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Haq IU, Rahim K, Paker NP. Exploring the historical roots, advantages and efficacy of phage therapy in plant diseases management. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112164. [PMID: 38908799 DOI: 10.1016/j.plantsci.2024.112164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/10/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
In the drug-resistance era, phage therapy has received considerable attention from worldwide researchers. Phage therapy has been given much attention in public health but is rarely applied to control plant diseases. Herein, we discuss phage therapy as a biocontrol approach against several plant diseases. The emergence of antibiotic resistance in agriculturally important pathogenic bacteria and the toxic nature of different synthetic compounds used to control microbes has driven researchers to rethink the century-old strategy of phage therapy''. Compared to other treatment strategies, phage therapy offers remarkable advantages such as high specificity, less chances of drug resistance, non-harmful nature, and benefit to soil microbial flora. The optimizations and protective formulations of phages are significant accomplishments; however, steps towards a better understanding of the physiologic characteristics of phages need to be preceded to commercialize their use. The future of phage therapy in the context of plant disease management is promising and could play a significant role in sustainable agriculture. Ongoing research will likely affirm the safety of phage therapy, ensuring that it does not harm non-target organisms, including beneficial soil microbes. Phage therapy could become vital in addressing global food security challenges, particularly in regions heavily impacted by plant bacterial diseases. Efforts to create formulations that enhance the stability and shelf-life of phages will be crucial, especially for their use in varied environmental conditions.
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Affiliation(s)
- Ihtisham Ul Haq
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, M. Strzody 9, Gliwice 44-100, Poland; Joint Doctoral School, Silesian University of Technology, Akademicka 2A, Gliwice 44-100, Poland; Programa de Pos-graduacao em Invacao Tecnologia, Universidade de Minas Gerais, Belo Horizonte, Brazil.
| | - Kashif Rahim
- School of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Najeeba Parre Paker
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.
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2
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Hu Y, Zhao W, Lv Y, Li H, Li J, Zhong M, Pu D, Jian F, Song J, Zhang Y. NLRP3-dependent pyroptosis exacerbates coxsackievirus A16 and coxsackievirus A10-induced inflammatory response and viral replication in SH-SY5Y cells. Virus Res 2024; 345:199386. [PMID: 38705479 PMCID: PMC11091677 DOI: 10.1016/j.virusres.2024.199386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Coxsackievirus A16 (CV-A16) and coxsackievirus A10 (CV-A10), more commonly etiological agents of hand, foot and mouth disease (HFMD), are capable of causing severe neurological syndromes with high fatalities, but their neuropathogenesis has rarely been studied. Mounting evidence indicated that pyroptosis is an inflammatory form of cell death that might be widely involved in the pathogenic mechanisms of neurotropic viruses. Our study was designed to examine the effects of NLRP3-mediated pyroptosis in CV-A16- and CV-A10-induced inflammatory neuropathologic formation. In this work, it was showed that SH-SY5Y cells were susceptible to CV-A16 and CV-A10, and meanwhile their infections could result in a decreasing cell viability and an increasing LDH release as well as Caspase1 activation. Moreover, CV-A16 and CV-A10 infections triggered NLRP3-mediated pyroptosis and promoted the release of inflammatory cytokines. Additionally, activated NLRP3 accelerated the pyroptosis formation and aggravated the inflammatory response, but inhibited NLRP3 had a dampening effect on the above situation. Finally, it was further revealed that NLRP3 agonist enhanced the viral replication, but NLRP3 inhibitor suppressed the viral replication, suggesting that NLRP3-driven pyroptosis might support CV-A16 and CV-A10 production in SH-SY5Y cells. Together, our findings demonstrated a mechanism by which CV-A16 and CV-A10 induce inflammatory responses by evoking NLRP3 inflammasome-regulated pyroptosis, which in turn further stimulated the viral replication, providing novel insights into the pathogenesis of CV-A16 and CV-A10 infections.
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Affiliation(s)
- Yajie Hu
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Wei Zhao
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yaming Lv
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Hui Li
- National and Local Engineering Center for Infectious Biological Products, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, China
| | - Jiang Li
- National and Local Engineering Center for Infectious Biological Products, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, China
| | - Mingmei Zhong
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Dandan Pu
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Fuping Jian
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Jie Song
- National and Local Engineering Center for Infectious Biological Products, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, China.
| | - Yunhui Zhang
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China.
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3
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Meidaninikjeh S, Mohammadi P, Elikaei A. A simplified method of bacteriophage preparation for transmission electron microscope. J Virol Methods 2024; 328:114951. [PMID: 38750823 DOI: 10.1016/j.jviromet.2024.114951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/21/2024]
Abstract
Bacteriophages are viruses that infect bacteria. Researchers use different methods to study the characteristics of bacteriophages. Transmission electron microscope (TEM) is considered the best method to analyze these characteristics. However, the quality of TEM micrographs is significantly influenced by the preparation methods used to prepare the bacteriophages sample. In this study, researchers compared two different methods for preparing the bacteriophage samples. In one method was used SM buffer, while in the other used deionized water. The results were analyzed by TEM and compared with each other. Additionally, the viability of bacteriophage in deionized water and SM buffer at 4°C was determined through plaque assay within 72 hours. TEM micrographs showed that the quality of bacteriophage sample prepared with deionized water is superior to those prepared with SM buffer. Furthermore, the titer of the bacteriophages did not show a significant reduction during 72 hours in both SM and deionized water. In conclusion, the results suggested that preparation method can significantly impact the quality of TEM micrographs. Using sterile deionized water for the preparation of bacteriophages is a simple way to improve the quality of TEM micrographs and it is advisable to send the samples to the laboratory within 72 hours.
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Affiliation(s)
- Sepideh Meidaninikjeh
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Parisa Mohammadi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran.
| | - Ameneh Elikaei
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran
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4
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Hosseininasab SS, Naderifar M, Akbarizadeh MR, Rahimzadeh M, Soltaninejad S, Makarem Z, Satarzadeh N, Sadeghi Dousari A. The use of phages for the biosynthesis of metal nanoparticles and their biological applications: A review. J Cell Mol Med 2024; 28:e18383. [PMID: 38837580 PMCID: PMC11149492 DOI: 10.1111/jcmm.18383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 04/19/2024] [Accepted: 04/27/2024] [Indexed: 06/07/2024] Open
Abstract
Nowadays, the use of biological methods of synthesis of nanoparticles as substitutes for methods that use high energy and consumption of expensive and dangerous materials is of interest to researchers all over the world. Biological methods of synthesising metal nanoparticles are very important because they are easy, affordable, safe, environmentally friendly and able to control the size and shape of nanoparticles. One of the methods that is of interest today is the use of bacteriophages as the most abundant organisms in nature in the synthesis of metal nanoparticles. Nanomaterials biosynthesized from phages have shown various clinical applications, including antimicrobial activities, biomedical sensors, drug and gene delivery systems, cancer treatment and tissue regeneration. Therefore, the purpose of this review is to investigate the biosynthesis of metal nanoparticles with phages and their biomedical applications.
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Affiliation(s)
| | - Mahin Naderifar
- School of Nursing & MidwiferyZabol University of Medical SciencesZabolIran
| | | | | | | | - Zohre Makarem
- Noncommunicable Diseases Research CenterBam University of Medical SciencesBamIran
| | - Naghmeh Satarzadeh
- Department of Pharmaceutical Biotechnology, Faculty of PharmacyKerman University of Medical SciencesKermanIran
| | - Amin Sadeghi Dousari
- Medical Mycology and Bacteriology Research CenterKerman University of Medical SciencesKermanIran
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5
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Choi Y, Kwak MJ, Kang MG, Kang AN, Lee W, Mun D, Choi H, Park J, Eor JY, Song M, Kim JN, Oh S, Kim Y. Molecular characterization and environmental impact of newly isolated lytic phage SLAM_phiST1N3 in the Cornellvirus genus for biocontrol of a multidrug-resistant Salmonella Typhimurium in the swine industry chain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171208. [PMID: 38408652 DOI: 10.1016/j.scitotenv.2024.171208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
Salmonella Typhimurium is a highly lethal pathogenic bacterium in weaned piglets, causing significant treatment costs and economic losses in the swine industry. Additionally, due to its ability to induce zoonotic diseases, resulting in harm to humans through the transmission of the pathogen from pork, it presents a serious public health issue. Bacteriophages (phages), viruses that infect specific bacterial strains, have been proposed as an alternative to antibiotics for controlling pathogenic bacteria. In this study, we isolated SLAM_phiST1N3, a phage infecting a multidrug-resistant (MDR) S. Typhimurium wild-type strain isolated from diseased pigs. First, comparative genomics and phylogenetic analysis revealed that SLAM_phiST1N3 belongs to the Cornellvirus genus. Moreover, utilizing a novel classification approach introduced in this study, SLAM_phiST1N3 was classified at the species level. Host range experiments demonstrated that SLAM_phiST1N3 did not infect other pathogenic bacteria or probiotics derived from pigs or other livestock. While complete eradication of Salmonella was not achievable in the liquid inhibition assay, surprisingly, we succeeded in largely eliminating Salmonella in the FIMM analysis, a gut simulation system using weaned piglet feces. Furthermore, using the C. elegans model, we showcased the potential of SLAM_phiST1N3 to prevent S. Typhimurium infection in living organisms. In addition, it was confirmed that bacterial control could be achieved when phage was applied to Salmonella-contaminated pork. pH and temperature stability experiments demonstrated that SLAM_phiST1N3 can endure swine industry processes and digestive conditions. In conclusion, SLAM_phiST1N3 demonstrates potential environmental impact as a substance for Salmonella prevention across various aspects of the swine industry chain.
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Affiliation(s)
- Youbin Choi
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Min-Jin Kwak
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Min-Geun Kang
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - An Na Kang
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Woogji Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Daye Mun
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyejin Choi
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeongkuk Park
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Ju Young Eor
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Minho Song
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jong Nam Kim
- Department of Food Science & Nutrition, Dongseo University, Busan 47011, Republic of Korea
| | - Sangnam Oh
- Department of Functional Food and Biotechnology, Jeonju University, Jeonju 55069, Republic of Korea.
| | - Younghoon Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea.
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6
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Panicker LR, Kummari S, Keerthanaa MR, Rao Bommi J, Koteshwara Reddy K, Yugender Goud K. Trends and challenges in electroanalytical biosensing methodologies for infectious viral diseases. Bioelectrochemistry 2024; 156:108594. [PMID: 37984310 DOI: 10.1016/j.bioelechem.2023.108594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023]
Abstract
Viral pandemic diseases have disruptive global consequences leading to millions of deaths and a severe impact on the global economy. Inadequate preventative protocols have led to an overwhelming demand for intensive care leading to uncontrollable burdens and even breakdown of healthcare sectors across many countries. The rapid detection of viral disease helps in the understanding of the relevant intricacies, helping to tackle infection with improved guidelines. Portable biosensor devices offer promising solutions by facilitating on-site detection of viral pathogens. This review summarizes the latest innovative strategies reported using electroanalytical methods for the screening of viral antigens. The structural components of viruses and their categories are presented followed by the various recognition elements and transduction techniques involved in biosensors. Core sections focus on biosensors reported for viral genomic detection(DNA and RNA) and antigenic capsid protein. Strategies for addressing the challenges of electroanalytical biosensing of viral components are also presented. The advantages, and disadvantages of biorecognition elements and nanozymes for the detection of viral disease are highlighted. Such technical insights will help researchers working in chemistry, and biochemistry as well as clinicians working in medical diagnostics.
