanzania Country Office, Dar es Salaam, Tanzania
| | - Phionah Atuhebwe
- World Health Organization, Regional Office for Africa, Brazzaville, Congo
| | - Yoti Zabulon
- World Health Organization, Tanzania Country Office, Dar es Salaam, Tanzania
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5
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Duette G, Lee E, Martins Costa Gomes G, Tungatt K, Doyle C, Stylianou VV, Lee A, Maddocks S, Taylor J, Khanna R, Bull RA, Martinello M, Sandgren KJ, Cunningham AL, Palmer S. Highly Networked SARS-CoV-2 Peptides Elicit T Cell Responses with Enhanced Specificity. Immunohorizons 2023; 7:508-527. [PMID: 37358499 PMCID: PMC10580120 DOI: 10.4049/immunohorizons.2300034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/27/2023] Open
Abstract
Identifying SARS-CoV-2-specific T cell epitope-derived peptides is critical for the development of effective vaccines and measuring the duration of specific SARS-CoV-2 cellular immunity. In this regard, we previously identified T cell epitope-derived peptides within topologically and structurally essential regions of SARS-CoV-2 spike and nucleocapsid proteins by applying an immunoinformatics pipeline. In this study, we selected 30 spike- and nucleocapsid-derived peptides and assessed whether these peptides induce T cell responses and avoid major mutations found in SARS-CoV-2 variants of concern. Our peptide pool was highly specific, with only a single peptide driving cross-reactivity in people unexposed to SARS-COV-2, and immunogenic, inducing a polyfunctional response in CD4+ and CD8+ T cells from COVID-19 recovered individuals. All peptides were immunogenic and individuals recognized broad and diverse peptide repertoires. Moreover, our peptides avoided most mutations/deletions associated with all four SARS-CoV-2 variants of concern while retaining their physicochemical properties even when genetic changes are introduced. This study contributes to an evolving definition of individual CD4+ and CD8+ T cell epitopes that can be used for specific diagnostic tools for SARS-CoV-2 T cell responses and is relevant to the development of variant-resistant and durable T cell-stimulating vaccines.
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Affiliation(s)
- Gabriel Duette
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Eunok Lee
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Katie Tungatt
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Chloe Doyle
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Vicki V. Stylianou
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Ashley Lee
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Susan Maddocks
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Janette Taylor
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Rajiv Khanna
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Rowena A. Bull
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, New South Wales, Australia
- The Kirby Institute, UNSW Australia, Sydney, New South Wales, Australia
| | - Marianne Martinello
- The Kirby Institute, UNSW Australia, Sydney, New South Wales, Australia
- Westmead Hospital, Sydney, New South Wales, Australia
- Blacktown & Mount Druitt Hospital, Blacktown, New South Wales, Australia
| | - Kerrie J. Sandgren
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Anthony L. Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
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Nasergivehchi S, Togha M, Jafari E, Sheikhvatan M, Shahamati D. Headache following vaccination against COVID-19 among healthcare workers with a history of COVID-19 infection: a cross-sectional study in Iran with a meta-analytic review of the literature. Head Face Med 2023; 19:19. [PMID: 37202794 DOI: 10.1186/s13005-023-00363-4] [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: 01/29/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND There is evidence of the occurrence of headache after vaccination against COVID-19. However, only a few studies have examined the headache characteristics and related determinants, especially among healthcare workers with a history of COVID-19 infection. METHODS We evaluated the incidence of headaches after injection of different types of COVID-19 vaccine to determine factors relating to the incidence of headache after vaccination among the Iranian healthcare workers who had previously contracted COVID-19. A group of 334 healthcare workers with a history of COVID-19 infection were included and vaccinated (at least one month after recovery without any COVID-19 related symptoms) with different COVID-19 vaccines. The baseline information, headache characteristics and vaccine specifications were recorded. RESULTS Overall, 39.2% reported experiencing a post-vaccination headache. Of those with a previous history of headache, 51.1% reported migraine-type, 27.4% tension-type and 21.5% other types. The mean time between vaccination and headache appearance was 26.78 ± 6.93 h, with the headache appearing less than 24 h after vaccination in most patients (83.2%). The headaches reached its peak within 8.62 ± 2.41 h. Most patients reported a compression-type headache. The prevalence of post-vaccination headaches was significantly different according to the type of vaccine used. The highest rates were reported for AstraZeneca, followed by Sputnik V. In regression analysis, the vaccine brand, female gender and initial COVID-19 severity were the main determinants for predicting post-vaccination headache. CONCLUSION Participants commonly experienced a headache following vaccination against COVID-19. Our study results indicated that this was slightly more common in females and in those with a history of severe COVID-19 infection.
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Affiliation(s)
- Somayeh Nasergivehchi
- Department of Headache, Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
- Department of Neurology, Baharloo University Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mansoureh Togha
- Department of Headache, Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran.
- Department of Headache, Neurology Ward, School of Medicine, Sina University Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - Elham Jafari
- Department of Headache, Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Sheikhvatan
- Tehran University of Medical Sciences, Tehran, Iran
- Heidelberg University Hospital, Heidelberg, Germany
| | - Donya Shahamati
- Faculty of Nutrition Sciences and Food Technology, National Nutrition and Food Technology Research Institute, Shahid Behehshti University of Medical Sciences Tehran, Tehran, Iran
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Scholkmann F, May CA. COVID-19, post-acute COVID-19 syndrome (PACS, "long COVID") and post-COVID-19 vaccination syndrome (PCVS, "post-COVIDvac-syndrome"): Similarities and differences. Pathol Res Pract 2023; 246:154497. [PMID: 37192595 DOI: 10.1016/j.prp.2023.154497] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/25/2023] [Accepted: 05/01/2023] [Indexed: 05/18/2023]
Abstract
Worldwide there have been over 760 million confirmed coronavirus disease 2019 (COVID-19) cases, and over 13 billion COVID-19 vaccine doses have been administered as of April 2023, according to the World Health Organization. An infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can lead to an acute disease, i.e. COVID-19, but also to a post-acute COVID-19 syndrome (PACS, "long COVID"). Currently, the side effects of COVID-19 vaccines are increasingly being noted and studied. Here, we summarise the currently available indications and discuss our conclusions that (i) these side effects have specific similarities and differences to acute COVID-19 and PACS, that (ii) a new term should be used to refer to these side effects (post-COVID-19 vaccination syndrome, PCVS, colloquially "post-COVIDvac-syndrome"), and that (iii) there is a need to distinguish between acute COVID-19 vaccination syndrome (ACVS) and post-acute COVID-19 vaccination syndrome (PACVS) - in analogy to acute COVID-19 and PACS ("long COVID"). Moreover, we address mixed forms of disease caused by natural SARS-CoV-2 infection and COVID-19 vaccination. We explain why it is important for medical diagnosis, care and research to use the new terms (PCVS, ACVS and PACVS) in order to avoid confusion and misinterpretation of the underlying causes of disease and to enable optimal medical therapy. We do not recommend to use the term "Post-Vac-Syndrome" as it is imprecise. The article also serves to address the current problem of "medical gaslighting" in relation to PACS and PCVS by raising awareness among the medical professionals and supplying appropriate terminology for disease.
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Affiliation(s)
- Felix Scholkmann
- University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland.
| | - Christian-Albrecht May
- Department of Anatomy, Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
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8
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Abu-Serie MM, Habashy NH. Major royal jelly proteins elicited suppression of SARS-CoV-2 entry and replication with halting lung injury. Int J Biol Macromol 2023; 228:715-731. [PMID: 36584778 PMCID: PMC9794390 DOI: 10.1016/j.ijbiomac.2022.12.251] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
For reasons of high transmissibility and virulence, Alpha (UK, B.1.1.7) and Beta (South African, B.1.351) SARS-CoV-2 variants are classified with other types as variants of concern. Here we report on the influence of royal jelly (RJ) protein fraction (PF)50 (major RJ protein 2 and its isoform X1) on the entry of these variants into the ACE2-human embryonic kidney (HEK) 293 cells using the lentiviral system. The efficiency of PF50 on SARS-CoV-2 replication (RNA-dependent RNA polymerase "RdRp" activity), as well as its impact on bleomycin-induced lung injury in vitro, were also assessed. The PF50 efficiently inhibited infection of kidney cells with the UK and S. African variant spikes of pseudotyped lentivirus particles (IC50 = 7.25 μM and 16.92 μM, respectively) and suppressed the RdRp activity (IC50 = 29.93 μM). Moreover, PF50 displayed protective and therapeutic efficacy against lung injury due to its antioxidant, anti-inflammatory, and angiotensin II blocking activities. The current findings, taken together, offer a novel perspective on PF50 as a promising agent against COVID-19.
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Affiliation(s)
- Marwa M. Abu-Serie
- Department of Medical Biotechnology, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications (SRTA-City), New Borg EL-Arab 21934, Alexandria, Egypt
| | - Noha H. Habashy
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt,Corresponding author
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9
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Khan A, Heng W, Imran K, Zhu G, Ji J, Zhang Y, Guan X, Ge G, Wei DQ. Discovery of Isojacareubin as a covalent inhibitor of SARS-CoV-2 main protease using structural and experimental approaches. J Med Virol 2023; 95:e28542. [PMID: 36727647 DOI: 10.1002/jmv.28542] [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: 11/23/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/03/2023]
Abstract
The ongoing pandemic with the emergence of immune evasion potential and, particularly, the current omicron subvariants intensified the situation further. Although vaccines are available, the immune evasion capabilities of the recent variants demand further efficient therapeutic choices to control the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Hence, considering the necessity of the small molecule inhibitor, we target the main protease (3CLpro), which is an appealing target for the development of antiviral drugs against SARS-CoV-2. High-throughput molecular in silico screening of South African natural compounds database reported Isojacareubin and Glabranin as the potential inhibitors for the main protease. The calculated docking scores were reported to be -8.47 and -8.03 kcal/mol, respectively. Moreover, the structural dynamic assessment reported that Isojacareubin in complex with 3CLpro exhibit a more stable dynamic behavior than Glabranin. Inhibition assay indicated that Isojacareubin could inhibit SARS-CoV-2 3CLpro in a time- and dose-dependent manner, with half maximal inhibitory concentration values of 16.00 ± 1.35 μM (60 min incubation). Next, the covalent binding sites of Isojacareubin on SARS-CoV-2 3CLpro was identified by biomass spectrometry, which reported that Isojacareubin can covalently bind to thiols or Cysteine through Michael addition. To evaluate the inactivation potency of Isojacareubin, the inactivation kinetics was further investigated. The inactivation kinetic curves were plotted according to various concentrations with gradient-ascending incubation times. The KI value of Isojacareubin was determined as 30.71 μM, whereas the Kinact value was calculated as 0.054 min-1 . These results suggest that Isojacareubin is a covalent inhibitor of SARS-CoV-2 3CLpro .
