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Fellenberg J, Dubrau D, Isken O, Tautz N. Packaging defects in pestiviral NS4A can be compensated by mutations in NS2 and NS3. J Virol 2023; 97:e0057223. [PMID: 37695056 PMCID: PMC10537661 DOI: 10.1128/jvi.00572-23] [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: 04/17/2023] [Accepted: 07/18/2023] [Indexed: 09/12/2023] Open
Abstract
The non-structural (NS) proteins of the Flaviviridae members play a dual role in genome replication and virion morphogenesis. For pestiviruses, like bovine viral diarrhea virus, the NS2-3 region and its processing by the NS2 autoprotease is of particular importance. While uncleaved NS2-3 in complex with NS4A is essential for virion assembly, it cannot replace free NS3/4A in the viral replicase. Furthermore, surface interactions between NS3 and the C-terminal cytosolic domain of NS4A were shown to serve as a molecular switch between RNA replication and virion morphogenesis. To further characterize the functionality of NS4A, we performed an alanine-scanning mutagenesis of two NS4A regions, a short highly conserved cytoplasmic linker downstream of the transmembrane domain and the C-terminal domain. NS4A residues critical for polyprotein processing, RNA replication, and/or virion morphogenesis were identified. Three double-alanine mutants, two in the linker region and one close to the C-terminus of NS4A, showed a selective effect on virion assembly. All three packaging defective mutants could be rescued by a selected set of two second-site mutations, located in NS2 and NS3, respectively. This phenotype was additionally confirmed by complementation studies providing the NS2-3/4A packaging molecules containing the rescue mutations in trans. This indicates that the linker region and the cytosolic C-terminal part of NS4A are critical for the formation of protein complexes required for virion morphogenesis. The ability of the identified sets of second-site mutations in NS2-3 to compensate for diverse NS4A defects highlights a surprising functional flexibility for pestiviral NS proteins. IMPORTANCE Positive-strand RNA viruses have a limited coding capacity due to their rather small genome size. To overcome this constraint, viral proteins often exhibit multiple functions that come into play at different stages during the viral replication cycle. The molecular basis for this multifunctionality is often unknown. For the bovine viral diarrhea virus, the non-structural protein (NS) 4A functions as an NS3 protease cofactor, a replicase building block, and a component in virion morphogenesis. Here, we identified the critical amino acids of its C-terminal cytosolic region involved in those processes and show that second-site mutations in NS2 and NS3 can compensate for diverse NS4A defects in virion morphogenesis. The ability to evolve alternative functional solutions by gain-of-function mutations highlights the astounding plasticity of the pestiviral system.
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Affiliation(s)
- Jonas Fellenberg
- Institute of Virology and Cell Biology, University of Luebeck, Luebeck, Germany
| | - Danilo Dubrau
- Institute of Virology and Cell Biology, University of Luebeck, Luebeck, Germany
| | - Olaf Isken
- Institute of Virology and Cell Biology, University of Luebeck, Luebeck, Germany
| | - Norbert Tautz
- Institute of Virology and Cell Biology, University of Luebeck, Luebeck, Germany
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52
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Pan J, Ji L, Wu H, Wang X, Wang Y, Wu Y, Yang S, Shen Q, Liu Y, Zhang W, Zhang K, Shan T. Metagenomic analysis of herbivorous mammalian viral communities in the Northwest Plateau. BMC Genomics 2023; 24:568. [PMID: 37749507 PMCID: PMC10521573 DOI: 10.1186/s12864-023-09646-1] [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: 06/06/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Mammals are potential hosts for many infectious diseases. However, studies on the viral communities of herbivorous mammals in the Northwest Plateau are limited. Here, we studied the viral communities of herbivorous mammals in the Northwest Plateau using virus metagenomic analysis to analyze and compare the viral community composition of seven animal species. RESULTS By library construction and next-generation sequencing, contigs and singlets reads with similar viral sequences were classified into 24 viral families. Analyzed from the perspective of sampling areas, the virus community composition was relatively similar in two areas of Wuwei and Jinchang, Gansu Province. Analyzed from the perspective of seven animal species, the viral reads of seven animal species were mostly ssDNA and dominated by CRESS-DNA viruses. Phylogenetic analysis based on viral marker genes indicated that CRESS-DNA viruses and microviruses have high genetic diversity. In addition to DNA viruses, nodaviruses, pepper mild mottle viruses and picornaviruses were RNA viruses that we performed by phylogenetic analysis. The CRESS-DNA viruses and nodaviruses are believed to infect plants and insects, and microviruses can infect bacteria, identifying that they were likely from the diet of herbivorous mammals. Notably, two picornaviruses were identified from red deer and wild horse, showing that the picornavirus found in red deer had the relatively high similarity with human hepatitis A virus, and the picornavirus carried by wild horse could potentially form a new species within the Picornaviridae family. CONCLUSIONS This study explored the herbivorous mammalian virus community in the Northwest Plateau and the genetic characteristics of viruses that potentially threaten human health. It reveals the diversity and stability of herbivorous mammalian virus communities in the Northwest Plateau and helps to expand our knowledge of various herbivorous mammalian potentially pathogenic viruses.
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Grants
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
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Affiliation(s)
- Jiamin Pan
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Haisheng Wu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yan Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yan Wu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yuwei Liu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
| | - Keshan Zhang
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
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53
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Hermanns K, Marklewitz M, Zirkel F, Kopp A, Kramer-Schadt S, Junglen S. Mosquito community composition shapes virus prevalence patterns along anthropogenic disturbance gradients. eLife 2023; 12:e66550. [PMID: 37702388 PMCID: PMC10547478 DOI: 10.7554/elife.66550] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 09/12/2023] [Indexed: 09/14/2023] Open
Abstract
Previously unknown pathogens often emerge from primary ecosystems, but there is little knowledge on the mechanisms of emergence. Most studies analyzing the influence of land-use change on pathogen emergence focus on a single host-pathogen system and often observe contradictory effects. Here, we studied virus diversity and prevalence patterns in natural and disturbed ecosystems using a multi-host and multi-taxa approach. Mosquitoes sampled along a disturbance gradient in Côte d'Ivoire were tested by generic RT-PCR assays established for all major arbovirus and insect-specific virus taxa including novel viruses previously discovered in these samples based on cell culture isolates enabling an unbiased and comprehensive approach. The taxonomic composition of detected viruses was characterized and viral infection rates according to habitat and host were analyzed. We detected 331 viral sequences pertaining to 34 novel and 15 previously identified viruses of the families Flavi-, Rhabdo-, Reo-, Toga-, Mesoni- and Iflaviridae and the order Bunyavirales. Highest host and virus diversity was observed in pristine and intermediately disturbed habitats. The majority of the 49 viruses was detected with low prevalence. However, nine viruses were found frequently across different habitats of which five viruses increased in prevalence towards disturbed habitats, in congruence with the dilution effect hypothesis. These viruses were mainly associated with one specific mosquito species (Culex nebulosus), which increased in relative abundance from pristine (3%) to disturbed habitats (38%). Interestingly, the observed increased prevalence of these five viruses in disturbed habitats was not caused by higher host infection rates but by increased host abundance, an effect tentatively named abundance effect. Our data show that host species composition is critical for virus abundance. Environmental changes that lead to an uneven host community composition and to more individuals of a single species are a key driver of virus emergence.
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Affiliation(s)
- Kyra Hermanns
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-Universtiy Berlin, and Berlin Institute of HealthBerlinGermany
| | - Marco Marklewitz
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-Universtiy Berlin, and Berlin Institute of HealthBerlinGermany
| | - Florian Zirkel
- Institute of Virology, University of Bonn Medical CentreBerlinGermany
| | - Anne Kopp
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-Universtiy Berlin, and Berlin Institute of HealthBerlinGermany
| | - Stephanie Kramer-Schadt
- Department of Ecological Dynamics, Leibniz Institute for Zoo and Wildlife ResearchBerlinGermany
- Institute of Ecology, Technische Universität BerlinBerlinGermany
| | - Sandra Junglen
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-Universtiy Berlin, and Berlin Institute of HealthBerlinGermany
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54
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Theerawatanasirikul S, Lueangaramkul V, Pantanam A, Mana N, Semkum P, Lekcharoensuk P. Small Molecules Targeting 3C Protease Inhibit FMDV Replication and Exhibit Virucidal Effect in Cell-Based Assays. Viruses 2023; 15:1887. [PMID: 37766293 PMCID: PMC10535379 DOI: 10.3390/v15091887] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Foot-and-mouth disease (FMD) is a highly contagious disease in cloven-hoofed animals, caused by the foot-and-mouth disease virus (FMDV). It is endemic in Asia and Africa but spreads sporadically throughout the world, resulting in significant losses in the livestock industry. Effective anti-FMDV therapeutics could be a supportive control strategy. Herein, we utilized computer-aided, structure-based virtual screening to filter lead compounds from the National Cancer Institute (NCI) diversity and mechanical libraries using FMDV 3C protease (3Cpro) as the target. Seven hit compounds were further examined via cell-based antiviral and intracellular protease assays, in which two compounds (NSC116640 and NSC332670) strongly inhibited FMDV, with EC50 values at the micromolar level of 2.88 µM (SI = 73.15) and 5.92 µM (SI = 11.11), respectively. These compounds could inactivate extracellular virus directly in a virucidal assay by reducing 1.00 to 2.27 log TCID50 of the viral titers in 0-60 min. In addition, the time-of-addition assay revealed that NSC116640 inhibited FMDV at the early stage of infection (0-8 h), while NSC332670 diminished virus titers when added simultaneously at infection (0 h). Both compounds showed good FMDV 3Cpro inhibition with IC50 values of 10.85 µM (NSC116640) and 4.21 µM (NSC332670). The molecular docking of the compounds on FMDV 3Cpro showed their specific interactions with amino acids in the catalytic triad of FMDV 3Cpro. Both preferentially reacted with enzymes and proteases in physicochemical and ADME analysis studies. The results revealed two novel small molecules with antiviral activities against FMDV and probably related picornaviruses.