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Affiliation(s)
- Lakshmi R Panicker
- Department of Chemistry, Indian Institute of Technology Palakkad, Palakkad, Kerala 678 557, India
| | - Shekher Kummari
- Department of Chemistry, Indian Institute of Technology Palakkad, Palakkad, Kerala 678 557, India
| | - M R Keerthanaa
- Department of Chemistry, Indian Institute of Technology Palakkad, Palakkad, Kerala 678 557, India
| | | | - K Koteshwara Reddy
- School of Material Science and Engineering, Purdue University, West Lafayette, IN, 47907, USA.
| | - K Yugender Goud
- Department of Chemistry, Indian Institute of Technology Palakkad, Palakkad, Kerala 678 557, India.
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7
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Bhandare S, Lawal OU, Colavecchio A, Cadieux B, Zahirovich-Jovich Y, Zhong Z, Tompkins E, Amitrano M, Kukavica-Ibrulj I, Boyle B, Wang S, Levesque RC, Delaquis P, Danyluk M, Goodridge L. Genomic and Phenotypic Analysis of Salmonella enterica Bacteriophages Identifies Two Novel Phage Species. Microorganisms 2024; 12:695. [PMID: 38674639 PMCID: PMC11052255 DOI: 10.3390/microorganisms12040695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Bacteriophages (phages) are potential alternatives to chemical antimicrobials against pathogens of public health significance. Understanding the diversity and host specificity of phages is important for developing effective phage biocontrol approaches. Here, we assessed the host range, morphology, and genetic diversity of eight Salmonella enterica phages isolated from a wastewater treatment plant. The host range analysis revealed that six out of eight phages lysed more than 81% of the 43 Salmonella enterica isolates tested. The genomic sequences of all phages were determined. Whole-genome sequencing (WGS) data revealed that phage genome sizes ranged from 41 to 114 kb, with GC contents between 39.9 and 50.0%. Two of the phages SB13 and SB28 represent new species, Epseptimavirus SB13 and genera Macdonaldcampvirus, respectively, as designated by the International Committee for the Taxonomy of Viruses (ICTV) using genome-based taxonomic classification. One phage (SB18) belonged to the Myoviridae morphotype while the remaining phages belonged to the Siphoviridae morphotype. The gene content analyses showed that none of the phages possessed virulence, toxin, antibiotic resistance, type I-VI toxin-antitoxin modules, or lysogeny genes. Three (SB3, SB15, and SB18) out of the eight phages possessed tailspike proteins. Whole-genome-based phylogeny of the eight phages with their 113 homologs revealed three clusters A, B, and C and seven subclusters (A1, A2, A3, B1, B2, C1, and C2). While cluster C1 phages were predominantly isolated from animal sources, cluster B contained phages from both wastewater and animal sources. The broad host range of these phages highlights their potential use for controlling the presence of S. enterica in foods.
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Affiliation(s)
- Sudhakar Bhandare
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham LE12 5RD, UK
| | - Opeyemi U. Lawal
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Anna Colavecchio
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Brigitte Cadieux
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Yella Zahirovich-Jovich
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Zeyan Zhong
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Elizabeth Tompkins
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Margot Amitrano
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Irena Kukavica-Ibrulj
- Institute for Integrative Systems Biology (IBIS), Laval University, Québec, QC G1V 0A6, Canada (R.C.L.)
| | - Brian Boyle
- Institute for Integrative Systems Biology (IBIS), Laval University, Québec, QC G1V 0A6, Canada (R.C.L.)
| | - Siyun Wang
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
| | - Roger C. Levesque
- Institute for Integrative Systems Biology (IBIS), Laval University, Québec, QC G1V 0A6, Canada (R.C.L.)
| | - Pascal Delaquis
- Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada
| | - Michelle Danyluk
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611, USA
| | - Lawrence Goodridge
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
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8
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Tan Y, Su J, Luo D, Liang B, Liu S, Zeng H. Isolation and genome-wide analysis of the novel Acinetobacter baumannii bacteriophage vB_AbaM_AB3P2. Arch Virol 2024; 169:66. [PMID: 38451338 DOI: 10.1007/s00705-024-05986-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/12/2024] [Indexed: 03/08/2024]
Abstract
A lytic Acinetobacter baumannii phage, isolate vB_AbaM_AB3P2, was isolated from a sewage treatment plant in China. A. baumannii phage vB_AbaM_AB3P2 has a dsDNA genome that is 44,824 bp in length with a G + C content of 37.75%. Ninety-six open reading frames were identified, and no genes for antibiotic resistance or virulence factors were found. Genomic and phylogenetic analysis of this phage revealed that it represents a new species in the genus Obolenskvirus. Phage vB_AbaM_AB3P2 has a short latent period (10 min) and high stability at 30-70°C and pH 2-10 and is potentially useful for controlling multi-drug-resistant A. baumannii.
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Affiliation(s)
- Yujing Tan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Waihuan West Road 100, Guangzhou, Guangdong Province, 510006, China
| | - Jianhui Su
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Waihuan West Road 100, Guangzhou, Guangdong Province, 510006, China
| | - Dandan Luo
- Yunnan Zhinong High-technology Company, Limited, Kunming, 650000, China
| | - Bingshao Liang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Shenshen Liu
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Waihuan West Road 100, Guangzhou, Guangdong Province, 510006, China
| | - Haiyan Zeng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Waihuan West Road 100, Guangzhou, Guangdong Province, 510006, China.
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9
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Veldsman WP, Yang C, Zhang Z, Huang Y, Chowdhury D, Zhang L. Structural and Functional Disparities within the Human Gut Virome in Terms of Genome Topology and Representative Genome Selection. Viruses 2024; 16:134. [PMID: 38257834 PMCID: PMC10820185 DOI: 10.3390/v16010134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Circularity confers protection to viral genomes where linearity falls short, thereby fulfilling the form follows function aphorism. However, a shift away from morphology-based classification toward the molecular and ecological classification of viruses is currently underway within the field of virology. Recent years have seen drastic changes in the International Committee on Taxonomy of Viruses' operational definitions of viruses, particularly for the tailed phages that inhabit the human gut. After the abolition of the order Caudovirales, these tailed phages are best defined as members of the class Caudoviricetes. To determine the epistemological value of genome topology in the context of the human gut virome, we designed a set of seven experiments to assay the impact of genome topology and representative viral selection on biological interpretation. Using Oxford Nanopore long reads for viral genome assembly coupled with Illumina short-read polishing, we showed that circular and linear virus genomes differ remarkably in terms of genome quality, GC skew, transfer RNA gene frequency, structural variant frequency, cross-reference functional annotation (COG, KEGG, Pfam, and TIGRfam), state-of-the-art marker-based classification, and phage-host interaction. Furthermore, the disparity profile changes during dereplication. In particular, our phage-host interaction results demonstrated that proportional abundances cannot be meaningfully compared without due regard for genome topology and dereplication threshold, which necessitates the need for standardized reporting. As a best practice guideline, we recommend that comparative studies of the human gut virome always report the ratio of circular to linear viral genomes along with the dereplication threshold so that structural and functional metrics can be placed into context when assessing biologically relevant metagenomic properties such as proportional abundance.
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Affiliation(s)
- Werner P. Veldsman
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China; (W.P.V.); (C.Y.); (Z.Z.)
| | - Chao Yang
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China; (W.P.V.); (C.Y.); (Z.Z.)
| | - Zhenmiao Zhang
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China; (W.P.V.); (C.Y.); (Z.Z.)
| | | | - Debajyoti Chowdhury
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China;
- Computational Medicine Laboratory, Hong Kong Baptist University, Hong Kong SAR, China
| | - Lu Zhang
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China; (W.P.V.); (C.Y.); (Z.Z.)
- Institute for Research and Continuing Education, Hong Kong Baptist University, Shenzhen 518057, China
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10
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Chaudhary V, Kajla P, Lather D, Chaudhary N, Dangi P, Singh P, Pandiselvam R. Bacteriophages: a potential game changer in food processing industry. Crit Rev Biotechnol 2024:1-25. [PMID: 38228500 DOI: 10.1080/07388551.2023.2299768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 10/03/2023] [Indexed: 01/18/2024]
Abstract
In the food industry, despite the widespread use of interventions such as preservatives and thermal and non-thermal processing technologies to improve food safety, incidences of foodborne disease continue to happen worldwide, prompting the search for alternative strategies. Bacteriophages, commonly known as phages, have emerged as a promising alternative for controlling pathogenic bacteria in food. This review emphasizes the potential applications of phages in biological sciences, food processing, and preservation, with a particular focus on their role as biocontrol agents for improving food quality and preservation. By shedding light on recent developments and future possibilities, this review highlights the significance of phages in the food industry. Additionally, it addresses crucial aspects such as regulatory status and safety concerns surrounding the use of bacteriophages. The inclusion of up-to-date literature further underscores the relevance of phage-based strategies in reducing foodborne pathogenic bacteria's presence in both food and the production environment. As we look ahead, new phage products are likely to be targeted against emerging foodborne pathogens. This will further advance the efficacy of approaches that are based on phages in maintaining the safety and security of food.
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Affiliation(s)
- Vandana Chaudhary
- Department of Dairy Technology, College of Dairy Science and Technology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Priyanka Kajla
- Department of Food Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India
| | - Deepika Lather
- Department of Veterinary Pathology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Nisha Chaudhary
- Department of Food Science and Technology, College of Agriculture, Agriculture University, Jodhpur, Rajasthan, India
| | - Priya Dangi
- Department of Food and Nutrition and Food Technology, Institute of Home Economics, University of Delhi, New Delhi, India
| | - Punit Singh
- Department of Mechanical Engineering, Institute of Engineering and Technology, GLA University Mathura, Mathura, Uttar Pradesh, India
| | - Ravi Pandiselvam
- Physiology, Biochemistry and Post-Harvest Technology Division, ICAR -Central Plantation Crops Research Institute, Kasaragod, Kerala, India
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11
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Marton HL, Bhatt A, Sagona AP, Kilbride P, Gibson MI. Screening of Hydrophilic Polymers Reveals Broad Activity in Protecting Phages during Cryopreservation. Biomacromolecules 2024; 25:413-424. [PMID: 38124388 PMCID: PMC10777348 DOI: 10.1021/acs.biomac.3c01042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023]
Abstract
Bacteriophages have many biotechnological and therapeutic applications, but as with other biologics, cryopreservation is essential for storage and distribution. Macromolecular cryoprotectants are emerging for a range of biologics, but the chemical space for polymer-mediated phage cryopreservation has not been explored. Here we screen the cryoprotective effect of a panel of polymers against five distinct phages, showing that nearly all the tested polymers provide a benefit. Exceptions were poly(methacrylic acid) and poly(acrylic acid), which can inhibit phage-infection with bacteria, making post-thaw recovery challenging to assess. A particular benefit of a polymeric cryopreservation formulation is that the polymers do not function as carbon sources for the phage hosts (bacteria) and hence do not interfere with post-thaw measurements. This work shows that phages are amenable to protection with hydrophilic polymers and opens up new opportunities for advanced formulations for future phage therapies and to take advantage of the additional functionality brought by the polymers.
