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Shum MHH, Lee Y, Tam L, Xia H, Chung OLW, Guo Z, Lam TTY. Binding affinity between coronavirus spike protein and human ACE2 receptor. Comput Struct Biotechnol J 2024; 23:759-770. [PMID: 38304547 PMCID: PMC10831124 DOI: 10.1016/j.csbj.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.
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Affiliation(s)
- Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Yang Lee
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Leighton Tam
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Hui Xia
- Department of Chemistry, South University of Science and Technology of China, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Oscar Lung-Wa Chung
- Department of Chemistry, South University of Science and Technology of China, China
| | - Zhihong Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
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Moiseenko A, Zhang Y, Vorovitch MF, Ivanova AL, Liu Z, Osolodkin DI, Egorov AM, Ishmukhametov AA, Sokolova OS. Structural diversity of tick-borne encephalitis virus particles in the inactivated vaccine based on strain Sofjin. Emerg Microbes Infect 2024; 13:2290833. [PMID: 38073510 DOI: 10.1080/22221751.2023.2290833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/29/2023] [Indexed: 03/12/2024]
Abstract
The main approach to preventing tick-borne encephalitis (TBE) is vaccination. Formaldehyde-inactivated TBE vaccines have a proven record of safety and efficiency but have never been characterized structurally with atomic resolution. We report a cryoelectron microscopy (cryo-EM) structure of the formaldehyde-inactivated TBE virus (TBEV) of Sofjin-Chumakov strain representing the Far-Eastern subtype. A 3.8 Å resolution reconstruction reveals the structural integrity of the envelope E proteins, specifically the E protein ectodomains. The comparative study shows a high structural similarity to the previously published structures of the TBEV European subtype strains Hypr and Kuutsalo-14. A fraction of inactivated virions exhibits asymmetric features including the deformations of the membrane profile. We propose that the heterogeneity is caused by inactivation and perform a local variability analysis on the small parts of the envelope protein shell to reveal membrane curvature features possibly induced by the inactivation. The results of this study will have implications for the design of novel vaccines against diseases caused by flaviviruses.
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Affiliation(s)
- Andrey Moiseenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yichen Zhang
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, People's Republic of China
| | - Mikhail F Vorovitch
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alla L Ivanova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Chinese University of Hong Kong, Shenzhen, People's Republic of China
| | - Dmitry I Osolodkin
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexey M Egorov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Aydar A Ishmukhametov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Olga S Sokolova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, People's Republic of China
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Landers VD, Thomas M, Isom CM, Karki D, Sokoloski KJ. Capsid protein mediated evasion of IRAK1-dependent signalling is essential to Sindbis virus neuroinvasion and virulence in mice. Emerg Microbes Infect 2024; 13:2300452. [PMID: 38164715 PMCID: PMC10773654 DOI: 10.1080/22221751.2023.2300452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
ABSTRACTAlphaviruses are arthropod-borne, single-stranded positive-sense RNA viruses that are recognized as rapidly emerging pathogens. Despite being exquisitely sensitive to the effects of the innate immune response alphaviruses can readily replicate, disseminate, and induce pathogenesis in immunologically competent hosts. Nonetheless, how alphaviruses evade the induction of an innate immune response prior to viral gene expression, or in non-permissive infections, is unknown. Previously we reported the identification of a novel host/pathogen interaction between the viral Capsid (CP) protein and the host IRAK1 protein. The CP/IRAK1 interaction was determined to negatively impact IRAK1-dependent PAMP detection in vitro, however, the precise importance of the CP/IRAK1 interaction to alphaviral infection remained unknown. Here we detail the identification of the CP/IRAK1 interaction determinants of the Sindbis virus (SINV) CP protein and examine the importance of the interaction to alphaviral infection and pathogenesis in vivo using an interaction deficient mutant of the model neurotropic strain of SINV. Importantly, these interaction determinants are highly conserved across multiple Old-World alphaviruses, including Ross River virus (RRV), Mayaro virus (MAYV), Chikungunya virus (CHIKV), and Semliki Forest virus (SFV). In the absence of a functional CP/IRAK1 interaction, SINV replication is significantly restricted and fails to disseminate from the primary site of inoculation due to the induction of a robust type-I Interferon response. Altogether these data indicate that the evasion of IRAK1-dependent signalling is critical to overcoming the host innate immune response and the in vivo data presented here demonstrate the importance of the CP/IRAK1 interaction to neurovirulence and pathogenesis.
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Affiliation(s)
- V Douglas Landers
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Milton Thomas
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Cierra M. Isom
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Deepa Karki
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Kevin J. Sokoloski
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY, USA
- Center for Predictive Medicine and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
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Chen GH, Dai YC, Hsieh SC, Tsai JJ, Sy AK, Jiz M, Pedroso C, Brites C, Netto EM, Kanki PJ, Saunders DRD, Vanlandingham DL, Higgs S, Huang YJS, Wang WK. Detection of anti-premembrane antibody as a specific marker of four flavivirus serocomplexes and its application to serosurveillance in endemic regions. Emerg Microbes Infect 2024; 13:2301666. [PMID: 38163752 PMCID: PMC10810658 DOI: 10.1080/22221751.2023.2301666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/30/2023] [Indexed: 01/03/2024]
Abstract
In the past few decades, several emerging/re-emerging mosquito-borne flaviviruses have resulted in disease outbreaks of public health concern in the tropics and subtropics. Due to cross-reactivities of antibodies recognizing the envelope protein of different flaviviruses, serosurveillance remains a challenge. Previously we reported that anti-premembrane (prM) antibody can discriminate between three flavivirus infections by Western blot analysis. In this study, we aimed to develop a serological assay that can discriminate infection or exposure with flaviviruses from four serocomplexes, including dengue (DENV), Zika (ZIKV), West Nile (WNV) and yellow fever (YFV) viruses, and explore its application for serosurveillance in flavivirus-endemic countries. We employed Western blot analysis including antigens of six flaviviruses (DENV1, 2 and 4, WNV, ZIKV and YFV) from four serocomplexes. We tested serum samples from YF-17D vaccinees, and from DENV, ZIKV and WNV panels that had been confirmed by RT-PCR or by neutralization assays. The overall sensitivity/specificity of anti-prM antibodies for DENV, ZIKV, WNV, and YFV infections/exposure were 91.7%/96.4%, 91.7%/99.2%, 88.9%/98.3%, and 91.3%/92.5%, respectively. When testing 48 samples from Brazil, we identified multiple flavivirus infections/exposure including DENV and ZIKV, DENV and YFV, and DENV, ZIKV and YFV. When testing 50 samples from the Philippines, we detected DENV, ZIKV, and DENV and ZIKV infections with a ZIKV seroprevalence rate of 10%, which was consistent with reports of low-level circulation of ZIKV in Asia. Together, these findings suggest that anti-prM antibody is a flavivirus serocomplex-specific marker and can be employed to delineate four flavivirus infections/exposure in regions where multiple flaviviruses co-circulate.
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Affiliation(s)
- Guan-Hua Chen
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Yu-Ching Dai
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Szu-Chia Hsieh
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Jih-Jin Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ava Kristy Sy
- National Reference Laboratory for Dengue and Other Arbovirus, Virology Department, Research Institute for Tropical Medicine, Muntinlupa City, Philippines
| | - Mario Jiz
- Immunology Department, Research Institute for Tropical Medicine, Muntinlupa City, Philippines
| | - Celia Pedroso
- LAPI-Laboratório de Pesquisa em Infectologia-School of Medicine, Federal University of Bahia, Salvador, Brazil
| | - Carlos Brites
- LAPI-Laboratório de Pesquisa em Infectologia-School of Medicine, Federal University of Bahia, Salvador, Brazil
| | - Eduardo Martins Netto
- LAPI-Laboratório de Pesquisa em Infectologia-School of Medicine, Federal University of Bahia, Salvador, Brazil
| | - Phyllis J. Kanki
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Dana L. Vanlandingham
- Biosecurity Research Institute and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Stephen Higgs
- Biosecurity Research Institute and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Yan-Jang S. Huang
- Biosecurity Research Institute and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Wei-Kung Wang
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
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Leveringhaus E, Poljakovic R, Herrmann G, Roman-Sosa G, Becher P, Postel A. Porcine low-density lipoprotein receptor plays an important role in classical swine fever virus infection. Emerg Microbes Infect 2024; 13:2327385. [PMID: 38514916 PMCID: PMC10962300 DOI: 10.1080/22221751.2024.2327385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024]
Abstract
Several cellular factors have been reported to be required for replication of classical swine fever virus (CSFV), a member of the genus Pestivirus within the family Flaviviridae. However, many steps of its replication cycle are still poorly understood. The low-density lipoprotein receptor (LDLR) is involved in cell entry and post-entry processes of different viruses including other members of the Flaviviridae. In this study, the relevance of LDLR in replication of CSFV and another porcine pestivirus, Bungowannah pestivirus (BuPV), was investigated by antibody-mediated blocking of LDLR and genetically engineered porcine cell lines providing altered LDLR expression levels. An LDLR-specific antibody largely blocked infection with CSFV, but had only a minor impact on BuPV. Infections of the genetically modified cells confirmed an LDLR-dependent replication of CSFV. Compared to wild type cells, lower and higher expression of LDLR resulted in a 3.5-fold decrease or increase in viral titers already 20 h post infection. Viral titers were 25-fold increased in LDLR-overexpressing cells compared to cells with reduced LDLR expression at 72 h post infection. The varying LDLR expression levels had no clear effect on permissivity to BuPV. A decoy receptor assay using recombinant soluble LDLR provided no evidence that LDLR may function as a receptor for CSFV or BuPV. Differences in their dependency on LDLR suggest that CSFV and BuPV likely use different mechanisms to interact with their host cells. Moreover, this study reveals similarities in the replication cycles of CSFV and other members of the family Flaviviridae that are dependent on LDLR.
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Affiliation(s)
- Elena Leveringhaus
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Robin Poljakovic
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Gina Herrmann
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Gleyder Roman-Sosa
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Paul Becher
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Alexander Postel
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
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Zhang Y, Fang L, Wang Z, Zhang C, Zhao J, Daemi HB, Zhang M, Yuan L, Han X, Li L, Fu ZF, Zhou M, Zhao L. A modified recombinant adenovirus vector containing dual rabies virus G expression cassettes confers robust and long-lasting humoral immunity in mice, cats, and dogs. Emerg Microbes Infect 2024; 13:2300461. [PMID: 38164714 PMCID: PMC10810672 DOI: 10.1080/22221751.2023.2300461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
During the COVID-19 epidemic, the incidence of rabies has increased in several countries, especially in remote and disadvantaged areas, due to inadequate surveillance and declining immunization coverage. Multiple vaccinations with inactivated rabies virus vaccines for pre- or post-exposure prophylaxis are considered inefficient, expensive and impractical in developing countries. Herein, three modified human recombinant adenoviruses type 5 designated Adv-RVG, Adv-E1-RVG, and Adv-RVDG, carrying rabies virus G (RVG) expression cassettes in various combinations within E1 or E3 genomic regions, were constructed to serve as rabies vaccine candidates. Adv-RVDG mediated greater RVG expression both in vitro and in vivo and induced a more robust and durable humoral immune response than the rabies vaccine strain SAD-L16, Adv-RVG, and Adv-E1-RVG by more effectively activating the dendritic cells (DCs) - follicular helper T (Tfh) cells - germinal centre (GC) / memory B cells (MBCs) - long-lived plasma cells (LLPCs) axis with 100% survival after a lethal RABV challenge in mice during the 24-week study period. Similarly, dogs and cats immunized with Adv-RVDG showed stronger and longer-lasting antibody responses than those vaccinated with a commercial inactivated rabies vaccine and showed good tolerance to Adv-RVDG. In conclusion, our study demonstrated that simultaneous insertion of protective antigens into the E1 and E3 genomic regions of adenovirus vector can significantly enhance the immunogenicity of adenoviral-vectored vaccines, providing a theoretical and practical basis for the subsequent development of multivalent and multi-conjugated vaccines using recombinant adenovirus platform. Meanwhile, our data suggest Adv-RVDG is a safe, efficient, and economical vaccine for mass-coverage immunization.