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Affiliation(s)
- Sirin Theerawatanasirikul
- Department of Anatomy, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
| | - Varanya Lueangaramkul
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (V.L.); (A.P.); (N.M.); (P.S.)
| | - Achiraya Pantanam
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (V.L.); (A.P.); (N.M.); (P.S.)
| | - Natjira Mana
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (V.L.); (A.P.); (N.M.); (P.S.)
| | - Ploypailin Semkum
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (V.L.); (A.P.); (N.M.); (P.S.)
| | - Porntippa Lekcharoensuk
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (V.L.); (A.P.); (N.M.); (P.S.)
- Center of Advanced Studies in Agriculture and Food, KU Institute, Bangkok 10900, Thailand
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55
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Viktorova EG, Gabaglio S, Moghimi S, Zimina A, Wynn BG, Sztul E, Belov GA. The development of resistance to an inhibitor of a cellular protein reveals a critical interaction between the enterovirus protein 2C and a small GTPase Arf1. PLoS Pathog 2023; 19:e1011673. [PMID: 37721955 PMCID: PMC10538752 DOI: 10.1371/journal.ppat.1011673] [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: 05/25/2023] [Revised: 09/28/2023] [Accepted: 09/08/2023] [Indexed: 09/20/2023] Open
Abstract
The cellular protein GBF1, an activator of Arf GTPases (ArfGEF: Arf guanine nucleotide exchange factor), is recruited to the replication organelles of enteroviruses through interaction with the viral protein 3A, and its ArfGEF activity is required for viral replication, however how GBF1-dependent Arf activation supports the infection remains enigmatic. Here, we investigated the development of resistance of poliovirus, a prototype enterovirus, to increasing concentrations of brefeldin A (BFA), an inhibitor of GBF1. High level of resistance required a gradual accumulation of multiple mutations in the viral protein 2C. The 2C mutations conferred BFA resistance even in the context of a 3A mutant previously shown to be defective in the recruitment of GBF1 to replication organelles, and in cells depleted of GBF1, suggesting a GBF1-independent replication mechanism. Still, activated Arfs accumulated on the replication organelles of this mutant even in the presence of BFA, its replication was inhibited by a pan-ArfGEF inhibitor LM11, and the BFA-resistant phenotype was compromised in Arf1-knockout cells. Importantly, the mutations strongly increased the interaction of 2C with the activated form of Arf1. Analysis of other enteroviruses revealed a particularly strong interaction of 2C of human rhinovirus 1A with activated Arf1. Accordingly, the replication of this virus was significantly less sensitive to BFA than that of poliovirus. Thus, our data demonstrate that enterovirus 2Cs may behave like Arf1 effector proteins and that GBF1 but not Arf activation can be dispensable for enterovirus replication. These findings have important implications for the development of host-targeted anti-viral therapeutics.
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Affiliation(s)
- Ekaterina G. Viktorova
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Samuel Gabaglio
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Seyedehmahsa Moghimi
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Anna Zimina
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Bridge G. Wynn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham; Birmingham, Alabama, United States of America
| | - Elizabeth Sztul
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham; Birmingham, Alabama, United States of America
| | - George A. Belov
- Department of Veterinary Medicine and Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
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56
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Chen S, Harris M. Mutational analysis reveals a novel role for hepatitis C virus NS5A domain I in cyclophilin-dependent genome replication. J Gen Virol 2023; 104:10.1099/jgv.0.001886. [PMID: 37672027 PMCID: PMC7615712 DOI: 10.1099/jgv.0.001886] [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: 09/07/2023] Open
Abstract
The hepatitis C virus (HCV) NS5A protein is comprised of three domains (D1-3). Previously, we observed that two alanine substitutions in D1 (V67A, P145A) abrogated replication of a genotype 2a isolate (JFH-1) sub-genomic replicon (SGR) in Huh7 cells, but this phenotype was partially restored in Huh7.5 cells. Here we demonstrate that five additional residues, surface-exposed and proximal to V67 or P145, exhibited the same phenotype. In contrast, the analogous mutants in a genotype 3a isolate (DBN3a) SGR exhibited different phenotypes in each cell line, consistent with fundamental differences in the functions of genotypes 2 and 3 NS5A. The difference between Huh7 and Huh7.5 cells was reminiscent of the observation that cyclophilin inhibitors are more potent against HCV replication in the former and suggested a role for D1 in cyclophilin dependence. Consistent with this, all JFH-1 and DBN3a mutants exhibited increased sensitivity to cyclosporin A treatment compared to wild-type. Silencing of cyclophilin A (CypA) in Huh7 cells inhibited replication of both JFH-1 and DBN3a. However, in Huh7.5 cells CypA silencing did not inhibit JFH-1 wild-type, but abrogated replication of all the JFH-1 mutants, and both DBN3a wild-type and all mutants. CypB silencing in Huh7 cells had no effect on DBN3a, but abrogated replication of JFH-1. CypB silencing in Huh7.5 cells had no effect on either SGR. Lastly, we confirmed that JFH-1 NS5A D1 interacted with CypA in vitro. These data demonstrate both a direct involvement of NS5A D1 in cyclophilin-dependent genome replication and functional differences between genotype 2 and 3 NS5A.
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Affiliation(s)
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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57
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Kumar V, Dahiya S, Budania S, Gupta AK, Sangwan P, Lather A, Kumar P, Kakker NK, Singh A. Characterization of Foot-and-Mouth Disease Virus Serotype O-Specific Single Domain Antibody Expressed in the pET Expression System. Indian J Microbiol 2023; 63:337-343. [PMID: 37781019 PMCID: PMC10533770 DOI: 10.1007/s12088-023-01095-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/16/2023] [Indexed: 10/03/2023] Open
Abstract
Foot and mouth disease (FMD) is an extremely contagious disease of cloven-hoofed domesticated and wild animals, resulting in significant economic losses in many parts of the world. FMD virus (FMDV) serotype O is responsible for approximately 70% of global outbreaks. For detection of FMDV antigen or antibody, ELISAs are used worldwide and have several limitations, such as batch-to-batch variation in generating immunobiologicals, high production cost and ethical concerns over animal sacrifice. The use of single domain antibody (sdAb) or variable N-terminal domain of the heavy chain of heavy chain antibody (VHH) found naturally in camels has proven their effectiveness in diagnostics and therapeutics. In the present study, the anti-FMDV serotype O-specific VHH-C1 gene sequence (Accession no. KJ751546) was retrieved from the NCBI database. The gene was synthesized commercially in the pBluescript KS+ cloning vector and expressed in E. coli BL21 (DE3) cells using the pET303/CT-His expression system with a C-terminal 6X-His tag. The expressed sdAb, verified by SDS‒PAGE and western blotting, was purified by Ni-chelate chromatography and used as a coating antibody in double antibody sandwich (DAS) ELISA for FMDV detection and typing. The sdAb exhibited a high binding affinity for FMDV serotype O, without any cross-reactivity toward serotypes A and Asia-1. It exhibited better thermostability up to 85 °C than conventional rabbit polyclonal anti-FMDV sera. The potential of sdAbs thus produced without sacrificing lab animals could be explored for replacing polyclonal sera in DAS-ELISA as well as for developing biosensors or lateral flow devices for FMDV type O detection.
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Affiliation(s)
- Vijay Kumar
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Swati Dahiya
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Savita Budania
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Akhil Kumar Gupta
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Punesh Sangwan
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Anshul Lather
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Pawan Kumar
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Naresh Kumar Kakker
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
| | - Ajit Singh
- Department of Veterinary Microbiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004 India
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58
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Smirnov A, Magri A, Lotz R, Han X, Yin C, Harris M, Osterburg C, Dötsch V, McKeating JA, Lu X. ASPP2 binds to hepatitis C virus NS5A protein via an SH3 domain/PxxP motif-mediated interaction and potentiates infection. J Gen Virol 2023; 104:10.1099/jgv.0.001895. [PMID: 37750869 PMCID: PMC7615710 DOI: 10.1099/jgv.0.001895] [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: 09/27/2023] Open
Abstract
Hepatitis C virus (HCV) infects millions of people worldwide and is a leading cause of liver disease. Despite recent advances in antiviral therapies, viral resistance can limit drug efficacy and understanding the mechanisms that confer viral escape is important. We employ an unbiased interactome analysis to discover host binding partners of the HCV non-structural protein 5A (NS5A), a key player in viral replication and assembly. We identify ASPP2, apoptosis-stimulating protein of p53, as a new host co-factor that binds NS5A via its SH3 domain. Importantly, silencing ASPP2 reduces viral replication and spread. Our study uncovers a previously unknown role for ASPP2 to potentiate HCV RNA replication.