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Affiliation(s)
- Huba L. Marton
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Apoorva Bhatt
- School
of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- Institute
of Microbiology and Infection, University
of Birmingham, Birmingham, B15 2TT, United
Kingdom
| | - Antonia P. Sagona
- School
of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Peter Kilbride
- Asymptote,
Cytiva, Chivers Way, Cambridge CB24 9BZ, United Kingdom
| | - Matthew I. Gibson
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
- Warwick
Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
- Department
of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Manchester
Institute of Biotechnology, University of
Manchester, 131 Princess
Street, Manchester, M1
7DN, United Kingdom
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12
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Turner D, Adriaenssens EM, Lehman SM, Moraru C, Kropinski AM. Bacteriophage Taxonomy: A Continually Evolving Discipline. Methods Mol Biol 2024; 2734:27-45. [PMID: 38066361 DOI: 10.1007/978-1-0716-3523-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
While taxonomy is an often underappreciated branch of science, it serves very important roles. Bacteriophage taxonomy has evolved from a discipline based mainly on morphology, characterized by the work of David Bradley and Hans-Wolfgang Ackermann, to the sequence-based approach that is taken today. The Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) takes a holistic approach to classifying prokaryote viruses by measuring overall DNA and protein similarity and phylogeny before making decisions about the taxonomic position of a new virus. The huge number of complete genomes being deposited with the National Center for Biotechnology Information (NCBI) and other public databases has resulted in a reassessment of the taxonomy of many viruses, and the future will see the introduction of new viral families and higher orders.
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Affiliation(s)
- Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, UK
| | | | - Susan M Lehman
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Cristina Moraru
- Department of The Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Andrew M Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
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13
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Yaacoub C, Wehbe R, Roufayel R, Fajloun Z, Coutard B. Bee Venom and Its Two Main Components-Melittin and Phospholipase A2-As Promising Antiviral Drug Candidates. Pathogens 2023; 12:1354. [PMID: 38003818 PMCID: PMC10674158 DOI: 10.3390/pathogens12111354] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/08/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
Viruses are known to infect most types of organisms. In humans, they can cause several diseases that range from mild to severe. Although many antiviral therapies have been developed, viral infections continue to be a leading cause of morbidity and mortality worldwide. Therefore, the discovery of new and effective antiviral agents is desperately needed. Animal venoms are a rich source of bioactive molecules found in natural goods that have been used since ancient times in alternative medicine to treat a variety of human diseases. Recently, and with the onset of the COVID-19 pandemic, scientists have regained their interest in the possible use of natural products, such as bee venom (BV), as a potential antiviral agent to treat viral infections. BV is known to exert many therapeutic activities such as anti-proliferative, anti-bacterial, and anti-inflammatory effects. However, there is limited discussion of the antiviral activity of BV in the literature. Therefore, this review aims to highlight the antiviral properties of BV and its two primary constituents, melittin (MEL) and phospholipase A2 (PLA2), against a variety of enveloped and non-enveloped viruses. Finally, the innovative strategies used to reduce the toxicity of BV and its two compounds for the development of new antiviral treatments are also considered.
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Affiliation(s)
- Carole Yaacoub
- Unité des Virus Emergents, Aix-Marseille University, IRD 190-Inserm 1207, IHU Méditerranée Infection, 13005 Marseille, France;
- Laboratory of Applied Biotechnology (LBA3B), Azm Center for Research in Biotechnology and Its Applications, Doctoral School for Sciences and Technology, Lebanese University, Tripoli 1300, Lebanon;
| | - Rim Wehbe
- Biology Department, Faculty of Arts and Sciences, American University of Beirut, Beirut 1107 2020, Lebanon;
| | - Rabih Roufayel
- College of Engineering and Technology, American University of the Middle East, Egaila 54200, Kuwait;
| | - Ziad Fajloun
- Laboratory of Applied Biotechnology (LBA3B), Azm Center for Research in Biotechnology and Its Applications, Doctoral School for Sciences and Technology, Lebanese University, Tripoli 1300, Lebanon;
- Faculty of Sciences III, Department of Biology, Michel Slayman Tripoli Campus, Lebanese University, Tripoli 1352, Lebanon
| | - Bruno Coutard
- Unité des Virus Emergents, Aix-Marseille University, IRD 190-Inserm 1207, IHU Méditerranée Infection, 13005 Marseille, France;
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14
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Hu Y, Liu C, Yang J, Zhong M, Qian B, Chen J, Zhang Y, Song J. HMGB1 is involved in viral replication and the inflammatory response in coxsackievirus A16-infected 16HBE cells via proteomic analysis and identification. Virol J 2023; 20:178. [PMID: 37559147 PMCID: PMC10410909 DOI: 10.1186/s12985-023-02150-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023] Open
Abstract
Coxsackievirus A16 (CV-A16) is still an important pathogen that causes hand, foot and mouth disease (HFMD) in young children and infants worldwide. Previous studies indicated that CV-A16 infection is usually mild or self-limiting, but it was also found that CV-A16 infection can trigger severe neurological complications and even death. However, there are currently no vaccines or antiviral compounds available to either prevent or treat CV-A16 infection. Therefore, investigation of the virus‒host interaction and identification of host proteins that play a crucial regulatory role in the pathogenesis of CV-A16 infection may provide a novel strategy to develop antiviral drugs. Here, to increase our understanding of the interaction of CV-A16 with the host cell, we analyzed changes in the proteome of 16HBE cells in response to CV-A16 using tandem mass tag (TMT) in combination with LC‒MS/MS. There were 6615 proteins quantified, and 172 proteins showed a significant alteration during CV-A16 infection. These differentially regulated proteins were involved in fundamental biological processes and signaling pathways, including metabolic processes, cytokine‒cytokine receptor interactions, B-cell receptor signaling pathways, and neuroactive ligand‒receptor interactions. Further bioinformatics analysis revealed the characteristics of the protein domains and subcellular localization of these differentially expressed proteins. Then, to validate the proteomics data, 3 randomly selected proteins exhibited consistent changes in protein expression with the TMT results using Western blotting and immunofluorescence methods. Finally, among these differentially regulated proteins, we primarily focused on HMGB1 based on its potential effects on viral replication and virus infection-induced inflammatory responses. It was demonstrated that overexpression of HMGB1 could decrease viral replication and upregulate the release of inflammatory cytokines, but deletion of HMGB1 increased viral replication and downregulated the release of inflammatory cytokines. In conclusion, the results from this study have helped further elucidate the potential molecular pathogenesis of CV-A16 based on numerous protein changes and the functions of HMGB1 Found to be involved in the processes of viral replication and inflammatory response, which may facilitate the development of new antiviral therapies as well as innovative diagnostic methods.
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Affiliation(s)
- Yajie Hu
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Chen Liu
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Jinghui Yang
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
- Department of Pediatrics, The First People's Hospital of Yunnan Province, Kunming, China
| | - Mingmei Zhong
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Baojiang Qian
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Juan Chen
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yunhui Zhang
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, Kunming, China.
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China.
| | - Jie Song
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.
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15
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Pilati GVT, Cadamuro RD, Filho VB, Dahmer M, Elois MA, Savi BP, Salles GBC, Muniz EC, Fongaro G. Bacteriophage-Associated Antimicrobial Resistance Genes in Avian Pathogenic Escherichia coli Isolated from Brazilian Poultry. Viruses 2023; 15:1485. [PMID: 37515172 PMCID: PMC10386125 DOI: 10.3390/v15071485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Colibacillosis is a disease caused by Escherichia coli and remains a major concern in poultry production, as it leads to significant economic losses due to carcass condemnation and clinical symptoms. The development of antimicrobial resistance is a growing problem of worldwide concern. Lysogenic bacteriophages are effective vectors for acquiring and disseminating antibiotic resistance genes (ARGs). The aim of this study was to investigate the complete genome of Escherichia coli isolates from the femurs of Brazilian broiler chickens in order to investigate the presence of antimicrobial resistance genes associated with bacteriophages. Samples were collected between August and November 2021 from broiler batches from six Brazilian states. Through whole genome sequencing (WGS), data obtained were analyzed for the presence of antimicrobial resistance genes. Antimicrobial resistance genes against the aminoglycosides class were detected in 79.36% of the isolates; 74.6% had predicted sulfonamides resistance genes, 63.49% had predicted resistance genes against β-lactams, and 49.2% of the isolates had at least one of the tetracycline resistance genes. Among the detected genes, 27 have been described in previous studies and associated with bacteriophages. The findings of this study highlight the role of bacteriophages in the dissemination of ARGs in the poultry industry.
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Affiliation(s)
- Giulia Von Tönnemann Pilati
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Rafael Dorighello Cadamuro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Vilmar Benetti Filho
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Mariane Dahmer
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Mariana Alves Elois
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Beatriz Pereira Savi
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Gleidson Biasi Carvalho Salles
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
- Zoetis Industry of Veterinary Products LTDA, São Paulo 04709-111, Brazil
| | | | - Gislaine Fongaro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
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16
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Baláž A, Kajsik M, Budiš J, Szemes T, Turňa J. PHERI-Phage Host ExploRation Pipeline. Microorganisms 2023; 11:1398. [PMID: 37374901 DOI: 10.3390/microorganisms11061398] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multidrug-resistant bacterial strains occurring in all regions. One of the possible future solutions is the use of bacteriophages. Phages are the most abundant form of life in the biosphere, so we can highly likely purify a specific phage against each target bacterium. The identification and consistent characterization of individual phages was a common form of phage work and included determining bacteriophages' host-specificity. With the advent of new modern sequencing methods, there was a problem with the detailed characterization of phages in the environment identified by metagenome analysis. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable of determining a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm-based tool called PHERI. PHERI predicts the suitable bacterial host genus for the purification of individual viruses from different samples. In addition, it can identify and highlight protein sequences that are important for host selection.
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Affiliation(s)
- Andrej Baláž
- Geneton Ltd., Ilkovicova 8, 841 04 Bratislava, Slovakia
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska dolina F1, 842 48 Bratislava, Slovakia
| | - Michal Kajsik
- Science Park, Comenius University, Ilkovicova 8, 841 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 841 04 Bratislava, Slovakia
- Medirex Group Academy n.o., Novozamocka 1, 949 05 Nitra, Slovakia
| | - Jaroslav Budiš
- Geneton Ltd., Ilkovicova 8, 841 04 Bratislava, Slovakia
- Science Park, Comenius University, Ilkovicova 8, 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information (SCSTI), Lamacska Cesta 8/A, 811 04 Bratislava, Slovakia
| | - Tomáš Szemes
- Geneton Ltd., Ilkovicova 8, 841 04 Bratislava, Slovakia
- Science Park, Comenius University, Ilkovicova 8, 841 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 841 04 Bratislava, Slovakia
| | - Ján Turňa
- Science Park, Comenius University, Ilkovicova 8, 841 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 841 04 Bratislava, Slovakia
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17
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Patil R, Dehari D, Chaudhuri A, Kumar DN, Kumar D, Singh S, Nath G, Agrawal AK. Recent advancements in nanotechnology-based bacteriophage delivery strategies against bacterial ocular infections. Microbiol Res 2023; 273:127413. [PMID: 37216845 DOI: 10.1016/j.micres.2023.127413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023]
Abstract
Antibiotic resistance is growing as a critical challenge in a variety of disease conditions including ocular infections leading to disastrous effects on the human eyes. Staphylococcus aureus (S. aureus) mediated ocular infections are very common affecting different parts of the eye viz. vitreous chamber, conjunctiva, cornea, anterior and posterior chambers, tear duct, and eyelids. Blepharitis, dacryocystitis, conjunctivitis, keratitis, endophthalmitis, and orbital cellulitis are some of the commonly known ocular infections caused by S. aureus. Some of these infections are so fatal that they could cause bilateral blindness like panophthalmitis and orbital cellulitis, which is caused by methicillin-resistant S. aureus (MRSA) and vancomycin-resistance S. aureus (VRSA). The treatment of S. aureus infections with known antibiotics is becoming gradually difficult because of the development of resistance against multiple antibiotics. Apart from the different combinations and formulation strategies, bacteriophage therapy is growing as an effective alternative to treat such infections. Although the superiority of bacteriophage therapy is well established, yet physical factors (high temperatures, acidic pH, UV-rays, and ionic strength) and pharmaceutical barriers (poor stability, low in-vivo retention, controlled and targeted delivery, immune system neutralization, etc.) have the greatest influence on the viability of phage virions (also phage proteins). A variety of Nanotechnology based formulations such as polymeric nanoparticles, liposomes, dendrimers, nanoemulsions, and nanofibres have been recently reported to overcome the above-mentioned obstacles. In this review, we have compiled all these recent reports and discussed bacteriophage-based nanoformulations techniques for the successful treatment of ocular infections caused by multidrug-resistant S. aureus and other bacteria.