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nayang, Henan, P.R., China
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R., China
| | - Wang Heng
- International School of Cosmetics, School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, P.R., China
| | - Kashif Imran
- Services Institute of Medical Sciences, Lahore, Punjab, Pakistan
| | - Guanghao Zhu
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jun Ji
- Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, P.R., China
| | - Yani Zhang
- Peng Cheng Laboratory, Vanke Cloud City, Nashan District, Shenzhen, Guangdong, P.R., China
| | - Xiaoqing Guan
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nayang, Henan, P.R., China
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R., China
- Peng Cheng Laboratory, Vanke Cloud City, Nashan District, Shenzhen, Guangdong, P.R., China
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10
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Zhang GF, Meng W, Chen L, Ding L, Sun S, Wang X, Huang Y, Guo H, Gao S. Infectivity of pseudotyped SARS-CoV-2 variants of concern in different human cell types and inhibitory effects of recombinant spike protein and entry-related cellular factors. J Med Virol 2023; 95:e28437. [PMID: 36573430 PMCID: PMC9880647 DOI: 10.1002/jmv.28437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 12/28/2022]
Abstract
Since the report of the first COVID-19 case in 2019, SARS-CoV-2 variants of concern (VOCs) have continued to emerge, manifesting diverse infectivity, evasion of host immunity and pathology. While ACE2 is the predominant receptor of SARS-CoV-2, TMPRSS2, Kim-1, NRP-1, CD147, furin, CD209L, and CD26 have also been implicated as viral entry-related cofactors. To understand the variations in infectivity and pathogenesis of VOCs, we conducted infection analysis in human cells from different organ systems using pseudoviruses of VOCs including Alpha, Beta, Gamma, and Delta. Recombinant spike S1, RBD, ACE2, Kim-1, and NRP-1 proteins were tested for their ability to block infection to dissect their roles in SARS-CoV-2 entry into cells. Compared with wild type SARS-CoV-2 (WT), numerous VOCs had significant increases of infectivity across a wide spectrum of cell types. Recombinant ACE2 protein more effectively inhibited the infection of VOCs including Delta and Omicron (BA.1 and BA.2) than that of WT. Interestingly, recombinant S1, RBD, Kim-1, and NRP-1 proteins inhibited the infection of all pseudoviruses in a manner dependent on the levels of ACE2 expression in different cell types. These results provide insights into the diverse infectivity of SARS-CoV-2 VOCs, which might be helpful for managing the emergence of new VOCs.
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Affiliation(s)
- George Fei Zhang
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Wen Meng
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Luping Chen
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Ling Ding
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Shenyu Sun
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Xian Wang
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Yufei Huang
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of MedicineUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Electrical and Computer EngineeringSwanson School and EngineeringPittsburghPennsylvaniaUSA
| | - Haitao Guo
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Shou‐Jiang Gao
- Cancer Virology Program, UPMC Hillman Cancer CenterUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of Microbiology and Molecular GeneticsUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
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11
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Hossain MJ, Rabaan AA, Mutair AA, Alhumaid S, Emran TB, Saikumar G, Mitra S, Dhama K. Strategies to tackle SARS-CoV-2 Mu, a newly classified variant of interest likely to resist currently available COVID-19 vaccines. Hum Vaccin Immunother 2022; 18:2027197. [PMID: 35172687 PMCID: PMC8862164 DOI: 10.1080/21645515.2022.2027197] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/17/2021] [Accepted: 01/06/2022] [Indexed: 12/18/2022] Open
Abstract
Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have recently been reported in many countries. These have exacerbated the coronavirus disease 2019 (COVID-19)-induced global health threats and hindered COVID-19 vaccine development and therapeutic progress. This commentary discusses the potential risk of the newly classified Mu variant of interest, seeming a highly vaccine-resistant variant, and the approaches that can be adopted to tackle this variant based on the available evidence. The SARS-CoV-2 B.1.621 (Mu variant) lineage has shown approximately ten times higher resistance to neutralizing sera obtained from COVID-19 survivors or BNT161b2-vaccinated people than the parenteral B.1 lineage. Several urgent and long-term strategic plans, including quick genomic surveillance for uncovering the genetic characteristics of the variants, equitable global mass vaccination, booster dose administration if required, and strict implementation of public health measures or non-pharmaceutical interventions, must be undertaken concertedly to restrict further infections, mutations, or recombination of the SARS-CoV-2 virus and its deadly strains.
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Affiliation(s)
- Md Jamal Hossain
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur, Pakistan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, Al-Ahsa, Saudi Arabia
- College of Nursing, Princess Norah Bint Abdulrahman University, Riyadh, Saudi Arabia
- School of Nursing, Wollongong University, Wollongong, NSW, Australia
| | - Saad Alhumaid
- Administration of Pharmaceutical Care, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - G Saikumar
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
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12
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Matthews AM, Biel TG, Ortega-Rodriguez U, Falkowski VM, Bush X, Faison T, Xie H, Agarabi C, Rao VA, Ju T. SARS-CoV-2 spike protein variant binding affinity to an angiotensin-converting enzyme 2 fusion glycoproteins. PLoS One 2022; 17:e0278294. [PMID: 36472974 PMCID: PMC9725131 DOI: 10.1371/journal.pone.0278294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the Coronavirus disease 2019 (Covid-19) pandemic, continues to evolve and circulate globally. Current prophylactic and therapeutic countermeasures against Covid-19 infection include vaccines, small molecule drugs, and neutralizing monoclonal antibodies. SARS-CoV-2 infection is mainly mediated by the viral spike glycoprotein binding to angiotensin converting enzyme 2 (ACE2) on host cells for viral entry. As emerging mutations in the spike protein evade efficacy of spike-targeted countermeasures, a potential strategy to counter SARS-CoV-2 infection is to competitively block the spike protein from binding to the host ACE2 using a soluble recombinant fusion protein that contains a human ACE2 and an IgG1-Fc domain (ACE2-Fc). Here, we have established Chinese Hamster Ovary (CHO) cell lines that stably express ACE2-Fc proteins in which the ACE2 domain either has or has no catalytic activity. The fusion proteins were produced and purified to partially characterize physicochemical properties and spike protein binding. Our results demonstrate the ACE2-Fc fusion proteins are heavily N-glycosylated, sensitive to thermal stress, and actively bind to five spike protein variants (parental, alpha, beta, delta, and omicron) with different affinity. Our data demonstrates a proof-of-concept production strategy for ACE2-Fc fusion glycoproteins that can bind to different spike protein variants to support the manufacture of potential alternative countermeasures for emerging SARS-CoV-2 variants.
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Affiliation(s)
- Alicia M. Matthews
- Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Thomas G. Biel
- Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Uriel Ortega-Rodriguez
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Vincent M. Falkowski
- Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Xin Bush
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, United States of America
| | - Talia Faison
- Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Hang Xie
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Cyrus Agarabi
- Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - V. Ashutosh Rao
- Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Tongzhong Ju
- Office of Biotechnology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail:
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13
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Alisoltani A, Jaroszewski L, Godzik A, Iranzadeh A, Simons LM, Dean TJ, Lorenzo-Redondo R, Hultquist JF, Ozer EA. ViralVar: A Web Tool for Multilevel Visualization of SARS-CoV-2 Genomes. Viruses 2022; 14:v14122714. [PMID: 36560718 PMCID: PMC9781208 DOI: 10.3390/v14122714] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/14/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
The unprecedented growth of publicly available SARS-CoV-2 genome sequence data has increased the demand for effective and accessible SARS-CoV-2 data analysis and visualization tools. The majority of the currently available tools either require computational expertise to deploy them or limit user input to preselected subsets of SARS-CoV-2 genomes. To address these limitations, we developed ViralVar, a publicly available, point-and-click webtool that gives users the freedom to investigate and visualize user-selected subsets of SARS-CoV-2 genomes obtained from the GISAID public database. ViralVar has two primary features that enable: (1) the visualization of the spatiotemporal dynamics of SARS-CoV-2 lineages and (2) a structural/functional analysis of genomic mutations. As proof-of-principle, ViralVar was used to explore the evolution of the SARS-CoV-2 pandemic in the USA in pediatric, adult, and elderly populations (n > 1.7 million genomes). Whereas the spatiotemporal dynamics of the variants did not differ between these age groups, several USA-specific sublineages arose relative to the rest of the world. Our development and utilization of ViralVar to provide insights on the evolution of SARS-CoV-2 in the USA demonstrates the importance of developing accessible tools to facilitate and accelerate the large-scale surveillance of circulating pathogens.
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Affiliation(s)
- Arghavan Alisoltani
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Correspondence: (A.A.); (E.A.O.)
| | - Lukasz Jaroszewski
- Biosciences Division, School of Medicine, University of California Riverside, Riverside, CA 92507, USA
| | - Adam Godzik
- Biosciences Division, School of Medicine, University of California Riverside, Riverside, CA 92507, USA
| | - Arash Iranzadeh
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lacy M. Simons
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Taylor J. Dean
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Judd F. Hultquist
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Egon A. Ozer
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Correspondence: (A.A.); (E.A.O.)
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14
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Ai H, Wang Q, Liu W. A mathematical prediction model of infectious diseases considering vaccine and temperature, and its prediction in Hong Kong. Heliyon 2022; 8:e12469. [PMID: 36568658 PMCID: PMC9767883 DOI: 10.1016/j.heliyon.2022.e12469] [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: 05/05/2022] [Revised: 09/24/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Since 2020, COVID-19 has launched a rather difficult challenge in public health all over the world. For the current situation of COVID-19 outbreaks in various places, predicting the trend of COVID-19 plays a vital role in later policy-making, allocating medical materials, and developing the economy and society. Although there may be corresponding specific drugs soon, which can reduce the mortality of COVID-19 to a relatively low level, but the main popular Omicron BA.1 and BA.2 strain is highly infectious, which has a great impact on the elderly population, so COVID-19 cannot be equated with general influenza. This paper aims to predict the trend of the number of infections over time and the final number of infections from the fifth wave of epidemic in Hong Kong. To establish a more practical infection model, this paper introduces an infectious disease transmission model with the influence of temperature and vaccine. The model shows that the fifth wave of the epidemic in Hong Kong will end at the end of April 2022. At that time, the cumulative number of infections is expected to reach about 1.6 million. By formulating and implementing reasonable policies, the final number of infections can be controlled at about 1.1 million. Therefore, we hope that the policymakers and managers of COVID-19 in Hong Kong will formulate and adopt reasonable measures to control these epidemic.