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Affiliation(s)
- Artem Smirnov
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, Rome 00133, Italy
| | - Andrea Magri
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Rebecca Lotz
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Xiaoyue Han
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Chunhong Yin
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Christian Osterburg
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Jane A. McKeating
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Xin Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
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59
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Chen QY, Sun ZH, Che YL, Chen RJ, Wu XM, Wu RJ, Wang LB, Zhou LJ. High Prevalence, Genetic Diversity, and Recombination of Porcine Sapelovirus in Pig Farms in Fujian, Southern China. Viruses 2023; 15:1751. [PMID: 37632093 PMCID: PMC10458035 DOI: 10.3390/v15081751] [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: 07/04/2023] [Revised: 08/12/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Porcine sapelovirus (PSV) is a ubiquitous virus in farmed pigs that is associated with SMEDI syndrome, polioencephalomyelitis, and diarrhea. However, there are few reports on the prevalence and molecular characterization of PSV in Fujian Province, Southern China. In this study, the prevalence of PSV and a poetical combinative strain PSV2020 were characterized using real-time PCR, sequencing, and bioinformatics analysis. As a result, an overall sample prevalence of 30.8% was detected in 260 fecal samples, and a farm prevalence of 76.7% was observed in 30 Fujian pig farms, from 2020 to 2022. Noteably, a high rate of PSV was found in sucking pigs. Bioinformatics analysis showed that the full-length genome of PSV2020 was 7550 bp, and the genetic evolution of its ORF region was closest to the G1 subgroup, which was isolated from Asia and America; the similarity of nucleotides and amino acids to other PSVs was 59.5~88.7% and 51.7~97.0%, respectively. However, VP1 genetic evolution analysis showed a distinct phylogenetic topology from the ORF region; PSV2020 VP1 was closer to the DIAPD5469-10 strain isolated from Italy than strains isolated from Asia and America, which comprise the G1 subgroup based on the ORF region. Amino acid discrepancy analysis illustrated that the PSV2020 VP1 gene inserted twelve additional nucleotides, corresponding to four additional amino acids (STAE) at positions 898-902 AAs. Moreover, a potential recombination signal was observed in the 2A coding region, near the 3' end of VP1, owing to recombination analysis. Additionally, 3D genetic evolutionary analysis showed that all reference strains demonstrated, to some degree, regional conservation. These results suggested that PSV was highly prevalent in Fujian pig farms, and PSV2020, a PSV-1 genotype strain, showed gene diversity and recombination in evolutionary progress. This study also laid a scientific foundation for the investigation of PSV epidemiology, molecular genetic characteristics, and vaccine development.
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Affiliation(s)
- Qiu-Yong Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences, Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China; (Q.-Y.C.); (Y.-L.C.); (R.-J.C.); (X.-M.W.); (R.-J.W.)
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Zhi-Hua Sun
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yong-Liang Che
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences, Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China; (Q.-Y.C.); (Y.-L.C.); (R.-J.C.); (X.-M.W.); (R.-J.W.)
| | - Ru-Jing Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences, Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China; (Q.-Y.C.); (Y.-L.C.); (R.-J.C.); (X.-M.W.); (R.-J.W.)
| | - Xue-Min Wu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences, Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China; (Q.-Y.C.); (Y.-L.C.); (R.-J.C.); (X.-M.W.); (R.-J.W.)
| | - Ren-Jie Wu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences, Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China; (Q.-Y.C.); (Y.-L.C.); (R.-J.C.); (X.-M.W.); (R.-J.W.)
| | - Long-Bai Wang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences, Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China; (Q.-Y.C.); (Y.-L.C.); (R.-J.C.); (X.-M.W.); (R.-J.W.)
| | - Lun-Jiang Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agriculture Sciences, Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China; (Q.-Y.C.); (Y.-L.C.); (R.-J.C.); (X.-M.W.); (R.-J.W.)
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Guo G, Wang M, Zhou D, He X, Han P, Chen G, Zeng J, Liu Z, Wu Y, Weng S, He J. Virome Analysis Provides an Insight into the Viral Community of Chinese Mitten Crab Eriocheir sinensis. Microbiol Spectr 2023; 11:e0143923. [PMID: 37358426 PMCID: PMC10433957 DOI: 10.1128/spectrum.01439-23] [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: 04/10/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023] Open
Abstract
Recent advances in viromics have led to the discovery of a great diversity of RNA viruses and the identification of a large number of viral pathogens. A systematic exploration of viruses in Chinese mitten crab (Eriocheir sinensis), one of the most important aquatic commercial species, is still lacking. Here, we characterized the RNA viromes of asymptomatic, milky disease (MD)-affected, and hepatopancreatic necrosis syndrome (HPNS)-affected Chinese mitten crabs collected from 3 regions in China. In total, we identified 31 RNA viruses belonging to 11 orders, 22 of which were first reported here. By comparing viral composition between samples, we observed high variation in viral communities across regions, with most of the viral species being region-specific. We proposed to establish several novel viral families or genera based on the phylogenetic relationships and genome structures of viruses discovered in this study, expanding our knowledge of viral diversity in brachyuran crustaceans. IMPORTANCE High-throughput sequencing and meta-transcriptomic analysis provide us with an efficient tool to discover unknown viruses and explore the composition of viral communities in specific species. In this study, we investigated viromes in asymptomatic and diseased Chinese mitten crabs collected from three distant locations. We observed high regional variation in the composition of viral species, highlighting the importance of multi-location sampling. In addition, we classified several novel and ICTV-unclassified viruses based on their genome structures and phylogenetic relationships, providing a new perspective on current viral taxa.
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Affiliation(s)
- Guangyu Guo
- State Key Laboratory of Biocontrol, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Muhua Wang
- State Key Laboratory of Biocontrol, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dandan Zhou
- State Key Laboratory of Biocontrol, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Xinyi He
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peiyun Han
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Gongrui Chen
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jiamin Zeng
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhi Liu
- State Key Laboratory of Biocontrol, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Yinqing Wu
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaoping Weng
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Zhao X, Dai C, Qian S, Tang Q, Li L, Hao Y, Zhou Z, Ge X, Gong C, Yuan J. Viral Diversity and Epidemiology in Critically Endangered Yangtze Finless Porpoises (Neophocaena asiaeorientalis asiaeorientalis). Microbiol Spectr 2023; 11:e0081023. [PMID: 37265414 PMCID: PMC10434060 DOI: 10.1128/spectrum.00810-23] [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: 02/24/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
The Yangtze finless porpoise (YFP) (Neophocaena asiaeorientalis asiaeorientalis) is a critically endangered freshwater cetacean, with about 1,249 individuals thought to be left in the wild. However, viral entities and viral diseases of YFPs remain obscure. In this study, anal swabs for virome analysis were collected during the physical examination of YFPs in the Tian-E-Zhou Oxbow (TEO) ex situ reserve. A total of 19 eukaryotic viral species belonging to 9 families, including Papillomaviridae, Herpesviridae, Picornaviridae, Picobirnaviridae, Caliciviridae, Retroviridae, Parvoviridae, Virgaviridae, and Narnaviridae, and other unclassified viruses were identified based on metasequencing. Among these detected viruses, a novel herpesvirus (NaHV), two different kobuviruses (NaKV1-2), and six different papillomaviruses (NaPV1 to -6) were considered potential risks to YFPs and confirmed by PCR or reverse transcription-PCR (RT-PCR). Most YFPs sampled were found to harbor one or more kinds of detected viral genomes (52/58 [89.7%]). Surveillance results demonstrated that kobuvirus and herpesvirus displayed obvious age distribution and PVs showed significant gender difference in YFPs. According to species demarcation criteria in individual genera in Papillomaviridae, two novel species (referred to as Omikronpapillomavirus 2 and 3) and four novel isolates of PV were identified in YFPs. Further evolutionary analysis suggested that NaPVs would occupy the mucosal niche and that virus-host codivergence mixed with duplications and host-switching events drives the evolution of cetacean PVs. Divergence times of PVs in YFP and other cetacean reflect the incipient speciation of YFPs. In summary, our findings revealed the potential viral entities, their prevalence, and their evolutionary history in YFPs, which raises an important issue regarding effects of viral infection on the fitness of YFPs. IMPORTANCE The Yangtze finless porpoise (YFP) is the only cetacean species in freshwater following the functional extinction of the baiji (Lipotes vexillifer). Health management, disease treatment, and other special measures are important for maintaining the existing YFP populations, especially in in situ and ex situ reserves. The discovery of potential viral entities and their prevalence in YFPs raises an important issue regarding the effects of viral infection on the fitness of YFPs and may contribute to the conservation of YFPs. The evolutionary history of papillomaviruses in YFP and other cetaceans reflects the phylogeny of their hosts and supports the status of incipient species, opening a window to investigate the evolutionary adaptation of cetaceans to freshwater as well as their phylogeny to remedy the deficiency of fossil evidence.
