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Vu NT, Kim H, Lee S, Hwang IS, Kwon CT, Oh CS. Bacteriophage cocktail for biocontrol of soft rot disease caused by Pectobacterium species in Chinese cabbage. Appl Microbiol Biotechnol 2024; 108:11. [PMID: 38159122 DOI: 10.1007/s00253-023-12881-x] [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: 06/18/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 01/03/2024]
Abstract
Pectobacterium spp. are necrotrophic plant pathogens that cause the soft rot disease in Chinese cabbage, resulting in severe yield loss. The use of conventional antimicrobial agents, copper-based bactericides, and antibiotics has encountered several limitations, such as bioaccumulation on plants and microbial resistance. Bacteriophages (phages) are considered promising alternative antimicrobial agents against diverse phytopathogens. In this study, we isolated and characterized two virulent phages (phiPccP-2 and phiPccP-3) to develop a phage cocktail. Morphological and genomic analyses revealed that two phages belonged to the Tevenvirinae and Mccorquodalevirinae subfamilies, respectively. The phiPccP-2 and phiPccP-3 phages, which have a broad host range, were stable at various environmental conditions, such as various pHs and temperatures and exposure to ultraviolet light. The phage cocktail developed using these two lytic phages inhibited the emergence of phage-resistant bacteria compared to single-phage treatments in in vitro challenge assays. The phage cocktail treatment effectively prevented the development of soft rot symptom in matured Chinese cabbage leaves. Additionally, the phage cocktail comprising three phages (phiPccP-1, phiPccP-2, and phiPccP-3) showed superior biocontrol efficacy against the mixture of Pectobacterium strains in Chinese cabbage seedlings. These results suggest that developing phage cocktails is an effective approach for biocontrol of soft rot disease caused by Pectobacterium strains in crops compared to single-phage treatments. KEY POINTS: •Two newly isolated Pectobacterium phages, phiPccP-2 and phiPccP-3, infected diverse Pectobacterium species and effectively inhibited the emergence of phage-resistant bacteria. •Genomic and physiological analyses suggested that both phiPccP-2 and phiPccP-3 are lytic phages and that their lytic activities are stable in the environmental conditions under which Chinese cabbage grows. •Treatment using a phage cocktail comprising phiPccP-2 and phiPccP-3 efficiently suppressed soft rot disease in detached mature leaves and seedlings of Chinese cabbage, indicating the applicability of the phage cocktail as an alternative antimicrobial agent.
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Affiliation(s)
- Nguyen Trung Vu
- Department of Green-Bio Science, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Hyeongsoon Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Soohong Lee
- Department of Green-Bio Science, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - In Sun Hwang
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Choon-Tak Kwon
- Department of Green-Bio Science, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Chang-Sik Oh
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
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2
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Leveringhaus E, Poljakovic R, Herrmann G, Roman-Sosa G, Becher P, Postel A. Porcine low-density lipoprotein receptor plays an important role in classical swine fever virus infection. Emerg Microbes Infect 2024; 13:2327385. [PMID: 38514916 PMCID: PMC10962300 DOI: 10.1080/22221751.2024.2327385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024]
Abstract
Several cellular factors have been reported to be required for replication of classical swine fever virus (CSFV), a member of the genus Pestivirus within the family Flaviviridae. However, many steps of its replication cycle are still poorly understood. The low-density lipoprotein receptor (LDLR) is involved in cell entry and post-entry processes of different viruses including other members of the Flaviviridae. In this study, the relevance of LDLR in replication of CSFV and another porcine pestivirus, Bungowannah pestivirus (BuPV), was investigated by antibody-mediated blocking of LDLR and genetically engineered porcine cell lines providing altered LDLR expression levels. An LDLR-specific antibody largely blocked infection with CSFV, but had only a minor impact on BuPV. Infections of the genetically modified cells confirmed an LDLR-dependent replication of CSFV. Compared to wild type cells, lower and higher expression of LDLR resulted in a 3.5-fold decrease or increase in viral titers already 20 h post infection. Viral titers were 25-fold increased in LDLR-overexpressing cells compared to cells with reduced LDLR expression at 72 h post infection. The varying LDLR expression levels had no clear effect on permissivity to BuPV. A decoy receptor assay using recombinant soluble LDLR provided no evidence that LDLR may function as a receptor for CSFV or BuPV. Differences in their dependency on LDLR suggest that CSFV and BuPV likely use different mechanisms to interact with their host cells. Moreover, this study reveals similarities in the replication cycles of CSFV and other members of the family Flaviviridae that are dependent on LDLR.
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Affiliation(s)
- Elena Leveringhaus
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Robin Poljakovic
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Gina Herrmann
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Gleyder Roman-Sosa
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Paul Becher
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Alexander Postel
- Institute of Virology, University of Veterinary Medicine Hannover, Hannover, Germany
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3
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Sedgwick RL, ElBohy O, Daly JM. Role of pseudotyped viruses in understanding epidemiology, pathogenesis and immunity of viral diseases affecting both horses and humans. Virology 2024; 597:110164. [PMID: 38959722 DOI: 10.1016/j.virol.2024.110164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024]
Abstract
In this review, we explore how pseudotyped viruses (PVs) are being applied to the study of viruses affecting both humans and horses. For the purposes of this review, we define PVs as non-replicative viruses with the core of one virus and the surface protein(s) of another and encapsulating a reporter gene such as luciferase. These 'reporter' PVs enable receptor-mediated entry into host cells to be quantified, and thus can be applied to study the initial stages of viral replication. They can also be used to test antiviral activity of compounds and measure envelope protein-specific antibodies in neutralisation tests.
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Affiliation(s)
- Rebecca L Sedgwick
- One Virology - WCGVR, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, UK
| | - Ola ElBohy
- One Virology - WCGVR, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, UK
| | - Janet M Daly
- One Virology - WCGVR, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, UK.
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4
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Wu L, Wu Q, Cao J, Wu X, Yang M, Liu H. Molecular characterization of a novel mitovirus from the plant-pathogenic fungus Nigrospora oryzae. Arch Virol 2024; 169:181. [PMID: 39150574 DOI: 10.1007/s00705-024-06110-7] [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: 05/17/2024] [Accepted: 07/06/2024] [Indexed: 08/17/2024]
Abstract
Here, we characterized a novel mitovirus from the fungus Nigrospora oryzae, which was named "Nigrospora oryzae mitovirus 3" (NoMV3). The NoMV3 genome is 2,492 nt in length with a G + C content of 33%, containing a single large open reading frame (ORF) using the fungal mitochondrial genetic code. The ORF encodes an RNA-dependent RNA polymerase (RdRp) of 775 amino acids with a molecular mass of 88.75 kDa. BLASTp analysis revealed that the RdRp of NoMV3 had 68.6%, 50.6%, and 48.6% sequence identity to those of Nigrospora oryzae mitovirus 2, Suillus luteus mitovirus 6, and Fusarium proliferatum mitovirus 3, respectively, which belong to the genus Unuamitovirus within the family Mitoviridae. Phylogenetic analysis based on amino acid sequences supported the classification of NoMV3 as a member of a new species in the genus Unuamitovirus within the family Mitoviridae.
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Affiliation(s)
- Lei Wu
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Qinxiang Wu
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Jiwu Cao
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Xizhi Wu
- College of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Manguo Yang
- Forestry Bureau of Shuangpai County, Yongzhou, China
| | - Hong Liu
- College of Forestry, Central South University of Forestry and Technology, Changsha, China.
- Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Changsha, China.
- Key Laboratory of National Forestry and Grassland Administration on Control of Artiffcial Forest Diseases and Pests, Changsha, China.
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5
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Calcraft T, Stanke-Scheffler N, Nans A, Lindemann D, Taylor IA, Rosenthal PB. Integrated cryoEM structure of a spumaretrovirus reveals cross-kingdom evolutionary relationships and the molecular basis for assembly and virus entry. Cell 2024; 187:4213-4230.e19. [PMID: 39013471 DOI: 10.1016/j.cell.2024.06.017] [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: 11/02/2023] [Revised: 02/26/2024] [Accepted: 06/11/2024] [Indexed: 07/18/2024]
Abstract
Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates for gene and oncolytic therapies. Structural studies of PFV contribute to the understanding of the mechanisms of FV replication, cell entry and infection, and retroviral evolution. Here we combine cryoEM and cryoET to determine high-resolution in situ structures of the PFV icosahedral capsid (CA) and envelope glycoprotein (Env), including its type III transmembrane anchor and membrane-proximal external region (MPER), and show how they are organized in an integrated structure of assembled PFV particles. The atomic models reveal an ancient retroviral capsid architecture and an unexpected relationship between Env and other class 1 fusion proteins of the Mononegavirales. Our results represent the de novo structure determination of an assembled retrovirus particle.
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Affiliation(s)
- Thomas Calcraft
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicole Stanke-Scheffler
- Institute of Medical Microbiology and Virology, University Hospital and Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, Fetscherstr. 74, 01307 Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Dirk Lindemann
- Institute of Medical Microbiology and Virology, University Hospital and Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, Fetscherstr. 74, 01307 Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany.
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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Dick A, Mikirtumov V, Fuchs J, Krupp F, Olal D, Bendl E, Sprink T, Diebolder C, Kudryashev M, Kochs G, Roske Y, Daumke O. Structural characterization of Thogoto Virus nucleoprotein provides insights into viral RNA encapsidation and RNP assembly. Structure 2024; 32:1068-1078.e5. [PMID: 38749445 DOI: 10.1016/j.str.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 03/11/2024] [Accepted: 04/18/2024] [Indexed: 08/11/2024]
Abstract
Orthomyxoviruses, such as influenza and thogotoviruses, are important human and animal pathogens. Their segmented viral RNA genomes are wrapped by viral nucleoproteins (NPs) into helical ribonucleoprotein complexes (RNPs). NP structures of several influenza viruses have been reported. However, there are still contradictory models of how orthomyxovirus RNPs are assembled. Here, we characterize the crystal structure of Thogoto virus (THOV) NP and found striking similarities to structures of influenza viral NPs, including a two-lobed domain architecture, a positively charged RNA-binding cleft, and a tail loop important for trimerization and viral transcription. A low-resolution cryo-electron tomography reconstruction of THOV RNPs elucidates a left-handed double helical assembly. By providing a model for RNP assembly of THOV, our study suggests conserved NP assembly and RNA encapsidation modes for thogoto- and influenza viruses.
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Affiliation(s)
- Alexej Dick
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Vasilii Mikirtumov
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Jonas Fuchs
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hermann-Herder-Straße 11, 79104 Freiburg, Germany
| | - Ferdinand Krupp
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Daniel Olal
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Elias Bendl
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hermann-Herder-Straße 11, 79104 Freiburg, Germany
| | - Thiemo Sprink
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Core facility for Cryo-Electron Microscopy, Charité, Berlin, Germany
| | | | - Mikhail Kudryashev
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Georg Kochs
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hermann-Herder-Straße 11, 79104 Freiburg, Germany.
| | - Yvette Roske
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany.
| | - Oliver Daumke
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany.
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7
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Camargo AP, Roux S, Schulz F, Babinski M, Xu Y, Hu B, Chain PSG, Nayfach S, Kyrpides NC. Identification of mobile genetic elements with geNomad. Nat Biotechnol 2024; 42:1303-1312. [PMID: 37735266 PMCID: PMC11324519 DOI: 10.1038/s41587-023-01953-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/17/2023] [Indexed: 09/23/2023]
Abstract
Identifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological applications and impact on public health. Here we introduce geNomad, a classification and annotation framework that combines information from gene content and a deep neural network to identify sequences of plasmids and viruses. geNomad uses a dataset of more than 200,000 marker protein profiles to provide functional gene annotation and taxonomic assignment of viral genomes. Using a conditional random field model, geNomad also detects proviruses integrated into host genomes with high precision. In benchmarks, geNomad achieved high classification performance for diverse plasmids and viruses (Matthews correlation coefficient of 77.8% and 95.3%, respectively), substantially outperforming other tools. Leveraging geNomad's speed and scalability, we processed over 2.7 trillion base pairs of sequencing data, leading to the discovery of millions of viruses and plasmids that are available through the IMG/VR and IMG/PR databases. geNomad is available at https://portal.nersc.gov/genomad .