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Affiliation(s)
- Rohit Patil
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, U.P., India
| | - Deepa Dehari
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, U.P., India
| | - Aiswarya Chaudhuri
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, U.P., India
| | - Dulla Naveen Kumar
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, U.P., India
| | - Dinesh Kumar
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, U.P., India
| | - Sanjay Singh
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, U.P., India; Babasaheb Bhimrao Ambedkar University, Lucknow 226025, U.P., India
| | - Gopal Nath
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, U.P., India
| | - Ashish Kumar Agrawal
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, U.P., India.
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18
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Friedrich B, Vogel P, Rückert MA, Lyer S, Günther J, Wernery U, Joseph S, Müller J, Behr VC, Alexiou C, Tietze R. Detection of viral antibodies in camel sera using magnetic particle spectroscopy. Appl Microbiol Biotechnol 2023; 107:3329-3339. [PMID: 37060465 PMCID: PMC10104765 DOI: 10.1007/s00253-023-12513-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/16/2023]
Abstract
Pandemics like SARS-Cov-2 very frequently have their origin in different animals and in particular herds of camels could be a source of zoonotic diseases. This study took advantage on a highly sensitive and adaptable method for the fast and reliable detection of viral antibodies in camels using low-cost equipment. Magnetic nanoparticles (MNP) have high variability in their functionalization with different peptides and proteins. We confirm that 3-aminopropyl triethoxysilane (APTES)-coated MNP could be functionalized with viral proteins. The protein loading could be confirmed by simple loading controls using FACS-analysis (p < 0.05). Complementary combination of antigen and antibody yields in a significant signal increase could be proven by both FACS and COMPASS. However, COMPASS needs only a few seconds for the measurement. In COMPASS, the phase φn on selected critical point of the fifth higher harmonic (n = 5th). Here, positive sera display highly significant signal increase over the control or negative sera. Furthermore, a clear distinction could be made in antibody detection as an immune response to closely related viruses (SARS-CoV2 and MERS). Using modified MNPs along with COMPASS offers a fast and reliable method that is less cost intensive than current technologies and offers the possibility to be quickly adapted in case of new occurring viral infections. KEY POINTS: • COMPASS (critical offset magnetic particle spectroscopy) allows the fast detection of antibodies. • Magnetic nanoparticles can be adapted by exchange of the linked bait molecule. • Antibodies could be detected in camel sera without washing steps within seconds.
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Affiliation(s)
- Bernhard Friedrich
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius-Stiftung Professorship, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Patrick Vogel
- Department of Experimental Physics 5 (Biophysics), Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Martin A Rückert
- Department of Experimental Physics 5 (Biophysics), Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Stefan Lyer
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius-Stiftung Professorship, Universitätsklinikum Erlangen, Erlangen, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Professorship for AI-Controlled Nanomaterials, University Hospital Erlangen, Erlangen, Germany
| | - Johanna Günther
- Department of Experimental Physics 5 (Biophysics), Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, P.O. Box 597, Dubai, UAE
| | - Sunitha Joseph
- Central Veterinary Research Laboratory, P.O. Box 597, Dubai, UAE
| | - Judith Müller
- Generatio - Center for Animal Genetics, Heidelberg, Germany
| | - Volker C Behr
- Department of Experimental Physics 5 (Biophysics), Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Christoph Alexiou
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius-Stiftung Professorship, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Rainer Tietze
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius-Stiftung Professorship, Universitätsklinikum Erlangen, Erlangen, Germany.
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19
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Ishibashi Y, Sung CYW, Grati M, Chien W. Immune responses in the mammalian inner ear and their implications for AAV-mediated inner ear gene therapy. Hear Res 2023; 432:108735. [PMID: 36965335 DOI: 10.1016/j.heares.2023.108735] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/17/2023] [Accepted: 03/04/2023] [Indexed: 03/13/2023]
Abstract
Adeno-associated virus (AAV)-mediated inner ear gene therapy is a promising treatment option for hearing loss and dizziness. Several studies have shown that AAV-mediated inner ear gene therapy can be applied to various mouse models of hereditary hearing loss to improve their auditory function. Despite the increase in AAV-based animal and clinical studies aiming to rescue auditory and vestibular functions, little is currently known about the host immune responses to AAV in the mammalian inner ear. It has been reported that the host immune response plays an important role in the safety and efficacy of viral-mediated gene therapy. Therefore, in order for AAV-mediated gene therapy to be successfully and safely translated into patients with hearing loss and dizziness, a better understanding of the host immune responses to AAV in the inner ear is critical. In this review, we summarize the current knowledge on host immune responses to AAV-mediated gene therapy in the mammalian inner ear and other organ systems. We also outline the areas of research that are critical for ensuring the safety and efficacy of AAV-mediated inner ear gene therapy in future clinical and translational studies.
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Affiliation(s)
- Yasuko Ishibashi
- Inner Ear Gene Therapy Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, 35A 1F220, 35A Covent Dr., Bethesda, MD 20892, USA; Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, USA
| | - Cathy Yea Won Sung
- Laboratory of Hearing Biology and Therapeutics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, USA
| | - Mhamed Grati
- Inner Ear Gene Therapy Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, 35A 1F220, 35A Covent Dr., Bethesda, MD 20892, USA
| | - Wade Chien
- Inner Ear Gene Therapy Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, 35A 1F220, 35A Covent Dr., Bethesda, MD 20892, USA; Department of Otolaryngology-Head & Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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20
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Karczewska M, Strzelecki P, Szalewska-Pałasz A, Nowicki D. How to Tackle Bacteriophages: The Review of Approaches with Mechanistic Insight. Int J Mol Sci 2023; 24:ijms24054447. [PMID: 36901878 PMCID: PMC10003480 DOI: 10.3390/ijms24054447] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
Bacteriophage-based applications have a renaissance today, increasingly marking their use in industry, medicine, food processing, biotechnology, and more. However, phages are considered resistant to various harsh environmental conditions; besides, they are characterized by high intra-group variability. Phage-related contaminations may therefore pose new challenges in the future due to the wider use of phages in industry and health care. Therefore, in this review, we summarize the current knowledge of bacteriophage disinfection methods, as well as highlight new technologies and approaches. We discuss the need for systematic solutions to improve bacteriophage control, taking into account their structural and environmental diversity.
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Affiliation(s)
- Monika Karczewska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Patryk Strzelecki
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg, CNRS, UMR7504, 23 rue du Loess, CEDEX 2, F-67034 Strasbourg, France
| | - Agnieszka Szalewska-Pałasz
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Dariusz Nowicki
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
- Correspondence: ; Tel.: +48-58-523-6065
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Oliveira LS, Reyes A, Dutilh BE, Gruber A. Rational Design of Profile HMMs for Sensitive and Specific Sequence Detection with Case Studies Applied to Viruses, Bacteriophages, and Casposons. Viruses 2023; 15:519. [PMID: 36851733 PMCID: PMC9966878 DOI: 10.3390/v15020519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Profile hidden Markov models (HMMs) are a powerful way of modeling biological sequence diversity and constitute a very sensitive approach to detecting divergent sequences. Here, we report the development of protocols for the rational design of profile HMMs. These methods were implemented on TABAJARA, a program that can be used to either detect all biological sequences of a group or discriminate specific groups of sequences. By calculating position-specific information scores along a multiple sequence alignment, TABAJARA automatically identifies the most informative sequence motifs and uses them to construct profile HMMs. As a proof-of-principle, we applied TABAJARA to generate profile HMMs for the detection and classification of two viral groups presenting different evolutionary rates: bacteriophages of the Microviridae family and viruses of the Flavivirus genus. We obtained conserved models for the generic detection of any Microviridae or Flavivirus sequence, and profile HMMs that can specifically discriminate Microviridae subfamilies or Flavivirus species. In another application, we constructed Cas1 endonuclease-derived profile HMMs that can discriminate CRISPRs and casposons, two evolutionarily related transposable elements. We believe that the protocols described here, and implemented on TABAJARA, constitute a generic toolbox for generating profile HMMs for the highly sensitive and specific detection of sequence classes.
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Affiliation(s)
- Liliane S. Oliveira
- Department of Parasitology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, 07743 Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Arthur Gruber
- Department of Parasitology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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Evseev P, Gutnik D, Shneider M, Miroshnikov K. Use of an Integrated Approach Involving AlphaFold Predictions for the Evolutionary Taxonomy of Duplodnaviria Viruses. Biomolecules 2023; 13:biom13010110. [PMID: 36671495 PMCID: PMC9855967 DOI: 10.3390/biom13010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/31/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
The evaluation of the evolutionary relationships is exceptionally important for the taxonomy of viruses, which is a rapidly expanding area of research. The classification of viral groups belonging to the realm Duplodnaviria, which include tailed bacteriophages, head-tailed archaeal viruses and herpesviruses, has undergone many changes in recent years and continues to improve. One of the challenging tasks of Duplodnaviria taxonomy is the classification of high-ranked taxa, including families and orders. At the moment, only 17 of 50 families have been assigned to orders. The evaluation of the evolutionary relationships between viruses is complicated by the high level of divergence of viral proteins. However, the development of structure prediction algorithms, including the award-winning AlphaFold, encourages the use of the results of structural predictions to clarify the evolutionary history of viral proteins. In this study, the evolutionary relationships of two conserved viral proteins, the major capsid protein and terminase, representing different viruses, including all classified Duplodnaviria families, have been analysed using AlphaFold modelling. This analysis has been undertaken using structural comparisons and different phylogenetic methods. The results of the analyses mainly indicated the high quality of AlphaFold modelling and the possibility of using the AlphaFold predictions, together with other methods, for the reconstruction of the evolutionary relationships between distant viral groups. Based on the results of this integrated approach, assumptions have been made about refining the taxonomic classification of bacterial and archaeal Duplodnaviria groups, and problems relating to the taxonomic classification of Duplodnaviria have been discussed.
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Affiliation(s)
- Peter Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- Correspondence: (P.E.); (K.M.)
| | - Daria Gutnik
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Mikhail Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
| | - Konstantin Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- Correspondence: (P.E.); (K.M.)