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Affiliation(s)
- Yuan Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Lingying Fang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Zongmei Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Chengguang Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Jianqing Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Hakimeh Baghaei Daemi
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Mai Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Liwen Yuan
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Xiaohu Han
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Linfeng Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Zhen F. Fu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Ming Zhou
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Ling Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Hubei Hongshan Laboratory, Wuhan, People’s Republic of China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
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Nakonieczna A, Topolska-Woś A, Łobocka M. New bacteriophage-derived lysins, LysJ and LysF, with the potential to control Bacillus anthracis. Appl Microbiol Biotechnol 2024; 108:76. [PMID: 38194144 PMCID: PMC10776502 DOI: 10.1007/s00253-023-12839-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 01/10/2024]
Abstract
Bacillus anthracis is an etiological agent of anthrax, a severe zoonotic disease that can be transmitted to people and cause high mortalities. Bacteriophages and their lytic enzymes, endolysins, have potential therapeutic value in treating infections caused by this bacterium as alternatives or complements to antibiotic therapy. They can also be used to identify and detect B. anthracis. Endolysins of two B. anthracis Wbetavirus phages, J5a and F16Ba which were described by us recently, differ significantly from the best-known B. anthracis phage endolysin PlyG from Wbetavirus genus bacteriophage Gamma and a few other Wbetavirus genus phages. They are larger than PlyG (351 vs. 233 amino acid residues), contain a signal peptide at their N-termini, and, by prediction, have a different fold of cell binding domain suggesting different structural basis of cell epitope recognition. We purified in a soluble form the modified versions of these endolysins, designated by us LysJ and LysF, respectively, and depleted of signal peptides. Both modified endolysins could lyse the B. anthracis cell wall in zymogram assays. Their activity against the living cells of B. anthracis and other species of Bacillus genus was tested by spotting on the layers of bacteria in soft agar and by assessing the reduction of optical density of bacterial suspensions. Both methods proved the effectiveness of LysJ and LysF in killing the anthrax bacilli, although the results obtained by each method differed. Additionally, the lytic efficiency of both proteins was different, which apparently correlates with differences in their amino acid sequence. KEY POINTS: • LysJ and LysF are B. anthracis-targeting lysins differing from lysins studied so far • LysJ and LysF could be overproduced in E. coli in soluble and active forms • LysJ and LysF are active in killing cells of B. anthracis virulent strains.
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Affiliation(s)
- Aleksandra Nakonieczna
- Military Institute of Hygiene and Epidemiology, Biological Threats Identification and Countermeasure Center, 24-100, Puławy, Poland.
| | | | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106, Warsaw, Poland
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Calzolari M, Callegari E, Grisendi A, Munari M, Russo S, Sgura D, Giannini A, Dalmonte G, Scremin M, Dottori M. Arbovirus screening of mosquitoes collected in 2022 in Emilia-Romagna, Italy, with the implementation of a real-time PCR for the detection of Tahyna virus. One Health 2024; 18:100670. [PMID: 38274566 PMCID: PMC10809124 DOI: 10.1016/j.onehlt.2023.100670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Several Arboviruses (Arthropod-borne virus) are a concrete health risk. While some arboviruses, such as the West Nile virus (WNV) and the Usutu virus (USUV) are actively surveyed, others are neglected, including the Tahyna virus (TAHV). In this work, we tested - searching for all the three viruses - 37,995 mosquitoes collected in 95 attractive traps, baited by carbon dioxide, distributed in the lowlands of Emilia-Romagna, northern Italy, between 19 July and 12 August 2022. Among the 668 pools obtained, WNV was detected in 45 pools of Culex (Cx.) pipiens and USUV was recorded in 24 pools of the same mosquito; ten of these Cx. pipiens pools tested positive for both WNV and USUV. Interestingly, we recorded a significant circulation of both WNV lineage 1 (WNV-L1) and lineage 2 (WNV-L2): WNV-L1 strains were detected in 40 pools, WNV-L2 strains in three pools and both lineages were detected in two pools. TAHV was detected in 8 different species of mosquitoes in a total of 37 pools: Aedes (Ae.) caspius (25), Ae. albopictus (5), Ae. vexans (3), Cx. pipiens (2), Ae. cinereus (1) and Anopheles maculipennis sl (1). The significant number of Ae. caspius-pools tested positive and the estimated viral load suggest that this mosquito is the principal vector in the surveyed area. The potential involvement of other mosquito species in the TAHV cycle could usefully be the subject of further experimental investigation. The results obtained demonstrate that, with adequate sampling effort, entomological surveillance is able to detect arboviruses circulating in a given area. Further efforts must be made to better characterise the TAHV cycle in the surveyed area and to define health risk linked to this virus.
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Affiliation(s)
- Mattia Calzolari
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, via Bianchi, 9-25124 Brescia, Italy
| | - Emanuele Callegari
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, via Bianchi, 9-25124 Brescia, Italy
| | - Annalisa Grisendi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, via Bianchi, 9-25124 Brescia, Italy
| | - Martina Munari
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, via Bianchi, 9-25124 Brescia, Italy
| | - Simone Russo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, via Bianchi, 9-25124 Brescia, Italy
| | - Danilo Sgura
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, via Bianchi, 9-25124 Brescia, Italy
| | - Antonio Giannini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, via Bianchi, 9-25124 Brescia, Italy
| | - Gastone Dalmonte
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, via Bianchi, 9-25124 Brescia, Italy
| | - Mara Scremin
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, via Bianchi, 9-25124 Brescia, Italy
| | - Michele Dottori
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, via Bianchi, 9-25124 Brescia, Italy
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9
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Sadiq S, Harvey E, Mifsud JCO, Minasny B, McBratney AB, Pozza LE, Mahar JE, Holmes EC. Australian terrestrial environments harbour extensive RNA virus diversity. Virology 2024; 593:110007. [PMID: 38346363 DOI: 10.1016/j.virol.2024.110007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 03/13/2024]
Abstract
Australia is home to a diverse range of unique native fauna and flora. To address whether Australian ecosystems also harbour unique viruses, we performed meta-transcriptomic sequencing of 16 farmland and sediment samples taken from the east and west coasts of Australia. We identified 2460 putatively novel RNA viruses across 18 orders, the vast majority of which belonged to the microbe-associated phylum Lenarviricota. In many orders, such as the Nodamuvirales and Ghabrivirales, the novel viruses identified here comprised entirely new clades. Novel viruses also fell between established genera or families, such as in the Cystoviridae and Picornavirales, while highly divergent lineages were identified in the Sobelivirales and Ghabrivirales. Viral read abundance and alpha diversity were influenced by sampling site, soil type and land use, but not by depth from the surface. In sum, Australian soils and sediments are home to remarkable viral diversity, reflecting the biodiversity of local fauna and flora.
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Affiliation(s)
- Sabrina Sadiq
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Budiman Minasny
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Alex B McBratney
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Liana E Pozza
- School of Life and Environmental Sciences & Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
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10
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Obonyo D, Ouma G, Ikawa R, Odeny DA. Meta-transcriptomic identification of groundnut RNA viruses in western Kenya and the novel detection of groundnut as a host for Cauliflower mosaic virus. Virology 2024; 593:110011. [PMID: 38367474 DOI: 10.1016/j.virol.2024.110011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND Groundnut (Arachis hypogaea L.) is the 13th most important global crop grown throughout the tropical and subtropical regions of the world. One of the major constraints to groundnut production is viruses, which are also the most economically important and most abundant pathogens among cultivated legumes. Only a few studies have reported the characterization of RNA viruses in cultivated groundnuts in western Kenya, most of which deployed classical methods of detecting known viruses. METHODS We sampled twenty-one symptomatic and three asymptomatic groundnut leaf samples from farmers' fields in western Kenya. Total RNA was extracted from the samples followed by First-strand cDNA synthesis and sequencing on the Illumina HiSeq 2500 platform. After removing host and rRNA sequences, high-quality viral RNA sequences were de novo assembled and viral genomes annotated using the publicly available NCBI virus database. Multiple sequence alignment and phylogenetic analysis were done using MEGA X. RESULTS Bioinformatics analyses using as low as ∼3.5 million reads yielded complete and partial genomes for Cauliflower mosaic virus (CaMV), Cowpea polerovirus 2 (CPPV2), Groundnut rosette assistor virus (GRAV), Groundnut rosette virus (GRV), Groundnut rosette virus satellite RNA (satRNA) and Peanut mottle virus (PeMoV) falling within the species demarcation criteria. This is the first report of CaMV and the second report of CPPV2 on groundnut hosts in the world. Confirmation of the detected viruses was further verified through phylogenetic analyses alongside reported publicly available highly similar viruses. PeMoV was the only seed-borne virus reported. CONCLUSION Our findings demonstrate the power of Next Generation Sequencing in the discovery and identification of novel viruses in groundnuts. The detection of the new viruses indicates the complexity of virus diseases in groundnuts and would require more focus in future studies to establish the effect of the viruses as sole or mixed infections on the crop. The detection of PeMoV with potential origin from Malawi indicates the importance of seed certification and cross-boundary seed health testing.
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Affiliation(s)
- Dennis Obonyo
- Department of Biotechnology, University of Eldoret, Kenya, P.O Box 1125-30100, Eldoret, Kenya; Centre for Biotechnology and Bioinformatics, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - George Ouma
- Institute for Climate Change and Adaptation, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - Rachel Ikawa
- Centre for Biotechnology and Bioinformatics, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Eastern and Southern Africa, P.O Box 39063-00623, Nairobi, Kenya.
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11
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Yu Y, Zhuo B, Xu W, Li L, Jin X, Ji Y, Ge Y. Diagnosis of an immunocompetent adult with acute headache and fever as Epstein-Barr virus encephalitis by mNGS of cerebrospinal fluid. Diagn Microbiol Infect Dis 2024; 109:116213. [PMID: 38359677 DOI: 10.1016/j.diagmicrobio.2024.116213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/31/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Complicated case with fever or headache of unknown origin is currently one of the main challenges in clinical diagnosis. A retrospective analysis was conducted on a 27-year-old female patient hospitalized with headache and fever, and the pathogen species were ultimately determined by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF). The culture results of CSF showed no bacterial or fungal growth. CSF cytology showed a significant increase in nucleated cells. Pathogenic index (corresponded to human gamma herpesvirus 4) of the microorganism after correcting for human background was 12846.77 with a host index (human resource) of 27822.48 by mNGS of CSF. The patient improved through antiviral treatment with ganciclovir. Epstein-Barr virus encephalitis is rare in immunocompetent adults, which can easily cause misdiagnosis and should be paid attention to. mNGS of CSF has significant advantages in the diagnosis of Epstein-Barr virus encephalitis.
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Affiliation(s)
- Yan Yu
- Center for Rehabilitation Medicine, Department of Ophthalmology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Bingqian Zhuo
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Wei Xu
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China; School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
| | - Lanhui Li
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
| | - Xinyue Jin
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Youqi Ji
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
| | - Yumei Ge
- Center for Rehabilitation Medicine, Department of Ophthalmology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China; Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China; School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China; Key Laboratory of Precision Medicine for Head and Neck Cancers of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, 310014, China.
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12
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Shi Z, Yang X, Shi X, Zhang D, Zhao D, Hao Y, Yang J, Bie X, Yan W, Chen G, Chen L, Liu X, Zheng H, Zhang K. Identification and verification of the role of key metabolites and metabolic pathways on ASFV replication. iScience 2024; 27:109345. [PMID: 38500823 PMCID: PMC10946325 DOI: 10.1016/j.isci.2024.109345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/06/2023] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
African swine fever virus (ASFV) infection usually causes viremia within a few days. However, the metabolic changes in pig serum after ASFV infection remain unclear. In this study, serum samples collected from ASFV-infected pigs at different times were analyzed using pseudotargeted metabolomics method. Metabolomic analysis revealed the dopaminergic synapse pathway has the highest rich factor in both ASFV5 and ASFV10 groups. By disrupting the dopamine synaptic pathway, dopamine receptor antagonists inhibited ASFV replication and L-dopa promoted ASFV replication. In addition, guanosine, one of the top20 changed metabolites in both ASFV5 and ASFV10 groups suppressed the replication of ASFV. Taken together, this study revealed the changed serum metabolite profiles of ASFV-infected pigs at various times after infection and verified the effect of the changed metabolites and metabolic pathways on ASFV replication. These findings may contribute to understanding the pathogenic mechanisms of ASFV and the development of target drugs to control ASF.
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Affiliation(s)
- Zunji Shi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Xing Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Xijuan Shi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Dajun Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Dengshuai Zhao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Yu Hao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Jinke Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Xintian Bie
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Wenqian Yan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Guohui Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Lingling Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Xiangtao Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Haixue Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Keshan Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
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13
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Qian J, Zhang S, Wang F, Li J, Zhang J. What makes SARS-CoV-2 unique? Focusing on the spike protein. Cell Biol Int 2024; 48:404-430. [PMID: 38263600 DOI: 10.1002/cbin.12130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.