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Affiliation(s)
- Antonio Pedro Camargo
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michal Babinski
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Yan Xu
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Bin Hu
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Stephen Nayfach
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Cho M, Min X, Been N, Son HS. The evolutionary and genetic patterns of African swine fever virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105612. [PMID: 38824981 DOI: 10.1016/j.meegid.2024.105612] [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: 10/11/2023] [Revised: 05/03/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
African swine fever (ASF) is a serious animal disease, and has spread to Africa, Europe and Asia, causing massive economic losses. African swine fever virus (ASFV) is transmitted from a reservoir host (warthog) to domestic pigs via a sylvatic cycle (transmission between warthogs and soft ticks) and a domestic cycle (transmission between domestic pigs) and survives by expressing a variety of genes related to virus-host interactions. We evaluated differences in codon usage patterns among ASFV genotypes and clades and explored the common and specific evolutionary and genetic characteristics of ASFV sequences. We analysed the evolutionary relationships, nucleotide compositions, codon usage patterns, selection pressures (mutational pressure and natural selection) and viral adaptation to host codon usage based on the coding sequences (CDS) of key functional genes of ASFV. AT bias was detected in the six genes analysed, irrespective of clade. The AT bias of genes (A224L, A179L, EP153R) encoding proteins involved in interaction with host cells after infection was high; among them, the AT bias of EP153R was the greatest at 78.3%. A large number of overrepresented codons were identified in EP153R, whereas there were no overrepresented codons with a relative synonymous codon usage (RSCU) value of ≥3 in B646L. In most genes, the pattern of selection pressure was similar for each clade, but in EP153R, diverse patterns of selection pressure were captured within the same clade and genotype. As a result of evaluating host adaptation based on the codon adaptation index (CAI), for B646L, E183L, CP204L and A179L, the codon usage patterns in all sequences were more similar to tick than domestic pig or wild boar. However, EP153R showed the lowest average CAI value of 0.52 when selecting tick as a reference set. The genes analysed in this study showed different magnitudes of selection pressure at the clade and genotype levels, which is likely to be related to the function of the encoded proteins and may determine key evolutionary traits of viruses, such as the level of genetic variation and host range. The diversity of codon adaptations at the genetic level in ASFV may account for differences in translational selection in ASFV hosts and provides insight into viral host adaptation and co-evolution.
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Affiliation(s)
- Myeongji Cho
- Laboratory of Computational Virology & Viroinformatics, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Health and Environment, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
| | - Xianglan Min
- Laboratory of Computational Virology & Viroinformatics, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
| | - Nara Been
- Laboratory of Computational Virology & Viroinformatics, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
| | - Hyeon S Son
- Laboratory of Computational Virology & Viroinformatics, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Health and Environment, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Interdisciplinary Graduate Program in Bioinformatics, College of Natural Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
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Liu H, Li T, Tang J, Ding S, Wang D. Complete genome sequence analysis of Reticuloendotheliosis virus integrated in nonhomologous Avipoxvirus. Microb Pathog 2024; 194:106827. [PMID: 39084308 DOI: 10.1016/j.micpath.2024.106827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024]
Abstract
Integration of nucleic acid sequences of Reticuloendotheliosis virus (REV) in Avipoxvirus(APV) has become commonplace. In this study, 4 strains of suspected Fowlpox virus (FPV) and 1 strain of suspected Pigeonpox virus (PPV) collected in Taiyuan, Shanxi Province were cultured in chicken embryos, and the 4b core protein gene was amplified by PCR, and the identity and genome similarity were determined by sequence analysis. The sequences between the end of ORF201 and the beginning of ORF203 of FPV and PPV were then amplified, sequenced, and subjected to sequence comparison to determine genome similarity. The results showed that the isolates were 4 strains of FPV and 1 strain of PPV. The 4 isolated strains of FPV belong to type A1 virus, with 100 % identity to each other and to the FWPV-09-Jilin strain isolated in Jilin, China, and the lowest identity to the type B2 virus TNPV5/NZL/2009, which is only 74 %. PPV belongs to type A2 virus, and its identity with local strain of fowlpox virus was 90.1 %, with the highest identity of 100 % with PPLH and ROPI/W370/ON/2012 and ow_2017_3 strains, which also belong to type A2 pigeonpox virus, and the lowest identity of 73.7 % with TNPV5/NZL/2009, a type B2 virus. The complete genome of REV sequences integrated into FPV and PPV were amplified, and 5 REV nucleic acid sequences were obtained after sequencing and concatenation, with lengths ranging from 7942 to 8005 bp. The identity analysis results indicate that it has high identity with isolates from Northeast China, Guangdong, and Guangxi regions in China. Based on its gp90 protein gene, the REV integrated into the poxvirus belong to type III, with the highest identity of 99.9% with strains such as APC-566 and CY1111, and the lowest identity with REV-Anhui1, at 95.4 %. The length of the pol gene varies among different strains of REV, and its encoded amino acid changes significantly after position 675, with deletions and alterations. This study indicates that all fowlpox viruses isolated in Taiyuan, Shanxi Province have integrated the entire REV gene sequence, with high identity between them. At the same time, it indicates that the pigeonpox virus isolate has also integrated the entire REV gene sequence, and has the highest identity with the integrated REV gene sequence in fowlpox virus.
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Affiliation(s)
- Huadong Liu
- College of Animal Science, Shanxi Agricultural University, Taiyuan, 030032, China.
| | - Tingting Li
- College of Animal Science, Shanxi Agricultural University, Taiyuan, 030032, China
| | - Juan Tang
- College of Animal Science, Shanxi Agricultural University, Taiyuan, 030032, China
| | - Shurong Ding
- College of Animal Science, Shanxi Agricultural University, Taiyuan, 030032, China
| | - Dongcai Wang
- College of Animal Science, Shanxi Agricultural University, Taiyuan, 030032, China
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10
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Erickson A, Ter Horst AM, Carlson CR, Falk BW, Kuo YW. Identification of a novel recombinant polerovirus and other emergent viruses and tombusvirus-like associated RNA species associated with carrot motley dwarf disease in the United States. Front Microbiol 2024; 15:1430445. [PMID: 39132135 PMCID: PMC11314183 DOI: 10.3389/fmicb.2024.1430445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/09/2024] [Indexed: 08/13/2024] Open
Abstract
Carrot motley dwarf (CMD) is a viral disease complex caused by co-infection of the polerovirus carrot red leaf virus with the umbraviruses carrot mottle virus or carrot mottle mimic virus, and/or a tombusvirus like associated RNA (tlaRNA), which depend on co-infection with a helper polerovirus to gain aphid transmissibility. In 2020 and 2021 carrot samples from Washington, United States (U.S.), and parsley and cilantro samples from California, U.S., exhibiting typical symptoms of CMD were submitted for diagnosis. Initial RT-PCR diagnostic assays identified the typical CMD viruses in the carrot samples, however only the umbraviruses and tlaRNAs were detected in the parsley and cilantro samples; as such, these samples were retested with another RT-PCR assay for generic polerovirus detection. Unexpectedly, the poleroviruses Torilis crimson leaf virus (TorCLV) and fennel motley virus were identified. Subsequent RNA sequencing analysis was conducted to confirm these results and look for other emergent viruses. In addition to confirming the diagnostic results, the recently described polerovirus Foeniculum vulgare polerovirus, the umbraviruses Pastinaca umbravirus 1 and wild carrot mottle virus, and the tlaRNA Arracacha latent virus E associated RNA were identified, making this the first report of these viruses and tlaRNA in the U.S. Using phylogenetic and pairwise identity comparisons and RDP4 recombination analyses, we also identified a putative novel polerovirus, for which we propose the name parsley polerovirus, that appears to be a recombinant between carrot polerovirus 1, sharing 92% amino acid (aa) identity with the RNA dependent RNA polymerase in the 5' gene block, and TorCLV, sharing >98% aa identity with the capsid protein in the 3 gene block. This work adds to the growing list of polerovirus species exhibiting recombination between the 5' and 3' gene blocks, and highlights the unique, variable, and dynamic associations that can occur in polerovirus, umbravirus, and tlaRNA disease complexes.
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Affiliation(s)
- Anna Erickson
- Department of Plant Pathology, University of California, Davis, CA, Unites States
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Szydło W, Wosula EN, Knoell E, Hein GL, Mondal S, Tatineni S. Helper Component-Proteinase of Triticum Mosaic Virus Is a Viral Determinant of Wheat Curl Mite Transmission. PHYTOPATHOLOGY 2024; 114:1672-1679. [PMID: 38579745 DOI: 10.1094/phyto-02-24-0073-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
Triticum mosaic virus (TriMV; genus Poacevirus; family Potyviridae) is an economically important virus in the Great Plains region of the United States. TriMV is transmitted by the wheat curl mite (Aceria tosichella) Type 2 genotype but not by Type 1. Helper component-proteinase (HC-Pro) is a vector transmission determinant for several potyvirids, but the role of HC-Pro in TriMV transmission is unknown. In this study, we examined the requirement of the HC-Pro cistron of TriMV for wheat curl mite (Type 2) transmission through deletion and point mutations and constructing TriMV chimeras with heterologous HC-Pros from other potyvirids. TriMV with complete deletion of HC-Pro failed to be transmitted by wheat curl mites at detectable levels. Furthermore, TriMV chimeras with heterologous HC-Pros from aphid-transmitted turnip mosaic virus and tobacco etch virus, or wheat curl mite-transmitted wheat streak mosaic virus, failed to be transmitted by wheat curl mites. These data suggest that heterologous HC-Pros did not complement TriMV for wheat curl mite transmission. A decreasing series of progressive nested in-frame deletions at the N-terminal region of HC-Pro comprising amino acids 3 to 125, 3 to 50, 3 to 25, 3 to 15, 3 to 8, and 3 and 4 abolished TriMV transmission by wheat curl mites. Additionally, mutation of conserved His20, Cys49, or Cys52 to Ala in HC-Pro abolished TriMV transmissibility by wheat curl mites. These data suggest that the N-terminal region of HC-Pro is crucial for TriMV transmission by wheat curl mites. Collectively, these data demonstrate that the HC-Pro cistron of TriMV is a viral determinant for wheat curl mite transmission.
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Affiliation(s)
- Wiktoria Szydło
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68503, U.S.A
- Center for Advanced Technology and Population Ecology Lab, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 10, 61-614 Poznań, Poland
| | - Everlyne N Wosula
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68503, U.S.A
| | - Elliot Knoell
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68503, U.S.A
| | - Gary L Hein
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68503, U.S.A
| | - Shaonpius Mondal
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68503, U.S.A
| | - Satyanarayana Tatineni
- U.S. Department of Agriculture-Agricultural Research Service, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
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12
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Santamaría-Corral G, Pagán I, Aguilera-Correa JJ, Esteban J, García-Quintanilla M. A Novel Bacteriophage Infecting Multi-Drug- and Extended-Drug-Resistant Pseudomonas aeruginosa Strains. Antibiotics (Basel) 2024; 13:523. [PMID: 38927189 PMCID: PMC11200629 DOI: 10.3390/antibiotics13060523] [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: 04/11/2024] [Revised: 05/13/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
The prevalence of carbapenem-resistant P. aeruginosa has dramatically increased over the last decade, and antibiotics alone are not enough to eradicate infections caused by this opportunistic pathogen. Phage therapy is a fresh treatment that can be administered under compassionate use, particularly against chronic cases. However, it is necessary to thoroughly characterize the virus before therapeutic application. Our work describes the discovery of the novel sequenced bacteriophage, vB_PaeP-F1Pa, containing an integrase, performs a phylogenetical analysis, describes its stability at a physiological pH and temperature, latent period (40 min), and burst size (394 ± 166 particles per bacterial cell), and demonstrates its ability to infect MDR and XDR P. aeruginosa strains. Moreover, this novel bacteriophage was able to inhibit the growth of bacteria inside preformed biofilms. The present study offers a road map to analyze essential areas for successful phage therapy against MDR and XDR P. aeruginosa infections, and shows that a phage containing an integrase is also able to show good in vitro results, indicating that it is very important to perform a genomic analysis before any clinical use, in order to prevent adverse effects in patients.
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Affiliation(s)
- Guillermo Santamaría-Corral
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (G.S.-C.); (J.J.A.-C.); (M.G.-Q.)
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA/CSIC and E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28223 Madrid, Spain;
| | - John Jairo Aguilera-Correa
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (G.S.-C.); (J.J.A.-C.); (M.G.-Q.)
- CIBERINFEC-Consorcio Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, 28029 Madrid, Spain
| | - Jaime Esteban
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (G.S.-C.); (J.J.A.-C.); (M.G.-Q.)