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Lephart ED, Naftolin F. Estrogen Action and Gut Microbiome Metabolism in Dermal Health. Dermatol Ther (Heidelb) 2022; 12:1535-1550. [PMID: 35752663 PMCID: PMC9276867 DOI: 10.1007/s13555-022-00759-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/08/2022] [Indexed: 01/14/2023] Open
Abstract
Emerging scientific advances in microbial research linking estrogens and the gut-skin microbiome in reference to dermal health are featured in this narrative review of journal reports and reviews from January 2018 through February 2022. Background information on advances in microbial research along with defining the microbiota and microbiome is presented in brief. The development of and factors that influence the gut microbiome in health and disease as well as the intrinsic and extrinsic factors influencing the skin microbiome and skin aging are summarized. New information on the development and changes of organ microbiomes have exposed similarities between skin and gut structure/function, microbial components/diversity/taxonomy and how they impact the immune response for combating disease and enhancing wellness. Estrogens promote health and support homeostasis in general and directly impact dermal health. Moreover, the gut, based upon the level of the microbial enzyme β-glucuronidase, which regulates estrogen’s enterohepatic recirculation, constitutes a gut-skin microbial axis. This axis revolves around the systemically available estrogen to support immune function, counteract inflammation and oxidative stress, and decrease the risk of hormone-dependent skin cancers. These data support the direct effect of estrogens on skin health and the interaction of diet on dermal health via effects on the gut microflora. Finally, the potential for bioactive botanicals containing phytoestrogens or selective estrogen receptor modulators (SERMs) to evade the effects of gut β-glucuronidase expressing flora is proposed that may have a positive impact on skin.
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Affiliation(s)
- Edwin D. Lephart
- Department of Cell Biology, Physiology and The Neuroscience Center LS 4005, College of Life Sciences, Brigham Young University, Provo, UT 84602 USA
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Andrade-Martínez JS, Camelo Valera LC, Chica Cárdenas LA, Forero-Junco L, López-Leal G, Moreno-Gallego JL, Rangel-Pineros G, Reyes A. Computational Tools for the Analysis of Uncultivated Phage Genomes. Microbiol Mol Biol Rev 2022; 86:e0000421. [PMID: 35311574 PMCID: PMC9199400 DOI: 10.1128/mmbr.00004-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Over a century of bacteriophage research has uncovered a plethora of fundamental aspects of their biology, ecology, and evolution. Furthermore, the introduction of community-level studies through metagenomics has revealed unprecedented insights on the impact that phages have on a range of ecological and physiological processes. It was not until the introduction of viral metagenomics that we began to grasp the astonishing breadth of genetic diversity encompassed by phage genomes. Novel phage genomes have been reported from a diverse range of biomes at an increasing rate, which has prompted the development of computational tools that support the multilevel characterization of these novel phages based solely on their genome sequences. The impact of these technologies has been so large that, together with MAGs (Metagenomic Assembled Genomes), we now have UViGs (Uncultivated Viral Genomes), which are now officially recognized by the International Committee for the Taxonomy of Viruses (ICTV), and new taxonomic groups can now be created based exclusively on genomic sequence information. Even though the available tools have immensely contributed to our knowledge of phage diversity and ecology, the ongoing surge in software programs makes it challenging to keep up with them and the purpose each one is designed for. Therefore, in this review, we describe a comprehensive set of currently available computational tools designed for the characterization of phage genome sequences, focusing on five specific analyses: (i) assembly and identification of phage and prophage sequences, (ii) phage genome annotation, (iii) phage taxonomic classification, (iv) phage-host interaction analysis, and (v) phage microdiversity.
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Affiliation(s)
- Juan Sebastián Andrade-Martínez
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Carolina Camelo Valera
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Luis Alberto Chica Cárdenas
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Forero-Junco
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Gamaliel López-Leal
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - J. Leonardo Moreno-Gallego
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Guillermo Rangel-Pineros
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
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Tewari DN, Biswas S, Chakrabarti AK, Dutta S. Viral Inactivation and Biocompatibility Study of Electrically Activated Water Mist. Microbiol Insights 2022; 15:11786361221096651. [PMID: 35591947 PMCID: PMC9112322 DOI: 10.1177/11786361221096651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/28/2022] [Indexed: 11/22/2022] Open
Abstract
In addition to the ongoing global problem of healthcare-acquired infections, the
COVID-19 pandemic continues to pose a serious threat to the health of the global
population. This unprecedented pandemic situation has reinforced the need for
the development of technologies that can curb the transmission of viruses among
human beings and help to control the infection. Existing disinfection techniques
using either ultraviolet light or harsh chemicals pose safety risks and are not
suitable for use in the presence of humans. Thus, the need for a safe and
effective disinfection technique that can be used in the presence of humans to
control viral transmission is evident. A technique that can continuously
disinfect air and surfaces in indoor environments, where the chances of viral
transmission are high, can be an indispensable tool to fight such a pandemic.
The Airlens Minus Corona (AMC) device provided by Persapien Innovations has been
developed to achieve this goal. In this study, the antiviral functionality and
biocompatibility of AMC were evaluated. Activated water mist (AWM) generated
from this device was tested in vitro and in vivo for its toxicity to cell lines
and in animal model. The AWM was found to be non-cytotoxic to L-929 cell lines
and had no sign of clinical toxicity in an animal model (rabbit). This device
was further used to inactivate animal viruses and bacteriophages. The AWM was
found to be effective in the complete inactivation of influenza A H1N1 virus
within 5 minutes of direct treatment. This device was also found to be effective
in inactivating >90% of bacteriophage particles.
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Affiliation(s)
- Devendra Nath Tewari
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Sanjoy Biswas
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | | | - Shanta Dutta
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
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26
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In Vivo Bacteriophages’ Application for the Prevention and Therapy of Aquaculture Animals–Chosen Aspects. Animals (Basel) 2022; 12:ani12101233. [PMID: 35625078 PMCID: PMC9137707 DOI: 10.3390/ani12101233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 12/14/2022] Open
Abstract
To meet the nutritional requirements of our growing population, animal production must double by 2050, and due to the exhaustion of environmental capacity, any growth will have to come from aquaculture. Aquaculture is currently undergoing a dynamic development, but the intensification of production increases the risk of bacterial diseases. In recent years, there has been a drastic development in the resistance of pathogenic bacteria to antibiotics and chemotherapeutic agents approved for use, which has also taken place in aquaculture. Consequently, animal mortality and economic losses in livestock have increased. The use of drugs in closed systems is an additional challenge as it can damage biological filters. For this reason, there has been a growing interest in natural methods of combating pathogens. One of the methods is the use of bacteriophages both for prophylactic purposes and therapy. This work summarizes the diverse results of the in vivo application of bacteriophages for the prevention and control of bacterial pathogens in aquatic animals to provide a reference for further research on bacteriophages in aquaculture and to compare major achievements in the field.
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Çelik A, Santosa AI, Gibbs AJ, Ertunç F. Prunus necrotic ringspot virus in Turkey: an immigrant population. Arch Virol 2022; 167:553-562. [DOI: 10.1007/s00705-022-05374-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022]
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Gorbalenya AE, Lauber C. Bioinformatics of virus taxonomy: foundations and tools for developing sequence-based hierarchical classification. Curr Opin Virol 2021; 52:48-56. [PMID: 34883443 DOI: 10.1016/j.coviro.2021.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/22/2021] [Accepted: 11/04/2021] [Indexed: 11/03/2022]
Abstract
The genome sequence is the only characteristic readily obtainable for all known viruses, underlying the growing role of comparative genomics in organizing knowledge about viruses in a systematic evolution-aware way, known as virus taxonomy. Overseen by the International Committee on Taxonomy of Viruses (ICTV), development of virus taxonomy involves taxa demarcation at 15 ranks of a hierarchical classification, often in host-specific manner. Outside the ICTV remit, researchers assess fitting numerous unclassified viruses into the established taxa. They employ different metrics of virus clustering, basing on conserved domain(s), separation of viruses in rooted phylogenetic trees and pair-wise distance space. Computational approaches differ further in respect to methodology, number of ranks considered, sensitivity to uneven virus sampling, and visualization of results. Advancing and using computational tools will be critical for improving taxa demarcation across the virosphere and resolving rank origins in research that may also inform experimental virology.
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Affiliation(s)
- Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands; Faculty of Bioengineering and Bioinformatics and Belozersky, Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899, Moscow, Russia.
| | - Chris Lauber
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, A Joint Venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
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He W, Li Q, Lu Y, Ju D, Gu Y, Zhao K, Dong C. Cancer treatment evolution from traditional methods to stem cells and gene therapy. Curr Gene Ther 2021; 22:368-385. [PMID: 34802404 DOI: 10.2174/1566523221666211119110755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 06/25/2021] [Accepted: 09/16/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Cancer, a malignant tumor, is caused by the failure of the mechanism that controls cell growth and proliferation. Late clinical symptoms often manifest as lumps, pain, ulcers, and bleeding. Systemic symptoms include weight loss, fatigue, and loss of appetite. It is a major disease that threatens human life and health. How to treat cancer is a long-standing problem that needs to be overcome in the history of medicine. METHOD Traditional tumor treatment methods are poorly targeted, and the side effects of treatment seriously damage the physical and mental health of patients. In recent years, with the advancement of medical science and technology, the research on gene combined with mesenchymal stem cells to treat tumors has been intensified. Mesenchymal stem cells carry genes to target cancer cells, which can achieve better therapeutic effects. DISCUSSION In the text, we systematically review the cancer treatment evolution from traditional methods to novel approaches that include immunotherapy, nanotherapy, stem cell theapy, and gene therapy. We provide the latest review of the application status, clinical trials and development prospects of mesenchymal stem cells and gene therapy for cancer, as well as their integration in cancer treatment. Mesenchymal stem cells are effective carriers carrying genes and provide new clinical ideas for tumor treatment. CONCLUSION This review focuses on the current status, application prospects and challenges of mesenchymal stem cell combined gene therapy for cancer, and provides new ideas for clinical research.
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Affiliation(s)
- Wenhua He
- Department of Anatomy, Medical College of Nantong University, Nantong 226001. China
| | - Qingxuan Li
- Department of Anatomy, Medical College of Nantong University, Nantong 226001. China
| | - Yan Lu
- Department of Anatomy, Medical College of Nantong University, Nantong 226001. China
| | - Dingyue Ju
- Department of Anatomy, Medical College of Nantong University, Nantong 226001. China
| | - Yu Gu
- Department of Anatomy, Medical College of Nantong University, Nantong 226001. China
| | - Kai Zhao
- Department of Anatomy, Medical College of Nantong University, Nantong 226001. China
| | - Chuanming Dong
- Department of Anatomy, Medical College of Nantong University, Nantong 226001. China
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Fuentes-Zacarías P, Murrieta-Coxca JM, Gutiérrez-Samudio RN, Schmidt A, Schmidt A, Markert UR, Morales-Prieto DM. Pregnancy and pandemics: Interaction of viral surface proteins and placenta cells. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166218. [PMID: 34311080 PMCID: PMC9188292 DOI: 10.1016/j.bbadis.2021.166218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/06/2021] [Accepted: 07/15/2021] [Indexed: 12/18/2022]
Abstract
Throughout history, pandemics of infectious diseases caused by emerging viruses have spread worldwide. Evidence from previous outbreaks demonstrated that pregnant women are at high risk of contracting the diseases and suffering from adverse outcomes. However, while some viruses can cause major health complications for the mother and her fetus, others do not appear to affect pregnancy. Viral surface proteins bind to specific receptors on the cellular membrane of host cells and begin therewith the infection process. During pregnancy, the molecular features of these proteins may determine specific target cells in the placenta, which may explain the different outcomes. In this review, we display information on Variola, Influenza, Zika and Corona viruses focused on their surface proteins, effects on pregnancy, and possible target placental cells. This will contribute to understanding viral entry during pregnancy, as well as to develop strategies to decrease the incidence of obstetrical problems in current and future infections.