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Affiliation(s)
- Jingbo Qian
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shichang Zhang
- Department of Clinical Laboratory Medicine, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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14
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Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
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Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
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15
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Zhang W, Chen Y, Yang F, Zhang H, Su T, Wang J, Zhang Y, Song X. Antiviral effect of palmatine against infectious bronchitis virus through regulation of NF-κB/IRF7/JAK-STAT signalling pathway and apoptosis. Br Poult Sci 2024; 65:119-128. [PMID: 38166582 DOI: 10.1080/00071668.2023.2296929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/29/2023] [Indexed: 01/04/2024]
Abstract
1. Infectious bronchitis virus (IBV), a gamma-coronavirus, can infect chickens of all ages and leads to an acute contact respiratory infection. This study evaluated the anti-viral activity of palmatine, a natural non-flavonoid alkaloid, against IBV in chicken embryo kidney (CEK) cells.2. The half toxic concentration (CC50) of palmatine was 672.92 μM, the half inhibitory concentration (IC50) of palmatine against IBV was 7.76 μM and the selection index (SI) was 86.74.3. Mode of action assay showed that palmatine was able to directly inactivate IBV and inhibited the adsorption, penetration and intracellular replication of IBV.4. Palmatine significantly upregulated TRAF6, TAB1 and IKK-β compared with the IBV-infected group, leading to the increased expressions of pro-inflammatory cytokines IL-1β and TNF-α in the downstream NF-κB signalling pathway.5. Palmatine significantly up-regulated the levels of MDA5, MAVS, IRF7, IFN-α and IFN-β in the IRF7 pathway, inducing type I interferon production. It up-regulated the expression of 2'5'-oligoadenylate synthase (OAS) in the JAK-STAT pathway.6. IBV infection induced cell apoptosis and palmatine-treatment delayed the process of apoptosis by regulation of the expression of apoptosis-related genes (BAX, BCL-2, CASPASE-3 and CASPASE-8).7. Palmatine could exert anti-IBV activity through regulation of NF-κB/IRF7/JAK-STAT signalling pathways and apoptosis, providing a theoretical basis for the utilisation of palmatine to treat IBV infection.
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Affiliation(s)
- W Zhang
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Y Chen
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - F Yang
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - H Zhang
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - T Su
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - J Wang
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Y Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - X Song
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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Yang D, Xiang Y, Song F, Li H, Ji X. Phage therapy: A renewed approach against oral diseases caused by Enterococcus faecalis infections. Microb Pathog 2024; 189:106574. [PMID: 38354990 DOI: 10.1016/j.micpath.2024.106574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 02/16/2024]
Abstract
Antibiotics play an important role in the treatment of infectious diseases. Long-term overuse or misuse of antibiotics, however, has triggered the global crisis of antibiotic resistance, bringing challenges to treating clinical infection. Bacteriophages (phages) are the viruses infecting bacterial cells. Due to high host specificity, high bactericidal activity, and good biosafety, phages have been used as natural alternative antibacterial agents to fight against multiple drug-resistant bacteria. Enterococcus faecalis is the main species detected in secondary persistent infection caused by failure of root canal therapy. Due to strong tolerance and the formation of biofilm, E. faecalis can survive the changes in pH, temperature, and osmotic pressure in the mouth and thus is one of the main causes of periapical lesions. This paper summarizes the advantages of phage therapy, its applications in treating oral diseases caused by E. faecalis infections, and the challenges it faces. It offers a new perspective on phage therapy in oral diseases.
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Affiliation(s)
- Dan Yang
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yingying Xiang
- Department of Stomatology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, 650031, China
| | - Fei Song
- Department of Minimally Invasive Intervention, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China.
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17
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Praveen M. Characterizing the West Nile Virus's polyprotein from nucleotide sequence to protein structure - Computational tools. J Taibah Univ Med Sci 2024; 19:338-350. [PMID: 38304694 PMCID: PMC10831166 DOI: 10.1016/j.jtumed.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Objectives West Nile virus (WNV) belongs to the Flaviviridae family and causes West Nile fever. The mechanism of transmission involves the culex mosquito species. Infected individuals are primarily asymptomatic, and few exhibit common symptoms. Moreover, 10 % of neuronal infection caused by this virus cause death. The proteins encoded by these genes had been uncharacterized, although understanding their function and structure is important for formulating antiviral drugs. Methods Herein, we used in silico approaches, including various bioinformatic tools and databases, to analyse the proteins from the WNV polyprotein individually. The characterization included GC content, physicochemical properties, conserved domains, soluble and transmembrane regions, signal localization, protein disorder, and secondary structure features and their respective 3D protein structures. Results Among 11 proteins, eight had >50 % GC content, eight proteins had basic pI values, three proteins were unstable under in vitro conditions, four were thermostable according to >100 AI values and some had negative GRAVY values in physicochemical analyses. All protein-conserved domains were shared among Flaviviridae family members. Five proteins were soluble and lacked transmembrane regions. Two proteins had signals for localization in the host endoplasmic reticulum. Non-structural (NS) 2A showed low protein disorder. The secondary structural features and tertiary structure models provide a valuable biochemical resource for designing selective substrates and synthetic inhibitors. Conclusions WNV proteins NS2A, NS2B, PM, NS3 and NS5 can be used as drug targets for the pharmacological design of lead antiviral compounds.
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Affiliation(s)
- Mallari Praveen
- Department of Zoology, Indira Gandhi National Tribal University, Amarkantak, Madhya Pradesh, India
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Merwaiss F, Lozano‐Sanchez E, Zulaica J, Rusu L, Vazquez‐Vilar M, Orzáez D, Rodrigo G, Geller R, Daròs J. Plant virus-derived nanoparticles decorated with genetically encoded SARS-CoV-2 nanobodies display enhanced neutralizing activity. Plant Biotechnol J 2024; 22:876-891. [PMID: 37966715 PMCID: PMC10955499 DOI: 10.1111/pbi.14230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Viral nanoparticles (VNPs) are a new class of virus-based formulations that can be used as building blocks to implement a variety of functions of potential interest in biotechnology and nanomedicine. Viral coat proteins (CP) that exhibit self-assembly properties are particularly appropriate for displaying antigens and antibodies, by generating multivalent VNPs with therapeutic and diagnostic potential. Here, we developed genetically encoded multivalent VNPs derived from two filamentous plant viruses, potato virus X (PVX) and tobacco etch virus (TEV), which were efficiently and inexpensively produced in the biofactory Nicotiana benthamiana plant. PVX and TEV-derived VNPs were decorated with two different nanobodies recognizing two different regions of the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein. The addition of different picornavirus 2A ribosomal skipping peptides between the nanobody and the CP allowed for modulating the degree of VNP decoration. Nanobody-decorated VNPs purified from N. benthamiana tissues successfully recognized the RBD antigen in enzyme-linked immunosorbent assays and showed efficient neutralization activity against pseudoviruses carrying the Spike protein. Interestingly, multivalent PVX and TEV-derived VNPs exhibited a neutralizing activity approximately one order of magnitude higher than the corresponding nanobody in a dimeric format. These properties, combined with the ability to produce VNP cocktails in the same N. benthamiana plant based on synergistic infection of the parent PVX and TEV, make these green nanomaterials an attractive alternative to standard antibodies for multiple applications in diagnosis and therapeutics.
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Affiliation(s)
- Fernando Merwaiss
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas – Universitat Politècnica de ValènciaValenciaSpain
| | - Enrique Lozano‐Sanchez
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas – Universitat Politècnica de ValènciaValenciaSpain
| | - João Zulaica
- Institute for Integrative Systems BiologyConsejo Superior de Investigaciones Científicas – Universitat de ValènciaPaternaSpain
| | - Luciana Rusu
- Institute for Integrative Systems BiologyConsejo Superior de Investigaciones Científicas – Universitat de ValènciaPaternaSpain
| | - Marta Vazquez‐Vilar
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas – Universitat Politècnica de ValènciaValenciaSpain
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas – Universitat Politècnica de ValènciaValenciaSpain
| | - Guillermo Rodrigo
- Institute for Integrative Systems BiologyConsejo Superior de Investigaciones Científicas – Universitat de ValènciaPaternaSpain
| | - Ron Geller
- Institute for Integrative Systems BiologyConsejo Superior de Investigaciones Científicas – Universitat de ValènciaPaternaSpain
| | - José‐Antonio Daròs
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas – Universitat Politècnica de ValènciaValenciaSpain
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19
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Capitanio JP, Del Rosso LA, Yee J, Lemoy MJMF. An analysis of risk factors for spontaneously occurring type 2 diabetes mellitus in rhesus macaques (Macaca mulatta). J Med Primatol 2024; 53:e12695. [PMID: 38454195 PMCID: PMC10936567 DOI: 10.1111/jmp.12695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Type 2 Diabetes Mellitus (T2D) is a chronic disease with a high prevalence worldwide. Human literature suggests factors beyond well-known risk factors (e.g., age, body mass index) for T2D: cytomegalovirus serostatus, season of birth, maternal age, birth weight, and depression. Nothing is known, however, about whether these variables are influential in primate models of T2D. METHODS Using a retrospective methodology, we identified 22 cases of spontaneously occurring T2D among rhesus monkeys at our facility. A control sample of n = 1199 was identified. RESULTS Animals born to mothers that were ≤5.5 years of age, and animals that showed heightened Activity and Emotionality in response to brief separation in infancy, had a greater risk for development of T2D in adulthood. CONCLUSIONS Knowledge of additional risk factors for T2D could help colony managers better identify at-risk animals and enable diabetes researchers to select animals that might be more responsive to their manipulations.
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Affiliation(s)
- John P Capitanio
- California National Primate Research Center, University of California, Davis, California, USA
| | - Laura A Del Rosso
- California National Primate Research Center, University of California, Davis, California, USA
| | - JoAnn Yee
- California National Primate Research Center, University of California, Davis, California, USA
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20
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Tam EH, Peng Y, Cheah MXY, Yan C, Xiao T. Neutralizing antibodies to block viral entry and for identification of entry inhibitors. Antiviral Res 2024; 224:105834. [PMID: 38369246 DOI: 10.1016/j.antiviral.2024.105834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
Neutralizing antibodies (NAbs) are naturally produced by our immune system to combat viral infections. Clinically, neutralizing antibodies with potent efficacy and high specificity have been extensively used to prevent and treat a wide variety of viral infections, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Human Immunodeficiency Virus (HIV), Dengue Virus (DENV) and Hepatitis B Virus (HBV). An overwhelmingly large subset of clinically effective NAbs operates by targeting viral envelope proteins to inhibit viral entry into the host cell. Binding of viral envelope protein to the host receptor is a critical rate limiting step triggering a cascade of downstream events, including endocytosis, membrane fusion and pore formation to allow viral entry. In recent years, improved structural knowledge on these processes have allowed researchers to also leverage NAbs as an indispensable tool in guiding discovery of novel antiviral entry inhibitors, providing drug candidates with high efficacy and pan-genus specificity. This review will summarize the latest progresses on the applications of NAbs as effective entry inhibitors and as important tools to develop antiviral therapeutics by high-throughput drug screenings, rational design of peptidic entry inhibitor mimicking NAbs and in silico computational modeling approaches.
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Affiliation(s)
- Ee Hong Tam
- School of Biological Sciences, Nanyang Technological University 637551, Singapore; Institute of Structural Biology, Nanyang Technological University 636921, Singapore
| | - Yu Peng
- School of Biological Sciences, Nanyang Technological University 637551, Singapore; Institute of Structural Biology, Nanyang Technological University 636921, Singapore
| | - Megan Xin Yan Cheah
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research) 138673, Singapore
| | - Chuan Yan
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research) 138673, Singapore
| | - Tianshu Xiao
- School of Biological Sciences, Nanyang Technological University 637551, Singapore; Institute of Structural Biology, Nanyang Technological University 636921, Singapore.
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21
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Sun Y, Nie W, Tian D, Ye Q. Human monkeypox virus: Epidemiologic review and research progress in diagnosis and treatment. J Clin Virol 2024; 171:105662. [PMID: 38432097 DOI: 10.1016/j.jcv.2024.105662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/22/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
Monkeypox virus (MPXV) is responsible for causing a zoonotic disease called monkeypox (mpox), which sporadically infects humans in West and Central Africa. It first infected humans in 1970 and, along with the variola virus, belongs to the genus Orthopoxvirus in the poxvirus family. Since the World Health Organization declared the MPXV outbreak a "Public Health Emergency of International Concern" on July 23, 2022, the number of infected patients has increased dramatically. To control this epidemic and address this previously neglected disease, MPXV needs to be better understood and reevaluated. In this review, we cover recent research on MPXV, including its genomic and pathogenic characteristics, transmission, mutations and mechanisms, clinical characteristics, epidemiology, laboratory diagnosis, and treatment measures, as well as prevention of MPXV infection in light of the 2022 and 2023 global outbreaks. The 2022 MPXV outbreak has been primarily associated with close intimate contact, including sexual activity, with most cases diagnosed among men who have sex with men. The incubation period of MPXV infection usually lasts from 6 to 13 days, and symptoms include fever, muscle pains, headache, swollen lymph nodes, and a characteristic painful rash, including several stages, such as macules, papules, blisters, pustules, scabs, and scab shedding involving the genitals and anus. Polymerase chain reaction (PCR) is usually used to detect MPXV in skin lesion material. Treatment includes supportive care, antivirals, and intravenous vaccinia immune globulin. Smallpox vaccines have been designed with four givens emergency approval for use against MPXV infection.
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Affiliation(s)
- Yanhong Sun
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Wenjian Nie
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Dandan Tian
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Qing Ye
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China.