- CIBERINFEC-Consorcio Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, 28029 Madrid, Spain
| | - Meritxell García-Quintanilla
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (G.S.-C.); (J.J.A.-C.); (M.G.-Q.)
- CIBERINFEC-Consorcio Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, 28029 Madrid, Spain
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13
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Roy SD, Ramasamy S, Obbineni JM. An evaluation of nucleic acid-based molecular methods for the detection of plant viruses: a systematic review. Virusdisease 2024; 35:357-376. [PMID: 39071869 PMCID: PMC11269559 DOI: 10.1007/s13337-024-00863-0] [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: 01/11/2024] [Accepted: 04/15/2024] [Indexed: 07/30/2024] Open
Abstract
Precise and timely diagnosis of plant viruses is a prerequisite for the implementation of efficient management strategies, considering factors like globalization of trade and climate change facilitating the spread of viruses that lead to agriculture yield losses of billions yearly worldwide. Symptomatic diagnosis alone may not be reliable due to the diverse symptoms and confusion with plant abiotic stresses. It is crucial to detect plant viruses accurately and reliably and do so with little time. A complete understanding of the various detection methods is necessary to achieve this. Enzyme-linked immunosorbent assay (ELISA), has become more popular as a method for detecting viruses but faces limitations such as antibody availability, cost, sample volume, and time. Advanced techniques like polymerase chain reaction (PCR) have surpassed ELISA with its various sensitive variants. Over the last decade, nucleic acid-based molecular methods have gained popularity and have quickly replaced other techniques, such as serological techniques for detecting plant viruses due to their specificity and accuracy. Hence, this review enables the reader to understand the strengths and weaknesses of each molecular technique starting with PCR and its variations, along with various isothermal amplification followed by DNA microarrays, and next-generation sequencing (NGS). As a result of the development of new technologies, NGS is becoming more and more accessible and cheaper, and it looks possible that this approach will replace others as a favoured approach for carrying out regular diagnosis. NGS is also becoming the method of choice for identifying novel viruses. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-024-00863-0.
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Affiliation(s)
- Subha Deep Roy
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu India
- School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | | | - Jagan M. Obbineni
- School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu India
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14
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Chernyshova AI, Zhirnov OP. Two Phylogenetic Cohorts of the Nucleocapsid Protein NP and Their Correlation with the Host Range of Influenza A Viruses. DOKL BIOCHEM BIOPHYS 2024; 516:93-97. [PMID: 38539009 DOI: 10.1134/s1607672924700789] [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: 12/10/2023] [Revised: 01/24/2024] [Accepted: 01/28/2024] [Indexed: 05/26/2024]
Abstract
Influenza A virus has a wide natural areal among birds, mammals, and humans. One of the main regulatory adaptors of the virus host range is the major NP protein of the viral nucleocapsid. Phylogenetic analysis of the NP protein of different viruses has revealed the existence of two phylogenetic cohorts in human influenza virus population. Cohort I includes classical human viruses that caused epidemics in 1957, 1968, 1977. Cohort II includes the H1N1/2009pdm virus, which had a mixed avian-swine origin but caused global human pandemic. Also, the highly virulent H5N1 avian influenza virus emerged in 2021 and caused outbreaks of lethal infections in mammals including humans, appeared to have the NP gene of the second phylogenetic cohort and, therefore, by the type of adaptation to human is similar to the H1N1/2009pdm virus and seems to possess a high epidemic potential for humans. The data obtained shed light on pathways and dynamics of adaptation of avian influenza viruses to humans and propose phylogenetic algorithm for systemic monitoring of dangerous virus strains to predict epidemic harbingers and take immediate preventive measures.
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Affiliation(s)
- A I Chernyshova
- Ivanovsky Institute of Virology, Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - O P Zhirnov
- Ivanovsky Institute of Virology, Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.
- Russian-German Academy of Medico-Social and Biotechnological Sciences, Skolkovo Innovation Center, Moscow, Russia.
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15
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Ke Z, Wen J, Wang Y, Li B, Wu S, Zhang D, Mo X, Li Y, Ren Y, Yin J, Shi C, Wang Q, Zheng S. Interferon regulatory factors inhibit TiLV replication by activating interferon-a3 in tilapia (Oreochromis niloticus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 155:105152. [PMID: 38408717 DOI: 10.1016/j.dci.2024.105152] [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: 10/17/2023] [Revised: 02/05/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
Tilapia lake virus (TiLV) is an emerging virus that seriously threatens the tilapia industries worldwide. Interferon regulatory factors (IRFs), which are the crucial mediators regulating the response of interferon (IFN) to combat invading viruses, have not yet been reported in tilapia during TiLV infection. Here, six IRF (IRF1, IRF2, IRF4, IRF7, IRF8, and IRF9) homologs from tilapia were characterized and analyzed. These IRFs typically shared the conserved domains and phylogenetic relationship with IRF homologs of other species. Tissue distribution analysis showed that all six IRF genes were expressed in various tissues, with the highest expression in immune-related tissues. Furthermore, overexpression of IRFs in tilapia brain (TiB) cells significantly inhibited TiLV propagation, as evidenced by decreased viral segment 8 gene transcripts and copy numbers of viral segment 1. More importantly, all six IRF genes significantly enhanced the promoter activity of type I interferon-a3 (IFNa3) in TiB cells, suggesting that tilapia IRF genes serve as positive regulators in activating IFNa3. Surprisingly, the promoter activity of IFNa3 mediated by IRF genes was markedly inhibited post-TiLV infection, indicating that TiLV antagonized IRF-mediated IFN immune response. Taken together, six IRF genes of tilapia are highly conserved transcription factors that inhibit TiLV infection by activating the promoter of IFNa3, which is in turn restrained by TiLV. These findings broaden our knowledge about the functionality of IRF-mediated antiviral immunity in tilapia against TiLV infection and host-TiLV interaction, which lays a foundation for developing antiviral strategies in tilapia cultural industries.
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Affiliation(s)
- Zishan Ke
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, 510380, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Jing Wen
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, 510380, China
| | - Yingying Wang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, 510380, China
| | - Bo Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, 510380, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Siyu Wu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Defeng Zhang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, 510380, China
| | - Xubing Mo
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, 510380, China
| | - Yingying Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, 510380, China
| | - Yan Ren
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, 510380, China
| | - Jiyuan Yin
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, 510380, China
| | - Cunbin Shi
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, 510380, China
| | - Qing Wang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, 510380, China.
| | - Shucheng Zheng
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, 510380, China; State Key Laboratory of Marine Pollution, Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong Special Administrative Region of China.
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16
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Lu X, Dai Z, Xue J, Li W, Ni P, Xu J, Zhou C, Zhang W. Discovery of novel RNA viruses through analysis of fungi-associated next-generation sequencing data. BMC Genomics 2024; 25:517. [PMID: 38797853 PMCID: PMC11129472 DOI: 10.1186/s12864-024-10432-w] [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: 03/19/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Like all other species, fungi are susceptible to infection by viruses. The diversity of fungal viruses has been rapidly expanding in recent years due to the availability of advanced sequencing technologies. However, compared to other virome studies, the research on fungi-associated viruses remains limited. RESULTS In this study, we downloaded and analyzed over 200 public datasets from approximately 40 different Bioprojects to explore potential fungal-associated viral dark matter. A total of 12 novel viral sequences were identified, all of which are RNA viruses, with lengths ranging from 1,769 to 9,516 nucleotides. The amino acid sequence identity of all these viruses with any known virus is below 70%. Through phylogenetic analysis, these RNA viruses were classified into different orders or families, such as Mitoviridae, Benyviridae, Botourmiaviridae, Deltaflexiviridae, Mymonaviridae, Bunyavirales, and Partitiviridae. It is possible that these sequences represent new taxa at the level of family, genus, or species. Furthermore, a co-evolution analysis indicated that the evolutionary history of these viruses within their groups is largely driven by cross-species transmission events. CONCLUSIONS These findings are of significant importance for understanding the diversity, evolution, and relationships between genome structure and function of fungal viruses. However, further investigation is needed to study their interactions.
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Affiliation(s)
- Xiang Lu
- Institute of Critical Care Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212002, China
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Ziyuan Dai
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People's Hospital, Yancheng, Jiangsu, China
| | - Jiaxin Xue
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wang Li
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China
| | - Ping Ni
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China
| | - Juan Xu
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China.
| | - Chenglin Zhou
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China.
| | - Wen Zhang
- Institute of Critical Care Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212002, China.
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, 225300, China.
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17
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Luigi M, Tiberini A, Taglienti A, Bertin S, Dragone I, Sybilska A, Tarchi F, Goggioli D, Lewandowski M, Simoni S, Faggioli F. Molecular Methods for the Simultaneous Detection of Tomato Fruit Blotch Virus and Identification of Tomato Russet Mite, a New Potential Virus-Vector System Threatening Solanaceous Crops Worldwide. Viruses 2024; 16:806. [PMID: 38793687 PMCID: PMC11126101 DOI: 10.3390/v16050806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Tomato fruit blotch virus (ToFBV) (Blunervirus solani, family Kitaviridae) was firstly identified in Italy in 2018 in tomato plants that showed the uneven, blotchy ripening and dimpling of fruits. Subsequent High-Throughput Sequencing (HTS) analysis allowed ToFBV to be identified in samples collected in Australia, Brazil, and several European countries, and its presence in tomato crops was dated back to 2012. In 2023, the virus was found to be associated with two outbreaks in Italy and Belgium, and it was included in the EPPO Alert list as a potential new threat for tomato fruit production. Many epidemiologic features of ToFBV need to be still clarified, including transmission. Aculops lycopersici Massee (Acariformes: Eriophyoidea), the tomato russet mite (TRM), is a likely candidate vector, since high population densities were found in most of the ToFBV-infected tomato cultivations worldwide. Real-time RT-PCR tests for ToFBV detection and TRM identification were developed, also as a duplex assay. The optimized tests were then transferred to an RT-ddPCR assay and validated according to the EPPO Standard PM 7/98 (5). Such sensitive, reliable, and validated tests provide an important diagnostic tool in view of the probable threat posed by this virus-vector system to solanaceous crops worldwide and can contribute to epidemiological studies by simplifying the efficiency of research. To our knowledge, these are the first molecular methods developed for the simultaneous detection and identification of ToFBV and TRM.
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Affiliation(s)
- Marta Luigi
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification, Via C.G. Bertero 22, 00156 Rome, Italy
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification, Via C.G. Bertero 22, 00156 Rome, Italy
| | - Anna Taglienti
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification, Via C.G. Bertero 22, 00156 Rome, Italy
| | - Sabrina Bertin
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification, Via C.G. Bertero 22, 00156 Rome, Italy
| | - Immacolata Dragone
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification, Via C.G. Bertero 22, 00156 Rome, Italy
| | - Anna Sybilska
- Department of Plant Protection, Warsaw University of Life Sciences, Nowoursynowska St. 159, 02-776 Warsaw, Poland
| | - Franca Tarchi
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification, Via Lanciola 12/a, 50125 Firenze, Italy
| | - Donatella Goggioli
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification, Via Lanciola 12/a, 50125 Firenze, Italy
| | - Mariusz Lewandowski
- Department of Plant Protection, Warsaw University of Life Sciences, Nowoursynowska St. 159, 02-776 Warsaw, Poland
| | - Sauro Simoni
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification, Via Lanciola 12/a, 50125 Firenze, Italy
| | - Francesco Faggioli
- Council for Agricultural Research and Economics, Research Centre for Plant Protection and Certification, Via C.G. Bertero 22, 00156 Rome, Italy
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18
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Zhirnov OP, Lvov DK. Avian flu: «for whom the bell tolls»? Vopr Virusol 2024; 69:101-118. [PMID: 38843017 DOI: 10.36233/10.36233/0507-4088-213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Indexed: 06/14/2024]
Abstract
The family Orthomyxoviridae consists of 9 genera, including Alphainfluenzavirus, which contains avian influenza viruses. In two subtypes H5 and H7 besides common low-virulent strains, a specific type of highly virulent avian virus have been described to cause more than 60% mortality among domestic birds. These variants of influenza virus are usually referred to as «avian influenza virus». The difference between high (HPAI) and low (LPAI) virulent influenza viruses is due to the structure of the arginine-containing proteolytic activation site in the hemagglutinin (HA) protein. The highly virulent avian influenza virus H5 was identified more than 100 years ago and during this time they cause outbreaks among wild and domestic birds on all continents and only a few local episodes of the disease in humans have been identified in XXI century. Currently, a sharp increase in the incidence of highly virulent virus of the H5N1 subtype (clade h2.3.4.4b) has been registered in birds on all continents, accompanied by the transmission of the virus to various species of mammals. The recorded global mortality rate among wild, domestic and agricultural birds from H5 subtype is approaching to the level of 1 billion cases. A dangerous epidemic factor is becoming more frequent outbreaks of avian influenza with high mortality among mammals, in particular seals and marine lions in North and South America, minks and fur-bearing animals in Spain and Finland, domestic and street cats in Poland. H5N1 avian influenza clade h2.3.4.4b strains isolated from mammals have genetic signatures of partial adaptation to the human body in the PB2, NP, HA, NA genes, which play a major role in regulating the aerosol transmission and the host range of the virus. The current situation poses a real threat of pre-adaptation of the virus in mammals as intermediate hosts, followed by the transition of the pre-adapted virus into the human population with catastrophic consequences.