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15
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Geerling E, Hameed M, Weger-Lucarelli J, Pinto AK. Metabolic syndrome and aberrant immune responses to viral infection and vaccination: Insights from small animal models. Front Immunol 2022; 13:1015563. [PMID: 36532060 PMCID: PMC9747772 DOI: 10.3389/fimmu.2022.1015563] [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: 08/09/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022] Open
Abstract
This review outlines the propensity for metabolic syndrome (MetS) to induce elevated disease severity, higher mortality rates post-infection, and poor vaccination outcomes for viral pathogens. MetS is a cluster of conditions including high blood glucose, an increase in circulating low-density lipoproteins and triglycerides, abdominal obesity, and elevated blood pressure which often overlap in their occurrence. MetS diagnoses are on the rise, as reported cases have increased by greater than 35% since 1988, resulting in one-third of United States adults currently diagnosed as MetS patients. In the aftermath of the 2009 H1N1 pandemic, a link between MetS and disease severity was established. Since then, numerous studies have been conducted to illuminate the impact of MetS on enhancing virally induced morbidity and dysregulation of the host immune response. These correlative studies have emphasized the need for elucidating the mechanisms by which these alterations occur, and animal studies conducted as early as the 1940s have linked the conditions associated with MetS with enhanced viral disease severity and poor vaccine outcomes. In this review, we provide an overview of the importance of considering overall metabolic health in terms of cholesterolemia, glycemia, triglyceridemia, insulin and other metabolic molecules, along with blood pressure levels and obesity when studying the impact of metabolism-related malignancies on immune function. We highlight the novel insights that small animal models have provided for MetS-associated immune dysfunction following viral infection. Such animal models of aberrant metabolism have paved the way for our current understanding of MetS and its impact on viral disease severity, dysregulated immune responses to viral pathogens, poor vaccination outcomes, and contributions to the emergence of viral variants.
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Affiliation(s)
- Elizabeth Geerling
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Muddassar Hameed
- Department of Biomedical Science and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States,Center for Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - James Weger-Lucarelli
- Department of Biomedical Science and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States,Center for Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Amelia K. Pinto
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, United States,*Correspondence: Amelia K. Pinto,
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16
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Guo L, Zafar F, Moeen N, Alshabrmi FM, Lin J, Ali SS, Munir M, Khan A, Wei D. Ultra-Large-Scale Screening of Natural Compounds and Free Energy Calculations Revealed Potential Inhibitors for the Receptor-Binding Domain (RBD) of SARS-CoV-2. Molecules 2022; 27:7317. [PMID: 36364143 PMCID: PMC9656483 DOI: 10.3390/molecules27217317] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/19/2023] Open
Abstract
The emergence of immune-evading variants of SARS-CoV-2 further aggravated the ongoing pandemic. Despite the deployments of various vaccines, the acquired mutations are capable of escaping both natural and vaccine-induced immune responses. Therefore, further investigation is needed to design a decisive pharmacological treatment that could efficiently block the entry of this virus into cells. Hence, the current study used structure-based methods to target the RBD of the recombinant variant (Deltacron) of SARS-CoV-2, which was used as a model variant. From the virtual drug screenings of various databases, a total of four hits were identified as potential lead molecules. Key residues were blocked by these molecules with favorable structural dynamic features. The binding free energies further validated the potentials of these molecules. The TBE for MNP was calculated to be -32.86 ± 0.10 kcal/mol, for SANC00222 the TBE was -23.41 ± 0.15 kcal/mol, for Liriodenine the TBE was -34.29 ± 0.07 kcal/mol, while for Carviolin the TBE was calculated to be -27.67 ± 0.12 kcal/mol. Moreover, each complex demonstrated distinct internal motion and a free energy profile, indicating a different strategy for the interaction with and inhibition of the RBD. In conclusion, the current study demands further in vivo and in vitro validation for the possible usage of these compounds as potential drugs against SARS-CoV-2 and its variants.
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Affiliation(s)
- Lisha Guo
- Zhongjing Chinese Medicine College, Nanyang Institute of Technology, 80 Changjiang Road, Nanyang 473004, China
| | - Faryar Zafar
- Nishtar Medical University, Multan 59341, Pakistan
| | - Nawal Moeen
- Nawaz Sharif Medical College, Gujrat 50700, Pakistan
| | - Fahad M. Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Junqi Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat 19120, Pakistan
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, Bailrigg, Lancaster LA1 4YW, UK
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang 473006, China
| | - Dongqing Wei
- Division of Biomedical and Life Sciences, Lancaster University, Bailrigg, Lancaster LA1 4YW, UK
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang 473006, China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen 518055, China
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
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17
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Khan T, Muzaffar A, Shoaib RM, Khan A, Waheed Y, Wei DQ. Towards specie-specific ensemble vaccine candidates against mammarenaviruses using optimized structural vaccinology pipeline and molecular modelling approaches. Microb Pathog 2022; 172:105793. [PMID: 36165863 DOI: 10.1016/j.micpath.2022.105793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 10/31/2022]
Abstract
Mammarena viruses are emerging pathogenic agents and cause hemorrhagic fevers in humans. These viruses accomplish host immune system evasion to replicate and spread in the host. There are only few available therapeutic options developed for Mammarena Virus (also called MMV). Currently, only a single candidate vaccine called Candid#1 is available against Junin virus. Similarly, the effective treatment Ribavirin is used only in Lassa fever treatments. Herein, immune-informatics pipeline has been used to annotate whole proteome of the seven human infecting Mammarena strains. The extensive immune based analysis reveals specie specific epitopes with a crucial role in immune response induction. This was achieved by construction of immunogenic epitopes (CTL "Cytotoxic T-Lymphocytes", HTL "Helper T-Lymphocytes", and B cell "B-Lymphocytes") based vaccine designs against seven different Mammarena virus species. Furthermore, validation of the vaccine constructs through exploring physiochemical properties was performed to confirm experimental feasibility. Additionally, in-silico cloning and receptor based immune simulation was performed to ensure induction of primary and secondary immune response. This was confirmed through expression of immune factors such as IL, cytokines, and antibodies. The current study provides with novel vaccine designs which needs further demonstrations through potential processing against MMVs. Future studies may be directed towards advanced evaluations to determine the efficacy and safety of the designed vaccines through further experimental procedures.
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Affiliation(s)
- Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | | | | | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China; Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nayang, Henan, 473006, PR China.
| | - Yasir Waheed
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China; Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nayang, Henan, 473006, PR China; Peng Cheng National Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China.
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18
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Ohishi T, Yamagishi T, Kurosu H, Kato H, Takayama Y, Anan H, Kunishima H. SARS-CoV-2 Delta AY.1 Variant Cluster in an Accommodation Facility for COVID-19: Cluster Report. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19159270. [PMID: 35954627 PMCID: PMC9367807 DOI: 10.3390/ijerph19159270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/23/2022] [Accepted: 07/27/2022] [Indexed: 11/22/2022]
Abstract
Background: This study aimed to examine the cause of and effective measures against cluster infections, including the delta AY.1 variant of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that occurred in an accommodation facility. Methods: We surveyed the zoning and ventilation systems of the cluster accommodation, examined the staff’s working conditions, conducted an interview, and administered a SARS-CoV-2 test (positive samples were further tested with molecular biological test). Results: Among the 99 employees working at the accommodation, 10 were infected with the delta AY.1 variant. The causes of the cluster infections were close-distance conversations without an unwoven-three-layer mask and contact for approximately five minutes with an unwoven mask under hypoventilated conditions. Conclusions: The Delta AY.1 infection may occur via aerosols and an unwoven mask might not prevent infection in poorly ventilated small spaces. Routine infection detection and responding quickly and appropriately to positive results helps to prevent clusters from spreading.
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Affiliation(s)
- Takayuki Ohishi
- Department of Infection Control and Prevention, Saiseikai Yokohama Eastern Tobu Hospital, 3-6-1 Shimosueyoshi, Tsurumi-ku, Yokohama 230-8765, Japan
- Kanagawa Prefectural Government, 1, Nihonodori, Naka-ku, Yokohama 231-0021, Japan; (H.K.); (Y.T.); (H.A.); (H.K.)
- Correspondence:
| | - Takuya Yamagishi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku Ward, Tokyo 162-8640, Japan; (T.Y.); (H.K.)
| | - Hitomi Kurosu
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku Ward, Tokyo 162-8640, Japan; (T.Y.); (H.K.)
| | - Hideaki Kato
- Kanagawa Prefectural Government, 1, Nihonodori, Naka-ku, Yokohama 231-0021, Japan; (H.K.); (Y.T.); (H.A.); (H.K.)
- Infection Prevention and Control Department, Yokohama City University Hospital, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Yoko Takayama
- Kanagawa Prefectural Government, 1, Nihonodori, Naka-ku, Yokohama 231-0021, Japan; (H.K.); (Y.T.); (H.A.); (H.K.)
- Department of Infection Control and Infectious Diseases, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, 1-15-1 Kitazato, Minami-ku, Sagamihara 252-0374, Japan
- Department of Infection Control and Prevention, Kitasato University Hospital, 1-15-1 Kitazato, Minami-ku, Sagamihara 252-0375, Japan
| | - Hideaki Anan
- Kanagawa Prefectural Government, 1, Nihonodori, Naka-ku, Yokohama 231-0021, Japan; (H.K.); (Y.T.); (H.A.); (H.K.)
- Fujisawa City Hospital, 2-6-1 Fujisawa, Fujisawa 251-8550, Japan
| | - Hiroyuki Kunishima
- Kanagawa Prefectural Government, 1, Nihonodori, Naka-ku, Yokohama 231-0021, Japan; (H.K.); (Y.T.); (H.A.); (H.K.)
- Infectious Diseases Course, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki 216-8511, Japan
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19
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Ward B, Yombi JC, Balligand JL, Cani PD, Collet JF, de Greef J, Dewulf JP, Gatto L, Haufroid V, Jodogne S, Kabamba B, Pyr dit Ruys S, Vertommen D, Elens L, Belkhir L. HYGIEIA: HYpothesizing the Genesis of Infectious Diseases and Epidemics through an Integrated Systems Biology Approach. Viruses 2022; 14:v14071373. [PMID: 35891354 PMCID: PMC9318602 DOI: 10.3390/v14071373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 12/13/2022] Open
Abstract
More than two years on, the COVID-19 pandemic continues to wreak havoc around the world and has battle-tested the pandemic-situation responses of all major global governments. Two key areas of investigation that are still unclear are: the molecular mechanisms that lead to heterogenic patient outcomes, and the causes of Post COVID condition (AKA Long-COVID). In this paper, we introduce the HYGIEIA project, designed to respond to the enormous challenges of the COVID-19 pandemic through a multi-omic approach supported by network medicine. It is hoped that in addition to investigating COVID-19, the logistics deployed within this project will be applicable to other infectious agents, pandemic-type situations, and also other complex, non-infectious diseases. Here, we first look at previous research into COVID-19 in the context of the proteome, metabolome, transcriptome, microbiome, host genome, and viral genome. We then discuss a proposed methodology for a large-scale multi-omic longitudinal study to investigate the aforementioned biological strata through high-throughput sequencing (HTS) and mass-spectrometry (MS) technologies. Lastly, we discuss how a network medicine approach can be used to analyze the data and make meaningful discoveries, with the final aim being the translation of these discoveries into the clinics to improve patient care.
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Affiliation(s)
- Bradley Ward
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (B.W.); (S.P.d.R.)