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22
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Debing Y, Vanrusselt H, Degrauwe L, Silva de Oliveira DA, Kariuki CK, Ebwanga EJ, Bashir S, Merckx W, Thatikonda SK, Rajwanshi V, Gohil V, Hong J, Kum DB, Acosta Sanchez A, Chanda S, Blatt LM, Jekle A, Symons JA, Smith DB, Raboisson P, Lin TI, Beigelman L, Paeshuyse J. An in vivo duck hepatitis B virus model recapitulates key aspects of nucleic acid polymer treatment outcomes in chronic hepatitis B patients. Antiviral Res 2024; 224:105835. [PMID: 38401714 DOI: 10.1016/j.antiviral.2024.105835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/30/2024] [Accepted: 02/13/2024] [Indexed: 02/26/2024]
Abstract
Nucleic acid polymers (NAPs) are an attractive treatment modality for chronic hepatitis B (CHB), with REP2139 and REP2165 having shown efficacy in CHB patients. A subset of patients achieve functional cure, whereas the others exhibit a moderate response or are non-responders. NAP efficacy has been difficult to recapitulate in animal models, with the duck hepatitis B virus (DHBV) model showing some promise but remaining underexplored for NAP efficacy testing. Here we report on an optimized in vivo DHBV duck model and explore several characteristics of NAP treatment. REP2139 was efficacious in reducing DHBV DNA and DHBsAg levels in approximately half of the treated ducks, whether administered intraperitoneally or subcutaneously. Intrahepatic or serum NAP concentrations did not correlate with efficacy, nor did the appearance of anti-DHBsAg antibodies. Furthermore, NAP efficacy was only observed in experimentally infected ducks, not in endogenously infected ducks (vertical transmission). REP2139 add-on to entecavir treatment induced a deeper and more sustained virological response compared to entecavir monotherapy. Destabilized REP2165 showed a different activity profile with a more homogenous antiviral response followed by a faster rebound. In conclusion, subcutaneous administration of NAPs in the DHBV duck model provides a useful tool for in vivo evaluation of NAPs. It recapitulates many aspects of this class of compound's efficacy in CHB patients, most notably the clear division between responders and non-responders.
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Affiliation(s)
| | | | - Lars Degrauwe
- Laboratory of Host Pathogen Interactions, Department of Biosystems, KU Leuven, Leuven, Belgium
| | | | | | - Ebanja Joseph Ebwanga
- Laboratory of Host Pathogen Interactions, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Shahbaz Bashir
- Laboratory of Host Pathogen Interactions, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Wouter Merckx
- TRANSfarm, Science, Engineering & Technology Group, KU Leuven, Leuven, Belgium
| | | | | | - Vikrant Gohil
- Aligos Therapeutics, Inc., South San Francisco, CA, USA
| | - Jin Hong
- Aligos Therapeutics, Inc., South San Francisco, CA, USA
| | | | | | | | | | - Andreas Jekle
- Aligos Therapeutics, Inc., South San Francisco, CA, USA
| | | | - David B Smith
- Aligos Therapeutics, Inc., South San Francisco, CA, USA
| | | | | | | | - Jan Paeshuyse
- Laboratory of Host Pathogen Interactions, Department of Biosystems, KU Leuven, Leuven, Belgium.
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23
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Hämmerle M, Rymbekova A, Gelabert P, Sawyer S, Cheronet O, Bernardi P, Calvignac-Spencer S, Kuhlwilm M, Guellil M, Pinhasi R. Link between Monkeypox Virus Genomes from Museum Specimens and 1965 Zoo Outbreak. Emerg Infect Dis 2024; 30:816-818. [PMID: 38526306 DOI: 10.3201/eid3004.231546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
We used pathogen genomics to test orangutan specimens from a museum in Bonn, Germany, to identify the origin of the animals and the circumstances of their death. We found monkeypox virus genomes in the samples and determined that they represent cases from a 1965 outbreak at Rotterdam Zoo in Rotterdam, the Netherlands.
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24
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Fleckenstein F, Stephan S, Hasse H. Elucidating the behavior of the SARS-CoV-2 virus surface at vapor-liquid interfaces using molecular dynamics simulation. Proc Natl Acad Sci U S A 2024; 121:e2317194121. [PMID: 38502700 DOI: 10.1073/pnas.2317194121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/15/2024] [Indexed: 03/21/2024] Open
Abstract
Aerosols play a major role in the transmission of the SARS-CoV-2 virus. The behavior of the virus within aerosols is therefore of fundamental importance. On the surface of a SARS-CoV-2 virus, there are about 40 spike proteins, which each have a length of about 20 nm. They are glycosylated trimers, which are highly flexible, due to their structure. These spike proteins play a central role in the intrusion of the virus into human host cells and are, therefore, a focus of vaccine development. In this work, we have studied the behavior of spike proteins of the SARS-CoV-2 virus in the presence of a vapor-liquid interface by molecular dynamics (MD) simulations. Systematically, the behavior of the spike protein at different distances to a vapor-liquid interface were studied. The results reveal that the spike protein of the SARS-CoV-2 virus is repelled from the vapor-liquid interface and has a strong affinity to stay inside the bulk liquid phase. Therefore, the spike protein bends when a vapor-liquid interface approaches the top of the protein. This has important consequences for understanding the behavior of the virus during the dry-out of aerosol droplets.
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Affiliation(s)
- Florian Fleckenstein
- Laboratory of Engineering Thermodynamics, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau (RPTU), Kaiserslautern 67663, Germany
| | - Simon Stephan
- Laboratory of Engineering Thermodynamics, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau (RPTU), Kaiserslautern 67663, Germany
| | - Hans Hasse
- Laboratory of Engineering Thermodynamics, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau (RPTU), Kaiserslautern 67663, Germany
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25
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Mwanga EP, Mchola IS, Makala FE, Mshani IH, Siria DJ, Mwinyi SH, Abbasi S, Seleman G, Mgaya JN, Jiménez MG, Wynne K, Sikulu-Lord MT, Selvaraj P, Okumu FO, Baldini F, Babayan SA. Rapid assessment of the blood-feeding histories of wild-caught malaria mosquitoes using mid-infrared spectroscopy and machine learning. Malar J 2024; 23:86. [PMID: 38532415 DOI: 10.1186/s12936-024-04915-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/22/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND The degree to which Anopheles mosquitoes prefer biting humans over other vertebrate hosts, i.e. the human blood index (HBI), is a crucial parameter for assessing malaria transmission risk. However, existing techniques for identifying mosquito blood meals are demanding in terms of time and effort, involve costly reagents, and are prone to inaccuracies due to factors such as cross-reactivity with other antigens or partially digested blood meals in the mosquito gut. This study demonstrates the first field application of mid-infrared spectroscopy and machine learning (MIRS-ML), to rapidly assess the blood-feeding histories of malaria vectors, with direct comparison to PCR assays. METHODS AND RESULTS Female Anopheles funestus mosquitoes (N = 1854) were collected from rural Tanzania and desiccated then scanned with an attenuated total reflectance Fourier-transform Infrared (ATR-FTIR) spectrometer. Blood meals were confirmed by PCR, establishing the 'ground truth' for machine learning algorithms. Logistic regression and multi-layer perceptron classifiers were employed to identify blood meal sources, achieving accuracies of 88%-90%, respectively, as well as HBI estimates aligning well with the PCR-based standard HBI. CONCLUSIONS This research provides evidence of MIRS-ML effectiveness in classifying blood meals in wild Anopheles funestus, as a potential complementary surveillance tool in settings where conventional molecular techniques are impractical. The cost-effectiveness, simplicity, and scalability of MIRS-ML, along with its generalizability, outweigh minor gaps in HBI estimation. Since this approach has already been demonstrated for measuring other entomological and parasitological indicators of malaria, the validation in this study broadens its range of use cases, positioning it as an integrated system for estimating pathogen transmission risk and evaluating the impact of interventions.
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Affiliation(s)
- Emmanuel P Mwanga
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania.
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Idrisa S Mchola
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Faraja E Makala
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Issa H Mshani
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Doreen J Siria
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Sophia H Mwinyi
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Said Abbasi
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Godian Seleman
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Jacqueline N Mgaya
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | | | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Maggy T Sikulu-Lord
- Faculty of Science, School of the Environment, The University of Queensland, Brisbane, QLD, Australia
| | - Prashanth Selvaraj
- Institute for Disease Modelling, Bill and Melinda Gates Foundation, Seattle, USA
| | - Fredros O Okumu
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Life Science and Bioengineering, The Nelson Mandela African, Institution of Science and Technology, P. O. Box 447, Arusha, Tanzania
| | - Francesco Baldini
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Simon A Babayan
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
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26
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Sánchez Romano J, Simón-Santamaría J, McCourt P, Smedsrød B, Mortensen KE, Sagona AP, Sørensen KK, Larsen AK. Liver sinusoidal cells eliminate blood-borne phage K1F. mSphere 2024; 9:e0070223. [PMID: 38415633 DOI: 10.1128/msphere.00702-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/30/2024] [Indexed: 02/29/2024] Open
Abstract
Phage treatment has regained attention due to an increase in multiresistant bacteria. For phage therapy to be successful, phages must reach their target bacteria in sufficiently high numbers. Blood-borne phages are believed to be captured by macrophages in the liver and spleen. Since liver sinusoids also consist of specialized scavenger liver sinusoidal endothelial cells (LSECs) and Kupffer cells (KCs), this study investigated the contribution of both cell types in the elimination of Escherichia coli phage K1Fg10b::gfp (K1Fgfp) in mice. Circulatory half-life, organ, and hepatocellular distribution of K1Fgfp were determined following intravenous administration. Internalization of K1Fgfp and effects of phage opsonization on uptake were explored using primary mouse and human LSEC and KC cultures. When inoculated with 107 virions, >95% of the total K1Fgfp load was eliminated from the blood within 20 min, and 94% of the total retrieved K1Fgfp was localized to the liver. Higher doses resulted in slower elimination, possibly reflecting temporary saturation of liver scavenging capacity. Phage DNA was detected in both cell types, with a KC:LSEC ratio of 12:1 per population following cell isolation. Opsonization with plasma proteins increased time-dependent cellular uptake in both LSECs and KCs in vitro. Internalized phages were rapidly transported along the endocytic pathway to lysosomal compartments. Reduced viability of intracellular K1Fgfp corroborated inactivation following endocytosis. This study is the first to identify phage distribution in the liver at the hepatocellular level, confirming clearance of K1Fgfp performed mostly by KCs with a significant uptake also in LSECs.IMPORTANCEFaced with the increasing amounts of bacteria with multidrug antimicrobial resistance, phage therapy has regained attention as a possible treatment option. The phage field has recently experienced an emergence in commercial interest as research has identified new and more efficient ways of identifying and matching phages against resistant superbugs. Currently, phages are unapproved drugs in most parts of the world. For phages to reach broad clinical use, they must be shown to be clinically safe and useful. The results presented herein contribute to increased knowledge about the pharmacokinetics of the T7-like phage K1F in the mammalian system. The cell types of the liver that are responsible for rapid phage blood clearance are identified. Our results highlight the need for more research about appropriate dose regimens when phage therapy is delivered intravenously and advise essential knowledge about cell systems that should be investigated further for detailed phage pharmacodynamics.
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Affiliation(s)
| | | | - Peter McCourt
- Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Bård Smedsrød
- Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kim Erlend Mortensen
- Gastrointestinal Surgery Unit, University Hospital of North Norway, Tromsø, Norway
| | - Antonia P Sagona
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | | | - Anett Kristin Larsen
- Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
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27
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Velásquez-López Y, Ruiz-Escudero A, Arrasate S, González-Díaz H. Implementation of IFPTML Computational Models in Drug Discovery Against Flaviviridae Family. J Chem Inf Model 2024; 64:1841-1852. [PMID: 38466369 DOI: 10.1021/acs.jcim.3c01796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The Flaviviridae family consists of single-stranded positive-sense RNA viruses, which contains the genera Flavivirus, Hepacivirus, Pegivirus, and Pestivirus. Currently, there is an outbreak of viral diseases caused by this family affecting millions of people worldwide, leading to significant morbidity and mortality rates. Advances in computational chemistry have greatly facilitated the discovery of novel drugs and treatments for diseases associated with this family. Chemoinformatic techniques, such as the perturbation theory machine learning method, have played a crucial role in developing new approaches based on ML models that can effectively aid drug discovery. The IFPTML models have shown its capability to handle, classify, and process large data sets with high specificity. The results obtained from different models indicates that this methodology is proficient in processing the data, resulting in a reduction of the false positive rate by 4.25%, along with an accuracy of 83% and reliability of 92%. These values suggest that the model can serve as a computational tool in assisting drug discovery efforts and the development of new treatments against Flaviviridae family diseases.