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Affiliation(s)
- O P Zhirnov
- The D.I. Ivaovsky Institute of Virology, The N.F. Gamaleya Research Center of Epidemiology and Microbiology, The Russian Ministry of Health
- The Russian-German Academy of Medical-Social and Biotechnological Sciences, Skolkovo Innovation Center
| | - D K Lvov
- The D.I. Ivaovsky Institute of Virology, The N.F. Gamaleya Research Center of Epidemiology and Microbiology, The Russian Ministry of Health
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19
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Graziosi G, Lupini C, Catelli E, Carnaccini S. Highly Pathogenic Avian Influenza (HPAI) H5 Clade 2.3.4.4b Virus Infection in Birds and Mammals. Animals (Basel) 2024; 14:1372. [PMID: 38731377 PMCID: PMC11083745 DOI: 10.3390/ani14091372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Avian influenza viruses (AIVs) are highly contagious respiratory viruses of birds, leading to significant morbidity and mortality globally and causing substantial economic losses to the poultry industry and agriculture. Since their first isolation in 2013-2014, the Asian-origin H5 highly pathogenic avian influenza viruses (HPAI) of clade 2.3.4.4b have undergone unprecedented evolution and reassortment of internal gene segments. In just a few years, it supplanted other AIV clades, and now it is widespread in the wild migratory waterfowl, spreading to Asia, Europe, Africa, and the Americas. Wild waterfowl, the natural reservoir of LPAIVs and generally more resistant to the disease, also manifested high morbidity and mortality with HPAIV clade 2.3.4.4b. This clade also caused overt clinical signs and mass mortality in a variety of avian and mammalian species never reported before, such as raptors, seabirds, sealions, foxes, and others. Most notably, the recent outbreaks in dairy cattle were associated with the emergence of a few critical mutations related to mammalian adaptation, raising concerns about the possibility of jumping species and acquisition of sustained human-to-human transmission. The main clinical signs and anatomopathological findings associated with clade 2.3.4.4b virus infection in birds and non-human mammals are hereby summarized.
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Affiliation(s)
- Giulia Graziosi
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell’Emilia, 40064 Bologna, Italy; (G.G.); (C.L.); (E.C.)
| | - Caterina Lupini
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell’Emilia, 40064 Bologna, Italy; (G.G.); (C.L.); (E.C.)
| | - Elena Catelli
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell’Emilia, 40064 Bologna, Italy; (G.G.); (C.L.); (E.C.)
| | - Silvia Carnaccini
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
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20
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Cook R, Crisci MA, Pye HV, Telatin A, Adriaenssens EM, Santini JM. Decoding huge phage diversity: a taxonomic classification of Lak megaphages. J Gen Virol 2024; 105:001997. [PMID: 38814706 PMCID: PMC11165621 DOI: 10.1099/jgv.0.001997] [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: 02/01/2024] [Accepted: 05/21/2024] [Indexed: 05/31/2024] Open
Abstract
High-throughput sequencing for uncultivated viruses has accelerated the understanding of global viral diversity and uncovered viral genomes substantially larger than any that have so far been cultured. Notably, the Lak phages are an enigmatic group of viruses that present some of the largest known phage genomes identified in human and animal microbiomes, and are dissimilar to any cultivated viruses. Despite the wealth of viral diversity that exists within sequencing datasets, uncultivated viruses have rarely been used for taxonomic classification. We investigated the evolutionary relationships of 23 Lak phages and propose a taxonomy for their classification. Predicted protein analysis revealed the Lak phages formed a deeply branching monophyletic clade within the class Caudoviricetes which contained no other phage genomes. One of the interesting features of this clade is that all current members are characterised by an alternative genetic code. We propose the Lak phages belong to a new order, the 'Grandevirales'. Protein and nucleotide-based analyses support the creation of two families, three sub-families, and four genera within the order 'Grandevirales'. We anticipate that the proposed taxonomy of Lak megaphages will simplify the future classification of related viral genomes as they are uncovered. Continued efforts to classify divergent viruses are crucial to aid common analyses of viral genomes and metagenomes.
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Affiliation(s)
- Ryan Cook
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Marco A. Crisci
- Department of Structural and Molecular Biology, Division of Biosciences, UCL, London, UK
| | - Hannah V. Pye
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Andrea Telatin
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Joanne M. Santini
- Department of Structural and Molecular Biology, Division of Biosciences, UCL, London, UK
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21
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Tan CCS, van Dorp L, Balloux F. The evolutionary drivers and correlates of viral host jumps. Nat Ecol Evol 2024; 8:960-971. [PMID: 38528191 DOI: 10.1038/s41559-024-02353-4] [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: 01/11/2024] [Accepted: 01/29/2024] [Indexed: 03/27/2024]
Abstract
Most emerging and re-emerging infectious diseases stem from viruses that naturally circulate in non-human vertebrates. When these viruses cross over into humans, they can cause disease outbreaks, epidemics and pandemics. While zoonotic host jumps have been extensively studied from an ecological perspective, little attention has gone into characterizing the evolutionary drivers and correlates underlying these events. To address this gap, we harnessed the entirety of publicly available viral genomic data, employing a comprehensive suite of network and phylogenetic analyses to investigate the evolutionary mechanisms underpinning recent viral host jumps. Surprisingly, we find that humans are as much a source as a sink for viral spillover events, insofar as we infer more viral host jumps from humans to other animals than from animals to humans. Moreover, we demonstrate heightened evolution in viral lineages that involve putative host jumps. We further observe that the extent of adaptation associated with a host jump is lower for viruses with broader host ranges. Finally, we show that the genomic targets of natural selection associated with host jumps vary across different viral families, with either structural or auxiliary genes being the prime targets of selection. Collectively, our results illuminate some of the evolutionary drivers underlying viral host jumps that may contribute to mitigating viral threats across species boundaries.
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Affiliation(s)
- Cedric C S Tan
- UCL Genetics Institute, University College London, London, UK.
- The Francis Crick Institute, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
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22
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Li C, Yang W, Zhang Y, Zhu F, Qiu Y, Du L, Lin F, Lan Y, Xu K, Zhou T. Investigation and characterization of rice dwarfing epidemic caused by southern rice black-streaked dwarf virus in Jiangsu in 2023. Virology 2024; 593:110027. [PMID: 38417251 DOI: 10.1016/j.virol.2024.110027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 03/01/2024]
Abstract
During the field surveys in Jiangsu Province, China, contiguous patches of rice plants with varying degrees of dwarfing, wax-white or dark brown enations at the base of stems, and abnormal heading symptoms were observed in the fields located in Jiangning District in Nanjing City, Jurong County in Zhenjiang City, and Zhangjiagang County in Suzhou City. Through molecular analyses, the presence of southern rice black-streaked dwarf virus was confirmed in symptomatic rice plants. The infections of other rice viruses that cause dwarfing were also ruled out. Additionally, Koch's postulates were fulfilled, further validating SRBSDV as the causal agent for the observed dwarfing disease epidemic. Furthermore, the phylogenetic analyses revealed that the SRBSDV prevalent in Jiangsu in 2023 may originate from multiple regions in Vietnam. Our study has documented the emergence of an SRBSDV epidemic in Jiangsu in 2023, marking the first incidence of southern rice black-streaked dwarf disease in this region.
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Affiliation(s)
- Chenyang Li
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Wenxuan Yang
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yuanming Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Feng Zhu
- Jiangsu Station of Plant Protection and Quarantine, Nanjing 210014, Jiangsu, China
| | - Yanglin Qiu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Linlin Du
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Feng Lin
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Ying Lan
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Kai Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Tong Zhou
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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23
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Lauber C, Zhang X, Vaas J, Klingler F, Mutz P, Dubin A, Pietschmann T, Roth O, Neuman BW, Gorbalenya AE, Bartenschlager R, Seitz S. Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates. PLoS Pathog 2024; 20:e1012163. [PMID: 38648214 PMCID: PMC11065284 DOI: 10.1371/journal.ppat.1012163] [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: 08/25/2023] [Revised: 05/02/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
Virus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization of pathogen epidemiology, and redefined our understanding of the natural genetic diversity of viruses with profound functional and structural implications. Here we employed a data-driven virus discovery approach that directly queries unprocessed sequencing data in a highly parallelized way and involves a targeted viral genome assembly strategy in a wide range of sequence similarity. By screening more than 269,000 datasets of numerous authors from the Sequence Read Archive and using two metrics that quantitatively assess assembly quality, we discovered 40 nidoviruses from six virus families whose members infect vertebrate hosts. They form 13 and 32 putative viral subfamilies and genera, respectively, and include 11 coronaviruses with bisegmented genomes from fishes and amphibians, a giant 36.1 kilobase coronavirus genome with a duplicated spike glycoprotein (S) gene, 11 tobaniviruses and 17 additional corona-, arteri-, cremega-, nanhypo- and nangoshaviruses. Genome segmentation emerged in a single evolutionary event in the monophyletic lineage encompassing the subfamily Pitovirinae. We recovered the bisegmented genome sequences of two coronaviruses from RNA samples of 69 infected fishes and validated the presence of poly(A) tails at both segments using 3'RACE PCR and subsequent Sanger sequencing. We report a genetic linkage between accessory and structural proteins whose phylogenetic relationships and evolutionary distances are incongruent with the phylogeny of replicase proteins. We rationalize these observations in a model of inter-family S recombination involving at least five ancestral corona- and tobaniviruses of aquatic hosts. In support of this model, we describe an individual fish co-infected with members from the families Coronaviridae and Tobaniviridae. Our results expand the scale of the known extraordinary evolutionary plasticity in nidoviral genome architecture and call for revisiting fundamentals of genome expression, virus particle biology, host range and ecology of vertebrate nidoviruses.
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Affiliation(s)
- 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
- Cluster of Excellence 2155 RESIST, Hannover, Germany
| | - Xiaoyu Zhang
- 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
| | - Josef Vaas
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Franziska Klingler
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Pascal Mutz
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Arseny Dubin
- Marine Evolutionary Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Thomas Pietschmann
- 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
- Cluster of Excellence 2155 RESIST, Hannover, Germany
| | - Olivia Roth
- Marine Evolutionary Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Benjamin W. Neuman
- Department of Biology and Texas A&M Global Health Research Complex, Texas A&M University, College Station, Texas, United States
| | - Alexander E. Gorbalenya
- Leiden University Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ralf Bartenschlager
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
| | - Stefan Seitz
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, Heidelberg, Germany
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24
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Zheng X, Li Y, Liu Y. Plant Immunity against Tobamoviruses. Viruses 2024; 16:530. [PMID: 38675873 PMCID: PMC11054417 DOI: 10.3390/v16040530] [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: 03/01/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Tobamoviruses are a group of plant viruses that pose a significant threat to agricultural crops worldwide. In this review, we focus on plant immunity against tobamoviruses, including pattern-triggered immunity (PTI), effector-triggered immunity (ETI), the RNA-targeting pathway, phytohormones, reactive oxygen species (ROS), and autophagy. Further, we highlight the genetic resources for resistance against tobamoviruses in plant breeding and discuss future directions on plant protection against tobamoviruses.