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Affiliation(s)
- Xin Zhao
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Caijiao Dai
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Shiyu Qian
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Qing Tang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Lijuan Li
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Hubei Engineering Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, People’s Republic of China
| | - Yujiang Hao
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology of the Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Zhijian Zhou
- College of Biology & Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Xingyi Ge
- College of Biology & Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Cheng Gong
- Tian-e-zhou National Reserve for Lipotes Vexillifer, Shishou, People’s Republic of China
| | - Junfa Yuan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Hubei Engineering Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, People’s Republic of China
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Shi W, Jin M, Chen H, Wu Z, Yuan L, Liang S, Wang X, Memon FU, Eldemery F, Si H, Ou C. Inflammasome activation by viral infection: mechanisms of activation and regulation. Front Microbiol 2023; 14:1247377. [PMID: 37608944 PMCID: PMC10440708 DOI: 10.3389/fmicb.2023.1247377] [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: 06/26/2023] [Accepted: 07/13/2023] [Indexed: 08/24/2023] Open
Abstract
Viral diseases are the most common problems threatening human health, livestock, and poultry industries worldwide. Viral infection is a complex and competitive dynamic biological process between a virus and a host/target cell. During viral infection, inflammasomes play important roles in the host and confer defense mechanisms against the virus. Inflammasomes are polymeric protein complexes and are considered important components of the innate immune system. These immune factors recognize the signals of cell damage or pathogenic microbial infection after activation by the canonical pathway or non-canonical pathway and transmit signals to the immune system to initiate the inflammatory responses. However, some viruses inhibit the activation of the inflammasomes in order to replicate and proliferate in the host. In recent years, the role of inflammasome activation and/or inhibition during viral infection has been increasingly recognized. Therefore, in this review, we describe the biological properties of the inflammasome associated with viral infection, discuss the potential mechanisms that activate and/or inhibit NLRP1, NLRP3, and AIM2 inflammasomes by different viruses, and summarize the reciprocal regulatory effects of viral infection on the NLRP3 inflammasome in order to explore the relationship between viral infection and inflammasomes. This review will pave the way for future studies on the activation mechanisms of inflammasomes and provide novel insights for the development of antiviral therapies.
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Affiliation(s)
- Wen Shi
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Mengyun Jin
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Hao Chen
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | | | - Liuyang Yuan
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Si Liang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Xiaohan Wang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Fareed Uddin Memon
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Fatma Eldemery
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Hongbin Si
- College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, China
| | - Changbo Ou
- College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, China
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Li R, Lin C, Dong S, Li J, Liang Z, Yang Y, Huo D, Gao Z, Jia L, Zhang D, Wang X, Wang Q. Phylogenetics and phylogeographic characteristics of coxsackievirus A16 in hand foot and mouth disease and herpangina cases collected in Beijing, China from 2019 to 2021. J Med Virol 2023; 95:e28991. [PMID: 37515317 DOI: 10.1002/jmv.28991] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/27/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023]
Abstract
Coxsackievirus A16 (CV-A16) is a significant pathogen responsible for causing hand foot and mouth disease (HFMD) and herpangina (HA). This study aimed to investigate the recent evolution and spread of CV-A16 by monitoring HFMD and HA cases in 29 hospitals across 16 districts in Beijing from 2019 to 2021. The first five cases of HFMD and the first five cases of HA each month in each hospital were included in the study. Real-time reverse transcription polymerase chain reaction was used to identify CV-A16, CV-A6, and EV-A71. From each district, two to four CV-A16 positive samples with a relatively long sampling time interval every month were selected for sequencing. A total of 3344 HFMD cases and 2704 HA cases were enrolled in this study, with 76.0% (2541/3344) of HFMD and 45.4% (1227/2704) of HA cases confirmed to be infected by enterovirus. Among the EV-positive samples, CV-A16 virus was detected in 33.61% (854/2541) of HFMD cases and 13.4% (165/1227) of HA cases, with the predominant cluster being B1a. Both B1a and B1b had a co-circulation of local and imported strains, with different origin time (1993 vs. 1995), different global distribution (14 countries vs. 10 countries), and different transmission centers but mainly distributed in the southern and eastern regions of Beijing. Strengthening surveillance of HFMD in southern and eastern regions will improve the prevention and control efficiency of enterovirus infections.
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Affiliation(s)
- Renqing Li
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Changying Lin
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Shuaibing Dong
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Jie Li
- Institute for HIV/AIDS and STD Prevention and Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Zhichao Liang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yang Yang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Da Huo
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
- School of Public Health, Capital Medical University, Beijing, China
| | - Zhiyong Gao
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Lei Jia
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Daitao Zhang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Xiaoli Wang
- School of Public Health, Capital Medical University, Beijing, China
- Beijing Office of Center for Global Health, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Quanyi Wang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing, China
- School of Public Health, Capital Medical University, Beijing, China
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Liang Y, Chen J, Wang C, Yu B, Zhang Y, Liu Z. Investigating the mechanism of Echovirus 30 cell invasion. Front Microbiol 2023; 14:1174410. [PMID: 37485505 PMCID: PMC10359910 DOI: 10.3389/fmicb.2023.1174410] [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: 02/26/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Viruses invade susceptible cells through a complex mechanism before injecting their genetic material into them. This causes direct damage to the host cell, as well as resulting in disease in the corresponding system. Echovirus type 30 (E30) is a member of the Enterovirus B group and has recently been reported to cause central nervous system (CNS) disorders, leading to viral encephalitis and viral meningitis in children. In this review, we aim to help in improving the understanding of the mechanisms of CNS diseases caused by E30 for the subsequent development of relevant drugs and vaccines.
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Affiliation(s)
- Yucai Liang
- Department of Microbiology, Weifang Medical University, Weifang, China
| | - Junbing Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing, China
| | - Congcong Wang
- Department of Microbiology, Weifang Medical University, Weifang, China
| | - Bowen Yu
- Department of Immunology, Weifang Medical University, Weifang, China
| | - Yong Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhijun Liu
- Department of Microbiology, Weifang Medical University, Weifang, China
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Aslam M, Alkheraije KA. The prevalence of foot-and-mouth disease in Asia. Front Vet Sci 2023; 10:1201578. [PMID: 37456961 PMCID: PMC10347409 DOI: 10.3389/fvets.2023.1201578] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/07/2023] [Indexed: 07/18/2023] Open
Abstract
Foot-and-mouth disease (FMD) is listed among the highly contagious diseases in animals and is endemic throughout the Asian continent. The disease is caused by the Foot-and-mouth disease virus (FMDV) and affects a wide variety of domesticated animals as well as wild ungulates. Clinically, the disease is described as a vesicular lesion on the tongue, muzzle, lips, gum, dental pad, interdigital cleft, coronary band, and heel of the foot. Sometimes these lesions give rise to lameness. Mastitis is also caused due to teat lesions. A biochemical test reveals that during FMD infection, there are elevated levels of interleukin-1 (IL-1), tumor necrosis factor-alpha, interferon-gamma (IFN-γ), interleukin-6, serum amyloid A protein, lactoferrin, mannose-binding lectin, and monocytes chemo-attractant protein-1 in the serum of infected animals. There is no specific treatment for FMD although some antivirals are given as prophylaxis and antibiotics are given to prevent secondary bacterial infection. This review presents comprehensive data on the prevalence of FMD and serotypes of FMDV that are attributable to the cause of FMD from a regional point of view. It also explains the worldwide dynamics of the seven serotypes of FMD and tries to identify epidemiological clusters of FMD in various geographical areas. Furthermore, the pathology associated with the foot and mouth disease virus along with the pathophysiology is discussed. The continent-wide prevalence and diversity patterns of FMD suggest that there is a need for stringent policies and legislation implementation regarding research and development aimed at manufacturing strain-specific vaccination, infection prevention, and control of the disease.