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
| | - Jean Cyr Yombi
- Department of Internal Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Jean-Luc Balligand
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Experimentale et Clinique (IREC), Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Patrice D. Cani
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Metabolism and Nutrition Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Jean-François Collet
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), de Duve Institute, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Julien de Greef
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Internal Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Joseph P. Dewulf
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
- Department of Biochemistry, de Duve Institute, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Laurent Gatto
- Computational Biology and Bioinformatics Unit (CBIO), de Duve Institute, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Vincent Haufroid
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Sébastien Jodogne
- Computer Science and Engineering Department (INGI), Institute of Information and Communication Technologies, Electronics and Applied Mathematics (ICTEAM), UCLouvain, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium;
| | - Benoît Kabamba
- Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
- Pôle de Microbiologie, Institut de Recherche Expérimentale et Clinique, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Sébastien Pyr dit Ruys
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (B.W.); (S.P.d.R.)
| | - Didier Vertommen
- De Duve Institute, and MASSPROT Platform, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Laure Elens
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (B.W.); (S.P.d.R.)
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Correspondence: (L.E.); (L.B.)
| | - Leïla Belkhir
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Internal Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
- Correspondence: (L.E.); (L.B.)
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20
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Albutti A. Proteome-Wide and Protein-Specific Multi-Epitope Vaccine Constructs Against the Rift Valley Fever Virus Outbreak Using Integrated Omics Approaches. Front Microbiol 2022; 13:921683. [PMID: 35711778 PMCID: PMC9195176 DOI: 10.3389/fmicb.2022.921683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Rift Valley fever (RVF) is a viral disease caused by a member of the Bunyavirales family causing severe infections in humans. The RVF virus is an enveloped, negative-sense, single-stranded RNA virus that can infect both animals and humans. The symptoms associated with these infections span from minor (fever and headaches) to severe (meningoencephalitis and hemorrhagic fever syndrome) symptoms. Despite the outbreaks of the RVF virus being reported in different parts of the world, no effective therapy is available. Herein, the development of an efficient vaccine is critical for the control of infections associated with the RVF virus. Moreover, computational vaccine approaches are helpful in the design of specific, safe, and stable peptide-based designs when compared to the conventional methods of vaccine development. In this study, the whole proteome of the virus, comprising four proteins (NP, L, GP, and NSP), was screened to find putative vaccine epitope sequences (T cell, B cell, and HTL) specific for each protein. These shortlisted epitopes were then combined with flexible linkers to design protein-specific and proteome-wide immunogenic multi-epitope-based vaccine constructs. The results revealed that these multi-epitope vaccine constructs (MEVCs) are strongly antigenic and non-allergenic in nature. The efficacy of these constructs was further validated by docking with immune receptors, which revealed strong binding interactions with human TLR8. Using the MD simulation approach, the binding stability and residual flexibility of the best vaccine construct (proteome-wide) were confirmed, which revealed stable dynamic and favorable features. Furthermore, in-silico cloning and immune simulation analysis confirmed the expression and production of immune factors, that is, IgM, IgG, and IL-6, against the proposed vaccine designs. Additionally, 3D models of all the MEVC constructs have been developed and evaluated for potential immunization against the RVF virus. Finally, the proteome-wide vaccine candidate (MEVC-PW-RVFV) with the highest immune reinforcement potential provides new insights into the development of future vaccines against the emerging RVF virus.
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Affiliation(s)
- Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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21
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Saberiyan M, Karimi E, Khademi Z, Movahhed P, Safi A, Mehri-Ghahfarrokhi A. SARS-CoV-2: phenotype, genotype, and characterization of different variants. Cell Mol Biol Lett 2022; 27:50. [PMID: 35715738 PMCID: PMC9204680 DOI: 10.1186/s11658-022-00352-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/31/2022] [Indexed: 12/31/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19), a major international public health concern. Because of very similar amino acid sequences of the seven domain names, SARS-CoV-2 belongs to the Coronavirinae subfamily of the family Coronaviridae, order Nidovirales, and realm Riboviria, placed in exceptional clusters, but categorized as a SARS-like species. As the RNA virus family with the longest genome, the Coronaviridae genome consists of a single strand of positive RNA (25–32 kb in length). Four major structural proteins of this genome include the spike (S), membrane (M), envelope (E), and the nucleocapsid (N) protein, all of which are encoded within the 3′ end of the genome. By engaging with its receptor, angiotensin-converting enzyme 2 (ACE2), SARS-CoV-2 infects host cells. According to the most recent epidemiological data, as the illness spread globally, several genetic variations of SARS-CoV-2 appeared quickly, with the World Health Organization (WHO) naming 11 of them. Among these, seven SARS-CoV-2 subtypes have received the most attention. Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.617.2) are now designated as variations of concern (VOC) (B.1.1.529). Lambda (C.37) and Mu are variations of interest (VOI) (B.1.621). The remaining six are either being monitored or are no longer considered a threat. On the basis of studies done so far, antiviral drugs, antibiotics, glucocorticoids, recombinant intravenous immunoglobulin, plasma therapy, and IFN-α2b have been used to treat patients. Moreover, full vaccination is associated with lower infection and helps prevent transmission, but the risk of infection cannot be eliminated completely in vaccinated people.
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Affiliation(s)
- Mohammadreza Saberiyan
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Elham Karimi
- Department of Medical Genetics, School of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Zahra Khademi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Parvaneh Movahhed
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Safi
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Ameneh Mehri-Ghahfarrokhi
- Clinical Research Development Unit, Hajar Hospital, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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22
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Naman ZT, Kadhim S, Al-Isawi ZJK, Butch CJ, Muhseen ZT. Computational Investigations of Traditional Chinese Medicinal Compounds against the Omicron Variant of SARS-CoV-2 to Rescue the Host Immune System. Pharmaceuticals (Basel) 2022; 15:ph15060741. [PMID: 35745660 PMCID: PMC9227372 DOI: 10.3390/ph15060741] [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: 05/04/2022] [Revised: 05/27/2022] [Accepted: 05/31/2022] [Indexed: 11/16/2022] Open
Abstract
Macrodomain-I of the NSP3 (non-structural protein 3) is responsible for immune response hijacking in the SARS-CoV-2 infection known as COVID-19. In the omicron variant (B.1.1.529), this domain harbors a new mutation, V1069I, which may increase the binding of ADPr and consequently the infection severity. This macrodomain-I, due to its significant role in infection, is deemed to be an important drug target. Hence, using structural bioinformatics and molecular simulation approaches, we performed a virtual screening of the traditional Chinese medicines (TCM) database for potential anti-viral drugs. The screening of 57,000 compounds yielded the 10 best compounds with docking scores better than the control ADPr. Among the top ten, the best three hits—TCM42798, with a docking score of −13.70 kcal/mol, TCM47007 of −13.25 kcal/mol, and TCM30675 of −12.49 kcal/mol—were chosen as the best hits. Structural dynamic features were explored including stability, compactness, flexibility, and hydrogen bonding, further demonstrating the anti-viral potential of these hits. Using the MM/GBSA approach, the total binding free energy for each complex was reported to be −69.78 kcal/mol, −50.11 kcal/mol, and −47.64 kcal/mol, respectively, which consequently reflect the stronger binding and inhibitory potential of these compounds. These agents might suppress NSP3 directly, allowing the host immune system to recuperate. The current study lays the groundwork for the development of new drugs to combat SARS-CoV-2 and its variants.
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Affiliation(s)
- Ziad Tareq Naman
- Department of Medical Laboratory Techniques, Al-Ma’Moon University College, Aladhamia, Baghdad 72029, Iraq;
| | - Salim Kadhim
- College of Pharmacy, University of Alkafeel, Najaf 61001, Iraq;
| | - Zahraa J. K. Al-Isawi
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Kufa, Najaf 61001, Iraq;
| | - Christopher J. Butch
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210093, China
- Correspondence: (C.J.B.); (Z.T.M.)
| | - Ziyad Tariq Muhseen
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
- Department of Pharmacy, Al-Mustaqbal University College, Hillah, Babylon 51001, Iraq
- Correspondence: (C.J.B.); (Z.T.M.)
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23
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Liang Y, Zou L, Lin H, Li B, Zhao J, Wang H, Sun J, Chen J, Mo Y, Yang X, Deng X, Tang S. Detection of Major SARS-CoV-2 Variants of Concern in Clinical Samples via CRISPR-Cas12a-Mediated Mutation-Specific Assay. ACS Synth Biol 2022; 11:1811-1823. [PMID: 35481381 DOI: 10.1021/acssynbio.1c00643] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Objectives: Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants pose a great threat and burden to global public health. Here, we evaluated a clustered regularly interspaced short palindromic repeat-associated enzyme 12a (CRISPR-Cas12a)-based method for detecting major SARS-CoV-2 variants of concern (VOCs) in SARS-CoV-2 positive clinical samples. Methods: Allele-specific CRISPR RNAs (crRNAs) targeting the signature mutations in the spike protein of SARS-CoV-2 are designed. A total of 59 SARS-CoV-2 positive oropharyngeal swab specimens were used to evaluate the performance of the CRISPR-Cas12a-mediated assay to identify major SARS-CoV-2 VOCs. Results: Compared with Sanger sequencing, the eight allele-specific crRNAs analyzed can specifically identify the corresponding mutations with a positive predictive value of 83.3-100% and a negative predictive value of 85.7-100%. Our CRISPR-Cas12a-mediated assay distinguished wild-type and four major VOCs (Alpha, Beta, Delta, and Omicron) of SARS-CoV-2 with a sensitivity of 93.8-100.0% and a specificity of 100.0%. The two methods showed a concordance of 98.3% (58/59) with a κ value of 0.956-1.000, while seven (11.9%) samples were found to be positive for extra mutations by the CRISPR-based assay. Furthermore, neither virus titers nor the sequences adjacent to the signature mutations were associated with the variation of fluorescence intensity detected or the false-positive reaction observed when testing clinical samples. In addition, there was no cross-reaction observed when detecting 33 SARS-CoV-2 negative clinical samples infected with common respiratory pathogens. Conclusions: The CRISPR-Cas12a-based genotyping assay is highly sensitive and specific when detecting both the SARS-CoV-2 wild-type strain and major VOCs. It is a simple and rapid assay that can monitor and track the circulating SARS-CoV-2 variants and the dynamics of the coronavirus disease 2019 (COVID-19) pandemic and can be easily implemented in resource-limited settings.