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Affiliation(s)
- Xiyin Zheng
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yiqing Li
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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25
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Ngoepe CE, Shumba W, Sabeta C. Evidence for a host switching in the maintenance of canid rabies variant in two wild carnivore species in the Northern Cape Province, South Africa. J S Afr Vet Assoc 2024; 95:16-25. [PMID: 38533811 DOI: 10.36303/jsava.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Rabies is a zoonotic infectious disease that causes at least 59 000 human deaths worldwide annually, with 95% of the cases occurring in the developing countries of Asia and Africa. There are two Lyssavirus rabies (RABV) variants circulating in South Africa, notably the canid and mongoose RABV biotypes. The canid RABV biotype is maintained in the domestic dog and two wild carnivore species, the black-backed jackal (Canis mesomelas) and the bat-eared fox (Otocyon megalotis). The yellow mongoose, a member of the Herpestidae family, is a reservoir and vector species for the mongoose RABV biotype. Rabies trends showed an increase in rabiespositive cases in aardwolves between 2011 and 2016 surpassing the bat-eared fox as the most rabies-affected wild carnivore in the Northern Cape Province of South Africa. The aim of the study was to establish the genetic relationships amongst rabies viruses recovered from both the aardwolves and bat-eared foxes. A partial region of the glycoprotein gene and the variable G-L intergenic region of the viral genome were analysed using nucleotide sequences generated from PCR amplicons. The rabies viruses recovered from the aardwolves between the year 2015 and 2017 were 100% nucleotide sequence identical, suggesting a single or common source and possible evidence for a host shift. Furthermore, the phylogenetic reconstruction demonstrated that the rabies viruses obtained from the two wild carnivore species from the Northern Cape Province clustered independently of each o ther with 96% nucleotide sequence identity, suggesting that the aardwolf may be able to maintain the canid RABV variant in this geographical area.
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Affiliation(s)
- C E Ngoepe
- WOAH Rabies Reference Laboratory, Agricultural Research Council, Onderstepoort Veterinary Research, South Africa
| | - W Shumba
- Epidemiology and Laboratory Services, Northern Cape Department of Agriculture, Environmental Affairs, Rural Development and Land Reform, South Africa
| | - C Sabeta
- WOAH Rabies Reference Laboratory, Agricultural Research Council, Onderstepoort Veterinary Research, South Africa
- Department of Veterinary Tropical Diseases, University of Pretoria, South Africa
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26
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Chamera S, Wycisk K, Czarnocki-Cieciura M, Nowotny M. Cryo-EM structure of rotavirus B NSP2 reveals its unique tertiary architecture. J Virol 2024; 98:e0166023. [PMID: 38421167 PMCID: PMC10949507 DOI: 10.1128/jvi.01660-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
Rotavirus (RV) NSP2 is a multifunctional RNA chaperone that exhibits numerous activities that are essential for replication and viral genome packaging. We performed an in silico analysis that highlighted a distant relationship of NSP2 from rotavirus B (RVB) to proteins from other human RVs. We solved a cryo-electron microscopy structure of RVB NSP2 that shows structural differences with corresponding proteins from other human RVs. Based on the structure, we identified amino acid residues that are involved in RNA interactions. Anisotropy titration experiments showed that these residues are important for nucleic acid binding. We also identified structural motifs that are conserved in all RV species. Collectively, our data complete the structural characterization of rotaviral NSP2 protein and demonstrate its structural diversity among RV species.IMPORTANCERotavirus B (RVB), also known as adult diarrhea rotavirus, has caused epidemics of severe diarrhea in China, India, and Bangladesh. Thousands of people are infected in a single RVB epidemic. However, information on this group of rotaviruses remains limited. As NSP2 is an essential protein in the viral life cycle, including its role in the formation of replication factories, it may be a target for future antiviral strategy against viruses with similar mechanisms.
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Affiliation(s)
- Sebastian Chamera
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Krzysztof Wycisk
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
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27
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Nandudu L, Strock C, Ogbonna A, Kawuki R, Jannink JL. Genetic analysis of cassava brown streak disease root necrosis using image analysis and genome-wide association studies. FRONTIERS IN PLANT SCIENCE 2024; 15:1360729. [PMID: 38562560 PMCID: PMC10982329 DOI: 10.3389/fpls.2024.1360729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
Cassava brown streak disease (CBSD) poses a substantial threat to food security. To address this challenge, we used PlantCV to extract CBSD root necrosis image traits from 320 clones, with an aim of identifying genomic regions through genome-wide association studies (GWAS) and candidate genes. Results revealed strong correlations among certain root necrosis image traits, such as necrotic area fraction and necrotic width fraction, as well as between the convex hull area of root necrosis and the percentage of necrosis. Low correlations were observed between CBSD scores obtained from the 1-5 scoring method and all root necrosis traits. Broad-sense heritability estimates of root necrosis image traits ranged from low to moderate, with the highest estimate of 0.42 observed for the percentage of necrosis, while narrow-sense heritability consistently remained low, ranging from 0.03 to 0.22. Leveraging data from 30,750 SNPs obtained through DArT genotyping, eight SNPs on chromosomes 1, 7, and 11 were identified and associated with both the ellipse eccentricity of root necrosis and the percentage of necrosis through GWAS. Candidate gene analysis in the 172.2kb region on the chromosome 1 revealed 24 potential genes with diverse functions, including ubiquitin-protein ligase, DNA-binding transcription factors, and RNA metabolism protein, among others. Despite our initial expectation that image analysis objectivity would yield better heritability estimates and stronger genomic associations than the 1-5 scoring method, the results were unexpectedly lower. Further research is needed to comprehensively understand the genetic basis of these traits and their relevance to cassava breeding and disease management.
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Affiliation(s)
- Leah Nandudu
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
- Root Crops Department, National Crops Resources Research Institute (NaCRRI), Kampala, Uganda
| | - Christopher Strock
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Alex Ogbonna
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Robert Kawuki
- Root Crops Department, National Crops Resources Research Institute (NaCRRI), Kampala, Uganda
| | - Jean-Luc Jannink
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
- US Department of Agriculture, Agricultural Research Service (USDA-ARS), Ithaca, NY, United States
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28
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Tarakanov RI, Evseev PV, Vo HTN, Troshin KS, Gutnik DI, Ignatov AN, Toshchakov SV, Miroshnikov KA, Jafarov IH, Dzhalilov FSU. Xanthomonas Phage PBR31: Classifying the Unclassifiable. Viruses 2024; 16:406. [PMID: 38543771 PMCID: PMC10975493 DOI: 10.3390/v16030406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/24/2024] [Accepted: 03/04/2024] [Indexed: 05/23/2024] Open
Abstract
The ability of bacteriophages to destroy bacteria has made them the subject of extensive research. Interest in bacteriophages has recently increased due to the spread of drug-resistant bacteria, although genomic research has not kept pace with the growth of genomic data. Genomic analysis and, especially, the taxonomic description of bacteriophages are often difficult due to the peculiarities of the evolution of bacteriophages, which often includes the horizontal transfer of genes and genomic modules. The latter is particularly pronounced for temperate bacteriophages, which are capable of integration into the bacterial chromosome. Xanthomonas phage PBR31 is a temperate bacteriophage, which has been neither described nor classified previously, that infects the plant pathogen Xanthomonas campestris pv. campestris. Genomic analysis, including phylogenetic studies, indicated the separation of phage PBR31 from known classified bacteriophages, as well as its distant relationship with other temperate bacteriophages, including the Lederbervirus group. Bioinformatic analysis of proteins revealed distinctive features of PBR31, including the presence of a protein similar to the small subunit of D-family DNA polymerase and advanced lysis machinery. Taxonomic analysis showed the possibility of assigning phage PBR31 to a new taxon, although the complete taxonomic description of Xanthomonas phage PBR31 and other related bacteriophages is complicated by the complex evolutionary history of the formation of its genome. The general biological features of the PBR31 phage were analysed for the first time. Due to its presumably temperate lifestyle, there is doubt as to whether the PBR31 phage is appropriate for phage control purposes. Bioinformatics analysis, however, revealed the presence of cell wall-degrading enzymes that can be utilised for the treatment of bacterial infections.
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Affiliation(s)
- Rashit I. Tarakanov
- Department of Plant Protection, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (K.S.T.)
| | - Peter V. Evseev
- Department of Plant Protection, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (K.S.T.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Laboratory of Molecular Microbiology, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Ha T. N. Vo
- Faculty of Agronomy, Nong Lam University, Quarter 6, Thu Duc District, Ho Chi Minh City 721400, Vietnam
| | - Konstantin S. Troshin
- Department of Plant Protection, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (K.S.T.)
| | - Daria I. Gutnik
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia;
| | - Aleksandr N. Ignatov
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str. 6, 117198 Moscow, Russia;
| | - Stepan V. Toshchakov
- Center for Genome Research, National Research Center “Kurchatov Institute”, Kurchatov Sq., 1, 123098 Moscow, Russia
| | - Konstantin A. Miroshnikov
- Department of Plant Protection, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (K.S.T.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Ibrahim H. Jafarov
- Azerbaijan Scientific Research Institute for Plant Protection and Industrial Crops, AZ 4200 Ganja, Azerbaijan
| | - Fevzi S.-U. Dzhalilov
- Department of Plant Protection, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (K.S.T.)
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29
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Flynn TG, Olortegui MP, Kosek MN. Viral gastroenteritis. Lancet 2024; 403:862-876. [PMID: 38340741 DOI: 10.1016/s0140-6736(23)02037-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/17/2023] [Accepted: 09/18/2023] [Indexed: 02/12/2024]
Abstract
Since the discovery of norovirus in 1972 as a cause of what was contemporarily known as acute infectious non-bacterial gastroenteritis, scientific understanding of the viral gastroenteritides has continued to evolve. It is now recognised that a small number of viruses are the predominant cause of acute gastroenteritis worldwide, in both high-income and low-income settings. Although treatment is still largely restricted to the replacement of fluid and electrolytes, improved diagnostics have allowed attribution of illness, enabling both targeted treatment of individual patients and prioritisation of interventions for populations worldwide. Questions remain regarding specific genetic and immunological factors underlying host susceptibility, and the optimal clinical management of patients who are susceptible to severe or prolonged manifestations of disease. Meanwhile, the worldwide implementation of rotavirus vaccines has led to substantial reductions in morbidity and mortality, and spurred interest in vaccine development to diminish the impact of the most prevalent viruses that are implicated in this syndrome.
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Affiliation(s)
- Thomas G Flynn
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | | | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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30
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Workman AM, Harhay GP, Groves JT, Vander Ley BL. Two bovine hepacivirus genome sequences from U.S. cattle. J Vet Diagn Invest 2024; 36:274-277. [PMID: 38414254 DOI: 10.1177/10406387231225656] [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] [Indexed: 02/29/2024] Open
Abstract
Bovine hepacivirus (BoHV) is closely related to the hepatitis C virus (HCV) in humans and can cause both acute and chronic liver infections in cattle. BoHV was first identified in Ghana and Germany in 2015 and since then it has been detected and characterized in other countries around the world, but no strains have been sequenced from U.S. cattle. To date, BoHV has been classified into 2 genotypes (1 and 2), with genotype 1 being further divided into 11 subtypes (A-K). However, the true genetic diversity of BoHV is likely underestimated given limited surveillance and a lack of published genome sequences. Here, we sequenced 2 nearly complete BoHV genomes from serum samples collected in 2019 from beef cattle in Missouri. Sequence comparisons and phylogenetic analysis showed that isolate MARC/2019/60 had high sequence homology with genotype 1, subtype E isolates from China. In contrast, isolate MARC/2019/50 represented a novel BoHV subtype within genotype 2. Thus, we report the first genomic characterization of BoHV isolates from U.S. cattle, and the second complete BoHV2 genome worldwide. This work increases our knowledge of the global genetic diversity of BoHV and demonstrates the co-circulation of divergent BoHV strains in U.S. cattle.
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Affiliation(s)
- Aspen M Workman
- U.S. Meat Animal Research Center, U.S. Department of Agriculture, Agricultural Research Service, Clay Center, NE, USA
| | - Gregory P Harhay
- U.S. Meat Animal Research Center, U.S. Department of Agriculture, Agricultural Research Service, Clay Center, NE, USA
| | | | - Brian L Vander Ley
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, NE, USA
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Chen L, Banfield JF. COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes. Nat Microbiol 2024; 9:737-750. [PMID: 38321183 PMCID: PMC10914622 DOI: 10.1038/s41564-023-01598-2] [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: 06/06/2023] [Accepted: 12/19/2023] [Indexed: 02/08/2024]
Abstract
Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.
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Affiliation(s)
- LinXing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Environmental Science Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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32
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Chen M, Xia Y, Wang Q. Identification and molecular characterization of a novel totivirus from Mangifera indica. Arch Virol 2024; 169:58. [PMID: 38424260 DOI: 10.1007/s00705-024-06001-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/20/2024] [Indexed: 03/02/2024]
Abstract
In this study, we determined the complete genome sequence of a novel totivirus, tentatively named "Mangifera indica totivirus 1" (MiTV1), identified in 'Apple' mango in China. The double-stranded RNA genome of MiTV1 is 4800 base pairs (bp) in length and contains two open reading frames (ORFs) encoding a putative coat protein (CP) and an RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis based on RdRp and CP amino acid sequences showed that MiTV1 is closely related to members of the genus Totivirus in the family Totiviridae. To our knowledge, this is the first report of a totivirus found in Mangifera indica.