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Affiliation(s)
- Yendrek Velásquez-López
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU. Apdo. 644. 48080 Bilbao (Spain)
- Bio-Cheminformatics Research Group, Universidad de Las Américas, Quito 170504, (Ecuador)
| | - Andrea Ruiz-Escudero
- Department of Pharmacology, University of the Basque Country UPV/EHU, 48940 Leioa, (Spain)
- IKERDATA S.L., ZITEK, University of Basque Country UPV/EHU, Rectorate Building, 48940 Leioa, Spain
| | - Sonia Arrasate
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU. Apdo. 644. 48080 Bilbao (Spain)
| | - Humberto González-Díaz
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU. Apdo. 644. 48080 Bilbao (Spain)
- BIOFISIKA, Basque Center for Biophysics CSIC-UPV/EHU, 48940 Bilbao (Spain)
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao (Spain)
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Li Y, Huo Y, Liang L, Li D, Zhang Z, Yang H. Bacillus phage phi18-2 is a novel temperate virus with an unintegrated genome present in the cytoplasm of lysogenic cells as a linear phage-plasmid. Arch Virol 2024; 169:81. [PMID: 38519716 DOI: 10.1007/s00705-024-06014-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/01/2024] [Indexed: 03/25/2024]
Abstract
Bacillus subtilis is a Gram-positive bacterium that is widely used in fermentation and in the pharmaceutical industry. Phage contamination occasionally occurs in various fermentation processes and causes significant economic loss. Here, we report the isolation and characterization of a temperate B. subtilis phage, termed phi18-2, from spore powder manufactured in a fermentation plant. Transmission electron microscopy showed that phi18-2 has a symmetrical polyhedral head and a long noncontractile tail. Receptor analysis showed that phi18-2 recognizes wall teichoic acid (WTA) for infection. The phage virions have a linear double-stranded DNA genome of 64,467 bp with identical direct repeat sequences of 309 bp at each end of the genome. In lysogenic cells, the phage genome was found to be present in the cytoplasm without integration into the host cell chromosome, and possibly as a linear phage-plasmid with unmodified ends. Our data may provide some insight into the molecular basis of the unique lysogenic cycle of phage phi18-2.
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Affiliation(s)
- Yutong Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Yansheng Huo
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Li Liang
- Shandong Vland Biotech Co., Ltd., Shandong, 251700, China
| | - Donghang Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Zhiqiang Zhang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Hongjiang Yang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
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29
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Popova P, Chen SP, Liao S, Sadarangani M, Blakney AK. Clinical perspective on topical vaccination strategies. Adv Drug Deliv Rev 2024:115292. [PMID: 38522725 DOI: 10.1016/j.addr.2024.115292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/01/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024]
Abstract
Vaccination is one of the most successful measures in modern medicine to combat diseases, especially infectious diseases, and saves millions of lives every year. Vaccine design and development remains critical and involves many aspects, including the choice of platform, antigen, adjuvant, and route of administration. Topical vaccination, defined herein as the introduction of a vaccine to any of the three layers of the human skin, has attracted interest in recent years as an alternative vaccination approach to the conventional intramuscular administration because of its potential to be needle-free and induce a superior immune response against pathogens. In this review, we describe recent progress in developing topical vaccines, highlight progress in the development of delivery technologies for topical vaccines, discuss potential factors that might impact the topical vaccine efficacy, and provide an overview of the current clinical landscape of topical vaccines.
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Affiliation(s)
- Petya Popova
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, British Columbia V6T 2B9, Canada; Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sunny P Chen
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, British Columbia V6T 2B9, Canada; Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Suiyang Liao
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, British Columbia V6T 2B9, Canada; Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada; Life Science Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Manish Sadarangani
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, 950 West 28th Ave, Vancouver, British Columbia V5Z 4H4, Canada; Department of Pediatrics, University of British Columbia, 4480 Oak St, Vancouver, BC V6H 0B3, Canada
| | - Anna K Blakney
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, British Columbia V6T 2B9, Canada; Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada.
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Mahillon M, Brodard J, Schoen R, Botermans M, Dubuis N, Groux R, Pannell JR, Blouin AG, Schumpp O. Revisiting a pollen-transmitted ilarvirus previously associated with angular mosaic of grapevine. Virus Res 2024; 344:199362. [PMID: 38508402 DOI: 10.1016/j.virusres.2024.199362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 03/22/2024]
Abstract
We report the characterization of a novel tri-segmented RNA virus infecting Mercurialis annua, a common crop weed and model species in plant science. The virus, named "Mercurialis latent virus" (MeLaV) was first identified in a mixed infection with the recently described Mercurialis orthotospovirus 1 (MerV1) on symptomatic plants grown in glasshouses in Lausanne (Switzerland). Both viruses were found to be transmitted by Thrips tabaci, which presumably help the inoculation of infected pollen in the case of MeLaV. Complete genome sequencing of the latter revealed a typical ilarviral architecture and close phylogenetic relationship with members of the Ilarvirus subgroup 1. Surprisingly, a short portion of MeLaV replicase was found to be identical to the partial sequence of grapevine angular mosaic virus (GAMV) reported in Greece in the early 1990s. However, we have compiled data that challenge the involvement of GAMV in angular mosaic of grapevine, and we propose alternative causal agents for this disorder. In parallel, three highly-conserved MeLaV isolates were identified in symptomatic leaf samples in The Netherlands, including a herbarium sample collected in 1991. The virus was also traced in diverse RNA sequencing datasets from 2013 to 2020, corresponding to transcriptomic analyses of M. annua and other plant species from five European countries, as well as metaviromics analyses of bees in Belgium. Additional hosts are thus expected for MeLaV, yet we argue that infected pollen grains have likely contaminated several sequencing datasets and may have caused the initial characterization of MeLaV as GAMV.
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Affiliation(s)
- Mathieu Mahillon
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Justine Brodard
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Ruben Schoen
- Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Netherlands Food and Consumer Product Safety Authority, Wageningen, The Netherlands
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Netherlands Food and Consumer Product Safety Authority, Wageningen, The Netherlands
| | - Nathalie Dubuis
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Raphaël Groux
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne (UNIL), Switzerland
| | - Arnaud G Blouin
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland.
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31
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Legarda EG, Elena SF, Mushegian AR. Emergence of two distinct spatial folds in a pair of plant virus proteins encoded by nested genes. J Biol Chem 2024:107218. [PMID: 38522515 DOI: 10.1016/j.jbc.2024.107218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024] Open
Abstract
Virus genomes may encode overlapping or nested open reading frames that increase their coding capacity. It is not known whether the constraints on spatial structures of the two encoded proteins limit evolvability of nested genes. We examine the evolution of a pair of proteins, p22 and p19, encoded by nested genes in plant viruses from the genus Tombusvirus. The known structure of p19, a suppressor of RNA silencing, belongs to the RAGNYA fold from the alpha+beta class. The structure of p22, the cell-to-cell movement protein from the 30K family widespread in plant viruses, is predicted with the AlphaFold approach, suggesting a single jelly-roll fold core from the all-beta class, structurally similar to capsid proteins from plant and animal viruses. The nucleotide and codon preferences impose modest constraints on the types of secondary structures encoded in the alternative reading frames, nonetheless allowing for compact, well-ordered folds from different structural classes in two similarly-sized nested proteins. Tombusvirus p22 emerged through radiation of the widespread 30K family, which evolved by duplication of a virus capsid protein early in the evolution of plant viruses, whereas lineage-specific p19 may have emerged by stepwise increase in the length of the overprinted gene and incremental acquisition of functionally active secondary structure elements by the protein product. This evolution of p19 towards the RAGNYA fold represents one of the first documented examples of protein structure convergence in naturally occurring proteins.
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Affiliation(s)
- Esmeralda G Legarda
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Paterna, 46980 València, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Paterna, 46980 València, Spain; The Santa Fe Institute, Santa Fe NM 87501, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Arlington VA 22314, USA.
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He Z, Zhao W, Fan Y, Wang L, Yang M, Yang Y, Zhou E. Genome characterization of a novel narnavirus infecting the plant-pathogenic fungus Ustilaginoidea virens. Arch Virol 2024; 169:78. [PMID: 38517587 DOI: 10.1007/s00705-024-06009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 02/15/2024] [Indexed: 03/24/2024]
Abstract
Mycoviruses are viruses that infect fungi and oomycetes. They are widespread in all major groups of plant-pathogenic fungi and oomycetes. To date, only the full genome of dsRNA mycoviruses and the contigs of positive-sense single-stranded RNA (+ssRNA) mycoviruses have been reported in Ustilaginoidea virens, which is the notorious causal agent of rice false smut (RFS). Here, we report the molecular characterization of a novel +ssRNA mycovirus, Ustilaginoidea virens narnavirus 4 (UvNV4), isolated from U. virens strain Uv418. UvNV4 has a genome of 3,131 nucleotides (nt) and possesses an open reading frame (ORF) predicted to encode an RNA-dependent RNA polymerase (RdRp) of 1,017 amino acids (aa) sequence with a molecular mass of 116.6 kDa. BLASTp analysis revealed that the RdRp showed 50.34% aa sequence identity to that of the previously described Zhangzhou Narna tick virus 1. Phylogenetic analysis indicated that UvNV4 is closely related to members of the family Narnaviridae. Taken together, these results clearly demonstrate that UvNV4 is a novel +ssRNA virus infecting U. virens.
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Affiliation(s)
- Zhenrui He
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Wenhua Zhao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Yu Fan
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Li Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Mei Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Yingqing Yang
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Erxun Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China.
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33
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Visalli MA, Nale Lovett DJ, Kornfeind EM, Herrington H, Xiao YT, Lee D, Plair P, Wilder SG, Garza BK, Young A, Visalli RJ. Mutagenesis and functional analysis of the varicella-zoster virus portal protein. J Virol 2024:e0060323. [PMID: 38517165 DOI: 10.1128/jvi.00603-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024] Open
Abstract
Herpesviruses replicate by cleaving concatemeric dsDNA into single genomic units that are packaged through an oligomeric portal present in preformed procapsids. In contrast to what is known about phage portal proteins, details concerning herpesvirus portal structure and function are not as well understood. A panel of 65 Varicella-Zoster virus (VZV) recombinant portal proteins with five amino acid in-frame insertions were generated by random transposon mutagenesis of the VZV portal gene, ORF54. Subsequently, 65 VZVLUC recombinant viruses (TNs) were generated via recombineering. Insertions were mapped to predicted portal domains (clip, wing, stem, wall, crown, and β-hairpin tunnel-loop) and recombinant viruses were characterized for plaque morphology, replication kinetics, pORF54 expression, and classified based on replication in non-complementing (ARPE19) or complementing (ARPE54C50) cell lines. The N- and C-termini were tolerant to insertion mutagenesis, as were certain clip sub-domains. The majority of mutants mapping to the wing, wall, β-hairpin tunnel loop, and stem domains were lethal. Elimination of the predicted ORF54 start codon revealed that the first 40 amino acids of the N-terminus were not required for viral replication. Stop codon insertions in the C-terminus showed that the last 100 amino acids were not required for viral replication. Lastly, a putative protease cleavage site was identified in the C-terminus of pORF54. Cleavage was likely orchestrated by a viral protease; however, processing was not required for DNA encapsidation and viral replication. The panel of recombinants should prove valuable in future studies to dissect mammalian portal structure and function.IMPORTANCEThough nucleoside analogs and a live-attenuated vaccine are currently available to treat some human herpesvirus family members, alternate methods of combating herpesvirus infection could include blocking viral replication at the DNA encapsidation stage. The approval of Letermovir provided proof of concept regarding the use of encapsidation inhibitors to treat herpesvirus infections in the clinic. We propose that small-molecule compounds could be employed to interrupt portal oligomerization, assembly into the capsid vertex, or affect portal function/dynamics. Targeting portal at any of these steps would result in disruption of viral DNA packaging and a decrease or absence of mature infectious herpesvirus particles. The oligomeric portals of herpesviruses are structurally conserved, and therefore, it may be possible to find a single compound capable of targeting portals from one or more of the herpesvirus subfamilies. Drug candidates from such a series would be effective against viruses resistant to the currently available antivirals.
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Affiliation(s)
- Melissa A Visalli
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Dakota J Nale Lovett
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Ellyn M Kornfeind
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Haley Herrington
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Yi Tian Xiao
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Daniel Lee
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Patience Plair
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - S Garrett Wilder
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Bret K Garza
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Ashton Young
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Robert J Visalli
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
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Lin W, Nagy PD. Co-opted cytosolic proteins form condensate substructures within membranous replication organelles of a positive-strand RNA virus. New Phytol 2024. [PMID: 38515267 DOI: 10.1111/nph.19691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
Positive-strand RNA viruses co-opt organellar membranes for biogenesis of viral replication organelles (VROs). Tombusviruses also co-opt pro-viral cytosolic proteins to VROs. It is currently not known what type of molecular organization keeps co-opted proteins sequestered within membranous VROs. In this study, we employed tomato bushy stunt virus (TBSV) and carnation Italian ringspot virus (CIRV) - Nicotiana benthamiana pathosystems to identify biomolecular condensate formation in VROs. We show that TBSV p33 and the CIRV p36 replication proteins sequester glycolytic and fermentation enzymes in unique condensate substructures associated with membranous VROs. We find that p33 and p36 form droplets in vitro driven by intrinsically disordered region. The replication protein organizes partitioning of co-opted host proteins into droplets. VRO-associated condensates are critical for local adenosine triphosphate production to support energy for virus replication. We find that co-opted endoplasmic reticulum membranes and actin filaments form meshworks within and around VRO condensates, contributing to unique composition and structure. We propose that p33/p36 organize liquid-liquid phase separation of co-opted concentrated host proteins in condensate substructures within membranous VROs. Overall, we demonstrate that subverted membranes and condensate substructures co-exist and are critical for VRO functions. The replication proteins induce and connect the two substructures within VROs.