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Affiliation(s)
| | - Jose M Murrieta-Coxca
- Placenta Lab, Department of Obstetrics, Jena University Hospital, 07747 Jena, Germany
| | | | - Astrid Schmidt
- Placenta Lab, Department of Obstetrics, Jena University Hospital, 07747 Jena, Germany
| | - Andre Schmidt
- Placenta Lab, Department of Obstetrics, Jena University Hospital, 07747 Jena, Germany
| | - Udo R Markert
- Placenta Lab, Department of Obstetrics, Jena University Hospital, 07747 Jena, Germany..
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Current challenges to virus discovery by meta-transcriptomics. Curr Opin Virol 2021; 51:48-55. [PMID: 34592710 DOI: 10.1016/j.coviro.2021.09.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 08/16/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022]
Abstract
Meta-transcriptomic next-generation sequencing has transformed virus discovery, dramatically expanding our knowledge of the known virosphere. Nevertheless, the use of meta-transcriptomics for virus discovery faces important challenges. As this technology becomes more widely adopted, the proportion of viral sequences in public databases with incorrect (e.g. mis-assignment of host) or limited information (e.g. lacking taxonomic classification) is likely to grow, limiting their utility in bioinformatic pipelines for virus discovery. In addition, we currently lack the bioinformatic tools that can accurately identify viruses showing little or no sequence similarity to database viruses or those that represent likely reagent contaminants. Herein, we outline some of the challenges to effective meta-transcriptomic virus discovery as well as their potential solutions.
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Zanotti G, Grinzato A. Structure of filamentous viruses. Curr Opin Virol 2021; 51:25-33. [PMID: 34592708 DOI: 10.1016/j.coviro.2021.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/21/2021] [Accepted: 09/12/2021] [Indexed: 12/17/2022]
Abstract
Despite filamentous viruses represent an important portion of the universe of viruses, their 3D structures available are quite limited, particularly if compared to the large number of structures of icosahedral viruses present in the Protein Data Bank. As a matter of fact, flexible filamentous viruses cannot be grown as single crystals and past structural studies have mostly been limited to X-ray fiber diffraction or to the determination of the structure of isolated viral proteins. Only very recently, several structures of filamentous viruses have become available, owing to the recent development of cryo-electron microscopy. This technique has given a strong impulse to the field and has allowed the building of reliable molecular models of entire viruses, in some cases at a nearly atomic resolution level. In this paper we briefly describe the architecture of filamentous viruses that infect bacteria, archaea, plants and humans. It is easy to foresee that more new structures of filamentous viruses will become available soon and they will allow a better understanding of the rules underlying the structural organization of these organisms so relevant for the life on our planet.
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Affiliation(s)
- Giuseppe Zanotti
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua, 35131, Italy.
| | - Alessandro Grinzato
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua, 35131, Italy.
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Van Regenmortel MHV. Design in biology and rational design in vaccinology: A conceptual analysis. Methods 2021; 195:120-127. [PMID: 34352372 DOI: 10.1016/j.ymeth.2021.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/20/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022] Open
Abstract
This review discusses the philosophical foundations of what used to be called "the scientific method" and is nowadays often known as the scientific attitude. It used to be believed that scientific theories and methods aimed at the truth especially in the case of physics, chemistry and astronomy because these sciences were able to develop numerous scientific laws that made it possible to understand and predict many physical phenomena. The situation is different in the case of the biological sciences which deal with highly complex living organisms made up of huge numbers of constituents that undergo continuous dynamic processes; this leads to novel emergent properties in organisms that cannot be predicted because they are not present in the constituents before they have interacted with each other. This is one of the reasons why there are no universal scientific laws in biology. Furthermore, all scientific theories can only achieve a restricted level of predictive success because they remain valid only under the limited range of conditions that were used for establishing the theory' in the first place. Many theories that used to be accepted were subsequently shown to be false, demonstrating that scientific theories always remain tentative and can never be proven beyond and doubt. It is ironical that as scientists have finally accepted that approximate truths are perfectly adequate and that absolute truth is an illusion, a new irrational sociological phenomenon called Post-Truth conveyed by social media, the Internet and fake news has developed in the Western world that is convincing millions of people that truth simply does not exist. Misleading information is circulated with the intention to deceive and science denialism is promoted by denying the remarkable achievements of science and technology during the last centuries. Although the concept of intentional design is widely used to describe the methods that biologists use to make discoveries and inventions, it will be argued that the term is not appropriate for explaining the appearance of life on our planet nor for describing the scientific creativity of scientific investigators. The term rational for describing the development of new vaccines is also unjustified. Because the analysis of the COVID-19 pandemic requires contributions from biomedical and psycho-socioeconomic sciences, one scientific method alone would be insufficient for combatting the pandemic.
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Rational Design of Profile Hidden Markov Models for Viral Classification and Discovery. Bioinformatics 2021. [DOI: 10.36255/exonpublications.bioinformatics.2021.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
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35
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Bartoszewicz JM, Seidel A, Renard BY. Interpretable detection of novel human viruses from genome sequencing data. NAR Genom Bioinform 2021; 3:lqab004. [PMID: 33554119 PMCID: PMC7849996 DOI: 10.1093/nargab/lqab004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/04/2021] [Accepted: 01/15/2021] [Indexed: 01/21/2023] Open
Abstract
Viruses evolve extremely quickly, so reliable methods for viral host prediction are necessary to safeguard biosecurity and biosafety alike. Novel human-infecting viruses are difficult to detect with standard bioinformatics workflows. Here, we predict whether a virus can infect humans directly from next-generation sequencing reads. We show that deep neural architectures significantly outperform both shallow machine learning and standard, homology-based algorithms, cutting the error rates in half and generalizing to taxonomic units distant from those presented during training. Further, we develop a suite of interpretability tools and show that it can be applied also to other models beyond the host prediction task. We propose a new approach for convolutional filter visualization to disentangle the information content of each nucleotide from its contribution to the final classification decision. Nucleotide-resolution maps of the learned associations between pathogen genomes and the infectious phenotype can be used to detect regions of interest in novel agents, for example, the SARS-CoV-2 coronavirus, unknown before it caused a COVID-19 pandemic in 2020. All methods presented here are implemented as easy-to-install packages not only enabling analysis of NGS datasets without requiring any deep learning skills, but also allowing advanced users to easily train and explain new models for genomics.
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Affiliation(s)
- Jakub M Bartoszewicz
- Bioinformatics (MF1), Department of Methodology and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany
- Department of Mathematics and Computer Science, Free University of Berlin, 14195 Berlin, Germany
- Data Analytics and Computational Statistics, Hasso Plattner Institute for Digital Engineering, 14482 Potsdam, Brandenburg, Germany
- Digital Engineering Faculty, University of Postdam, 14482 Potsdam, Brandenburg, Germany
| | - Anja Seidel
- Bioinformatics (MF1), Department of Methodology and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany
- Department of Mathematics and Computer Science, Free University of Berlin, 14195 Berlin, Germany
| | - Bernhard Y Renard
- Bioinformatics (MF1), Department of Methodology and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany
- Data Analytics and Computational Statistics, Hasso Plattner Institute for Digital Engineering, 14482 Potsdam, Brandenburg, Germany
- Digital Engineering Faculty, University of Postdam, 14482 Potsdam, Brandenburg, Germany
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36
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Host cell glutamine metabolism as a potential antiviral target. Clin Sci (Lond) 2021; 135:305-325. [PMID: 33480424 DOI: 10.1042/cs20201042] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 12/08/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022]
Abstract
A virus minimally contains a nucleic acid genome packaged by a protein coat. The genome and capsid together are known as the nucleocapsid, which has an envelope containing a lipid bilayer (mainly phospholipids) originating from host cell membranes. The viral envelope has transmembrane proteins that are usually glycoproteins. The proteins in the envelope bind to host cell receptors, promoting membrane fusion and viral entry into the cell. Virus-infected host cells exhibit marked increases in glutamine utilization and metabolism. Glutamine metabolism generates ATP and precursors for the synthesis of macromolecules to assemble progeny viruses. Some compounds derived from glutamine are used in the synthesis of purines and pyrimidines. These latter compounds are precursors for the synthesis of nucleotides. Inhibitors of glutamine transport and metabolism are potential candidate antiviral drugs. Glutamine is also an essential nutrient for the functions of leukocytes (lymphocyte, macrophage, and neutrophil), including those in virus-infected patients. The increased glutamine requirement for immune cell functions occurs concomitantly with the high glutamine utilization by host cells in virus-infected patients. The development of antiviral drugs that target glutamine metabolism must then be specifically directed at virus-infected host cells to avoid negative effects on immune functions. Therefore, the aim of this review was to describe the landscape of cellular glutamine metabolism to search for potential candidates to inhibit glutamine transport or glutamine metabolism.
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Pons JC, Paez-Espino D, Riera G, Ivanova N, Kyrpides NC, Llabrés M. VPF-Class: Taxonomic assignment and host prediction of uncultivated viruses based on viral protein families. Bioinformatics 2021; 37:1805-1813. [PMID: 33471063 PMCID: PMC8830756 DOI: 10.1093/bioinformatics/btab026] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/11/2020] [Accepted: 01/13/2021] [Indexed: 12/03/2022] Open
Abstract
Motivation Two key steps in the analysis of uncultured viruses recovered from metagenomes are the taxonomic classification of the viral sequences and the identification of putative host(s). Both steps rely mainly on the assignment of viral proteins to orthologs in cultivated viruses. Viral Protein Families (VPFs) can be used for the robust identification of new viral sequences in large metagenomics datasets. Despite the importance of VPF information for viral discovery, VPFs have not yet been explored for determining viral taxonomy and host targets. Results In this work, we classified the set of VPFs from the IMG/VR database and developed VPF-Class. VPF-Class is a tool that automates the taxonomic classification and host prediction of viral contigs based on the assignment of their proteins to a set of classified VPFs. Applying VPF-Class on 731K uncultivated virus contigs from the IMG/VR database, we were able to classify 363K contigs at the genus level and predict the host of over 461K contigs. In the RefSeq database, VPF-class reported an accuracy of nearly 100% to classify dsDNA, ssDNA and retroviruses, at the genus level, considering a membership ratio and a confidence score of 0.2. The accuracy in host prediction was 86.4%, also at the genus level, considering a membership ratio of 0.3 and a confidence score of 0.5. And, in the prophages dataset, the accuracy in host prediction was 86% considering a membership ratio of 0.6 and a confidence score of 0.8. Moreover, from the Global Ocean Virome dataset, over 817K viral contigs out of 1 million were classified. Availability and implementation The implementation of VPF-Class can be downloaded from https://github.com/biocom-uib/vpf-tools. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joan Carles Pons
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain
| | | | - Gabriel Riera
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Berkeley, 94720, USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Berkeley, 94720, USA
| | - Mercè Llabrés
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain
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Abstract
The risk of emergence and spread of novel human pathogens originating from an animal reservoir has increased in the past decades. However, the unpredictable nature of disease emergence makes surveillance and preparedness challenging. Knowledge of general risk factors for emergence and spread, combined with local level data is needed to develop a risk-based methodology for early detection. This involves the implementation of the One Health approach, integrating human, animal and environmental health sectors, as well as social sciences, bioinformatics and more. Recent technical advances, such as metagenomic sequencing, will aid the rapid detection of novel pathogens on the human-animal interface.