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Affiliation(s)
- Mengyi Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510316, China
| | - Yujia Xia
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products/ Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs of China, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, 524000, China
- South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Qihua Wang
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products/ Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs of China, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, 524000, China.
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33
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Feng L, Chen H, Qian C, Zhao Y, Wang W, Liu Y, Xu M, Cao J, Zhou T, Wu Q. Resistance, mechanism, and fitness cost of specific bacteriophages for Pseudomonas aeruginosa. mSphere 2024; 9:e0055323. [PMID: 38299825 PMCID: PMC10900902 DOI: 10.1128/msphere.00553-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/20/2023] [Indexed: 02/02/2024] Open
Abstract
The bacteriophage is an effective adjunct to existing antibiotic therapy; however, in the course of bacteriophage therapy, host bacteria will develop resistance to bacteriophages, thus affecting the efficacy. Therefore, it is important to describe how bacteria evade bacteriophage attack and the consequences of the biological changes that accompany the development of bacteriophage resistance before the bacteriophage is applied. The specific bacteriophage vB3530 of Pseudomonas aeruginosa (P. aeruginosa) has stable biological characteristics, short incubation period, strong in vitro cleavage ability, and absence of virulence or resistance genes. Ten bacteriophage-resistant strains (TL3780-R) were induced using the secondary infection approach, and the plaque assay showed that vB3530 was less sensitive to TL3780-R. Identification of bacteriophage adsorption receptors showed that the bacterial surface polysaccharide was probably the adsorption receptor of vB3530. In contrast to the TL3780 parental strain, TL3780-R is characterized by the absence of long lipopolysaccharide chains, which may be caused by base insertion of wzy or deletion of galU. It is also intriguing to observe that, in comparison to the parent strain, the bacteriophage-resistant strains TL3780-R mostly exhibited a large cost of fitness (growth rate, biofilm formation, motility, and ability to produce enhanced pyocyanin). In addition, TL3780-R9 showed increased susceptibility to aminoglycosides and chlorhexidine, which may be connected to the loss and down-regulation of mexX expression. Consequently, these findings fully depicted the resistance mechanism of P. aeruginosa to vB3530 and the fitness cost of bacteriophage resistance, laying a foundation for further application of bacteriophage therapy.IMPORTANCEThe bacteriophage is an effective adjunct to existing antibiotic therapy; However, bacteria also develop defensive mechanisms against bacteriophage attack. Thus, there is an urgent need to deeply understand the resistance mechanism of bacteria to bacteriophages and the fitness cost of bacteriophage resistance so as to lay the foundation for subsequent application of the phage. In this study, a specific bacteriophage vB3530 of P. aeruginosa had stable biological characteristics, short incubation period, strong in vitro cleavage ability, and absence of virulence or resistance genes. In addition, we found that P. aeruginosa may lead to phage resistance due to the deletion of galU and the base insertion of wzy, involved in the synthesis of lipopolysaccharides. Simultaneously, we showed the association with the biological state of the bacteria after bacteria acquire bacteriophage resistance, which is extremely relevant to guide the future application of therapeutic bacteriophages.
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Affiliation(s)
- Luozhu Feng
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Department of Clinical Laboratory, the First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang Province, China
| | - Huanchang Chen
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Changrui Qian
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yining Zhao
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Weixiang Wang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yan Liu
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Mengxin Xu
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jianming Cao
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Tieli Zhou
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qing Wu
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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Kamiński B, Paczesny J. Bacteriophage Challenges in Industrial Processes: A Historical Unveiling and Future Outlook. Pathogens 2024; 13:152. [PMID: 38392890 PMCID: PMC10893365 DOI: 10.3390/pathogens13020152] [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: 12/30/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Humans have used fermentation processes since the Neolithic period, mainly to produce beverages. The turning point occurred in the 1850s, when Louis Pasteur discovered that fermentation resulted from the metabolism of living microorganisms. This discovery led to the fast development of fermented food production. The importance of industrial processes based on fermentation significantly increased. Many branches of industry rely on the metabolisms of bacteria, for example, the dairy industry (cheese, milk, yogurts), pharmaceutical processes (insulin, vaccines, antibiotics), or the production of chemicals (acetone, butanol, acetic acid). These are the mass production processes involving a large financial outlay. That is why it is essential to minimize threats to production. One major threat affecting bacteria-based processes is bacteriophage infections, causing substantial economic losses. The first reported phage infections appeared in the 1930s, and companies still struggle to fight against phages. This review shows the cases of phage infections in industry and the most common methods used to prevent phage infections.
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Affiliation(s)
| | - Jan Paczesny
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
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Lamichhane B, Brockway C, Evasco K, Nicholson J, Neville PJ, Levy A, Smith D, Imrie A. Metatranscriptomic Sequencing of Medically Important Mosquitoes Reveals Extensive Diversity of RNA Viruses and Other Microbial Communities in Western Australia. Pathogens 2024; 13:107. [PMID: 38392845 PMCID: PMC10892203 DOI: 10.3390/pathogens13020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Mosquitoes harbor a wide diversity of microorganisms, including viruses that are human pathogens, or that are insect specific. We used metatranscriptomics, an unbiased high-throughput molecular approach, to describe the composition of viral and other microbial communities in six medically important mosquito species from across Western Australia: Aedes vigilax, Culex annulirostris, Cx. australicus, Cx. globocoxitus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. We identified 42 viral species, including 13 novel viruses, from 19 families. Culex mosquitoes exhibited a significantly higher diversity of viruses than Aedes mosquitoes, and no virus was shared between the two genera. Comparison of mosquito populations revealed a heterogenous distribution of viruses between geographical regions and between closely related species, suggesting that geography and host species may play a role in shaping virome composition. We also detected bacterial and parasitic microorganisms, among which Wolbachia bacteria were detected in three members of the Cx. pipiens complex, Cx. australicus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. In summary, our unbiased metatranscriptomics approach provides important insights into viral and other microbial diversity in Western Australian mosquitoes that vector medically important viruses.
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Affiliation(s)
- Binit Lamichhane
- School of Biomedical Sciences, The University of Western Australia, Nedlands, WA 6009, Australia;
| | - Craig Brockway
- Biological and Applied Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (C.B.); (K.E.); (J.N.); (P.J.N.)
| | - Kimberly Evasco
- Biological and Applied Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (C.B.); (K.E.); (J.N.); (P.J.N.)
| | - Jay Nicholson
- Biological and Applied Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (C.B.); (K.E.); (J.N.); (P.J.N.)
| | - Peter J. Neville
- Biological and Applied Environmental Health Hazards, Department of Health, Perth, WA 6000, Australia; (C.B.); (K.E.); (J.N.); (P.J.N.)
| | - Avram Levy
- PathWest Laboratory Medicine, Nedlands, WA 6009, Australia; (A.L.); (D.S.)
| | - David Smith
- PathWest Laboratory Medicine, Nedlands, WA 6009, Australia; (A.L.); (D.S.)
- UWA Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Allison Imrie
- School of Biomedical Sciences, The University of Western Australia, Nedlands, WA 6009, Australia;
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Nishimura L, Tanino A, Ajimoto M, Katsumura T, Ogawa M, Koganebuchi K, Waku D, Kumagai M, Sugimoto R, Nakaoka H, Oota H, Inoue I. Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. PLoS One 2024; 19:e0295924. [PMID: 38265980 PMCID: PMC10807776 DOI: 10.1371/journal.pone.0295924] [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: 03/08/2023] [Accepted: 12/03/2023] [Indexed: 01/26/2024] Open
Abstract
Coprolites contain various kinds of ancient DNAs derived from gut micro-organisms, viruses, and foods, which can help to determine the gut environment of ancient peoples. Their genomic information should be helpful in elucidating the interaction between hosts and microbes for thousands of years, as well as characterizing the dietary behaviors of ancient people. We performed shotgun metagenomic sequencing on four coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. The coprolites were found in the layers of the Early Jomon period, corresponding stratigraphically to 7000 to 5500 years ago. After shotgun sequencing, we found that a significant number of reads showed homology with known gut microbe, viruses, and food genomes typically found in the feces of modern humans. We detected reads derived from several types of phages and their host bacteria simultaneously, suggesting the coexistence of viruses and their hosts. The food genomes provide biological evidence for the dietary behavior of the Jomon people, consistent with previous archaeological findings. These results indicate that ancient genomic analysis of coprolites is useful for understanding the gut environment and lifestyle of ancient peoples.
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Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Akio Tanino
- Kitasato University Graduate School of Medical Sciences, Sagamihara, Kanagawa, Japan
| | | | - Takafumi Katsumura
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Motoyuki Ogawa
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Kae Koganebuchi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Daisuke Waku
- Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Tokyo, Japan
| | - Masahiko Kumagai
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Ryota Sugimoto
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, Sasaki Institute, Tokyo, Japan
| | - Hiroki Oota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
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Rozwalak P, Barylski J, Wijesekara Y, Dutilh BE, Zielezinski A. Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces. Nat Commun 2024; 15:495. [PMID: 38263397 PMCID: PMC10805732 DOI: 10.1038/s41467-023-44370-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
Bacteriophages are widely recognised as rapidly evolving biological entities. However, knowledge about ancient bacteriophages is limited. Here, we analyse DNA sequence datasets previously generated from ancient palaeofaeces and human gut-content samples, and identify an ancient phage genome nearly identical to present-day Mushuvirus mushu, a virus that infects gut commensal bacteria. The DNA damage patterns of the genome are consistent with its ancient origin and, despite 1300 years of evolution, the ancient Mushuvirus genome shares 97.7% nucleotide identity with its modern counterpart, indicating a long-term relationship between the prophage and its host. In addition, we reconstruct and authenticate 297 other phage genomes from the last 5300 years, including those belonging to unknown families. Our findings demonstrate the feasibility of reconstructing ancient phage genome sequences, thus expanding the known virosphere and offering insights into phage-bacteria interactions spanning several millennia.
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Affiliation(s)
- Piotr Rozwalak
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Jakub Barylski
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Yasas Wijesekara
- Institute of Bioinformatics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475, Greifswald, Germany
| | - 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, Science4Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
| | - Andrzej Zielezinski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, 61-614, Poland.
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38
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Olivo D, Khalifeh A, Custer JM, Kraberger S, Varsani A. Diverse Small Circular DNA Viruses Identified in an American Wigeon Fecal Sample. Microorganisms 2024; 12:196. [PMID: 38258021 PMCID: PMC10821283 DOI: 10.3390/microorganisms12010196] [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: 12/24/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
American wigeons (Mareca americana) are waterfowls that are widely distributed throughout North America. Research of viruses associated with American wigeons has been limited to orthomyxoviruses, coronaviruses, and circoviruses. To address this poor knowledge of viruses associated with American wigeons, we undertook a pilot study to identify small circular DNA viruses in a fecal sample collected in January 2021 in the city of Tempe, Arizona (USA). We identified 64 diverse circular DNA viral genomes using a viral metagenomic workflow biased towards circular DNA viruses. Of these, 45 belong to the phylum Cressdnaviricota based on their replication-associated protein sequence, with 3 from the Genomoviridae family and the remaining 42 which currently cannot be assigned to any established virus group. It is most likely that these 45 viruses infect various organisms that are associated with their diet or environment. The remaining 19 virus genomes are part of the Microviridae family and likely associated with the gut enterobacteria of American wigeons.
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Affiliation(s)
- Diego Olivo
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Anthony Khalifeh
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Joy M. Custer
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Simona Kraberger
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Arvind Varsani
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
- Structural Biology Research Unit, Department of Integrative, Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa
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Zhou K, Zhang T, Chen XW, Xu Y, Zhang R, Qian PY. Viruses in Marine Invertebrate Holobionts: Complex Interactions Between Phages and Bacterial Symbionts. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:467-485. [PMID: 37647612 DOI: 10.1146/annurev-marine-021623-093133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Marine invertebrates are ecologically and economically important and have formed holobionts by evolving symbiotic relationships with cellular and acellular microorganisms that reside in and on their tissues. In recent decades, significant focus on symbiotic cellular microorganisms has led to the discovery of various functions and a considerable expansion of our knowledge of holobiont functions. Despite this progress, our understanding of symbiotic acellular microorganisms remains insufficient, impeding our ability to achieve a comprehensive understanding of marine holobionts. In this review, we highlight the abundant viruses, with a particular emphasis on bacteriophages; provide an overview of their diversity, especially in extensively studied sponges and corals; and examine their potential life cycles. In addition, we discuss potential phage-holobiont interactions of various invertebrates, including participating in initial bacterial colonization, maintaining symbiotic relationships, and causing or exacerbating the diseases of marine invertebrates. Despite the importance of this subject, knowledge of how viruses contribute to marine invertebrate organisms remains limited. Advancements in technology and greater attention to viruses will enhance our understanding of marine invertebrate holobionts.