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Affiliation(s)
- Wenwu Lin
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40543, USA
| | - Peter D Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40543, USA
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35
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Ao Y, Grover JR, Gifford L, Han Y, Zhong G, Katte R, Li W, Bhattacharjee R, Zhang B, Sauve S, Qin W, Ghimire D, Haque MA, Arthos J, Moradi M, Mothes W, Lemke EA, Kwong PD, Melikyan GB, Lu M. Bioorthogonal click labeling of an amber-free HIV-1 provirus for in-virus single molecule imaging. Cell Chem Biol 2024; 31:487-501.e7. [PMID: 38232732 PMCID: PMC10960674 DOI: 10.1016/j.chembiol.2023.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/13/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024]
Abstract
Structural dynamics of human immunodeficiency virus 1 (HIV-1) envelope (Env) glycoprotein mediate cell entry and facilitate immune evasion. Single-molecule FRET using peptides for Env labeling revealed structural dynamics of Env, but peptide use risks potential effects on structural integrity/dynamics. While incorporating noncanonical amino acids (ncAAs) into Env by amber stop-codon suppression, followed by click chemistry, offers a minimally invasive approach, this has proved to be technically challenging for HIV-1. Here, we develope an intact amber-free HIV-1 system that overcomes hurdles of preexisting viral amber codons. We achieved dual-ncAA incorporation into Env on amber-free virions, enabling single-molecule Förster resonance energy transfer (smFRET) studies of click-labeled Env that validated the previous peptide-based labeling approaches by confirming the intrinsic propensity of Env to dynamically sample multiple conformational states. Amber-free click-labeled Env also enabled real-time tracking of single virion internalization and trafficking in cells. Our system thus permits in-virus bioorthogonal labeling of proteins, compatible with studies of virus entry, trafficking, and egress from cells.
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Affiliation(s)
- Yuanyun Ao
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Jonathan R Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Levi Gifford
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yang Han
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Guohua Zhong
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Revansiddha Katte
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Wenwei Li
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Rajanya Bhattacharjee
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; International PhD Program of the Institute of Molecular Biology, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephanie Sauve
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Wenyi Qin
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Dibya Ghimire
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Md Anzarul Haque
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Edward A Lemke
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gregory B Melikyan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Maolin Lu
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA.
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36
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Antillon SF, Bernhardt TG, Chamakura K, Young R. Physiological characterization of single-gene lysis proteins. J Bacteriol 2024; 206:e0038423. [PMID: 38426721 PMCID: PMC10955853 DOI: 10.1128/jb.00384-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Single-strand RNA (ssRNA) and single-strand DNA phages elicit host lysis using a single gene, in each case designated as sgl. Of the 11 identified Sgls, three have been shown to be specific inhibitors of different steps in the pathway that supplies lipid II to the peptidoglycan (PG) biosynthesis machinery. These Sgls have been called "protein antibiotics" because the lytic event is a septal catastrophe indistinguishable from that caused by cell wall antibiotics. Here, we designate these as type I Sgls. In this formalism, the other eight Sgls are assigned to type II, the best-studied of which is protein L of the paradigm F-specific ssRNA phage MS2. Comparisons have suggested that type II Sgls have four sequence elements distinguished by hydrophobic and polar character. Environmental metatranscriptomics has revealed thousands of new ssRNA phage genomes, each of which presumably has an Sgl. Here, we describe methods to distinguish type I and type II Sgls. Using phase contrast microscopy, we show that both classes of Sgls cause the formation of blebs prior to lysis, but the location of the blebs differs significantly. In addition, we show that L and other type II Sgls do not inhibit the net synthesis of PG, as measured by radio-labeling of PG. Finally, we provide direct evidence that the Sgl from Pseudomonas phage PP7 is a type I Sgl, in support of a recent report based on a genetic selection. This shows that the putative four-element sequence structure suggested for L is not a reliable discriminator for the operational characterization of Sgls. IMPORTANCE The ssRNA phage world has recently undergone a metagenomic expansion upward of a thousandfold. Each genome likely carries at least one single-gene lysis (sgl) cistron encoding a protein that single-handedly induces host autolysis. Here, we initiate an approach to segregate the Sgls into operational types based on physiological analysis, as a first step toward the alluring goal of finding many new ways to induce bacterial death and the attendant expectations for new antibiotic development.
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Affiliation(s)
- S. Francesca Antillon
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
| | - Thomas G. Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Karthik Chamakura
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
| | - Ry Young
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
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37
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Hassan A, Tapp ZA, Tran DK, Rychtář J, Taylor D. Mathematical model of rabies vaccination in the United States. Theor Popul Biol 2024:S0040-5809(24)00032-7. [PMID: 38521097 DOI: 10.1016/j.tpb.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
Rabies is one of the oldest viral diseases and it has been present on every continent except Antarctica. Within the U.S. human rabies cases are quite rare. In the eastern USA, raccoons are the main reservoir hosts and pet vaccination serves as an important barrier against human rabies exposure. In this paper, we develop a compartmental model for rabies transmission amongst raccoons and domestic pets. We find the disease-free equilibria, reproduction numbers for the raccoons and domestic pets. We also determine the vaccination coverage/rates, both for raccoons and pets, needed to achieve the elimination of rabies.
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Affiliation(s)
- Annalise Hassan
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Zoe A Tapp
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Dan K Tran
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Jan Rychtář
- Department of Mathematics and Applied Mathematics, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Dewey Taylor
- Department of Mathematics and Applied Mathematics, Virginia Commonwealth University, Richmond, VA 23284, USA.
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Yamashita W, Ojima S, Tamura A, Azam AH, Kondo K, Yuancheng Z, Cui L, Shintani M, Suzuki M, Takahashi Y, Watashi K, Tsuneda S, Kiga K. Harnessing a T1 Phage-Derived Spanin for Developing Phage-Based Antimicrobial Development. Biodes Res 2024; 6:0028. [PMID: 38516182 PMCID: PMC10954549 DOI: 10.34133/bdr.0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/27/2023] [Indexed: 03/23/2024] Open
Abstract
The global increase in the prevalence of drug-resistant bacteria has necessitated the development of alternative treatments that do not rely on conventional antimicrobial agents. Using bacteriophage-derived lytic enzymes in antibacterial therapy shows promise; however, a thorough comparison and evaluation of their bactericidal efficacy are lacking. This study aimed to compare and investigate the bactericidal activity and spectrum of such lytic enzymes, with the goal of harnessing them for antibacterial therapy. First, we examined the bactericidal activity of spanins, endolysins, and holins derived from 2 Escherichia coli model phages, T1 and T7. Among these, T1-spanin exhibited the highest bactericidal activity against E. coli. Subsequently, we expressed T1-spanin within bacterial cells and assessed its bactericidal activity. T1-spanin showed potent bactericidal activity against all clinical isolates tested, including bacterial strains of 111 E. coli, 2 Acinetobacter spp., 3 Klebsiella spp., and 3 Pseudomonas aeruginosa. In contrast, T1 phage-derived endolysin showed bactericidal activity against E. coli and P. aeruginosa, yet its efficacy against other bacteria was inferior to that of T1-spanin. Finally, we developed a phage-based technology to introduce the T1-spanin gene into target bacteria. The synthesized non-proliferative phage exhibited strong antibacterial activity against the targeted bacteria. The potent bactericidal activity exhibited by spanins, combined with the novel phage synthetic technology, holds promise for the development of innovative antimicrobial agents.
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Affiliation(s)
- Wakana Yamashita
- Research Center for Drug and Vaccine Development,
National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Department of Life Science and Medical Bioscience,
Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Shinjiro Ojima
- Research Center for Drug and Vaccine Development,
National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Azumi Tamura
- Research Center for Drug and Vaccine Development,
National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Division of Infectious Diseases, Advanced Clinical Research Center, The Institute of Medical Science,
The University of Tokyo, Tokyo 108-8639, Japan
| | - Aa Haeruman Azam
- Research Center for Drug and Vaccine Development,
National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Kohei Kondo
- Research Center for Drug and Vaccine Development,
National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Antimicrobial Resistance Research Center,
National Institute of Infectious Diseases, Tokyo, Japan
| | - Zhang Yuancheng
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine,
Jichi Medical University, Shimotsuke-shi, Tochigi 329-0498, Japan
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine,
Jichi Medical University, Shimotsuke-shi, Tochigi 329-0498, Japan
| | - Masaki Shintani
- Department of Engineering,
Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka, 432-8561, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center,
National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development,
National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Department of Life Science and Medical Bioscience,
Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Koichi Watashi
- Research Center for Drug and Vaccine Development,
National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience,
Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Phage Therapy Institute,
Comprehensive Research Organization, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kotaro Kiga
- Research Center for Drug and Vaccine Development,
National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine,
Jichi Medical University, Shimotsuke-shi, Tochigi 329-0498, Japan
- Phage Therapy Institute,
Comprehensive Research Organization, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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39
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Tamura T, Yamamoto H, Ogino S, Morioka Y, Tsujino S, Suzuki R, Hiono T, Suzuki S, Isoda N, Sakoda Y, Fukuhara T. A rapid and versatile reverse genetics approach for generating recombinant positive-strand RNA viruses that use IRES-mediated translation. J Virol 2024; 98:e0163823. [PMID: 38353536 PMCID: PMC10949505 DOI: 10.1128/jvi.01638-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/24/2024] [Indexed: 03/20/2024] Open
Abstract
Reverse genetics systems have played a central role in developing recombinant viruses for a wide spectrum of virus research. The circular polymerase extension reaction (CPER) method has been applied to studying positive-strand RNA viruses, allowing researchers to bypass molecular cloning of viral cDNA clones and thus leading to the rapid generation of recombinant viruses. However, thus far, the CPER protocol has only been established using cap-dependent RNA viruses. Here, we demonstrate that a modified version of the CPER method can be successfully applied to positive-strand RNA viruses that use cap-independent, internal ribosomal entry site (IRES)-mediated translation. As a proof-of-concept, we employed mammalian viruses with different types (classes I, II, and III) of IRES to optimize the CPER method. Using the hepatitis C virus (HCV, class III), we found that inclusion in the CPER assembly of an RNA polymerase I promoter and terminator, instead of those from polymerase II, allowed greater viral production. This approach was also successful in generating recombinant bovine viral diarrhea virus (class III) following transfection of MDBK/293T co-cultures to overcome low transfection efficiency. In addition, we successfully generated the recombinant viruses from clinical specimens. Our modified CPER could be used for producing hepatitis A virus (HAV, type I) as well as de novo generation of encephalomyocarditis virus (type II). Finally, we generated recombinant HCV and HAV reporter viruses that exhibited replication comparable to that of the wild-type parental viruses. The recombinant HAV reporter virus helped evaluate antivirals. Taking the findings together, this study offers methodological advances in virology. IMPORTANCE The lack of versatility of reverse genetics systems remains a bottleneck in viral research. Especially when (re-)emerging viruses reach pandemic levels, rapid characterization and establishment of effective countermeasures using recombinant viruses are beneficial in disease control. Indeed, numerous studies have attempted to establish and improve the methods. The circular polymerase extension reaction (CPER) method has overcome major obstacles in generating recombinant viruses. However, this method has not yet been examined for positive-strand RNA viruses that use cap-independent, internal ribosome entry site-mediated translation. Here, we engineered a suitable gene cassette to expand the CPER method for all positive-strand RNA viruses. Furthermore, we overcame the difficulty of generating recombinant viruses because of low transfection efficiency. Using this modified method, we also successfully generated reporter viruses and recombinant viruses from a field sample without virus isolation. Taking these findings together, our adapted methodology is an innovative technology that could help advance virologic research.