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Affiliation(s)
- Munazza Aslam
- Department of Pathology, Faculty of Veterinary Science, University of Agriculture, Faisalabad, Pakistan
| | - Khalid A. Alkheraije
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia
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Zhang Y, Ye ZX, Feng XX, Xu ZT, Chen JP, Zhang CX, Li JM. Prevalence of Reversed Genome Organizations for Viruses in the Family Iflaviridae, Order Picornavirales. Microbiol Spectr 2023; 11:e0473822. [PMID: 37125908 PMCID: PMC10269833 DOI: 10.1128/spectrum.04738-22] [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: 11/19/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Viruses in the order Picornavirales possess a positive-strand RNA genome that encodes structural proteins (SPs) and nonstructural proteins (NSPs). According to the recent report of the International Committee on Taxonomy of Viruses (ICTV), there are 8 families in Picornavirales, and monopartite picornaviruses in each family exhibit distinct types of genome organizations with rearranged genes coding for SPs and NSPs, namely, TypeI (5'-SPs-NSPs-3') and TypeII (5'-NSPs-SPs-3'). In the present study, 2 iflaviruses with the 2 genome types were unexpectedly identified in a damselfly host species, suggesting that these 2 genome types coexisted in the same host species, and the families of order Picornavirales might be more complex than previously thought. The consequent systematic homologous screening with all the publicly available picornaviruses successfully revealed a considerable number of candidates rearranged genome types of picornaviruses in various families of Picornavirales. Subsequently, phylogenetic trees were reconstructed based on RNA dependent RNA polymerase and coat protein, which evidently confirmed the prevalence of the 10 typeII iflaviruses in the Iflaviridae family. This suggests that genome types may not be relevant to viral taxonomy in this family. However, candidate picornaviruses with reversed genome types in the Secoviridae and Dicistroviridae families require further investigation. All in all, as the number of newly discovered viruses increases, more viruses with non-canonical genome arrangements will be uncovered, which can expand our current knowledge on the genome complexity and evolution of picornaviruses. IMPORTANCE Monopartite viruses in the order Picornavirales exhibit distinct genome arrangement of nonstructural proteins and structural proteins for each of the 8 families. Recent studies indicated that at least 4 ifla-like viruses possessed reversed genome organization in the family Iflaviridae, raising the possibility that this phenomenon may commonly present in different families of picornaviruses. Since we discovered 2 iflaviruses with exchanged structural and nonstructural proteins simultaneously in the damselfly, a systematic screening was subsequently performed for all of the current available picornaviruses (1,543 candidates). The results revealed 10 picornaviruses with reversed genome organization in the family Iflaviridae, implying that this phenomenon might prevalence in the order Picornavirales. These results will contribute to a better understanding for the future study on the genome complexity and taxonomy of picornaviruses.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
- College of Plant Protection, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Zhuang-Xin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Xiao-Xiao Feng
- Agricultural Experiment Station, Zhejiang University, Hangzhou, China
| | - Zhong-Tian Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
- College of Plant Protection, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
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Mbani CJ, Nekoua MP, Moukassa D, Hober D. The Fight against Poliovirus Is Not Over. Microorganisms 2023; 11:1323. [PMID: 37317297 DOI: 10.3390/microorganisms11051323] [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: 04/26/2023] [Revised: 05/13/2023] [Accepted: 05/14/2023] [Indexed: 06/16/2023] Open
Abstract
Poliovirus (PV), the virus that causes both acute poliomyelitis and post-polio syndrome, is classified within the Enterovirus C species, and there are three wild PV serotypes: WPV1, WPV2 and WPV3. The launch of the Global Polio Eradication Initiative (GPEI) in 1988 eradicated two of the three serotypes of WPV (WPV2 and WPV3). However, the endemic transmission of WPV1 persists in Afghanistan and Pakistan in 2022. There are cases of paralytic polio due to the loss of viral attenuation in the oral poliovirus vaccine (OPV), known as vaccine-derived poliovirus (VDPV). Between January 2021 and May 2023, a total of 2141 circulating VDPV (cVDPV) cases were reported in 36 countries worldwide. Because of this risk, inactivated poliovirus (IPV) is being used more widely, and attenuated PV2 has been removed from OPV formulations to obtain bivalent OPV (containing only types 1 and 3). In order to avoid the reversion of attenuated OPV strains, the new OPV, which is more stable due to genome-wide modifications, as well as sabin IPV and virus-like particle (VLP) vaccines, is being developed and offers promising solutions for eradicating WP1 and VDPV.
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Affiliation(s)
- Chaldam Jespère Mbani
- Laboratoire de Virologie URL3610, Université de Lille, CHU Lille, 59000 Lille, France
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences et Technique, Université Marien Ngouabi, Brazzaville BP 69, Congo
| | | | - Donatien Moukassa
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences et Technique, Université Marien Ngouabi, Brazzaville BP 69, Congo
| | - Didier Hober
- Laboratoire de Virologie URL3610, Université de Lille, CHU Lille, 59000 Lille, France
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Hadj Hassine I, Gharbi J, Amara I, Alyami A, Subei R, Almalki M, Hober D, M'hadheb MB. Cloning and Molecular Characterization of the Recombinant CVB4E2 Immunogenic Viral Protein (rVP1), as a Potential Subunit Protein for Vaccine and Immunodiagnostic Reagent Candidate. Microorganisms 2023; 11:1192. [PMID: 37317166 DOI: 10.3390/microorganisms11051192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 06/16/2023] Open
Abstract
The aim of the present study was, first, to clone the VP1 gene of the human coxsackievirus B4 strain E2 (CVB4E2) in the prokaryotic pUC19 plasmid expression vector then to compare it with the structural capsid proteins of the same strain using bioinformatic tools. PCR colony amplification followed through a restriction digestion analysis and sequencing process which affirmed the success of the cloning process. SDS-PAGE and Western Blotting were used to characterize the purified recombinant viral protein expressed in bacteria cells. The BLASTN tool revealed that the nucleotide sequence of the recombinant VP1 (rVP1) expressed by pUC19 highly matched the target nucleotide sequence of the diabetogenic CVB4E2 strain. Secondary structure and three-dimension structure prediction suggested that rVP1, such as wild-type VP1, is chiefly composed of random coils and a high percentage of exposed amino acids. Linear B-cell epitope prediction showed that several antigenic epitopes are likely present in rVP1 and CVB4E2 VP1 capsid protein. Additionally, phosphorylation site prediction revealed that both proteins may affect the signal transduction of host cells and can be involved in virus virulence. The present work highlights the usefulness of cloning and bioinformatics characterizations for gene investigation. Furthermore, the collected data are helpful for future experimental research related to the development of immunodiagnostic reagents and subunit vaccines based on the expression of immunogenic viral capsid proteins.
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Affiliation(s)
- Ikbel Hadj Hassine
- Virology and Antiviral Strategies Research Unit, Institute of Biotechnology, University of Monastir, BP74, Monastir 5000, Tunisia
| | - Jawhar Gharbi
- Department of Biological Sciences, College of Science, King Faisal University, P.O. Box 380, Al-Ahsa 31982, Saudi Arabia
| | - Imene Amara
- Virology and Antiviral Strategies Research Unit, Institute of Biotechnology, University of Monastir, BP74, Monastir 5000, Tunisia
| | - Ameera Alyami
- Department of Biological Sciences, College of Science, King Faisal University, P.O. Box 380, Al-Ahsa 31982, Saudi Arabia
| | - Reem Subei
- Department of Biological Sciences, College of Science, King Faisal University, P.O. Box 380, Al-Ahsa 31982, Saudi Arabia
| | - Mohammed Almalki
- Department of Biological Sciences, College of Science, King Faisal University, P.O. Box 380, Al-Ahsa 31982, Saudi Arabia
| | - Didier Hober
- Laboratoire de Virologie ULR3610, Université de Lille et CHU de Lille, 59000 Lille, France
| | - Manel Ben M'hadheb
- Virology and Antiviral Strategies Research Unit, Institute of Biotechnology, University of Monastir, BP74, Monastir 5000, Tunisia
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69
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Zhou L, Lu X, Zhao C, Zhang Y, Ning S, Zhang W. Characterization of a novel picornavirus prevalent in experimental rabbits ( Oryctolagus cuniculus). Heliyon 2023; 9:e15702. [PMID: 37159695 PMCID: PMC10163628 DOI: 10.1016/j.heliyon.2023.e15702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/11/2023] Open
Abstract
Here, using viral metagenomic method a novel picornavirus (named UJS-2019picorna, GenBank accession number OP821762) was discovered in fecal and blood samples of experimental rabbits (Oryctolagus cuniculus). The complete genome size of UJS-2019picorna is 7832 bp excluding the poly(A)-tail, with GC content of 44.00% and a nucleotide composition of 28.0% A, 28.0% U, 21.5% G, and 22.5% C. The viral genome has a typical picornavirus organization pattern from the 5'-3' direction: VPg-5' UTR-(L)-P1, (VP4-VP2-VP3-VP1)-P2, (2 A-2B-2C)-P3, (3 A-3B-3C-3D)-3' UTR-poly(A). The P1 region of UJS-2019picorna is related to Erbovirus with amino acid identity of 37.31%, while the P2 and P3 regions are the closest to Bopivirus with amino acid identity of 35.66%-39.53%. According to the Picornaviridae Study Group guidelines, UJS-2019picorna should be presumed to be a new genus belonging to the Picornaviridae family. Epidemiologic study revealed that this novel picornavirus was prevalent in a cohort of experimental rabbits, with prevalence rate of 23.68% (9/38) in feces and 18.4% (7/38) in blood samples. Further work is required to elucidate whether this virus is pathogenic to rabbits and whether it has influence on studies using rabbits as experimental animal.
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Affiliation(s)
- Liye Zhou
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Xiang Lu
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Chunyan Zhao
- Medical School, Wuxi Taihu University, Wuxi, Jiangsu, China
| | - Yu Zhang
- Key Laboratory of Cellular Physiology, Ministry of Education, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Songyi Ning
- School of Medicine, Jiangsu University, Zhenjiang, China
- Corresponding author.
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
- Corresponding author.
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70
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Li X, Yang E, Li X, Fan T, Guo S, Yang H, Wu B, Wang H. MAVS-Based Reporter Systems for Real-Time Imaging of EV71 Infection and Antiviral Testing. Viruses 2023; 15:v15051064. [PMID: 37243150 DOI: 10.3390/v15051064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Enterovirus consists of a variety of viruses that could cause a wide range of illness in human. The pathogenesis of these viruses remains incompletely understood and no specific treatment is available. Better methods to study enterovirus infection in live cells will help us better understand the pathogenesis of these viruses and might contribute to antiviral development. Here in this study, we developed fluorescent cell-based reporter systems that allow sensitive distinction of individual cells infected with enterovirus 71 (EV71). More importantly, these systems could be easily used for live-cell imaging by monitoring viral-induced fluorescence translocation after EV71 infection. We further demonstrated that these reporter systems could be used to study other enterovirus-mediated MAVS cleavage and they are sensitive for antiviral activity testing. Therefore, integration of these reporters with modern image-based analysis has the potential to generate new insights into enterovirus infection and facilitate antiviral development.