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Affiliation(s)
- Yuanhao Liang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Lirong Zou
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou 511430, China
| | - Hongqing Lin
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Baisheng Li
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou 511430, China
| | - Jianhui Zhao
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Haiying Wang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Jiufeng Sun
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou 511430, China
| | - Jingdiao Chen
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou 511430, China
| | - Yanling Mo
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou 511430, China
| | - Xingfen Yang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Xiaoling Deng
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou 511430, China
| | - Shixing Tang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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24
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Kim J, Cheon S, Ahn I. NGS data vectorization, clustering, and finding key codons in SARS-CoV-2 variations. BMC Bioinformatics 2022; 23:187. [PMID: 35581558 PMCID: PMC9113074 DOI: 10.1186/s12859-022-04718-7] [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: 09/26/2021] [Accepted: 05/06/2022] [Indexed: 11/10/2022] Open
Abstract
The rapid global spread and dissemination of SARS-CoV-2 has provided the virus with numerous opportunities to develop several variants. Thus, it is critical to determine the degree of the variations and in which part of the virus those variations occurred. Therefore, in this study, methods that could be used to vectorize the sequence data, perform clustering analysis, and visualize the results were proposed using machine learning methods. To conduct this study, a total of 224,073 cases of SARS-CoV-2 sequence data were collected through NCBI and GISAID, and the data were visualized using dimensionality reduction and clustering analysis models such as T-SNE and DBSCAN. The SARS-CoV-2 virus, which was first detected, was distinguished from different variations, including Omicron and Delta, in the cluster results. Furthermore, it was possible to examine which codon changes in the spike protein caused the variants to be distinguished using feature importance extraction models such as Random Forest or Shapely Value. The proposed method has the advantage of being able to analyse and visualize a large amount of data at once compared to the existing tree-based sequence data analysis. The proposed method was able to identify and visualize significant changes between the SARS-CoV-2 virus, which was first detected in Wuhan, China, in December 2019, and the newly formed mutant virus group. As a result of clustering analysis using sequence data, it was possible to confirm the formation of clusters among various variants in a two-dimensional graph, and by extracting the importance of variables, it was possible to confirm which codon changes played a major role in distinguishing variants. Furthermore, since the proposed method can handle a variety of data sequences, it can be used for all kinds of diseases, including influenza and SARS-CoV-2. Therefore, the proposed method has the potential to become widely used for the effective analysis of disease variations.
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Affiliation(s)
- Juhyeon Kim
- Department of Data-Centric Problem Solving Research, Korea Institute of Science and Technology Information, Yuseong-gu, Daejeon, Korea.,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Yuseong-gu, Daejeon, Korea.,Department of Industrial Engineering, Ajou University, Suwon, South Korea
| | - Saeyeon Cheon
- Applied Artificial Intelligence Major, University of Science & Technology, Yuseong-gu, Daejeon, Korea
| | - Insung Ahn
- Department of Data-Centric Problem Solving Research, Korea Institute of Science and Technology Information, Yuseong-gu, Daejeon, Korea. .,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Yuseong-gu, Daejeon, Korea. .,Applied Artificial Intelligence Major, University of Science & Technology, Yuseong-gu, Daejeon, Korea.
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25
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Alagheband Bahrami A, Azargoonjahromi A, Sadraei S, Aarabi A, Payandeh Z, Rajabibazl M. An overview of current drugs and prophylactic vaccines for coronavirus disease 2019 (COVID-19). Cell Mol Biol Lett 2022; 27:38. [PMID: 35562685 PMCID: PMC9100302 DOI: 10.1186/s11658-022-00339-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 04/21/2022] [Indexed: 02/06/2023] Open
Abstract
Designing and producing an effective vaccine is the best possible way to reduce the burden and spread of a disease. During the coronavirus disease 2019 (COVID-19) pandemic, many large pharmaceutical and biotechnology companies invested a great deal of time and money in trying to control and combat the disease. In this regard, due to the urgent need, many vaccines are now available earlier than scheduled. Based on their manufacturing technology, the vaccines available for COVID-19 (severe acute respiratory syndrome coronavirus 2 (SAR-CoV2)) infection can be classified into four platforms: RNA vaccines, adenovirus vector vaccines, subunit (protein-based) vaccines, and inactivated virus vaccines. Moreover, various drugs have been deemed to negatively affect the progression of the infection via various actions. However, adaptive variants of the SARS-CoV-2 genome can alter the pathogenic potential of the virus and increase the difficulty of both drug and vaccine development. In this review, along with drugs used in COVID-19 treatment, currently authorized COVID-19 vaccines as well as variants of the virus are described and evaluated, considering all platforms.
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Affiliation(s)
- Armina Alagheband Bahrami
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Samin Sadraei
- Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aryan Aarabi
- Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Payandeh
- Department Medical Biochemistry and Biophysics, Division Medical Inflammation Research, Karolinska Institute, Stockholm, Sweden
| | - Masoumeh Rajabibazl
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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26
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Cojocaru C, Cojocaru E, Turcanu A, Zaharia D. Clinical challenges of SARS‑CoV‑2 variants (Review). Exp Ther Med 2022; 23:416. [PMID: 35601074 PMCID: PMC9117961 DOI: 10.3892/etm.2022.11343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/08/2022] [Indexed: 11/06/2022] Open
Abstract
Since the first cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, there have been challenges recognizing the clinical features of SARS-CoV-2 and identifying therapeutic options. This has been compounded by viral mutations that affect clinical response and primary epidemiological indicators. Multiple variants of SARS-CoV-2 have been identified and classified on the basis of nomenclature implemented by scientific organizations and the World Health Organisation (WHO). A total of five variants of concern (VOCs) have been identified to date. The present study aimed to analyse clinical and epidemiological features of each variant. Based on these characteristics, predictions were made about potential future evolution. Considering the time and location of SARS-CoV-2 VOC emergence, it was hypothesised that mutations were not due to pressure caused by the vaccines introduced in December 2020 but were dependent on natural characteristics of the virus. In the process of adapting to the human body, SARS-CoV-2 is expected to undergo evolution to become more contagious but less deadly. SARS-CoV-2 was hypothesized to continue spread through isolated epidemic outbreaks due to the unimmunized population, mostly unvaccinated children and adults, and for coronaviruses to continue to present a public health problem.
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Affiliation(s)
- Cristian Cojocaru
- Medical III Department, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Elena Cojocaru
- Morpho‑Functional Sciences II Department, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Adina Turcanu
- Medical III Department, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Dragos Zaharia
- Department 4 Cardio‑thoracic Pathology, Faculty of Medicine, University of Medicine and Pharmacy ‘Carol Davila’, 050471 Bucharest, Romania
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Khoshnood S, Arshadi M, Akrami S, Koupaei M, Ghahramanpour H, Shariati A, Sadeghifard N, Heidary M. An overview on inactivated and live-attenuated SARS-CoV-2 vaccines. J Clin Lab Anal 2022; 36:e24418. [PMID: 35421266 PMCID: PMC9102488 DOI: 10.1002/jcla.24418] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/20/2022] [Accepted: 03/25/2022] [Indexed: 12/18/2022] Open
Abstract
After about 2 years since severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2), first infections were detected in Wuhan city of China in December 2019, which was followed by a worldwide pandemic with a record of 5.41 million deaths. Due to urgent need for the development of a safe and effective vaccine for coronavirus disease 2019 (COVID‐19), attempts for producing efficient vaccines are inexhaustibly continuing. According to a report by the World Health Organization (WHO) on COVID‐19 vaccine tracker and landscape, there are 149 vaccine candidates all over the world. Inactivated SARS‐CoV‐2 vaccines as a conventional vaccine platform consist of whole virus particles grown in cell culture and inactivated by chemicals. Because of benefits such as antigenic similarity to real virion inducing humoral and cellular immune responses and ease for transport and storage, these vaccines, including the vaccines produced by Bharat Biotech, Sinopharm, and Sinovac, are in use at large scales. In this study, we have a review on inactivated SARS‐CoV‐2 vaccines that are passing their phase 3 and 4 clinical trials, population which was included in the trials, vaccine producers, the efficiency, adverse effects, and components of vaccines, and other vaccine features.
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Affiliation(s)
- Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Maniya Arshadi
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sousan Akrami
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Koupaei
- Department of Microbiology and Immunology, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Hossein Ghahramanpour
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Aref Shariati
- Molecular and Medicine Research Center, Khomein University of Medical Sciences, Khomein, Iran
| | - Nourkhoda Sadeghifard
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar, Iran.,Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
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Konozy E, Osman M, Dirar A. Plant Lectins as Potent Anti-coronaviruses, Anti-inflammatory, Antinociceptive and Antiulcer Agents. Saudi J Biol Sci 2022; 29:103301. [PMID: 35475119 PMCID: PMC9026953 DOI: 10.1016/j.sjbs.2022.103301] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/12/2022] [Accepted: 04/17/2022] [Indexed: 12/14/2022] Open
Abstract
Lectins are defined as carbohydrate-binding proteins/glycoproteins of none immune origin, they are ubiquitous in nature, exist from bacteria to human cells. And due to their carbohydrate-binding recognition capacity, they have been a useful biological tool for the purification of glycoproteins and their subsequent characterization. Some plant lectins have also been revealed to own antinociceptive, antiulcer, and anti-inflammatory properties, where these features, in many instances, depending on the lectin carbohydrate-binding site. Coronavirus disease of 2019 (COVID-19) is a respiratory disease that struck the entire world leaving millions of people dead and more infected. Although COVID-19 vaccines have been made available, and quite a large number of world populations have already been immunized, the viral infection rates remained in acceleration, which continues to provoke major concern about the vaccines' efficacy. The belief in the ineffectiveness of the vaccine has been attributed in part to the recurrent mutations that occur in the epitope determinant fragments of the virus. Coronavirus envelope surface is extensively glycosylated being covered by more than sixty N-linked oligomannose, composite, and hybrid glycans with a core of Man3GlcNAc2Asn. In addition some O–linked glycans are also detected. Of these glyco-chains, many have also been exposed to several mutations, and a few remained conserved. Therefore, numerous plant lectins with a specificity directed towards these viral envelope sugars have been found to interact preferentially with them and are suggested to be scrutinized as a possible future tool to combat coronaviruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through blocking the viral attachment to the host cells. In this review, we will discuss the possible applications of plant lectins as anti-coronaviruses including SARS-CoV-2, antinociceptive, anti-inflammatory, and antiulcer agents with the proposed mechanism of their actions.