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Affiliation(s)
- Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Hirotaka Yamamoto
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Saho Ogino
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Yuhei Morioka
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Shuhei Tsujino
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Takahiro Hiono
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Saori Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Norikazu Isoda
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yoshihiro Sakoda
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
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40
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Thomas MN, Zanella GC, Cowan B, Caceres CJ, Rajao DS, Perez DR, Gauger PC, Vincent Baker AL, Anderson TK. Nucleoprotein reassortment enhanced transmissibility of H3 1990.4.a clade influenza A virus in swine. J Virol 2024; 98:e0170323. [PMID: 38353535 PMCID: PMC10949443 DOI: 10.1128/jvi.01703-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/22/2024] [Indexed: 03/20/2024] Open
Abstract
The increased detection of H3 C-IVA (1990.4.a) clade influenza A viruses (IAVs) in US swine in 2019 was associated with a reassortment event to acquire an H1N1pdm09 lineage nucleoprotein (pdmNP) gene, replacing a TRIG lineage NP (trigNP). We hypothesized that acquiring the pdmNP conferred a selective advantage over prior circulating H3 viruses with a trigNP. To investigate the role of NP reassortment in transmission, we identified two contemporary 1990.4.a representative strains (NC/19 and MN/18) with different evolutionary origins of the NP gene. A reverse genetics system was used to generate wild-type (wt) strains and swap the pdm and TRIG lineage NP genes, generating four viruses: wtNC/19-pdmNP, NC/19-trigNP, wtMN/18-trigNP, and MN/18-pdmNP. The pathogenicity and transmission of the four viruses were compared in pigs. All four viruses infected 10 primary pigs and transmitted to five indirect contact pigs per group. Pigs infected via contact with MN/18-pdmNP shed virus 2 days earlier than pigs infected with wtMN/18-trigNP. The inverse did not occur for wtNC/19-pdmNP and NC/19-trigNP. This suggests that pdmNP reassortment resulted in a combination of genes that improved transmission efficiency when paired with the 1990.4.a hemagglutinin (HA). This is likely a multigenic trait, as replacing the trigNP gene did not diminish the transmission of a wild-type IAV in swine. This study demonstrates how reassortment and evolutionary change of internal genes can result in more transmissible viruses that influence HA clade detection frequency. Thus, rapidly identifying novel reassortants paired with dominant hemagglutinin/neuraminidase may improve the prediction of strains to include in vaccines.IMPORTANCEInfluenza A viruses (IAVs) are composed of eight non-continuous gene segments that can reassort during coinfection of a host, creating new combinations. Some gene combinations may convey a selective advantage and be paired together preferentially. A reassortment event was detected in swine in the United States that involved the exchange of two lineages of nucleoprotein (NP) genes (trigNP to pdmNP) that became a predominant genotype detected in surveillance. Using a transmission study, we demonstrated that exchanging the trigNP for a pdmNP caused the virus to shed from the nose at higher levels and transmit to other pigs more rapidly. Replacing a pdmNP with a trigNP did not hinder transmission, suggesting that transmission efficiency depends on interactions between multiple genes. This demonstrates how reassortment alters IAV transmission and that reassortment events can provide an explanation for why genetically related viruses with different internal gene combinations experience rapid fluxes in detection frequency.
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Affiliation(s)
- Megan N. Thomas
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, USA
| | - Giovana Ciacci Zanella
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
| | - Brianna Cowan
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - C. Joaquin Caceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Daniela S. Rajao
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Daniel R. Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Phillip C. Gauger
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Amy L. Vincent Baker
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
| | - Tavis K. Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
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41
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Zhou Y, Routh AL. Bipartite viral RNA genome heterodimerization influences genome packaging and virion thermostability. J Virol 2024; 98:e0182023. [PMID: 38329331 PMCID: PMC10949487 DOI: 10.1128/jvi.01820-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/18/2023] [Indexed: 02/09/2024] Open
Abstract
Multi-segmented viruses often multimerize their genomic segments to ensure efficient and stoichiometric packaging of the correct genetic cargo. In the bipartite Nodaviridae family, genome heterodimerization is also observed and conserved among different species. However, the nucleotide composition and biological function for this heterodimer remain unclear. Using Flock House virus as a model system, we developed a next-generation sequencing approach ("XL-ClickSeq") to probe heterodimer site sequences. We identified an intermolecular base-pairing site which contributed to heterodimerization in both wild-type and defective virus particles. Mutagenic disruption of this heterodimer site exhibited significant deficiencies in genome packaging and encapsidation specificity to viral genomic RNAs. Furthermore, the disruption of this intermolecular interaction directly impacts the thermostability of the mature virions. These results demonstrate that the intermolecular RNA-RNA interactions within the encapsidated genome of an RNA virus have an important role on virus particle integrity and thus may impact its transmission to a new host.IMPORTANCEFlock House virus is a member of Nodaviridae family of viruses, which provides a well-studied model virus for non-enveloped RNA virus assembly, cell entry, and replication. The Flock House virus genome consists of two separate RNA molecules, which can form a heterodimer upon heating of virus particles. Although similar RNA dimerization is utilized by other viruses (such as retroviruses) as a packaging mechanism and is conserved among Nodaviruses, the role of heterodimerization in the Nodavirus replication cycle is unclear. In this research, we identified the RNA sequences contributing to Flock House virus genome heterodimerization and discovered that such RNA-RNA interaction plays an essential role in virus packaging efficiency and particle integrity. This provides significant insight into how the interaction of packaged viral RNA may have a broader impact on the structural and functional properties of virus particles.
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Affiliation(s)
- Yiyang Zhou
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, Texas, USA
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew L. Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
- Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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42
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Idrovo-Hidalgo T, Pignataro MF, Bredeston LM, Elias F, Herrera MG, Pavan MF, Foscaldi S, Suireszcz M, Fernández NB, Wetzler DE, Paván CH, Craig PO, Roman EA, Ruberto LAM, Noseda DG, Ibañez LI, Czibener C, Ugalde JE, Nadra AD, Santos J, D'Alessio C. Deglycosylated RBD produced in Pichia pastoris as a low-cost sera COVID-19 diagnosis tool and a vaccine candidate. Glycobiology 2024; 34:cwad089. [PMID: 37944064 DOI: 10.1093/glycob/cwad089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
During the COVID-19 outbreak, numerous tools including protein-based vaccines have been developed. The methylotrophic yeast Pichia pastoris (synonymous to Komagataella phaffii) is an eukaryotic cost-effective and scalable system for recombinant protein production, with the advantages of an efficient secretion system and the protein folding assistance of the secretory pathway of eukaryotic cells. In a previous work, we compared the expression of SARS-CoV-2 Spike Receptor Binding Domain in P. pastoris with that in human cells. Although the size and glycosylation pattern was different between them, their protein structural and conformational features were indistinguishable. Nevertheless, since high mannose glycan extensions in proteins expressed by yeast may be the cause of a nonspecific immune recognition, we deglycosylated RBD in native conditions. This resulted in a highly pure, homogenous, properly folded and monomeric stable protein. This was confirmed by circular dichroism and tryptophan fluorescence spectra and by SEC-HPLC, which were similar to those of RBD proteins produced in yeast or human cells. Deglycosylated RBD was obtained at high yields in a single step, and it was efficient in distinguishing between SARS-CoV-2-negative and positive sera from patients. Moreover, when the deglycosylated variant was used as an immunogen, it elicited a humoral immune response ten times greater than the glycosylated form, producing antibodies with enhanced neutralizing power and eliciting a more robust cellular response. The proposed approach may be used to produce at a low cost, many antigens that require glycosylation to fold and express, but do not require glycans for recognition purposes.
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Affiliation(s)
- Tommy Idrovo-Hidalgo
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
| | - María F Pignataro
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
- Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Universidad de Buenos Aires, Junín 965 C1113AAD. Buenos Aires, Argentina
| | - Luis M Bredeston
- Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Universidad de Buenos Aires, Junín 965 C1113AAD. Buenos Aires, Argentina
- Instituto de Química y Fisicoquímica Biológicas, (IQUIFIB), CONICET-Universidad de Buenos Aires, Junín 956 C1113AAD, Buenos Aires, Argentina
| | - Fernanda Elias
- Consejo Nacional de Investigaciones Científicas y Técnicas-Fundación Pablo Cassará, Instituto de Ciencia y Tecnología Dr. César Milstein, Saladillo 2468 C1440FFX, Buenos Aires, Argentina
| | - María G Herrera
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
| | - María F Pavan
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 C1425FQB, Buenos Aires, Argentina
| | - Sabrina Foscaldi
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
| | - Mayra Suireszcz
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
| | - Natalia B Fernández
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
| | - Diana E Wetzler
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
| | - Carlos H Paván
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 C1425FQB, Buenos Aires, Argentina
- Facultad de Farmacia y Bioquímica, LANAIS-PROEM, Instituto de Química y Fisicoquímica Biológicas, (IQUIFIB), CONICET-Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Patricio O Craig
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
| | - Ernesto A Roman
- Instituto de Química y Fisicoquímica Biológicas, (IQUIFIB), CONICET-Universidad de Buenos Aires, Junín 956 C1113AAD, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
| | - Lucas A M Ruberto
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 965, C1113AAD, Buenos Aires, Argentina
- Instituto de Nanobiotecnología (NANOBIOTEC), CONICET-Universidad de Buenos Aires, Junín 965, C1113AAD, Buenos Aires, Argentina
- Instituto Antártico Argentino, Ministerio de Relaciones Exteriores y Culto, Av. 25 de Mayo 1147, B1650HMP, San Martín, Prov. de Buenos Aires, Argentina
| | - Diego G Noseda
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 C1425FQB, Buenos Aires, Argentina
- Instituto de Investigaciones Biotecnológicas (IIBio), Universidad Nacional de San Martín-CONICET, Av. 25 de Mayo y Francia S/N, B1650HMP, San Martín, Prov. de Buenos Aires, Argentina
| | - Lorena I Ibañez
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 C1425FQB, Buenos Aires, Argentina
| | - Cecilia Czibener
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 C1425FQB, Buenos Aires, Argentina
- Instituto de Investigaciones Biotecnológicas (IIBio), Universidad Nacional de San Martín-CONICET, Av. 25 de Mayo y Francia S/N, B1650HMP, San Martín, Prov. de Buenos Aires, Argentina
| | - Juan E Ugalde
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 C1425FQB, Buenos Aires, Argentina
- Instituto de Investigaciones Biotecnológicas (IIBio), Universidad Nacional de San Martín-CONICET, Av. 25 de Mayo y Francia S/N, B1650HMP, San Martín, Prov. de Buenos Aires, Argentina
| | - Alejandro D Nadra
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 C1425FQB, Buenos Aires, Argentina
| | - Javier Santos
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 C1425FQB, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
| | - Cecilia D'Alessio
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología y Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 C1425FQB, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EGA, Buenos Aires, Argentina
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43
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Cao X, Tang L, Song J. Circular Single-Stranded DNA: Discovery, Biological Effects, and Applications. ACS Synth Biol 2024. [PMID: 38501391 DOI: 10.1021/acssynbio.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The field of nucleic acid therapeutics has witnessed a significant surge in recent times, as evidenced by the increasing number of approved genetic drugs. However, current platform technologies containing plasmids, lipid nanoparticle-mRNAs, and adeno-associated virus vectors encounter various limitations and challenges. Thus, we are devoted to finding a novel nucleic acid vector and have directed our efforts toward investigating circular single-stranded DNA (CssDNA), an ancient form of nucleic acid. CssDNAs are ubiquitous, but generally ignored. Accumulating evidence suggests that CssDNAs possess exceptional properties as nucleic acid vectors, exhibiting great potential for clinical applications in genetic disorders, gene editing, and immune cell therapy. Here, we comprehensively review the discovery and biological effects of CssDNAs as well as their applications in the field of biomedical research for the first time. Undoubtedly, as an ancient form of DNA, CssDNA holds immense potential and promises novel insights for biomedical research.
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Affiliation(s)
- Xisen Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
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Zhang J, Zhao L, Bai Y, Li S, Zhang M, Wei B, Wang X, Xue Y, Li L, Ma G, Tang Y, Wang X. An ascidian Polycarpa aurata-derived pan-inhibitor against coronaviruses targeting M pro. Bioorg Med Chem Lett 2024; 103:129706. [PMID: 38508325 DOI: 10.1016/j.bmcl.2024.129706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/09/2024] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
Abstract
Coronaviruses (CoVs) are responsible for a wide range of illnesses in both animals and human. The main protease (Mpro) of CoVs is an attractive drug target, owing its critical and highly conserved role in viral replication. Here, we developed and refined an enzymatic technique to identify putative Mpro inhibitors from 189 marine chemicals and 46 terrestrial natural products. The IC50 values of Polycarpine (1a), a marine natural substance we studied and synthesized, are 30.0 ± 2.5 nM for SARS-CoV-2 Mpro and 0.12 ± 0.05 μM for PEDV Mpro. Our research further demonstrated that pretreatment with Polycarpine (1a) inhibited the betacoronavirus SARS-CoV-2 and alphacoronavirus PEDV multiplication in Vero-E6 cells. As a result, Polycarpine (1a), a pan-inhibitor of Mpro, will function as an effective and promising antiviral option to combat CoVs infection and as a foundation for further therapeutic research.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Lili Zhao
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China.
| | - Yuxin Bai
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China
| | - Shanshan Li
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Meifang Zhang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Bo Wei
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Xianyang Wang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yan Xue
- Department of Physiology, School of Basic Medicine, Qingdao University, Qingdao 266000, China
| | - Li Li
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China
| | - Guiliang Ma
- Department of General Surgery, Qingdao Municipal Hospital, No. 5, Donghaizhong Road, Qingdao 266071, China.
| | - Yu Tang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China.
| | - Xin Wang
- Key Laboratory of Marine Drugs of Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Center for Innovation Marine Drug Screening & Evaluation of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Marine Biomedical Research Institute of Qingdao, Qingdao 266003, China.