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Affiliation(s)
- Xiaozhen Li
- Department of Pathogen Biology and Immunology, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - E Yang
- Department of Pathogen Biology and Immunology, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Xinyu Li
- Department of Pathogen Biology and Immunology, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Tingting Fan
- Department of Pathogen Biology and Immunology, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Shangrui Guo
- Department of Pathogen Biology and Immunology, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Hang Yang
- Department of Pathogen Biology and Immunology, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Bo Wu
- Department of Pathogen Biology and Immunology, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Hongliang Wang
- Department of Pathogen Biology and Immunology, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an 710061, China
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71
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Rolton A, Charles Webb S, López-Sanmartín M, Suzanne Hutson K. Bivalve digestive epithelial virosis (DEV): a cause of disease or a natural process? J Invertebr Pathol 2023; 198:107924. [PMID: 37085110 DOI: 10.1016/j.jip.2023.107924] [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: 12/06/2022] [Revised: 03/20/2023] [Accepted: 04/16/2023] [Indexed: 04/23/2023]
Abstract
Epithelial hyperplasia and sloughing of the digestive gland in bivalve mollusks are a global phenomenon and occur in species of commercial interest and cultural significance to indigenous peoples. Where hemocytosis, hyperplasia, and necrosis of digestive tubule cells have been observed associated with electron-dense uncoated virus-like particles (VLPs) 25-45nm in diameter, the condition has been named digestive epithelial virosis (DEV). This condition has been associated with mortalities of some bivalve species in New Zealand. Similar digestive gland alterations, but without detection of associated VLPs, have been reported in other bivalve species worldwide and are termed "DEV-like" since no virus link has been demonstrated. It remains unclear if DEV is an infectious condition and whether associated VLPs are the cause, a contributor, or simply associated with the observed condition. It is also unclear whether DEV or DEV-like conditions pose a biosecurity or economic threat, or alternatively, whether they reflect a natural cyclic event that does not require disease management. In this mini-review, we summarize the history of digestive epithelial alteration with VLPs (i.e., DEV) or without observation of VLPs (i.e., DEV-like), and we examine the evidence for and against viral-like particles as the cause of DEV in bivalves. We also explore other viral afflictions of bivalves and non-infectious agents, such as harmful algae and xenotoxins, that could elicit similar tissue alterations. Future recommendations for approaches to identify key risk factors that lead to the development of digestive epithelial alterations such as DEV include histological characterization of the digestive gland of marine mollusks; the use of metagenome analysis to design primers that could be used for detection of VLPs and to study host microbiota; disease challenges demonstrating that DEV causes pathology and the relationship between DEV intensity and morbidity/mortality.
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Affiliation(s)
- Anne Rolton
- Cawthron Institute, Nelson, 7010, New Zealand.
| | | | - Monserrat López-Sanmartín
- Laboratorio de Bioquímica, Facultad de Ciencias Experimentales, Campus de Excelencia Internacional del Mar (CEIMAR), Universidad de Huelva, 2110, Huelva, Spain
| | - Kate Suzanne Hutson
- Cawthron Institute, Nelson, 7010, New Zealand; College of Science and Engineering, Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, 4811, Australia
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Tushabe P, Bwogi J, Eliku JP, Aine F, Birungi M, Gaizi J, Nakabazzi L, Kabaliisa T, Turyahabwe I, Namuwulya P, Nanteza MB, Bukenya H, Kanyesigye C, Katushabe E, Ampeire I, Kisakye A, Bakamutumaho B, Byabamazima CR. Environmental surveillance detects circulating vaccine-derived poliovirus type 2 that was undetected by acute flaccid paralysis surveillance in 2021 in Uganda. Arch Virol 2023; 168:140. [PMID: 37059887 PMCID: PMC10104764 DOI: 10.1007/s00705-023-05759-w] [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: 01/10/2023] [Accepted: 03/14/2023] [Indexed: 04/16/2023]
Abstract
The success of the global polio eradication initiative is threatened by the genetic instability of the oral polio vaccine, which can result in the emergence of pathogenic vaccine-derived polioviruses following prolonged replication in the guts of individuals with primary immune deficiencies or in communities with low vaccination coverage. Through environmental surveillance, circulating vaccine-derived poliovirus type 2 was detected in Uganda in the absence of detection by acute flaccid paralysis (AFP) surveillance. This underscores the sensitivity of environmental surveillance and emphasizes its usefulness in supplementing AFP surveillance for poliovirus infections in the race towards global polio eradication.
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Affiliation(s)
- Phionah Tushabe
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda.
| | - Josephine Bwogi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - James Peter Eliku
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Francis Aine
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Molly Birungi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joseph Gaizi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Lucy Nakabazzi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Theopista Kabaliisa
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Irene Turyahabwe
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Prossy Namuwulya
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Mary Bridget Nanteza
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Henry Bukenya
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Edson Katushabe
- World Health Organization, Uganda Country Office, Kampala, Uganda
| | | | - Annet Kisakye
- World Health Organization, Uganda Country Office, Kampala, Uganda
| | - Barnabas Bakamutumaho
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Charles R Byabamazima
- WHO Inter-Country Support Team Office for Eastern and Southern Africa (IST/ESA), Harare, Zimbabwe
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73
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Masmoudi F, Santos-Ferreira N, Pajkrt D, Wolthers KC, DeGroot J, Vlaming MLH, Rocha-Pereira J, Buti L. Evaluation of 3D Human Intestinal Organoids as a Platform for EV-A71 Antiviral Drug Discovery. Cells 2023; 12:cells12081138. [PMID: 37190047 DOI: 10.3390/cells12081138] [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: 01/18/2023] [Revised: 03/24/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Enteroviruses are a leading cause of upper respiratory tract, gastrointestinal, and neurological infections. Management of enterovirus-related diseases has been hindered by the lack of specific antiviral treatment. The pre-clinical and clinical development of such antivirals has been challenging, calling for novel model systems and strategies to identify suitable pre-clinical candidates. Organoids represent a new and outstanding opportunity to test antiviral agents in a more physiologically relevant system. However, dedicated studies addressing the validation and direct comparison of organoids versus commonly used cell lines are lacking. Here, we described the use of human small intestinal organoids (HIOs) as a model to study antiviral treatment against human enterovirus 71 (EV-A71) infection and compared this model to EV-A71-infected RD cells. We used reference antiviral compounds such as enviroxime, rupintrivir, and 2'-C-methylcytidine (2'CMC) to assess their effects on cell viability, virus-induced cytopathic effect, and viral RNA yield in EV-A71-infected HIOs and cell line. The results indicated a difference in the activity of the tested compounds between the two models, with HIOs being more sensitive to infection and drug treatment. In conclusion, the outcome reveals the value added by using the organoid model in virus and antiviral studies.
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Affiliation(s)
- Fatma Masmoudi
- Charles River Laboratories, 2333 CR Leiden, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC Location Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Nanci Santos-Ferreira
- Laboratory of Virology and Chemotherapy, KU Leuven-Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000 Leuven, Belgium
| | - Dasja Pajkrt
- OrganoVIR Labs, Pediatric Infectious Diseases, Emma Children's Hospital, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Katja C Wolthers
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC Location Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Jeroen DeGroot
- Charles River Laboratories, 2333 CR Leiden, The Netherlands
| | | | - Joana Rocha-Pereira
- Laboratory of Virology and Chemotherapy, KU Leuven-Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000 Leuven, Belgium
| | - Ludovico Buti
- Charles River Laboratories, 2333 CR Leiden, The Netherlands
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74
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Zhang Y, Wu S, Liu W, Hu Z. Current status and future direction of duck hepatitis A virus vaccines. Avian Pathol 2023; 52:89-99. [PMID: 36571394 DOI: 10.1080/03079457.2022.2162367] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Duck viral hepatitis (DVH), mainly caused by duck hepatitis A virus (DHAV), is a highly fatal and rapidly spreading infectious disease of young ducklings that seriously jeopardizes the duck industry worldwide. DHAV type 1 (DHAV-1) is the main genotype responsible for disease outbreaks since 1945, and the disease situation is complicated by the emergence and dissemination of a novel genotype (DHAV-3) in some countries in Asia and Africa. Live attenuated DHAV vaccines are widely used to induce a considerable degree of protection in ducklings. Breeder ducks are immunized with inactivated or/and live DHAV vaccines to achieve satisfactory levels of passive immunity in progeny. In addition, novel characteristics of virus transmission, pathogenicity and pathogenesis of DHAV were recently characterized, necessitating the development of new vaccines and effective vaccination programmes against DVH. Therefore, a systematic dissection of the profiles, strengths and shortcomings of the available DHAV vaccines is essential. Moreover, to further increase the efficiency of vaccine production and administration, the development of next-generation DHAV vaccines using cutting-edge technologies is also required. In this review, based on a comprehensive summary of the research advances in the epidemiology, pathogenicity, and genomic features of DHAV, we focus on reviewing and analysing the features of the commercial and experimental DHAV vaccines. We also propose perspectives for disease control based on the specific disease situations in different countries. This review provides essential information for vaccine development and disease control of DVH.