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Affiliation(s)
- Emadeldin Konozy
- Department of Biotechnology, Africa City of Technology, Khartoum, Sudan
- Corresponding author.
| | - Makarim Osman
- Department of Zoology, University of Khartoum, Khartoum, Sudan
| | - Amina Dirar
- Medicinal, Aromatic Plants and Traditional Medicine Research Institute (MAPTRI), National Center for Research, Mek Nimr Street, Khartoum, Sudan
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Ullah M, Mubashir M, Atique H, Aslam F, Tahir M, Naqvi M. COVID-19 Infection in Vaccinated Healthcare Professionals. Cureus 2022; 14:e23386. [PMID: 35475110 PMCID: PMC9022484 DOI: 10.7759/cureus.23386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2022] [Indexed: 11/16/2022] Open
Abstract
Background: There are different types of Coronavirus disease (COVID-19) vaccines available presently, and their emergency use has been approved by WHO worldwide on a mass scale. COVID-19 vaccine breakthrough infections have been reported worldwide. In Pakistan, there are limited data on COVID-19 vaccine breakthrough infections and their clinical course, especially in healthcare professionals (HCPs). Our study aims to investigate COVID-19 infections among vaccinated HCPs. Methods: A prospective study was conducted on 425 healthcare professionals. Data collected from healthcare professionals included names, age, gender, number of vaccination doses, COVID-19 infection pre and post-vaccination, the severity of COVID-19 infection (if positive), and co-morbid conditions. Ethical board approval was taken. Statistical Package for Social Sciences (SPSS) version 23 (IBM Corp., Armonk, NY) was used to analyze the data. Results: After complete vaccination, 17.27% acquired COVID-19 infection; 2.47% had COVID-19 infection both pre and post-vaccination. The mean age was 32.46 years (n=71) with a standard deviation of ±9.376. The male to female ratio was 1.53. COVID-19 PCR was positive in 95.77%. During the course of the disease, 4.2% were asymptomatic, 92.95% had mild symptoms, 1.4% were hospitalized, and 1.4% had to be managed in the intensive care unit. None of the HCPs who had received booster doses acquired a COVID-19 infection. Conclusion: It was found that prior COVID-19 infection and vaccination do not confer immunity from infection. However, proper vaccination limits the severity, morbidity, and mortality of COVID-19 infection.
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Akelew Y, Andualem H, Ebrahim E, Atnaf A, Hailemichael W. Immunomodulation of COVID‐19 severity by helminth co‐infection: Implications for COVID‐19 vaccine efficacy. Immun Inflamm Dis 2022; 10:e573. [PMID: 34861106 PMCID: PMC8926508 DOI: 10.1002/iid3.573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/07/2021] [Accepted: 11/24/2021] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), an emerging virus in late 2019 causing coronavirus disease 2019 (COVID‐19), has caused a catastrophic effect, resulting in an unprecedented global crisis. The immunopathology of COVID‐19 appears to be clearly associated with a dysregulated immune response leading to organ failure and death. Similarly, over two billion people worldwide are infected with helminth, with those living in low‐middle‐income countries disproportionately affected. Helminth infections have been shown to possess immunomodulatory effects in several conditions. Helminth co‐infection in COVID‐19 patients is one of the potential reasons for global attention to answer why COVID‐19 severity is still lower in helminth endemic countries. Recent studies have shown that helminth endemic countries showed fewer cases and deaths so far and helminth co‐infection might reduce the severity of COVID‐19. Moreover, lessons from other diseases with helminth co‐infection have been shown to substantially reduce vaccine efficacy that could also be implicated for COVID‐19. This immunomodulatory effect of helminth has intended and unintended consequences, both advantageous and disadvantageous which could decrease the severity of COVID‐19 and COVID‐19 vaccine efficacy respectively. Herewith, we discuss the overview of COVID‐19 immune response, immunomodulatory effects of helminth co‐infections in COVID‐19, lessons from other diseases, and perspectives on the efficacy of COVID‐19 vaccines.
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Affiliation(s)
- Yibeltal Akelew
- Immunology and Molecular Biology, Medical Laboratory Sciences, College of Health Sciences Debre Markos University Debre Markos Ethiopia
| | - Henok Andualem
- Immunology and Molecular Biology, Medical Laboratory Sciences, College of Health Sciences Debre Tabor University Debre Tabor Ethiopia
| | - Endris Ebrahim
- Immunology and Molecular Biology, Medical Laboratory Sciences, College of Health Sciences Wollo University Dessie Ethiopia
| | - Aytenew Atnaf
- Hematology and Immunohematology, Medical Laboratory Sciences, College of Health Sciences Debre Markos University Debre Markos Ethiopia
| | - Wasihun Hailemichael
- Immunology and Molecular Biology, Medical Laboratory Sciences, College of Health Sciences Debre Tabor University Debre Tabor Ethiopia
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Khan A, Waris H, Rafique M, Suleman M, Mohammad A, Ali SS, Khan T, Waheed Y, Liao C, Wei DQ. The Omicron (B.1.1.529) variant of SARS-CoV-2 binds to the hACE2 receptor more strongly and escapes the antibody response: Insights from structural and simulation data. Int J Biol Macromol 2022; 200:438-448. [PMID: 35063482 PMCID: PMC8767976 DOI: 10.1016/j.ijbiomac.2022.01.059] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 02/07/2023]
Abstract
As SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) continues to inflict chaos globally, a new variant officially known as B.1.1.529 was reported in South Africa and was found to harbor 30 mutations in the spike protein. It is too early to speculate on transmission and hospitalizations. Hence, more analyses are required, particularly to connect the genomic patterns to the phenotypic attributes to reveal the binding differences and antibody response for this variant, which can then be used for therapeutic interventions. Given the urgency of the required analysis and data on the B.1.1.529 variant, we have performed a detailed investigation to provide an understanding of the impact of these novel mutations on the structure, function, and binding of RBD to hACE2 and mAb to the NTD of the spike protein. The differences in the binding pattern between the wild type and B.1.1.529 variant complexes revealed that the key substitutions Asn417, Ser446, Arg493, and Arg498 in the B.1.1.529 RBD caused additional interactions with hACE2 and the loss of key residues in the B.1.1.529 NTD resulted in decreased interactions with three CDR regions (1-3) in the mAb. Further investigation revealed that B.1.1.529 displayed a stable dynamic that follows a global stability trend. In addition, the dissociation constant (KD), hydrogen bonding analysis, and binding free energy calculations further validated the findings. Hydrogen bonding analysis demonstrated that significant hydrogen bonding reprogramming took place, which revealed key differences in the binding. The total binding free energy using MM/GBSA and MM/PBSA further validated the docking results and demonstrated significant variations in the binding. This study is the first to provide a basis for the higher infectivity of the new SARS-CoV-2 variants and provides a strong impetus for the development of novel drugs against them.
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Hira Waris
- Rawalpindi Medical College, Rawalpindi, Punjab, Pakistan
| | | | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Khyber Pakhtunkhwa, Pakistan
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Khyber Pakhtunkhwa, Pakistan
| | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, Islamabad, Pakistan
| | - Chenguang Liao
- College of Software, Zhengzhou University, Daxue Road, Zhengzhou, China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China; State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Laboratory of Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, PR China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, PR China.
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Celik I, Tallei TE. A computational comparative analysis of the binding mechanism of molnupiravir's active metabolite to RNA-dependent RNA polymerase of wild-type and Delta subvariant AY.4 of SARS-CoV-2. J Cell Biochem 2022; 123:807-818. [PMID: 35132671 DOI: 10.1002/jcb.30226] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 01/18/2023]
Abstract
The antiviral drug molnupiravir targets the SARS-CoV-2 RNA-dependent RNA polymerase (RdRP) enzyme. Early treatment with molnupiravir reduced the risk of hospitalization or death in at-risk, unvaccinated adults with COVID-19, according to phase 3 clinical trials. Many mutations have occurred within this virus as a result of its widespread distribution. The current study sought to determine whether mutations in the RdRP of Delta subvariant AY.4 (D-AY.4 RdRP) influence the interaction of the enzyme with molnupiravir triphosphate (MTP), the active metabolite of molnupiravir. The interactions between the wild-type (WT) RdRP and D-AY.4 RdRP with MTP were evaluated based on molecular docking and dynamic simulation (MD) studies. The results show that the MTP interaction is stronger and more stable with D-AY.4 RdRP than with WT RdRP. This study provides insight into the potential significance of administering MTP to patients infected with D-AY.4 RdRP, which may have a more favorable chance of alleviating the illness. According to the findings of this study, MTP has a high likelihood of becoming widely used as an anti-SARS-CoV-2 agent. The fact that MTP is not only cytotoxic but also mutagenic to mammalian cells, as well as the possibility that it may cause DNA damage in the host, have all been raised as potential concerns.
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Affiliation(s)
- Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Trina E Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, North Sulawesi, Indonesia
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Targeting the RBD of Omicron Variant (B.1.1.529) with Medicinal Phytocompounds to Abrogate the Binding of Spike Glycoprotein with the hACE2 Using Computational Molecular Search and Simulation Approach. BIOLOGY 2022; 11:biology11020258. [PMID: 35205124 PMCID: PMC8869371 DOI: 10.3390/biology11020258] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 01/23/2023]
Abstract
Simple Summary The current study based on virtual drugs screening and simulations identified novel drugs to target the RBD of the spike protein from Omicron variant of SARS-CoV-2. Using molecular modeling tools to search for a good binding drugs we identified SANC00944, SANC01032, SANC00992, and SANC00317 from South African natural compounds database as potential inhibitor of the Spike-ACE2 complex. In sum, this study will help in the design and discovery of novel drug therapeutics, which may be used against the emerging Omicron variant of SARS-CoV-2. Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus continues to inflict chaos globally. The emergence of a novel Omicron variant (B.1.1.529) in South Africa harbors 30 mutations in the spike protein. The variant is distinguished from other variants of concern (VOCs) with an increased (15) number of mutations in the receptor-binding domain (RBD) and suggests higher chances of causing reinfections. Initial reports also claimed that this variant escapes all the neutralizing antibodies, thus demanding a novel strategy against it. Thus, in this study, we performed a computational molecular screening against the RBD of the Omicron (B.1.1.529) variant and assessed the binding affinity of potent drugs against the RBD. The multi-steps screening of the South African Natural Compounds Database (SANCDB) revealed four medicinal compounds as excellent (potential) anti-viral agents against the Omicron variant, namely SANC00944, SANC01032, SANC00992, and SANC00317. The simulation analysis of these compounds in complex with the RBD demonstrated stable dynamics and structural compactness. Moreover, the residual flexibility analysis revealed that the flexibility of three loops required for interaction with hACE2 has been reduced by the binding of these drugs. The post-simulation validation of these compounds such as binding free energy, in silico bioactivity, and dissociation constant prediction validated the anti-viral potency of these compounds. The total binding free energy (TBFE) for the SANC01032–RBD complex was reported to be −46.54 kcal/mol; for the SANC01032–RBD complex, the TBFE was −41.88 kcal/mol; for the SANC00992–RBD complex the TBFE was −29.05 kcal/mol, while for the SANC00317–RBD complex the TBFE was −31.03 kcal/mol. The results showed the inhibition potential of these compounds by targeting the RBD. In conclusion, this study will help in the design and discovery of novel drug therapeutics, which may be used against the emerging Omicron variant of SARS-CoV-2.