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Affiliation(s)
- Kun Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China;
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Ting Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Xiao-Wei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China;
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China;
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China;
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
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40
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Ligeti B, Szepesi-Nagy I, Bodnár B, Ligeti-Nagy N, Juhász J. ProkBERT family: genomic language models for microbiome applications. Front Microbiol 2024; 14:1331233. [PMID: 38282738 PMCID: PMC10810988 DOI: 10.3389/fmicb.2023.1331233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/11/2023] [Indexed: 01/30/2024] Open
Abstract
Background In the evolving landscape of microbiology and microbiome analysis, the integration of machine learning is crucial for understanding complex microbial interactions, and predicting and recognizing novel functionalities within extensive datasets. However, the effectiveness of these methods in microbiology faces challenges due to the complex and heterogeneous nature of microbial data, further complicated by low signal-to-noise ratios, context-dependency, and a significant shortage of appropriately labeled datasets. This study introduces the ProkBERT model family, a collection of large language models, designed for genomic tasks. It provides a generalizable sequence representation for nucleotide sequences, learned from unlabeled genome data. This approach helps overcome the above-mentioned limitations in the field, thereby improving our understanding of microbial ecosystems and their impact on health and disease. Methods ProkBERT models are based on transfer learning and self-supervised methodologies, enabling them to use the abundant yet complex microbial data effectively. The introduction of the novel Local Context-Aware (LCA) tokenization technique marks a significant advancement, allowing ProkBERT to overcome the contextual limitations of traditional transformer models. This methodology not only retains rich local context but also demonstrates remarkable adaptability across various bioinformatics tasks. Results In practical applications such as promoter prediction and phage identification, the ProkBERT models show superior performance. For promoter prediction tasks, the top-performing model achieved a Matthews Correlation Coefficient (MCC) of 0.74 for E. coli and 0.62 in mixed-species contexts. In phage identification, ProkBERT models consistently outperformed established tools like VirSorter2 and DeepVirFinder, achieving an MCC of 0.85. These results underscore the models' exceptional accuracy and generalizability in both supervised and unsupervised tasks. Conclusions The ProkBERT model family is a compact yet powerful tool in the field of microbiology and bioinformatics. Its capacity for rapid, accurate analyses and its adaptability across a spectrum of tasks marks a significant advancement in machine learning applications in microbiology. The models are available on GitHub (https://github.com/nbrg-ppcu/prokbert) and HuggingFace (https://huggingface.co/nerualbioinfo) providing an accessible tool for the community.
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Affiliation(s)
- Balázs Ligeti
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - István Szepesi-Nagy
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Babett Bodnár
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Noémi Ligeti-Nagy
- Language Technology Research Group, HUN-REN Hungarian Research Centre for Linguistics, Budapest, Hungary
| | - János Juhász
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
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Kapytina A, Kolchenko M, Kerimbek N, Pozharskiy AS, Nizamdinova G, Taskuzhina A, Adilbayeva K, Khusnitdinova M, Amidullayeva M, Moisseyev R, Kachiyeva Z, Gritsenko D. Distribution of Wheat-Infecting Viruses and Genetic Variability of Wheat Streak Mosaic Virus and Barley Stripe Mosaic Virus in Kazakhstan. Viruses 2024; 16:96. [PMID: 38257796 PMCID: PMC10819362 DOI: 10.3390/v16010096] [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: 11/29/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Wheat is an essential cereal crop for the economy and food safety of Kazakhstan. In the present work, a screening of wheat and barley from different regions of Kazakhstan was conducted using newly developed specific primers for reverse transcription PCR and loop-mediated isothermal amplification (LAMP) assays. In total, 82 and 19 of 256 samples of wheat and barley tested positive for wheat streak mosaic virus (WSMV) and barley stripe mosaic virus (BSMV), respectively. A phylogenetic analysis using two independent methods revealed that most of the analyzed isolates had a European origin. Molecular data on the distribution and diversity of cereal viruses in Kazakhstan were obtained for the first time and will help lay a foundation for the implementation of genetics and genomics in wheat phyto-epidemiology in the country.
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Affiliation(s)
- Anastasiya Kapytina
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Mariya Kolchenko
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Nazym Kerimbek
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
- Department of Molecular Biology and Genetics, Al Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Alexandr S. Pozharskiy
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Gulnaz Nizamdinova
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Aisha Taskuzhina
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
- Department of Molecular Biology and Genetics, Al Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Kamila Adilbayeva
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Marina Khusnitdinova
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Malika Amidullayeva
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
| | - Ruslan Moisseyev
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
- Department of Molecular Biology and Genetics, Al Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Zulfiya Kachiyeva
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
- Research Institute of Applied and Fundamental Medicine, Kazakh National Medical University, Almaty 050000, Kazakhstan
| | - Dilyara Gritsenko
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.K.); (N.K.); (M.A.); (Z.K.)
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Marian L, Withoeft JA, Esser M, Dal Molin SR, Hamckmeier D, Baumbach LF, Canal CW, Casagrande RA. Uncommon bovine viral diarrhea virus subtype 1e associated with abortions in cattle in southern Brazil. J Vet Diagn Invest 2024; 36:115-119. [PMID: 37908042 PMCID: PMC10734589 DOI: 10.1177/10406387231209739] [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: 11/02/2023] Open
Abstract
We characterized bovine viral diarrhea virus (BVDV)-related abortions in cattle and identified the species and subgenotypes in the state of Santa Catarina, southern Brazil. Our RT-PCR assay was positive for BVDV in 5 fetuses from different farms; however, 3 of the 5 fetuses were also PCR-positive for Neospora caninum. In the 5 BVDV-positive fetuses, gross lesions included fetal mummification (1), hepatomegaly (1), subcutaneous edema (1), and perirenal edema (1). Predominant histologic lesions included epicarditis and mild-to-moderate lymphoplasmacytic myocarditis (5), mild multifocal lymphoplasmacytic interlobular pneumonia (4), nephrosis associated with moderate multifocal interstitial nephritis (1), moderate multifocal lymphoplasmacytic necrotic hepatitis (1), and mild multifocal lymphoplasmacytic meningitis (1). The amplification products from the Pestivirus 5'UTR region of 4 of the 5 fetuses had 96.3-100% similarity between fetal strains and reference strains. The samples were distributed into 2 branches of the phylogenetic tree; strains UDESC:01, UDESC:02, and UDESC:05 clustered in the BVDV-1e branch, uncommon in the Americas, and strain UDESC:04 clustered in the BVDV-2b branch. The three 1e strains had 96.9-97.4% similarity.
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Affiliation(s)
- Lucas Marian
- Laboratório de Patologia Animal, Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina (UDESC), Lages, Santa Catarina, Brazil
| | - Jéssica A. Withoeft
- Laboratório de Patologia Animal, Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina (UDESC), Lages, Santa Catarina, Brazil
| | - Maiara Esser
- Laboratório de Patologia Animal, Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina (UDESC), Lages, Santa Catarina, Brazil
| | - Stephane R. Dal Molin
- Laboratório de Patologia Animal, Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina (UDESC), Lages, Santa Catarina, Brazil
| | - Deise Hamckmeier
- Prefeitura de Pouso Redondo, Pouso Redondo, Santa Catarina, Brazil
| | - Letícia F. Baumbach
- Laboratorio de Virologia Veterinária, Faculdade de Medicina Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Cláudio W. Canal
- Laboratorio de Virologia Veterinária, Faculdade de Medicina Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Renata A. Casagrande
- Laboratório de Patologia Animal, Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina (UDESC), Lages, Santa Catarina, Brazil
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Dharmayanti NI, Nurjanah D, Nuradji H, Suyatno T, Indriani R. Newcastle disease virus: the past and current situation in Indonesia. J Vet Sci 2024; 25:e3. [PMID: 38311318 PMCID: PMC10839176 DOI: 10.4142/jvs.23022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/25/2023] [Accepted: 07/29/2023] [Indexed: 02/07/2024] Open
Abstract
The Newcastle disease virus (NDV) outbreak was first reported in Java Island, Indonesia, in 1926, which was then reported further in Newcastle-upon-Tyne, England. Nevertheless, the NDV is still endemic in Indonesia, with outbreaks occurring in free-range and commercial chicken farms. The dynamic evolution of the NDV has led to the further development of vaccines and diagnostic tools for more effective control of this virus. This paper discusses the history of the NDV occurrence, vaccines, the development of diagnostic tools, and the epidemiological condition of the NDV in Indonesia. Indonesia, which has the largest poultry population in the world after China, has challenges in preventing and controlling this virus that causes economic losses to the farmers and has an impact on the welfare of the poultry farming community in Indonesia.
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Affiliation(s)
- Nlp Indi Dharmayanti
- Research Organization for Health, National Research and Innovation Agency, Cibinong 16911, Indonesia
| | - Diana Nurjanah
- Research Center for Veterinary Science, Research Organization for Health, National Research and Innovation Agency, Cibinong 16911, Indonesia
- Master's Programme in Biomedical Sciences Faculty of Medicine Universitas Indonesia, Depok 16424, Indonesia.
| | - Harimurti Nuradji
- Research Center for Veterinary Science, Research Organization for Health, National Research and Innovation Agency, Cibinong 16911, Indonesia
| | - Teguh Suyatno
- Research Center for Veterinary Science, Research Organization for Health, National Research and Innovation Agency, Cibinong 16911, Indonesia
| | - Risa Indriani
- Research Center for Veterinary Science, Research Organization for Health, National Research and Innovation Agency, Cibinong 16911, Indonesia
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Atwa AS, Gomaa L, Elmenofy W, Amer HM, Ahmed BM. Expression of recombinant Florida clade 2 hemagglutinin in baculovirus expression system: A step for subunit vaccine development against H3N8 equine influenza virus. Open Vet J 2024; 14:350-359. [PMID: 38633177 PMCID: PMC11018420 DOI: 10.5455/ovj.2024.v14.i1.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/15/2023] [Indexed: 04/19/2024] Open
Abstract
Background Equine influenza (EI) is a transmissible viral respiratory sickness of the Equidae family. Two viruses, H7N7 and H3N8 caused EI; however, H7N7 has not been detected for decades. H3N8 has circulated and bifurcated into Eurasian and American lineages. The latter subsequently diversified into Kentucky, South America, and Florida sub-lineages. Florida clade 1 (FC1) and Florida clade 2 (FC2) strains are the only circulating EI viruses (EIVs) in the meantime. Immunization is considered the major means for the prevention and control of EI infection. Using disparate technologies and platforms, several vaccines have been developed and commercialized. According to the recommendations of the World Organization for Animal Health (WOAH), all commercial vaccines shall comprise representatives of both FC1 and FC2 strains. Unfortunately, most of the commercially available vaccines were not updated to incorporate a representative of FC2 strains. Aim The purpose of this research was to develop a new EI vaccine candidate that incorporates the hemagglutinin (HA) antigen from the currently circulating FC2. Methods In this study, we report the expression of the full-length recombinant HA gene of FC2 in the baculovirus expression system. Results The HA recombinant protein has been proven to maintain its biological characteristics by hemadsorption (HAD) and hemagglutination tests. Moreover, using a reference-specific serum, the specificity of the HA has been confirmed through the implementation of immunoperoxidase and western immunoblotting assays. Conclusion In conclusion, we report the expression of specific biologically active recombinant HA of FC2, which would act as a foundation for the generation of an updated EI subunit or virus vector vaccine candidates.