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Affiliation(s)
- Yanyan Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, People's Republic of China.,Key Laboratory of Animal Infectious Diseases, School of Veterinary Medicine, Yangzhou University, Yangzhou, People's Republic of China
| | - Shuang Wu
- Jiangsu Agri-animal Husbandry Vocational College, Jiangsu Key Laboratory for High-Tech Research and Development of Veterinary Biopharmaceuticals, Taizhou, People's Republic of China
| | - Wenbo Liu
- Key Laboratory of Animal Infectious Diseases, School of Veterinary Medicine, Yangzhou University, Yangzhou, People's Republic of China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, People's Republic of China
| | - Zenglei Hu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, People's Republic of China.,Key Laboratory of Animal Infectious Diseases, School of Veterinary Medicine, Yangzhou University, Yangzhou, People's Republic of China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, People's Republic of China
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Abstract
Viruses lack the properties to replicate independently due to the limited resources encoded in their genome; therefore, they hijack the host cell machinery to replicate and survive. Picornaviruses get the prerequisite for effective protein synthesis through specific sequences known as internal ribosome entry sites (IRESs). In the past 2 decades, significant progress has been made in identifying different types of IRESs in picornaviruses. This review will discuss the past and current findings related to the five different types of IRESs and various internal ribosome entry site trans-acting factors (ITAFs) that either promote or suppress picornavirus translation and replication. Some IRESs are inefficient and thus require ITAFs. To achieve their full efficiency, they recruit various ITAFs, which enable them to translate more effectively and efficiently, except type IV IRES, which does not require any ITAFs. Although there are two kinds of ITAFs, one promotes viral IRES-dependent translation, and the second type restricts. Picornaviruses IRESs are classified into five types based on their use of sequence, ITAFs, and initiation factors. Some ITAFs regulate IRES activity by localizing to the viral replication factories in the cytoplasm. Also, some drugs, chemicals, and herbal extracts also regulate viral IRES-dependent translation and replication. Altogether, this review will elaborate on our understanding of the past and recent advancements in the IRES-dependent translation and replication of picornaviruses. IMPORTANCE The family Picornaviridae is divided into 68 genera and 158 species. The viruses belonging to this family range from public health importance, such as poliovirus, enterovirus A71, and hepatitis A virus, to animal viruses of great economic importance, such as foot-and-mouth disease virus. The genomes of picornaviruses contain 5' untranslated regions (5' UTRs), which possess crucial and highly structured stem-loops known as IRESs. IRES assemble the ribosomes and facilitate the cap-independent translation. Virus-host interaction is a hot spot for researchers, which warrants deep insight into understanding viral pathogenesis better and discovering new tools and ways for viral restriction to improve human and animal health. The cap-independent translation in the majority of picornaviruses is modulated by ITAFs, which bind to various IRES regions to initiate the translation. The discoveries of ITAFs substantially contributed to understanding viral replication behavior and enhanced our knowledge about virus-host interaction more effectively than ever before. This review discussed the various types of IRESs found in Picornaviridae, past and present discoveries regarding ITAFs, and their mechanism of action. The herbal extracts, drugs, and chemicals, which indicated their importance in controlling viruses, were also summarized. In addition, we discussed the movement of ITAFs from the nucleus to viral replication factories. We believe this review will stimulate researchers to search for more novel ITAFs, drugs, herbal extracts, and chemicals, enhancing the understanding of virus-host interaction.
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Viljakainen L, Fürst MA, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei T, Cremer S. Antiviral immune response reveals host-specific virus infections in natural ant populations. Front Microbiol 2023; 14:1119002. [PMID: 37007485 PMCID: PMC10060816 DOI: 10.3389/fmicb.2023.1119002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management.
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Affiliation(s)
- Lumi Viljakainen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
- *Correspondence: Lumi Viljakainen,
| | - Matthias A. Fürst
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Anna V. Grasse
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jaana Jurvansuu
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Jinook Oh
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Lassi Tolonen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Thomas Eder
- Centre for Microbiology and Environmental Systems Science, Division of Computational System Biology, University of Vienna, Vienna, Austria
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, Division of Computational System Biology, University of Vienna, Vienna, Austria
| | - Sylvia Cremer
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Sylvia Cremer,
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77
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Detection and genetic characterization of canine kobuvirus from stray dogs in Shanghai, China. Arch Virol 2023; 168:112. [PMID: 36918497 PMCID: PMC10013983 DOI: 10.1007/s00705-023-05710-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/23/2022] [Indexed: 03/16/2023]
Abstract
In this study, rectal samples collected from 60 stray dogs in dog shelters were screened for canine kobuvirus and other enteroviruses by quantitative real-time reverse transcription polymerase chain reaction. Canine kobuvirus was detected in 25% (15/60) of the samples. In the 15 positive samples, the coinfection rates of canine distemper virus, canine coronavirus, canine astrovirus, canine norovirus, and canine rotavirus were 26.67%, 20.00%, 73.33%, 0%, and 20.00%, respectively. Phylogenetic analysis based on partial VP1 sequences identified a novel canine kobuvirus that was a recombinant of canine and feline kobuvirus. Bayesian evolutionary analysis revealed that the rate of evolution of the VP1 gene of canine kobuvirus was 1.36 × 10-4 substitutions per site per year (95% highest posterior density interval, 6.28 × 10-7 - 4.30 × 10-4 substitutions per site per year). Finally, the divergence time of VP1 was around 19.44 years ago (95% highest posterior density interval, 12.96-27.57 years).
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78
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Luo Y, Liu H, Zou Y, Qiao C, Su Y, Zhu X, Zhang G, Huang W, Qin Y, Pan Y, Huang W. Molecular Epidemiology of Bovine Enteroviruses and Genome Characterization of Two Novel Bovine Enterovirus Strains in Guangxi, China. Microbiol Spectr 2023; 11:e0378522. [PMID: 36877012 PMCID: PMC10101013 DOI: 10.1128/spectrum.03785-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/04/2023] [Indexed: 03/07/2023] Open
Abstract
Bovine enterovirus (BEV) is a highly infectious pathogen that may cause respiratory and gastrointestinal disease outbreaks in cattle. This study aimed to investigate the prevalence and genetic characteristics of BEVs in Guangxi Province, China. A total of 1,168 fecal samples from 97 different bovine farms were collected between October 2021 and July 2022 in Guangxi Province, China. BEV was confirmed using a reverse transcription-PCR (RT-PCR) method targeting the 5' untranslated region (UTR), and isolates were genotyped by sequencing their genomes. The nearly complete genome sequences of eight BEV strains showing cytopathic effects in MDBK cells were determined and analyzed. In total, 125 (10.7%) of 1,168 fecal samples were positive for BEV. BEV infection was significantly associated with farming patterns and clinical symptoms (P < 0.05; odds ratio [OR] > 1). Molecular characterization indicated that five BEV strains from this study belonged to EV-E2 and one strain to EV-E4. Two BEV strains (GXNN2204 and GXGL2215) could not be assigned to a known type. Strain GXGL2215 showed the closest genetic relationship with GX1901 (GenBank accession number MN607030; China) in its VP1 (67.5%) and P1 (74.7%) and with NGR2017 (MH719217; Nigeria) in its polyprotein (72.0%). It was also close to the EV-E4 strain GXYL2213 from this study when the complete genome (81.7%) was compared. Strain GXNN2204 showed the closest genetic relationship with Ho12 (LC150008; Japan) in the VP1 (66.5%), P1 (71.6%), and polyprotein (73.2%). Genome sequence analysis suggested that strains GXNN2204 and GXGL2215 originated from the genomic recombination of EV-E4 and EV-F3 and EV-E2 and EV-E4, respectively. This study reports the cocirculation of multiple BEV types and the identification of two novel BEV strains in Guangxi, China, and it will provide further insights into the epidemiology and evolution of BEV in China. IMPORTANCE Bovine enterovirus (BEV) is a pathogen that causes intestinal, respiratory, and reproductive disease infections in cattle. This study reports on the widespread prevalence and biological characteristics of the different BEV types which currently exist in Guangxi Province, China. It also provides a reference for the study of the prevalence of BEV in China.
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Affiliation(s)
- Yuhang Luo
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, China
| | - Huanghao Liu
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, China
| | - Yanlin Zou
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, China
| | - Chengpeng Qiao
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, China
| | - Yaquan Su
- Guangxi Agricultural Vocational University, Nanning, China
| | - Xinyue Zhu
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, China
| | - Guangxin Zhang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, China
| | - Wenfei Huang
- Guangxi Agricultural Vocational University, Nanning, China
| | - Yifeng Qin
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, China
| | - Yan Pan
- Guangxi Agricultural Vocational University, Nanning, China
| | - Weijian Huang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
- Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, China
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Imai R, Rongduo W, Kaixin L, Borjigin S, Matsumura H, Masuda T, Ozawa T, Oba M, Makino S, Nagai M, Mizutani T. Novel recombinant porcine enterovirus G viruses lacking structural proteins are maintained in pig farms in Japan. J Vet Med Sci 2023; 85:252-265. [PMID: 36543238 PMCID: PMC10017297 DOI: 10.1292/jvms.22-0505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Type 1 recombinant enterovirus G (EV-G), which carries the papain-like cysteine protease (PLCP) gene of torovirus between its 2C/3A regions, and type 2 recombinant EV-G, which carries the torovirus PLCP gene with its flanking regions having non-EV-G sequences in place of the viral structural genes, have been detected in pig farms in several countries. In a previous study, we collected 222 fecal samples from 77 pig farms from 2104 to 2016 and detected one type 2 recombinant EV-G genome by metagenomics sequencing. In this study, we reanalyzed the metagenomic data and detected 11 type 2 recombinant EV-G genomes. In addition, we discovered new type 2 recombinant EV-G genomes of the two strains from two pig farms samples in 2018 and 2019. Thus, we identified the genomes of 13 novel type 2 recombinant EV-Gs isolated from several pig farms in Japan. Type 2 recombinant EV-G has previously been detected only in neonatal piglets. The present findings suggest that type 2 recombinant EV-G replicates in weaning piglets and sows. The detection of type 1 recombinant EV-Gs and type 2 recombinant EV-Gs at 3-year and 2-year intervals, respectively, from the same pig farm suggests that the viruses were persistently infecting or circulating in these farms.