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Khan T, Abdullah M, Toor TF, Almajhdi FN, Suleman M, Iqbal A, Ali L, Khan A, Waheed Y, Wei DQ. Evaluation of the Whole Proteome of Achromobacter xylosoxidans to Identify Vaccine Targets for mRNA and Peptides-Based Vaccine Designing Against the Emerging Respiratory and Lung Cancer-Causing Bacteria. Front Med (Lausanne) 2022; 8:825876. [PMID: 35186980 PMCID: PMC8854494 DOI: 10.3389/fmed.2021.825876] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/29/2021] [Indexed: 02/05/2023] Open
Abstract
Achromobacter xylosoxidans is a rod-shaped Gram-negative bacterium linked with causing several infections which mostly includes hematological malignancies. It has been recently reported to be associated with the development and progression of lung cancer and is an emerging respiratory disease-causing bacterium. The treatment of individuals infected with A. xylosoxidans bacteremia is difficult due to the fact that this pathogen has both intrinsic and acquired resistance mechanisms, typically resulting in a phenotype of multidrug resistance (MDR). Efforts are needed to design effective therapeutic strategies to curtail the emergence of this bacterium. Computational vaccine designing has proven its effectiveness, specificity, safety, and stability compared to conventional approaches of vaccine development. Therefore, the whole proteome of A. xylosoxidans was screened for the characterization of potential vaccine targets through subtractive proteomics pipeline for therapeutics design. Annotation of the whole proteome confirmed the three immunogenic vaccine targets, such as (E3HHR6), (E3HH04), and (E3HWA2), which were used to map the putative immune epitopes. The shortlisted epitopes, specific against Cytotoxic T Lymphocytes, Helper T-cell Lymphocytes, and linear B-Cell, were used to design the mRNA and multi-epitopes vaccine (MEVC). Initial validations confirmed the antigenic and non-allergenic properties of these constructs, followed by docking with the immune receptor, TLR-5, which resulted in robust interactions. The interaction pattern that followed in the docking complex included formation of 5 hydrogen bonds, 2 salt bridges, and 165 non-bonded contacts. This stronger binding affinity was also assessed through using the mmGBSA approach, showing a total of free binding energy of -34.64 kcal/mol. Further validations based on in silico cloning revealed a CAI score of 0.98 and an optimal percentage of GC contents (54.4%) indicated a putatively higher expression of the vaccine construct in Escherichia coli. Moreover, immune simulation revealed strong antibodies production upon the injection of the designed MEVC that resulted in the highest peaks of IgM+ IgG production (>3,500) between 10 and 15 days. In conclusion the current study provide basis for vaccine designing against the emerging A. xylosoxidans, which demands further experimental studies for in vitro and in vivo validations.
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Affiliation(s)
- Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | | | - Fahad N. Almajhdi
- Department of Botany and Microbiology, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Kanju, Pakistan
| | - Arshad Iqbal
- Centre for Biotechnology and Microbiology, University of Swat, Kanju, Pakistan
| | - Liaqat Ali
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, Islamabad, Pakistan
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, China
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Structural and Dynamic Insights into the W68L, L85P, and T87A Mutations of Mycobacterium tuberculosis Inducing Resistance to Pyrazinamide. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19031615. [PMID: 35162636 PMCID: PMC8835092 DOI: 10.3390/ijerph19031615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/05/2022] [Accepted: 01/19/2022] [Indexed: 12/10/2022]
Abstract
Tuberculosis (TB), the most frequent bacterium-mediated infectious disease caused by Mycobacterium tuberculosis, has been known to infect humans since ancient times. Although TB is common worldwide, the most recent report by the WHO (World Health Organization) listed the three countries of India, China, and Russia with 27%, 14%, and 8% of the global burden of TB, respectively. It has been reported that resistance to TB drugs, particularly by the pncA gene to the pyrazinamide drug due to mutations, significantly affects the effective treatment of TB. Understanding the mechanism of drug resistance using computational methods is of great interest to design effective TB treatment, exploring the structural features with these tools. Thus, keeping in view the importance of these methods, we employed state-of-the-art computational methods to study the mechanism of resistance caused by the W68L, L85P, and T87A mutations recently reported in 2021. We employed a molecular docking approach to predict the binding conformation and studied the dynamic properties of each complex using molecular dynamics simulation approaches. Our analysis revealed that compared to the wildtype, these three mutations altered the binding pattern and reduced the binding affinity. Moreover, the structural dynamic features also showed that these mutations significantly reduced the structural stability and packing, particularly by the W68L and L85P mutations. Moreover, principal component analysis, free energy landscape, and the binding free energy results revealed variation in the protein’s motion and the binding energy. The total binding free energy was for the wildtype −9.61 kcal/mol, W68L −7.57 kcal/mol, L85P −6.99 kcal/mol, and T87A −7.77 kcal/mol. Our findings can help to design a structure-based drug against the MDR (multiple drug-resistant) TB.
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Kolesov DE, Sinegubova MV, Safenkova IV, Vorobiev II, Orlova NA. Antigenic properties of the SARS-CoV-2 nucleoprotein are altered by the RNA admixture. PeerJ 2022; 10:e12751. [PMID: 35036106 PMCID: PMC8744485 DOI: 10.7717/peerj.12751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/15/2021] [Indexed: 01/07/2023] Open
Abstract
Determining the presence of antibodies to the SARS-CoV-2 antigens is the best way to identify infected people, regardless of the development of symptoms of COVID-19. The nucleoprotein (NP) of the SARS-CoV-2 is an immunodominant antigen of the virus; anti-NP antibodies are detected in persons previously infected with the virus with the highest titers. Many test systems for detecting antibodies to SARS-CoV-2 contain NP or its fragments as antigen. The sensitivity and specificity of such test systems differ significantly, which can be explained by variations in the antigenic properties of NP caused by differences in the methods of its cultivation, isolation and purification. We investigated this effect for the Escherichia coli-derived SARS-CoV-2 NP, obtained from the cytoplasm in the soluble form. We hypothesized that co-purified nucleic acids that form a strong complex with NP might negatively affect NP's antigenic properties. Therefore, we have established the NP purification method, which completely eliminates the RNA in the NP preparation. Two stages of RNA removal were used: treatment of the crude lysate of E. coli with RNase A and subsequent selective RNA elution with 2 M NaCl solution. The resulting NP without RNA has a significantly better signal-to-noise ratio when used as an ELISA antigen and tested with a control panel of serum samples with antibodies to SARS-CoV-2; therefore, it is preferable for in vitro diagnostic use. The same increase of the signal-to-noise ratio was detected for the free N-terminal domain of the NP. Complete removal of RNA complexed with NP during purification will significantly improve its antigenic properties, and the absence of RNA in NP preparations should be controlled during the production of this antigen.
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Affiliation(s)
- Denis E. Kolesov
- Laboratory of Mammalian Cell Bioengineering, Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Maria V. Sinegubova
- Laboratory of Mammalian Cell Bioengineering, Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Irina V. Safenkova
- Laboratory of Immunobiochemistry, Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia, Moscow, Russia
| | - Ivan I. Vorobiev
- Laboratory of Mammalian Cell Bioengineering, Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda A. Orlova
- Laboratory of Mammalian Cell Bioengineering, Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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Khan A, Hussain S, Ahmad S, Suleman M, Bukhari I, Khan T, Rashid F, Azad AK, Waseem M, Khan W, Hussain Z, Khan A, Ali SS, Qin Q, Wei DQ. Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Comput Biol Med 2022; 141:105163. [PMID: 34979405 PMCID: PMC8716154 DOI: 10.1016/j.compbiomed.2021.105163] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/16/2021] [Accepted: 12/19/2021] [Indexed: 12/28/2022]
Abstract
The spike protein of SARS-CoV-2 and the host ACE2 receptor plays a vital role in the entry to the cell. Among which the hotspot residue 501 is continuously subjected to positive selection pressure and induces unusual virulence. Keeping in view the importance of the hot spot residue 501, we predicted the potentially emerging structural variants of 501 residue. We analyzed the binding pattern of wild type and mutants (Spike RBD) to the ACE2 receptor by deciphering variations in the amino acids’ interaction networks by graph kernels along with evolutionary, network metrics, and energetic information. Our analysis revealed that N501I, N501T, and N501V increase the binding affinity and alter the intra and inter-residue bonding networks. The N501T has shown strong positive selection and fitness in other animals. Docking results and repeated simulations (three times) confirmed the structural stability and tighter binding of these three variants, correlated with the previous results following the global stability trend. Consequently, we reported three variants N501I, N501T, and N501V could worsen the situation further if they emerged. The relations between the viral fitness and binding affinity is a complicated game thus the emergence of high affinity mutations in the SARS-CoV-2 RBD brings up the question of whether or not positive selection favours these mutations or not?
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Sarfaraz Hussain
- Institute of Food Sciences and Technology, Chinese Academy of Agriculture Sciences, Beijing, 100193, China
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat, KP, Pakistan
| | - Imrana Bukhari
- Department of Botany, University of Okara, Punjab, Pakistan
| | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Farooq Rashid
- School of Public Health, Department of Epidemiology, Southern Medical University, Dermatology Hospital, Guangzhou, China
| | - Abul Kalam Azad
- Advanced Drug Delivery Laboratory, Department of Pharmaceutical Technology, Faculty of Pharmacy, International Islamic University Malaysia, 25200, Kuantan, Pahang, Malaysia
| | - Muhammad Waseem
- Faculty of Rehabilitation and Allied Health Science, Riphah International University, Islamabad, Pakistan
| | - Wajid Khan
- Center for Biotechnology and Microbiology, University of Swat, Swat, KP, Pakistan
| | - Zahid Hussain
- Center for Biotechnology and Microbiology, University of Swat, Swat, KP, Pakistan
| | - Asghar Khan
- Saidu Teaching Hospital, Saidu Sharif, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, KP, Pakistan
| | - Qiyao Qin
- School of Statistics, Renmin University of China, PR China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China; State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China.
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Karlebach G, Aronow B, Baylin SB, Butler D, Foox J, Levy S, Meydan C, Mozsary C, Saravia-Butler AM, Taylor DM, Wurtele E, Mason CE, Beheshti A, Robinson PN. Betacoronavirus-specific alternate splicing. Genomics 2022; 114:110270. [PMID: 35074468 PMCID: PMC8782732 DOI: 10.1016/j.ygeno.2022.110270] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/15/2021] [Accepted: 01/16/2022] [Indexed: 11/04/2022]
Abstract
Viruses can subvert a number of cellular processes including splicing in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to suppress global mRNA splicing, and at least 10 SARS-CoV-2 proteins bind specifically to one or more human RNAs. Here, we investigate 17 published experimental and clinical datasets related to SARS-CoV-2 infection, datasets from the betacoronaviruses SARS-CoV and MERS, as well as Streptococcus pneumonia, HCV, Zika virus, Dengue virus, influenza H3N2, and RSV. We show that genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those of SARS-CoV and MERS and affect a diverse set of genes and biological functions, including many closely related to virus biology. Additionally, the differentially spliced transcripts of cells infected by coronaviruses were more likely to undergo intron-retention, contain a pseudouridine modification, and have a smaller number of exons as compared with differentially spliced transcripts in the control groups. Viral load in clinical COVID-19 samples was correlated with isoform distribution of differentially spliced genes. A significantly higher number of ribosomal genes are affected by differential alternative splicing and gene expression in betacoronavirus samples, and the betacoronavirus differentially spliced genes are depleted for binding sites of RNA-binding proteins. Our results demonstrate characteristic patterns of differential splicing in cells infected by SARS-CoV-2, SARS-CoV, and MERS. The alternative splicing changes observed in betacoronaviruses infection potentially modify a broad range of cellular functions, via changes in the functions of the products of a diverse set of genes involved in different biological processes.