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Seasonal and diel patterns of abundance and activity of viruses in the Red Sea. Proc Natl Acad Sci U S A 2020; 117:29738-29747. [PMID: 33172994 DOI: 10.1073/pnas.2010783117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Virus-microbe interactions have been studied in great molecular details for many years in cultured model systems, yielding a plethora of knowledge on how viruses use and manipulate host machinery. Since the advent of molecular techniques and high-throughput sequencing, methods such as cooccurrence, nucleotide composition, and other statistical frameworks have been widely used to infer virus-microbe interactions, overcoming the limitations of culturing methods. However, their accuracy and relevance is still debatable as cooccurrence does not necessarily mean interaction. Here we introduce an ecological perspective of marine viral communities and potential interaction with their hosts, using analyses that make no prior assumptions on specific virus-host pairs. By size fractionating water samples into free viruses and microbes (i.e., also viruses inside or attached to their hosts) and looking at how viral group abundance changes over time along both fractions, we show that the viral community is undergoing a change in rank abundance across seasons, suggesting a seasonal succession of viruses in the Red Sea. We use abundance patterns in the different size fractions to classify viral clusters, indicating potential diverse interactions with their hosts and potential differences in life history traits between major viral groups. Finally, we show hourly resolved variations of intracellular abundance of similar viral groups, which might indicate differences in their infection cycles or metabolic capacities.
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Naureen Z, Malacarne D, Anpilogov K, Dautaj A, Camilleri G, Cecchin S, Bressan S, Casadei A, Albion E, Sorrentino E, Beccari T, Dundar M, Bertelli M. Comparison between American and European legislation in the therapeutical and alimentary bacteriophage usage. ACTA BIO-MEDICA : ATENEI PARMENSIS 2020; 91:e2020023. [PMID: 33170166 PMCID: PMC8023134 DOI: 10.23750/abm.v91i13-s.10815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 10/23/2020] [Indexed: 01/21/2023]
Abstract
Bacteriophages, though discovered a century ago, still lag behind in the race of antimicrobials due to scarce information about their biology, pharmacology, safety and suitability as therapeutic agents. Although they possess several capabilities of practical utility in medicine, they are still unable to satisfy the regulatory standards set by the regulatory authorities in both United States (US) and European Union (EU). Bacteriophages and their products (lysins) are considered as drugs, therefore they should follow the same route of the chemical drugs in order to achieve regulatory approvals for commercial production and application. However, lack of definitive guidelines and regulations has rendered bacteriophages less attractive to pharmaceutical companies and funding agencies, making it difficult for clinicians and researchers to set up wide scale clinical trials in order to prove efficacy, safety and stability of bacteriophages and their products. In this review, we will discuss the current regulations for developing phages and phage-based products for therapeutic purposes in the US and EU.
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Affiliation(s)
- Zakira Naureen
- Department of Biological Sciences and Chemistry, College of Arts and Sciences, University of Nizwa, Nizwa, Oman.
| | | | | | | | | | | | | | | | | | | | - Tommaso Beccari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy.
| | - Munis Dundar
- Department of Medical Genetics, Erciyes University Medical School, Kayseri, Turkey.
| | - Matteo Bertelli
- MAGI'S LAB, Rovereto (TN), Italy; MAGI EUREGIO, Bolzano, Italy; EBTNA-LAB, Rovereto (TN), Italy.
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A brief history of the species concept in virology and an opinion on the proposal to introduce Linnaean binomial virus species names. Arch Virol 2020; 165:3073-3077. [DOI: 10.1007/s00705-020-04795-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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42
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Neurological Components in Coronavirus Induced Disease: A Review of the Literature Related to SARS, MERS, and COVID-19. Neurol Res Int 2020. [DOI: 10.1155/2020/6587875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background. COVID-19 has been declared the pandemic of the 21st century, causing more than 45,000 deaths worldwide. The abrupt release of SARS-CoV-2 demonstrated the potential infection, morbidity, and lethality of zoonotic viruses and human-to-human transmission. Fever, cough, and fatigue are reported as the most common symptoms of the disease, including acute respiratory distress syndrome, and also signs of severe illness, such as shock, acute cardiac injury, and renal lesions, are described. Considering the previous works related to human coronavirus and other zoonotic infections, it has been demonstrated that the neuroinvasive propensity is a common characteristic of coronaviruses, especially in SARS-CoV and MERS-CoV. Objective. In the present review, we analyzed the potential neurological components involved in coronavirus infections and detailed the neurological syndromes related to COVID-19. We also examined the mechanism of transmission and CNS pathology related to other viruses with similar structures such as SARS-CoV and MERS-CoV. Methods. A comprehensive search of different original articles and clinical, experimental, and review studies was conducted in MEDLINE/PubMed, Scopus, and Web of Science. We selected 92 articles that have been published in journals or preprints according to the search words and the inclusion and exclusion criteria. Results. COVID-19 patients may experience neurological symptoms such as headache, impaired mental status, confusion, dizziness, nausea and vomiting, anosmia/hyposmia, and dysgeusia/hypogeusia as initial symptoms, with more severe manifestations such as seizures or coma later on. The neurological signs shown are clinical symptoms similar to those reported for SARS-CoV and MERS-CoV. Given that both SARS-CoV and MERS-CoV have similar structures, these viruses may share comparable neurological symptoms and similar progression. Coronaviruses are linked to central nervous system dysfunction, and they are also reported as the probable cause of multiple sclerosis, encephalitis, and meningitis.
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Ortega MÁ, Guzmán Merino A, Fraile-Martínez O, Recio-Ruiz J, Pekarek L, G. Guijarro L, García-Honduvilla N, Álvarez-Mon M, Buján J, García-Gallego S. Dendrimers and Dendritic Materials: From Laboratory to Medical Practice in Infectious Diseases. Pharmaceutics 2020; 12:pharmaceutics12090874. [PMID: 32937793 PMCID: PMC7560085 DOI: 10.3390/pharmaceutics12090874] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/11/2020] [Accepted: 09/11/2020] [Indexed: 02/07/2023] Open
Abstract
Infectious diseases are one of the main global public health risks, predominantly caused by viruses, bacteria, fungi, and parasites. The control of infections is founded on three main pillars: prevention, treatment, and diagnosis. However, the appearance of microbial resistance has challenged traditional strategies and demands new approaches. Dendrimers are a type of polymeric nanoparticles whose nanometric size, multivalency, biocompatibility, and structural perfection offer boundless possibilities in multiple biomedical applications. This review provides the reader a general overview about the uses of dendrimers and dendritic materials in the treatment, prevention, and diagnosis of highly prevalent infectious diseases, and their advantages compared to traditional approaches. Examples of dendrimers as antimicrobial agents per se, as nanocarriers of antimicrobial drugs, as well as their uses in gene transfection, in vaccines or as contrast agents in imaging assays are presented. Despite the need to address some challenges in order to be used in the clinic, dendritic materials appear as an innovative tool with a brilliant future ahead in the clinical management of infectious diseases and many other health issues.
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Affiliation(s)
- Miguel Ángel Ortega
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (M.Á.O.); (A.G.M.); (O.F.-M.); (L.P.); (N.G.-H.); (M.Á.-M.); (J.B.)
- Institute Ramón y Cajal for Health Research (IRYCIS), 28034 Madrid, Spain
- Tumour Registry, Pathological Anatomy Service, University Hospital Príncipe de Asturias, 28805 Alcalá de Henares, Spain
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
| | - Alberto Guzmán Merino
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (M.Á.O.); (A.G.M.); (O.F.-M.); (L.P.); (N.G.-H.); (M.Á.-M.); (J.B.)
| | - Oscar Fraile-Martínez
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (M.Á.O.); (A.G.M.); (O.F.-M.); (L.P.); (N.G.-H.); (M.Á.-M.); (J.B.)
| | - Judith Recio-Ruiz
- Department of Organic and Inorganic Chemistry, Faculty of Sciences, and Research Institute in Chemistry “Andrés M. del Río” (IQAR), University of Alcalá, 28801 Alcalá de Henares, Spain;
| | - Leonel Pekarek
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (M.Á.O.); (A.G.M.); (O.F.-M.); (L.P.); (N.G.-H.); (M.Á.-M.); (J.B.)
| | - Luis G. Guijarro
- Department of Systems Biology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain;
- Networking Research Centre on Hepatic and Digestive Diseases (CIBER-EHD), 28029 Madrid, Spain
| | - Natalio García-Honduvilla
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (M.Á.O.); (A.G.M.); (O.F.-M.); (L.P.); (N.G.-H.); (M.Á.-M.); (J.B.)
- Institute Ramón y Cajal for Health Research (IRYCIS), 28034 Madrid, Spain
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
| | - Melchor Álvarez-Mon
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (M.Á.O.); (A.G.M.); (O.F.-M.); (L.P.); (N.G.-H.); (M.Á.-M.); (J.B.)
- Institute Ramón y Cajal for Health Research (IRYCIS), 28034 Madrid, Spain
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
- Immune System Diseases-Rheumatology, Oncology and Medicine Service, University Hospital Príncipe de Asturias, 28805 Alcalá de Henares, Madrid, Spain
| | - Julia Buján
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (M.Á.O.); (A.G.M.); (O.F.-M.); (L.P.); (N.G.-H.); (M.Á.-M.); (J.B.)
- Institute Ramón y Cajal for Health Research (IRYCIS), 28034 Madrid, Spain
- Tumour Registry, Pathological Anatomy Service, University Hospital Príncipe de Asturias, 28805 Alcalá de Henares, Spain
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
| | - Sandra García-Gallego
- Institute Ramón y Cajal for Health Research (IRYCIS), 28034 Madrid, Spain
- Department of Organic and Inorganic Chemistry, Faculty of Sciences, and Research Institute in Chemistry “Andrés M. del Río” (IQAR), University of Alcalá, 28801 Alcalá de Henares, Spain;
- Correspondence:
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Nomura S, Taniura T, Ito T. Extracellular Vesicle-Related Thrombosis in Viral Infection. Int J Gen Med 2020; 13:559-568. [PMID: 32904587 PMCID: PMC7457561 DOI: 10.2147/ijgm.s265865] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/28/2020] [Indexed: 12/17/2022] Open
Abstract
Although the outcomes of viral infectious diseases are remarkably varied, most infections cause acute diseases after a short period. Novel coronavirus disease 2019, which recently spread worldwide, is no exception. Extracellular vesicles (EVs) are small circulating membrane-enclosed entities shed from the cell surface in response to cell activation or apoptosis. EVs transport various kinds of bioactive molecules between cells, including functional RNAs, such as viral RNAs and proteins. Therefore, when EVs are at high levels, changes in cell activation, inflammation, angioplasty and transportation suggest that EVs are associated with various diseases. Clinical research on EVs includes studies on the coagulatory system. In particular, abnormal enhancement of the coagulatory system through EVs can cause thrombosis. In this review, we address the functions of EVs, thrombosis, and their involvement in viral infection.