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Umer BA, Noyce RS, Kieser Q, Favis NA, Shenouda MM, Rans KJ, Middleton J, Hitt MM, Evans DH. Oncolytic vaccinia virus immunotherapy antagonizes image-guided radiotherapy in mouse mammary tumor models. PLoS One 2024; 19:e0298437. [PMID: 38498459 PMCID: PMC10947714 DOI: 10.1371/journal.pone.0298437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/23/2024] [Indexed: 03/20/2024] Open
Abstract
Ionizing radiation (IR) and oncolytic viruses are both used to treat cancer, and the effectiveness of both agents depends upon stimulating an immune response against the tumor. In this study we tested whether combining image guided ionizing radiation (IG-IR) with an oncolytic vaccinia virus (VACV) could yield a better therapeutic response than either treatment alone. ΔF4LΔJ2R VACV grew well on irradiated human and mouse breast cancer cells, and the virus can be combined with 4 or 8 Gy of IR to kill cells in an additive or weakly synergistic manner. To test efficacy in vivo we used immune competent mice bearing orthotopic TUBO mammary tumors. IG-IR worked well with 10 Gy producing 80% complete responses, but this was halved when the tumors were treated with VACV starting 2 days after IG-IR. VACV monotherapy was ineffective in this model. The antagonism was time dependent as waiting for 21 days after IG-IR eliminated the inhibitory effect but without yielding any further benefits over IR alone. In irradiated tumors, VACV replication was also lower, suggesting that irradiation created an environment that did not support infection as well in vivo as in vitro. A study of how four different treatment regimens affected the immune composition of the tumor microenvironment showed that treating irradiated tumors with VACV altered the immunological profiles in tumors exposed to IR or VACV alone. We detected more PD-1 and PD-L1 expression in tumors exposed to IR+VACV but adding an αPD-1 antibody to the protocol did not change the way VACV interferes with IG-IR therapy. VACV encodes many immunosuppressive gene products that may interfere with the ability of radiotherapy to induce an effective anti-tumor immune response through the release of danger-associated molecular patterns. These data suggest that infecting irradiated tumors with VACV, too soon after exposure, may interfere in the innate and linked adaptive immune responses that are triggered by radiotherapy to achieve a beneficial impact.
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Affiliation(s)
- Brittany A. Umer
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Ryan S. Noyce
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute for Virology, University of Alberta, Edmonton, Alberta, Canada
| | - Quinten Kieser
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Nicole A. Favis
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Mira M. Shenouda
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Kim J. Rans
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Jackie Middleton
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Mary M. Hitt
- Li Ka Shing Institute for Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - David H. Evans
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute for Virology, University of Alberta, Edmonton, Alberta, Canada
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Subong BJJ, Ozawa T. Bio-Chemoinformatics-Driven Analysis of nsp7 and nsp8 Mutations and Their Effects on Viral Replication Protein Complex Stability. Curr Issues Mol Biol 2024; 46:2598-2619. [PMID: 38534781 DOI: 10.3390/cimb46030165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024] Open
Abstract
The nonstructural proteins 7 and 8 (nsp7 and nsp8) of SARS-CoV-2 are highly important proteins involved in the RNA-dependent polymerase (RdRp) protein replication complex. In this study, we analyzed the global mutation of nsp7 and nsp8 in 2022 and 2023 and analyzed the effects of mutation on the viral replication protein complex using bio-chemoinformatics. Frequently occurring variants are found to be single amino acid mutations for both nsp7 and nsp8. The most frequently occurring mutations for nsp7 which include L56F, L71F, S25L, M3I, D77N, V33I and T83I are predicted to cause destabilizing effects, whereas those in nsp8 are predicted to cause stabilizing effects, with the threonine to isoleucine mutation (T89I, T145I, T123I, T148I, T187I) being a frequent mutation. A conserved domain database analysis generated critical interaction residues for nsp7 (Lys-7, His-36 and Asn-37) and nsp8 (Lys-58, Pro-183 and Arg-190), which, according to thermodynamic calculations, are prone to destabilization. Trp-29, Phe-49 of nsp7 and Trp-154, Tyr-135 and Phe-15 of nsp8 cause greater destabilizing effects to the protein complex based on a computational alanine scan suggesting them as possible new target sites. This study provides an intensive analysis of the mutations of nsp7 and nsp8 and their possible implications for viral complex stability.
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Affiliation(s)
- Bryan John J Subong
- Department of Chemistry, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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Wang J, Ni Y, Zhao H, Liu X, Qiu R, Li S, Liu H. Complete genome sequence of a novel dsRNA virus from the phytopathogenic fungus Fusarium oxysporum. Arch Virol 2024; 169:75. [PMID: 38492088 DOI: 10.1007/s00705-024-05976-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/13/2023] [Indexed: 03/18/2024]
Abstract
Fusarium oxysporum is a widespread plant pathogen that causes fusarium wilt and fusarium root rot in many economically significant crops. Here, a novel dsRNA virus tentatively named "Fusarium oxysporum virus 1" (FoV1) was identified in F. oxysporum strain 3S-18. The genome of FoV1 is 2,944 nucleotides (nt) in length and contains two non-overlapping open reading frames (ORF1 and 2). The larger of these, ORF2, encodes an RNA-dependent RNA polymerase (RdRp) of 590 amino acids with a molecular mass of 67.52 kDa. ORF1 encodes a putative nucleocapsid protein consisting of 134 amino acids with a molecular mass of 34.25 kDa. The RdRp domain of FoV1 shares 60.00% to 84.24% sequence identity with non-segmented dsRNA viruses. Phylogenetic analysis further suggested that FoV1 is a new member of the proposed genus "Unirnavirus" accommodating unclassified monopartite dsRNA viruses.
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Affiliation(s)
- Jing Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Yunxia Ni
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Hui Zhao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Xintao Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Rui Qiu
- Institute of Tobacco, Henan Academy of Agricultural Sciences, Key Laboratory for Green Preservation & Control of Tobacco Diseases and Pest in Huanghuai Growing Area, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Shujun Li
- Institute of Tobacco, Henan Academy of Agricultural Sciences, Key Laboratory for Green Preservation & Control of Tobacco Diseases and Pest in Huanghuai Growing Area, Zhengzhou, 450002, Henan Province, People's Republic of China.
| | - Hongyan Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan Province, People's Republic of China.
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Leng X, Yang H, Zhao L, Feng J, Jin K, Liao L, Zhang F. Dengue encephalopathy in an adult due to dengue virus type 1 infection. BMC Infect Dis 2024; 24:319. [PMID: 38491361 PMCID: PMC10943806 DOI: 10.1186/s12879-024-09198-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Dengue is an important public health problem, which caused by the dengue virus (DENV), a single-stranded RNA virus consisted of four serotypes. Central nervus system (CNS) impairment in dengue usually results from DENV-2 or DENV-3 infection, which lead to life-threatening outcomes. Furthermore, neurological complications due to DENV-1 was rare especially in adult patients. CASE PRESENTATION A 44-year-old man without comorbidities had lethargy after hyperpyrexia and a positive DENV NS1 antigen was detected for confirming the diagnosis of dengue on day 8 of onset. Then logagnosia, decreased muscle strength, delirium and irritability were occurred even radiographic examination were normal. He was treated with low-dose hormone, sedatives and gamma goblin with a short duration of 6 days. The cerebrospinal fluid (CSF) tests were persistent normal. However, presence of DENV-1 RNA was confirmed both in CSF and serum. Furthermore, the complete sequence of the DENV isolated from the patient's serum was performed (GenBank No.: MW261838). The cytokines as IL-6, IL-10 and sVCAM-1 were increased in critical phase of disease. Finally, the patient was discharged on day 24 of onset without any neurological sequelae. CONCLUSION Encephalopathy caused by a direct CNS invasion due to DENV-1 during viremia was described in an adult patient. Treatment with low-dose hormone and gamma goblin was helpful for admission.
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Affiliation(s)
- Xingyu Leng
- Guangzhou Medical Research Institute of Infectious Diseases, Department of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, 510000, Guangzhou, P.R. China
| | - Huiqin Yang
- Guangzhou Medical Research Institute of Infectious Diseases, Department of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, 510000, Guangzhou, P.R. China
| | - Lingzhai Zhao
- Guangzhou Medical Research Institute of Infectious Diseases, Department of Clinical Laboratory, Guangzhou Eighth People's Hospital, Guangzhou Medical University, 510000, Guangzhou, P. R. China
| | - Jiamin Feng
- Guangzhou Medical Research Institute of Infectious Diseases, Institution of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, 510000, Guangzhou, P.R. China
| | - Kanghong Jin
- Guangzhou Medical Research Institute of Infectious Diseases, Department of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, 510000, Guangzhou, P.R. China
| | - Lu Liao
- Guangzhou Medical Research Institute of Infectious Diseases, Department of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, 510000, Guangzhou, P.R. China
| | - Fuchun Zhang
- Guangzhou Medical Research Institute of Infectious Diseases, Department of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, 510000, Guangzhou, P.R. China.
- Guangzhou Medical Research Institute of Infectious Diseases, Institution of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, 510000, Guangzhou, P.R. China.
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49
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Olajiga OM, Jameson SB, Carter BH, Wesson DM, Mitzel D, Londono-Renteria B. Artificial Feeding Systems for Vector-Borne Disease Studies. Biology (Basel) 2024; 13:188. [PMID: 38534457 DOI: 10.3390/biology13030188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/28/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024]
Abstract
This review examines the advancements and methodologies of artificial feeding systems for the study of vector-borne diseases, offering a critical assessment of their development, advantages, and limitations relative to traditional live host models. It underscores the ethical considerations and practical benefits of such systems, including minimizing the use of live animals and enhancing experimental consistency. Various artificial feeding techniques are detailed, including membrane feeding, capillary feeding, and the utilization of engineered biocompatible materials, with their respective applications, efficacy, and the challenges encountered with their use also being outlined. This review also forecasts the integration of cutting-edge technologies like biomimicry, microfluidics, nanotechnology, and artificial intelligence to refine and expand the capabilities of artificial feeding systems. These innovations aim to more accurately simulate natural feeding conditions, thereby improving the reliability of studies on the transmission dynamics of vector-borne diseases. This comprehensive review serves as a foundational reference for researchers in the field, proposing a forward-looking perspective on the potential of artificial feeding systems to revolutionize vector-borne disease research.
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Affiliation(s)
- Olayinka M Olajiga
- Department of Tropical Medicine and Infectious Disease, Tulane University, New Orleans, LA 70112, USA
| | - Samuel B Jameson
- Department of Tropical Medicine and Infectious Disease, Tulane University, New Orleans, LA 70112, USA
| | - Brendan H Carter
- Department of Tropical Medicine and Infectious Disease, Tulane University, New Orleans, LA 70112, USA
| | - Dawn M Wesson
- Department of Tropical Medicine and Infectious Disease, Tulane University, New Orleans, LA 70112, USA
| | - Dana Mitzel
- Animal Diseases Research Unit, National Bio- and Agro-Defense Facility, United States Department of Agriculture, Agricultural Research Service, Manhattan, KS 66506, USA
| | - Berlin Londono-Renteria
- Department of Tropical Medicine and Infectious Disease, Tulane University, New Orleans, LA 70112, USA
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50
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de Wit MM, Dimas Martins A, Delecroix C, Heesterbeek H, ten Bosch QA. Mechanistic models for West Nile virus transmission: a systematic review of features, aims and parametrization. Proc Biol Sci 2024; 291:20232432. [PMID: 38471554 PMCID: PMC10932716 DOI: 10.1098/rspb.2023.2432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Mathematical models within the Ross-Macdonald framework increasingly play a role in our understanding of vector-borne disease dynamics and as tools for assessing scenarios to respond to emerging threats. These threats are typically characterized by a high degree of heterogeneity, introducing a range of possible complexities in models and challenges to maintain the link with empirical evidence. We systematically identified and analysed a total of 77 published papers presenting compartmental West Nile virus (WNV) models that use parameter values derived from empirical studies. Using a set of 15 criteria, we measured the dissimilarity compared with the Ross-Macdonald framework. We also retrieved the purpose and type of models and traced the empirical sources of their parameters. Our review highlights the increasing refinements in WNV models. Models for prediction included the highest number of refinements. We found uneven distributions of refinements and of evidence for parameter values. We identified several challenges in parametrizing such increasingly complex models. For parameters common to most models, we also synthesize the empirical evidence for their values and ranges. The study highlights the potential to improve the quality of WNV models and their applicability for policy by establishing closer collaboration between mathematical modelling and empirical work.
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Affiliation(s)
- Mariken M. de Wit
- Quantitative Veterinary Epidemiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Afonso Dimas Martins
- Department of Population Health Sciences, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, The Netherlands
| | - Clara Delecroix
- Quantitative Veterinary Epidemiology, Wageningen University and Research, Wageningen, The Netherlands
- Department of Environmental Sciences, Wageningen University and Research, Wageningen, The Netherlands
| | - Hans Heesterbeek
- Department of Population Health Sciences, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, The Netherlands
| | - Quirine A. ten Bosch
- Quantitative Veterinary Epidemiology, Wageningen University and Research, Wageningen, The Netherlands
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