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Affiliation(s)
- Ahmed S. Atwa
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Lamis Gomaa
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza, Egypt
| | - Wael Elmenofy
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza, Egypt
- Department of Arid Land Agriculture, College of Agricultural and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Haitham M. Amer
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Basem M. Ahmed
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
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Werid GM, Miller D, Hemmatzadeh F, Messele YE, Petrovski K. An overview of the detection of bovine respiratory disease complex pathogens using immunohistochemistry: emerging trends and opportunities. J Vet Diagn Invest 2024; 36:12-23. [PMID: 37982437 PMCID: PMC10734592 DOI: 10.1177/10406387231210489] [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] [Indexed: 11/21/2023] Open
Abstract
The bovine respiratory disease complex (BRDC) is caused by a variety of pathogens, as well as contributing environmental and host-related risk factors. BRDC is the costliest disease for feedlot cattle globally. Immunohistochemistry (IHC) is a valuable tool for enhancing our understanding of BRDC given its specificity, sensitivity, cost-effectiveness, and capacity to provide information on antigen localization and immune response. Emerging trends in IHC include the use of multiplex IHC for the detection of coinfections, the use of digital imaging and automation, improved detection systems using enhanced fluorescent dyes, and the integration of IHC with spatial transcriptomics. Overall, identifying biomarkers for early detection, utilizing high-throughput IHC for large-scale studies, developing standardized protocols and reagents, and integrating IHC with other technologies are some of the opportunities to enhance the accuracy and applicability of IHC. We summarize here the various techniques and protocols used in IHC and highlight their current and potential role in BRDC research.
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Affiliation(s)
- Gebremeskel Mamu Werid
- Davies Livestock Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Darren Miller
- Davies Livestock Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Farhid Hemmatzadeh
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Yohannes E. Messele
- Davies Livestock Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Kiro Petrovski
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
- Davies Livestock Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
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46
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McKelvy U, Brelsford M, Burrows M. Evaluation of Seed Transmission Rates of Wheat Streak Mosaic Virus in Mechanically Inoculated Winter and Spring Wheat Cultivars in Montana. PLANT DISEASE 2023; 107:3727-3730. [PMID: 37415357 DOI: 10.1094/pdis-04-22-0898-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Wheat streak mosaic disease is caused by wheat streak mosaic virus (WSMV) and two other viruses and persistently limits wheat yields in the Great Plains region of the United States. Seed transmission of viruses is an important consideration in international movement and is important epidemiologically. Seed transmission of WSMV in wheat was first reported from Australia in 2005, but there is little data from United States cultivars on the rate of seed transmission. In 2018, mechanically inoculated winter and spring wheat cultivars were evaluated in Montana. We found differences in WSMV seed transmission rates between winter and spring wheat, with average transmission rates in spring wheat (3.1%) being five times higher compared to winter wheat (0.6%). Seed transmission rates in spring wheat were twice as high as the highest previously reported transmission rate for individual genotypes, 1.5%. The results from this study provide a strong argument for increasing the current testing of seed for breeding purposes prior to international movement when WSMV has been observed and caution against using grain from WSMV-infected fields as seed source because it can heighten the risk of wheat streak mosaic outbreaks.
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Affiliation(s)
- Uta McKelvy
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717
| | - Monica Brelsford
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717
| | - Mary Burrows
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717
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Fan Y, Hou Y, Li Q, Dian Z, Wang B, Xia X. RNA virus diversity in rodents. Arch Microbiol 2023; 206:9. [PMID: 38038743 DOI: 10.1007/s00203-023-03732-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023]
Abstract
Many zoonotic disease emergencies are associated with RNA viruses in rodents that substantially impact public health. With the widespread application of meta-genomics and meta-transcriptomics for virus discovery over the last decade, viral sequences deposited in public databases have expanded rapidly, and the number of novel viruses discovered in rodents has increased. As important reservoirs of zoonotic viruses, rodents have attracted increasing attention for the risk of potential spillover of rodent-borne viruses. However, knowledge of rodent viral diversity and the major factors contributing to the risk of zoonotic epidemic outbreaks remains limited. Therefore, this study analyzes the diversity and composition of rodent RNA viruses using virus records from the Database of Rodent-associated Viruses (DRodVir/ZOVER), which covers the published literatures and records in GenBank database, reviews the main rodent RNA virus-induced human infectious diseases, and discusses potential challenges in this field.
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Affiliation(s)
- Yayu Fan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Ziqin Dian
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, People's Republic of China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China.
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China.
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Nikolic N, Anagnostidis V, Tiwari A, Chait R, Gielen F. Droplet-based methodology for investigating bacterial population dynamics in response to phage exposure. Front Microbiol 2023; 14:1260196. [PMID: 38075890 PMCID: PMC10703435 DOI: 10.3389/fmicb.2023.1260196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/23/2023] [Indexed: 02/12/2024] Open
Abstract
An alarming rise in antimicrobial resistance worldwide has spurred efforts into the search for alternatives to antibiotic treatments. The use of bacteriophages, bacterial viruses harmless to humans, represents a promising approach with potential to treat bacterial infections (phage therapy). Recent advances in microscopy-based single-cell techniques have allowed researchers to develop new quantitative methodologies for assessing the interactions between bacteria and phages, especially the ability of phages to eradicate bacterial pathogen populations and to modulate growth of both commensal and pathogen populations. Here we combine droplet microfluidics with fluorescence time-lapse microscopy to characterize the growth and lysis dynamics of the bacterium Escherichia coli confined in droplets when challenged with phage. We investigated phages that promote lysis of infected E. coli cells, specifically, a phage species with DNA genome, T7 (Escherichia virus T7) and two phage species with RNA genomes, MS2 (Emesvirus zinderi) and Qβ (Qubevirus durum). Our microfluidic trapping device generated and immobilized picoliter-sized droplets, enabling stable imaging of bacterial growth and lysis in a temperature-controlled setup. Temporal information on bacterial population size was recorded for up to 25 h, allowing us to determine growth rates of bacterial populations and helping us uncover the extent and speed of phage infection. In the long-term, the development of novel microfluidic single-cell and population-level approaches will expedite research towards fundamental understanding of the genetic and molecular basis of rapid phage-induced lysis and eco-evolutionary aspects of bacteria-phage dynamics, and ultimately help identify key factors influencing the success of phage therapy.
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Affiliation(s)
- Nela Nikolic
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
- Translational Research Exchange @ Exeter, University of Exeter, Exeter, United Kingdom
| | - Vasileios Anagnostidis
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Anuj Tiwari
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Remy Chait
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Fabrice Gielen
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
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49
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de Almeida PR, Weber MN, Sonne L, Spilki FR. Aedes-borne orthoflavivirus infections in neotropical primates - Ecology, susceptibility, and pathogenesis. Exp Biol Med (Maywood) 2023; 248:2030-2038. [PMID: 38230520 PMCID: PMC10800122 DOI: 10.1177/15353702231220659] [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: 01/18/2024] Open
Abstract
Arboviral diseases comprise a group of important infectious diseases imposing a heavy burden to public health in many locations of the world. Orthoflaviviruses are viruses belonging to the genus Orthoflavivirus; this genus includes some of the most relevant arboviruses to human health. Orthoflaviviruses can infect several different hosts, with some species being transmitted in cycles involving birds and anthropophilic mosquitoes and others transmitted between mammals and mostly Aedes sp. mosquitoes. Some of the most important sylvatic reservoirs of orthoflaviviruses are non-human primates (NHPs). Many flaviviruses that infect NHPs in nature have the potential to cause epidemics in humans, as has been observed in the cases of Orthoflavivirus denguei (dengue virus - DENV), Orthoflavivirus flavi (yellow fever virus - YFV), and Orthoflavivirus zikaense (Zika virus - ZIKV). In this minireview, we discuss important aspects regarding history, ecology involving NHP, distribution, disease outcome, and pathogenesis of these three major orthoflaviviruses that affect humans and NHP and relate this information to the potential of using NHP as experimental models. In addition, we suggest some orthoflaviviruses that could be better investigated, both in nature and in experimental studies, in light of the recent revolution in molecular biology.
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Affiliation(s)
- Paula Rodrigues de Almeida
- Molecular Microbiology Laboratory, Institute of Health Sciences, Feevale University, Novo Hamburgo, RS 93352-000, Brazil
| | - Matheus Nunes Weber
- Molecular Microbiology Laboratory, Institute of Health Sciences, Feevale University, Novo Hamburgo, RS 93352-000, Brazil
| | - Luciana Sonne
- Veterinary Pathology Sector, Veterinary Clinical Pathology Department, College of Veterinary Medicine, Federal University of Rio Grande do Sul, Porto Alegre, RS 91540-000, Brazil
| | - Fernando Rosado Spilki
- Molecular Microbiology Laboratory, Institute of Health Sciences, Feevale University, Novo Hamburgo, RS 93352-000, Brazil
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50
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Mohanto S, Faiyazuddin M, Dilip Gholap A, Jc D, Bhunia A, Subbaram K, Gulzar Ahmed M, Nag S, Shabib Akhtar M, Bonilla-Aldana DK, Sah S, Malik S, Haleem Al-Qaim Z, Barboza JJ, Sah R. Addressing the resurgence of global monkeypox (Mpox) through advanced drug delivery platforms. Travel Med Infect Dis 2023; 56:102636. [PMID: 37633474 DOI: 10.1016/j.tmaid.2023.102636] [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: 06/11/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 08/28/2023]
Abstract
Monkeypox (Mpox) is a transmissible infection induced by the Monkeypox virus (a double-stranded DNA virus), recognised under the family orthopoxvirus genus. Monkeypox, like endemic diseases, is a substantial concern worldwide; thus, comprehending the pathogenesis and mutagenesis of amino acids is indispensable to combat the infection. According to the World Health Organization's report, about 89 thousand cases with 160 mortalities have been reported from 114 countries worldwide. The conventional orthopoxvirus vaccines developed on live attenuated viruses exempted any clinical validation from combating monkeypox due to inadequate immunogenicity, toxicity, instability, and multiple doses. Therefore, novel drug delivery systems come into the conception with high biological and mechanical characteristics to address the resurgence of Global Monkeypox. The edges of metallic biomaterials, novel molecules, and vaccine development in targeted therapy increase the modulation of the immune response and blockage of host-virus interaction, with enhanced stability for the antigens. Thus, this review strives to comprehend the viral cell pathogenesis concerning amino acid mutagenesis and current epidemiological standards of the Monkeypox disease across the globe. Furthermore, the review also recapitulates the various clinical challenges, current therapies, and progressive nanomedicine utilisation in the Monkeypox outbreak reinforced by various clinical trial reports. The contemporary challenges of novel drug delivery systems in Monkeypox treatment cannot be overlooked, and thus, authors have outlined the future strategies to develop successful nanomedicine to combat monkeypox. Future pandemics are inevitable but can be satisfactorily handled if we comprehend the crises, innovate, and develop cutting-edge technologies, especially by delving into frontiers like nanotechnology.
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Affiliation(s)
- Sourav Mohanto
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Md Faiyazuddin
- School of Pharmacy, Al-Karim University, Katihar, Bihar, 845106, India; Nano Drug Delivery®, Chapel Hill, NC, USA
| | - Amol Dilip Gholap
- Department of Pharmaceutics, St. John Institute of Pharmacy and Research, Palghar, Maharashtra, 401404, India
| | - Darshan Jc
- Department of Pharmacy Practice, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Adrija Bhunia
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Kannan Subbaram
- School of Medicine, The Maldives National University, Male', Maldives
| | - Mohammed Gulzar Ahmed
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Sagnik Nag
- Department of Bio-Sciences, School of Bio-Sciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Mohammad Shabib Akhtar
- Department of Clinical Pharmacy, College of Pharmacy, Najran University, Najran, Kingdom of Saudi Arabia
| | | | - Sanjit Sah
- Global Consortium for Public Health and Research, Datta Meghe Institute of Higher Education and Research, Jawaharlal Nehru Medical College, Wardha, 442001, India; SR Sanjeevani Hospital, Kalyanpur-10, Siraha, Nepal
| | - Sumira Malik
- Amity Institute of Biotechnology, Amity University, Jharkhand, 834002, Ranchi, India; School of Applied Sciences, Uttaranchal University, Dehradun, India
| | - Zahraa Haleem Al-Qaim
- Department of Anesthesia Techniques, Al-Mustaqbal University College, 51001, Hillah, Babylon, Iraq
| | - Joshuan J Barboza
- Escuela de Medicina, Universidad César Vallejo, Trujillo, 13007, Peru
| | - Ranjit Sah
- Tribhuvan University Teaching Hospital, Kathmandu, 46000, Nepal; Department of Clinical Microbiology, DY Patil Medical College, Hospital and Research Centre, DY Patil Vidyapeeth, Pune, 411000, Maharashtra, India; Department of Public Health Dentistry, Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, 411018, Maharashtra, India
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