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Affiliation(s)
- Shosaku Nomura
- First Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | | | - Tomoki Ito
- First Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
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Mahmoud ERA, Ahmed HAH, Abo-senna ASM, Riad OKM, Abo- Shadi MMAA–R. Isolation and characterization of six gamma-irradiated bacteriophages specific for MRSA and VRSA isolated from skin infections. JOURNAL OF RADIATION RESEARCH AND APPLIED SCIENCES 2020. [DOI: 10.1080/16878507.2020.1795564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | - Hala Ahmed Hussein Ahmed
- Department of Radiation Microbiology, National Center for Radiation Research and Technology, Egyptian Atomic, Energy Authority, Cairo, Egypt
| | | | - Omnia Karem M. Riad
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
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Zhu W, Chen CZ, Gorshkov K, Xu M, Lo DC, Zheng W. RNA-Dependent RNA Polymerase as a Target for COVID-19 Drug Discovery. SLAS DISCOVERY 2020; 25:1141-1151. [PMID: 32660307 PMCID: PMC7684788 DOI: 10.1177/2472555220942123] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
COVID-19 respiratory disease caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly become a global health issue since it emerged in December 2019. While great global efforts are underway to develop vaccines and to discover or repurpose therapeutic agents for this disease, as of this writing only the nucleoside drug remdesivir has been approved under Emergency Use Authorization to treat COVID-19. The RNA-dependent RNA polymerase (RdRP), a viral enzyme for viral RNA replication in host cells, is one of the most intriguing and promising drug targets for SARS-CoV-2 drug development. Because RdRP is a viral enzyme with no host cell homologs, selective SARS-CoV-2 RdRP inhibitors can be developed that have improved potency and fewer off-target effects against human host proteins and thus are safer and more effective therapeutics for treating COVID-19. This review focuses on biochemical enzyme and cell-based assays for RdRPs that could be used in high-throughput screening to discover new and repurposed drugs against SARS-CoV-2.
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Affiliation(s)
- Wei Zhu
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Catherine Z Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Kirill Gorshkov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Donald C Lo
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
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47
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Awan FM, Yang BB, Naz A, Hanif A, Ikram A, Obaid A, Malik A, Janjua HA, Ali A, Sharif S. The emerging role and significance of circular RNAs in viral infections and antiviral immune responses: possible implication as theranostic agents. RNA Biol 2020; 18:1-15. [PMID: 32615049 DOI: 10.1080/15476286.2020.1790198] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs) are ubiquitously expressed, covalently closed rings, produced by pre-mRNA splicing in a reversed order during post-transcriptional processing. Circularity endows 3'-5'-linked circRNAs with stability and resistance to exonucleolytic degradation which raises the question whether circRNAs may be relevant as potential therapeutic targets or agents. High stability in biological systems is the most remarkable property and a major criterion for why circRNAs could be exploited for a range of RNA-centred medical applications. Even though various biological roles and regulatory functions of circRNAs have been reported, their in-depth study is challenging because of their circular structure and sequence-overlap with linear mRNA counterparts. Moreover, little is known about their role in viral infections and in antiviral immune responses. We believe that an in-depth and detailed understanding of circRNA mediated viral protein regulations will increase our knowledge of the biology of these novel molecules. In this review, we aimed to provide a comprehensive basis and overview on the biogenesis, significance and regulatory roles of circRNAs in the context of antiviral immune responses and viral infections including hepatitis C virus infection, hepatitis B virus infection, hepatitis delta virus infection, influenza A virus infection, Epstein-Barr virus infection, kaposi's sarcoma herpesvirus infection, human cytomegalovirus infection, herpes simplex virus infection, human immunodeficiency virus infection, porcine epidemic diarrhoea virus infection, ORF virus infection, avian leukosis virus infection, simian vacuolating virus 40 infection, transmissible gastroenteritis coronavirus infection, and bovine viral diarrhoea virus infection. We have also discussed the critical regulatory role of circRNAs in provoking antiviral immunity, providing evidence for implications as therapeutic agents and as diagnostic markers.
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Affiliation(s)
- Faryal Mehwish Awan
- Institute of Molecular Biology and Biotechnology (IMBB), the University of Lahore (UOL) , Lahore, Pakistan
| | - Burton B Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre , Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto , Toronto, Canada.,Institute of Medical Sciences, University of Toronto , Toronto, Canada
| | - Anam Naz
- Institute of Molecular Biology and Biotechnology (IMBB), the University of Lahore (UOL) , Lahore, Pakistan
| | - Aneeqa Hanif
- Institute of Molecular Biology and Biotechnology (IMBB), the University of Lahore (UOL) , Lahore, Pakistan
| | - Aqsa Ikram
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) , Pakistan
| | - Ayesha Obaid
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) , Pakistan
| | - Arif Malik
- Institute of Molecular Biology and Biotechnology (IMBB), the University of Lahore (UOL) , Lahore, Pakistan
| | - Hussnain Ahmed Janjua
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) , Pakistan
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) , Pakistan
| | - Sumaira Sharif
- Institute of Molecular Biology and Biotechnology (IMBB), the University of Lahore (UOL) , Lahore, Pakistan
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48
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Coperchini F, Chiovato L, Croce L, Magri F, Rotondi M. The cytokine storm in COVID-19: An overview of the involvement of the chemokine/chemokine-receptor system. Cytokine Growth Factor Rev 2020; 53:25-32. [PMID: 32446778 PMCID: PMC7211650 DOI: 10.1016/j.cytogfr.2020.05.003] [Citation(s) in RCA: 877] [Impact Index Per Article: 219.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 01/08/2023]
Abstract
In 2019-2020 a new coronavirus named SARS-CoV-2 was identified as the causative agent of a several acute respiratory infection named COVID-19, which is causing a worldwide pandemic. There are still many unresolved questions regarding the pathogenesis of this disease and especially the reasons underlying the extremely different clinical course, ranging from asymptomatic forms to severe manifestations, including the Acute Respiratory Distress Syndrome (ARDS). SARS-CoV-2 showed phylogenetic similarities to both SARS-CoV and MERS-CoV viruses, and some of the clinical features are shared between COVID-19 and previously identified beta-coronavirus infections. Available evidence indicate that the so called "cytokine storm" an uncontrolled over-production of soluble markers of inflammation which, in turn, sustain an aberrant systemic inflammatory response, is a major responsible for the occurrence of ARDS. Chemokines are low molecular weight proteins with powerful chemoattractant activity which play a role in the immune cell recruitment during inflammation. This review will be aimed at providing an overview of the current knowledge on the involvement of the chemokine/chemokine-receptor system in the cytokine storm related to SARS-CoV-2 infection. Basic and clinical evidences obtained from previous SARS and MERS epidemics and available data from COVID-19 will be taken into account.
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Affiliation(s)
- Francesca Coperchini
- Istituti Clinici Scientifici Maugeri IRCCS, Unit of Internal Medicine and Endocrinology, Laboratory for Endocrine Disruptors, 27100 Pavia, PV, Italy
| | - Luca Chiovato
- Istituti Clinici Scientifici Maugeri IRCCS, Unit of Internal Medicine and Endocrinology, Laboratory for Endocrine Disruptors, 27100 Pavia, PV, Italy; Department of Internal Medicine and Therapeutics, University of Pavia, 27100 Pavia, PV, Italy
| | - Laura Croce
- Istituti Clinici Scientifici Maugeri IRCCS, Unit of Internal Medicine and Endocrinology, Laboratory for Endocrine Disruptors, 27100 Pavia, PV, Italy; Department of Internal Medicine and Therapeutics, University of Pavia, 27100 Pavia, PV, Italy
| | - Flavia Magri
- Istituti Clinici Scientifici Maugeri IRCCS, Unit of Internal Medicine and Endocrinology, Laboratory for Endocrine Disruptors, 27100 Pavia, PV, Italy; Department of Internal Medicine and Therapeutics, University of Pavia, 27100 Pavia, PV, Italy
| | - Mario Rotondi
- Istituti Clinici Scientifici Maugeri IRCCS, Unit of Internal Medicine and Endocrinology, Laboratory for Endocrine Disruptors, 27100 Pavia, PV, Italy; Department of Internal Medicine and Therapeutics, University of Pavia, 27100 Pavia, PV, Italy.
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49
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Petrovic Fabijan A, Khalid A, Maddocks S, Ho J, Gilbey T, Sandaradura I, Lin RCY, Ben Zakour N, Venturini C, Bowring B, Iredell JR. Phage therapy for severe bacterial infections: a narrative review. Med J Aust 2020; 212:279-285. [PMID: 31587298 PMCID: PMC9545287 DOI: 10.5694/mja2.50355] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bacteriophage (phage) therapy is re-emerging a century after it began. Activity against antibiotic-resistant pathogens and a lack of serious side effects make phage therapy an attractive treatment option in refractory bacterial infections. Phages are highly specific for their bacterial targets, but the relationship between in vitro activity and in vivo efficacy remains to be rigorously evaluated. Pharmacokinetic and pharmacodynamic principles of phage therapy are generally based on the classic predator-prey relationship, but numerous other factors contribute to phage clearance and optimal dosing strategies remain unclear. Combinations of fully characterised, exclusively lytic phages prepared under good manufacturing practice are limited in their availability. Safety has been demonstrated but randomised controlled trials are needed to evaluate efficacy.
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Affiliation(s)
- Aleksandra Petrovic Fabijan
- Centre for Infectious Diseases and MicrobiologyWestmead HospitalSydneyNSW
- Westmead Institute for Medical ResearchSydneyNSW
| | - Ali Khalid
- Centre for Infectious Diseases and MicrobiologyWestmead HospitalSydneyNSW
- Westmead Institute for Medical ResearchSydneyNSW
- University of SydneySydneyNSW
| | - Susan Maddocks
- Centre for Infectious Diseases and MicrobiologyWestmead HospitalSydneyNSW
- University of SydneySydneyNSW
- Westmead HospitalSydneyNSW
| | - Josephine Ho
- Centre for Infectious Diseases and MicrobiologyWestmead HospitalSydneyNSW
- Westmead Institute for Medical ResearchSydneyNSW
- Westmead HospitalSydneyNSW
| | | | - Indy Sandaradura
- Centre for Infectious Diseases and MicrobiologyWestmead HospitalSydneyNSW
- University of SydneySydneyNSW
| | - Ruby CY Lin
- Centre for Infectious Diseases and MicrobiologyWestmead HospitalSydneyNSW
- Westmead Institute for Medical ResearchSydneyNSW
- University of SydneySydneyNSW
| | - Nouri Ben Zakour
- Centre for Infectious Diseases and MicrobiologyWestmead HospitalSydneyNSW
- Westmead Institute for Medical ResearchSydneyNSW
- University of SydneySydneyNSW
| | - Carola Venturini
- Centre for Infectious Diseases and MicrobiologyWestmead HospitalSydneyNSW
- Westmead Institute for Medical ResearchSydneyNSW
- University of SydneySydneyNSW
| | - Bethany Bowring
- Centre for Infectious Diseases and MicrobiologyWestmead HospitalSydneyNSW
- Westmead Institute for Medical ResearchSydneyNSW
| | - Jonathan R Iredell
- Centre for Infectious Diseases and MicrobiologyWestmead HospitalSydneyNSW
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50
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Obbard DJ, Shi M, Roberts KE, Longdon B, Dennis AB. A new lineage of segmented RNA viruses infecting animals. Virus Evol 2020; 6:vez061. [PMID: 31976084 PMCID: PMC6966834 DOI: 10.1093/ve/vez061] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called 'dark' virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose 'dark' virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.
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Affiliation(s)
- Darren J Obbard
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Mang Shi
- Charles Perkins Center, The University of Sydney, NSW 2006, Australia
| | - Katherine E Roberts
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Ben Longdon
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Alice B Dennis
- Department of Evolutionary Biology & Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
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