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Farahani M, Niknam Z, Mohammadi Amirabad L, Amiri-Dashatan N, Koushki M, Nemati M, Danesh Pouya F, Rezaei-Tavirani M, Rasmi Y, Tayebi L. Molecular pathways involved in COVID-19 and potential pathway-based therapeutic targets. Biomed Pharmacother 2022; 145:112420. [PMID: 34801852 PMCID: PMC8585639 DOI: 10.1016/j.biopha.2021.112420] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/05/2021] [Accepted: 11/10/2021] [Indexed: 01/08/2023] Open
Abstract
Deciphering the molecular downstream consequences of severe acute respiratory syndrome coronavirus (SARS-CoV)- 2 infection is important for a greater understanding of the disease and treatment planning. Furthermore, greater understanding of the underlying mechanisms of diagnostic and therapeutic strategies can help in the development of vaccines and drugs against COVID-19. At present, the molecular mechanisms of SARS-CoV-2 in the host cells are not sufficiently comprehended. Some of the mechanisms are proposed considering the existing similarities between SARS-CoV-2 and the other members of the β-CoVs, and others are explained based on studies advanced in the structure and function of SARS-CoV-2. In this review, we endeavored to map the possible mechanisms of the host response following SARS-CoV-2 infection and surveyed current research conducted by in vitro, in vivo and human observations, as well as existing suggestions. We addressed the specific signaling events that can cause cytokine storm and demonstrated three forms of cell death signaling following virus infection, including apoptosis, pyroptosis, and necroptosis. Given the elicited signaling pathways, we introduced possible pathway-based therapeutic targets; ADAM17 was especially highlighted as one of the most important elements of several signaling pathways involved in the immunopathogenesis of COVID-19. We also provided the possible drug candidates against these targets. Moreover, the cytokine-cytokine receptor interaction pathway was found as one of the important cross-talk pathways through a pathway-pathway interaction analysis for SARS-CoV-2 infection.
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Affiliation(s)
- Masoumeh Farahani
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Niknam
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Nasrin Amiri-Dashatan
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mehdi Koushki
- Department of Clinical Biochemistry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohadeseh Nemati
- Department of Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Fahima Danesh Pouya
- Department of Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Yousef Rasmi
- Department of Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran; Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran.
| | - Lobat Tayebi
- Marquette University School of Dentistry, Milwaukee, WI 53233, USA
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Muhseen ZT, Kadhim S, Yahiya YI, Alatawi EA, Aba Alkhayl FF, Almatroudi A. Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. BIOLOGY 2021; 10:1310. [PMID: 34943225 PMCID: PMC8698945 DOI: 10.3390/biology10121310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022]
Abstract
Recently, a new variant, B.1620, with mutations (S477N-E484K) in the spike protein's receptor-binding domain (RBD) has been reported in Europe. In order to design therapeutic strategies suitable for B.1.620, further studies are required. A detailed investigation of the structural features and variations caused by these substitutions, that is, a molecular level investigation, is essential to uncover the role of these changes. To determine whether and how the binding affinity of ACE2-RBD is affected, we used protein-protein docking and all-atom simulation approaches. Our analysis revealed that B.1.620 binds more strongly than the wild type and alters the hydrogen bonding network. The docking score for the wild type was reported to be -122.6 +/- 0.7 kcal/mol, while for B.1.620, the docking score was -124.9 +/- 3.8 kcal/mol. A comparative binding investigation showed that the wild-type complex has 11 hydrogen bonds and one salt bridge, while the B.1.620 complex has 14 hydrogen bonds and one salt bridge, among which most of the interactions are preserved between the wild type and B.1.620. A dynamic analysis of the two complexes revealed stable dynamics, which corroborated the global stability trend, compactness, and flexibility of the three essential loops, providing a better conformational optimization opportunity and binding. Furthermore, binding free energy revealed that the wild type had a total binding energy of -51.14 kcal/mol, while for B.1.628, the total binding energy was -68.25 kcal/mol. The current findings based on protein complex modeling and bio-simulation methods revealed the atomic features of the B.1.620 variant harboring S477N and E484K mutations in the RBD and the basis for infectivity. In conclusion, the current study presents distinguishing features of B.1.620, which can be used to design structure-based drugs against the B.1.620 variant.
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Affiliation(s)
- Ziyad Tariq Muhseen
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
- School of Life Sciences, Shaanxi Normal University, Xi’an 710062, China
| | - Salim Kadhim
- Department of Pharmacology, College of Pharmacy, University of Alkafeel, Najaf 61001, Iraq; (S.K.); (Y.I.Y.)
| | - Yahiya Ibrahim Yahiya
- Department of Pharmacology, College of Pharmacy, University of Alkafeel, Najaf 61001, Iraq; (S.K.); (Y.I.Y.)
| | - Eid A. Alatawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia;
| | - Faris F. Aba Alkhayl
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia;
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Dentistry and Pharmacy, Buraydah Colleges, Buraydah 51418, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia;
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Khan A, Mohammad A, Haq I, Nasar M, Ahmad W, Yousafi Q, Suleman M, Ahmad S, Albutti A, Khan T, Marafie SK, Alshawaf E, Ali SS, Abubaker J, Wei DQ. Structural-Dynamics and Binding Analysis of RBD from SARS-CoV-2 Variants of Concern (VOCs) and GRP78 Receptor Revealed Basis for Higher Infectivity. Microorganisms 2021; 9:2331. [PMID: 34835456 PMCID: PMC8619099 DOI: 10.3390/microorganisms9112331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 01/21/2023] Open
Abstract
Glucose-regulated protein 78 (GRP78) might be a receptor for SARS-CoV-2 to bind and enter the host cell. Recently reported mutations in the spike glycoprotein unique to the receptor-binding domain (RBD) of different variants might increase the binding and pathogenesis. However, it is still not known how these mutations affect the binding of RBD to GRP78. The current study provides a structural basis for the binding of GRP78 to the different variants, i.e., B.1.1.7, B.1.351, B.1.617, and P.1 (spike RBD), of SARS-CoV-2 using a biomolecular simulation approach. Docking results showed that the new variants bound stronger than the wild-type, which was further confirmed through the free energy calculation results. All-atom simulation confirmed structural stability, which was consistent with previous results by following the global stability trend. We concluded that the increased binding affinity of the B.1.1.7, B.1.351, and P.1 variants was due to a variation in the bonding network that helped the virus induce a higher infectivity and disease severity. Consequently, we reported that the aforementioned new variants use GRP78 as an alternate receptor to enhance their seriousness.
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (T.K.)
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (A.M.); (S.K.M.); (E.A.); (J.A.)
| | - Inamul Haq
- Department of Animal Sciences, Jeonbuk National University, 567 Baekji-Daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, Jeonju 54896, Korea;
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun 55365, Korea
| | - Mohammad Nasar
- Department of Biosciences, COMSATS University, Islamabad-Sahiwal Campus, Punjab 57000, Pakistan; (M.N.); (Q.Y.)
| | - Waqar Ahmad
- Department of Microbiology, Abdul Wali Khan University (AWKUM), Mardan 23200, Khyber Pakhtunkhwa, Pakistan;
| | - Qudsia Yousafi
- Department of Biosciences, COMSATS University, Islamabad-Sahiwal Campus, Punjab 57000, Pakistan; (M.N.); (Q.Y.)
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat 19200, KP, Pakistan; (M.S.); (S.S.A.)
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25120, Pakistan;
| | - Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia;
| | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (T.K.)
| | - Sulaiman K. Marafie
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (A.M.); (S.K.M.); (E.A.); (J.A.)
| | - Eman Alshawaf
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (A.M.); (S.K.M.); (E.A.); (J.A.)
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat 19200, KP, Pakistan; (M.S.); (S.S.A.)
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (A.M.); (S.K.M.); (E.A.); (J.A.)
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (T.K.)
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen 518055, China
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National Holidays and Social Mobility Behaviors: Alternatives for Forecasting COVID-19 Deaths in Brazil. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182111595. [PMID: 34770108 PMCID: PMC8582864 DOI: 10.3390/ijerph182111595] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/30/2021] [Accepted: 10/31/2021] [Indexed: 01/08/2023]
Abstract
In this paper, we investigate the influence of holidays and community mobility on the transmission rate and death count of COVID-19 in Brazil. We identify national holidays and hallmark holidays to assess their effect on disease reports of confirmed cases and deaths. First, we use a one-variate model with the number of infected people as input data to forecast the number of deaths. This simple model is compared with a more robust deep learning multi-variate model that uses mobility and transmission rates (R0, Re) from a SEIRD model as input data. A principal components model of community mobility, generated by the principal component analysis (PCA) method, is added to improve the input features for the multi-variate model. The deep learning model architecture is an LSTM stacked layer combined with a dense layer to regress daily deaths caused by COVID-19. The multi-variate model incremented with engineered input features can enhance the forecast performance by up to 18.99% compared to the standard one-variate data-driven model.
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Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Comput Biol Med 2021; 138:104936. [PMID: 34655895 PMCID: PMC8501515 DOI: 10.1016/j.compbiomed.2021.104936] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 12/26/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Reports of new variants that potentially increase virulence and viral transmission, as well as reduce the efficacy of available vaccines, have recently emerged. In this study, we computationally analyzed the N439K, S477 N, and T478K variants for their ability to bind Angiotensin-converting enzyme 2 (ACE2). We used the protein-protein docking approach to explore whether the three variants displayed a higher binding affinity to the ACE2 receptor than the wild type. We found that these variants alter the hydrogen bonding network and the cluster of interactions. Additional salt bridges, hydrogen bonds, and a high number of non-bonded contacts (i.e., non-bonded interactions between atoms in the same molecule and those in other molecules) were observed only in the mutant complexes, allowing efficient binding to the ACE2 receptor. Furthermore, we used a 2.0-μs all-atoms simulation approach to detect differences in the structural dynamic features of the resulting protein complexes. Our findings revealed that the mutant complexes possessed stable dynamics, consistent with the global trend of mutations yielding variants with improved stability and enhanced affinity. Binding energy calculations based on molecular mechanics/generalized Born surface area (MM/GBSA) further revealed that electrostatic interactions principally increased net binding energies. The stability and binding energies of N439K, S477 N, and T478K variants were enhanced compared to the wild-type-ACE2 complex. The net binding energy of the systems was -31.86 kcal/mol for the wild-type-ACE2 complex, -67.85 kcal/mol for N439K, -69.82 kcal/mol for S477 N, and -69.64 kcal/mol for T478K. The current study provides a basis for exploring the enhanced binding abilities and structural features of SARS-CoV-2 variants to design novel therapeutics against the virus.
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