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Affiliation(s)
- Ryo Imai
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Graduate School of Agriculture Cooperative Division of Veterinary Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Wen Rongduo
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Graduate School of Agriculture Cooperative Division of Veterinary Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Li Kaixin
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Sumiya Borjigin
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hirofumi Matsumura
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | | | - Takuji Ozawa
- Japanese Animal Hospital Association, Tokyo, Japan
| | - Mami Oba
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Shinji Makino
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Makoto Nagai
- Laboratory of Infectious Diseases, Department of Veterinary Medicine, Faculty of Veterinary Medicine, Azabu University, Kanagawa, Japan
| | - Tetsuya Mizutani
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Graduate School of Agriculture Cooperative Division of Veterinary Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
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80
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Xiao J, Wang J, Lu H, Song Y, Sun D, Han Z, Li J, Yang Q, Yan D, Zhu S, Pei Y, Wang X, Xu W, Zhang Y. Genomic Epidemiology and Transmission Dynamics of Global Coxsackievirus B4. Viruses 2023; 15:v15020569. [PMID: 36851788 PMCID: PMC9961479 DOI: 10.3390/v15020569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The aim of this study was to determine the global genetic diversity and transmission dynamics of coxsackievirus B4 (CVB4) and to propose future directions for disease surveillance. Next-generation sequencing was performed to obtain the complete genome sequence of CVB4, and the genetic diversity and transmission dynamics of CVB4 worldwide were analyzed using bioinformatics methods such as phylogenetic analysis, evolutionary dynamics, and phylogeographic analysis. Forty complete genomes of CVB4 were identified from asymptomatic infected individuals and hand, foot, and mouth disease (HFMD) patients. Frequent recombination between CVB4 and EV-B multiple serotypes in the 3Dpol region was found and formed 12 recombinant patterns (A-L). Among these, the CVB4 isolated from asymptomatic infected persons and HFMD patients belonged to lineages H and I, respectively. Transmission dynamics analysis based on the VP1 region revealed that CVB4 epidemics in countries outside China were dominated by the D genotype, whereas the E genotype was dominant in China, and both genotypes evolved at a rate of > 6.50 × 10-3 substitutions/site/year. CVB4 spreads through the population unseen, with the risk of disease outbreaks persisting as susceptible individuals accumulate. Our findings add to publicly available CVB4 genomic sequence data and deepen our understanding of CVB4 molecular epidemiology.
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Affiliation(s)
- Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis and National Health Commission Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jianxing Wang
- Shandong Center for Disease Control and Prevention, Jinan 250014, China
| | - Huanhuan Lu
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis and National Health Commission Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis and National Health Commission Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Dapeng Sun
- Shandong Center for Disease Control and Prevention, Jinan 250014, China
| | - Zhenzhi Han
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing 102206, China
| | - Jichen Li
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis and National Health Commission Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Qian Yang
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis and National Health Commission Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis and National Health Commission Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis and National Health Commission Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yaowen Pei
- Shandong Center for Disease Control and Prevention, Jinan 250014, China
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Jinan 250014, China
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis and National Health Commission Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis and National Health Commission Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- Correspondence:
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81
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Oba M, Obinata S, Takemae H, Kazama K, Oguro M, Ito K, Kakinuma S, Ishida H, Murakami H, Sakaguchi S, Mizutani T, Nagai M. Prevalence and genetic diversity in bovine parechovirus infecting Japanese cattle. Arch Virol 2023; 168:91. [PMID: 36786868 DOI: 10.1007/s00705-023-05712-x] [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: 12/07/2022] [Accepted: 01/02/2023] [Indexed: 02/15/2023]
Abstract
The first bovine parechovirus (Bo_ParV) was reported in 2021, and currently, only two nearly complete genome sequences of Bo_ParV are available. In this study, we detected Bo_ParVs in 10 out of 158 bovine fecal samples tested using real-time RT-PCR, and Bo_ParVs were isolated from three of these samples using MA104 cells. Analysis of the P1 region revealed that Bo_ParVs shared high pairwise amino acid sequence similarity (≥ 95.7% identity), suggesting antigenic similarity among Bo_ParVs, whereas nucleotide sequence identity values (≥ 84.8%) indicated more variability. A recombination breakpoint was identified in the 2B region, which may influence the evolution of this virus.
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Affiliation(s)
- Mami Oba
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 183-8509, Fuchu, Tokyo, Japan.,School of Veterinary Medicine, Azabu University, 252-5201, Sagamihara, Kanagawa, Japan
| | - Shiho Obinata
- School of Veterinary Medicine, Azabu University, 252-5201, Sagamihara, Kanagawa, Japan
| | - Hitoshi Takemae
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 183-8509, Fuchu, Tokyo, Japan
| | - Kei Kazama
- School of Veterinary Medicine, Azabu University, 252-5201, Sagamihara, Kanagawa, Japan
| | | | - Kazuki Ito
- Veterinary Clinic, Saitama Agricultural Mutual Aid Association, 360-0843, Kumagaya, Saitama, Japan
| | - Seiichi Kakinuma
- Kakinuma Veterinary Hospital, Kodama-chou, 367-0212, Kodama, Honjou, Saitama, Japan
| | - Hiroho Ishida
- School of Veterinary Medicine, Azabu University, 252-5201, Sagamihara, Kanagawa, Japan
| | - Hironobu Murakami
- School of Veterinary Medicine, Azabu University, 252-5201, Sagamihara, Kanagawa, Japan
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 569-8686, Osaka, Japan
| | - Tetsuya Mizutani
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 183-8509, Fuchu, Tokyo, Japan
| | - Makoto Nagai
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 183-8509, Fuchu, Tokyo, Japan. .,School of Veterinary Medicine, Azabu University, 252-5201, Sagamihara, Kanagawa, Japan.
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82
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Zhang Q, Zhang F, Chang X, Hu J, Zhang Z, Cui X, Zheng X, Wang X. A Neonatal Murine Model for Caprine Enterovirus Infection and the Viral Tissue Tropism. Viruses 2023; 15:v15020475. [PMID: 36851688 PMCID: PMC9962493 DOI: 10.3390/v15020475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
As the first caprine enterovirus identified from goat herds characterized by severe diarrhea with a high morbidity and mortality rate, the underlying pathogenesis and tissue tropism for CEV-JL14 remains largely unknown. Here, we reported the establishment of a neonatal murine model for caprine enterovirus and the unveiling of the tissue tropism and underlying pathogenesis for CEV-JL14 enterovirus. Susceptible murine strains, the infective dose, the infective routes, viral loads, and tissue tropism for CEV-JL14 infection were determined. The findings showed that ICR mice were susceptible to CEV-JL14 infection via all infection routes. Tissue viral load analysis showed that CEV-JL14 was detected in almost all tissues including the heart, liver, spleen, lung, kidney, intestine, brain, and muscle, with significantly higher viral loads in the heart, liver, lung, kidney, and intestine. These results revealed the pattern of viral load and tropism for CEV-JL14 and provided a model system for elucidating the pathogenesis of CEV-JL14 viruses.
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83
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Miyamoto M, Himeda T, Ishihara K, Okuwa T, Kobayashi D, Nameta M, Karasawa Y, Chunhaphinyokul B, Yoshida Y, Tanaka N, Higuchi M, Komuro A. Theilovirus 3C Protease Cleaves the C-Terminal Domain of the Innate Immune RNA Sensor, Melanoma Differentiation-Associated Gene 5, and Impairs Double-Stranded RNA-Mediated IFN Response. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:335-347. [PMID: 36525065 DOI: 10.4049/jimmunol.2200565] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/09/2022] [Indexed: 01/04/2023]
Abstract
Melanoma differentiation-associated gene 5 (MDA5), a member of the retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), has pivotal roles in innate immune responses against many positive-stranded RNA viruses, including picornavirus and coronavirus. Upon engagement with dsRNA derived from viral infection, MDA5 initiates coordinated signal transduction leading to type I IFN induction to restrict viral replication. In this study, we describe a targeted cleavage events of MDA5 by the 3C protease from Theilovirus. Upon ectopic expression of theilovirus 3C protease from Saffold virus or Theiler's murine encephalomyelitis virus but not encephalomyocarditis virus, fragments of cleaved MDA5 were observed in a dose-dependent manner. When enzymatically inactive Theilovirus 3C protease was expressed, MDA5 cleavage was completely abrogated. Mass spectrometric analysis identified two cleavage sites at the C terminus of MDA5, cleaving off one of the RNA-binding domains. The same cleavage pattern was observed during Theilovirus infection. The cleavage of MDA5 by Theilovirus protease impaired ATP hydrolysis, RNA binding, and filament assembly on RNA, resulting in dysfunction of MDA5 as an innate immune RNA sensor for IFN induction. Furthermore, the cleavage-resistant MDA5 mutant against the 3C protease showed an enhanced IFN response during Saffold virus infection, indicating that Theilovirus has a strategy to circumvent the antiviral immune response by cleaving MDA5 using 3C protease. In summary, these data suggest MDA5 cleavage by 3C protease as a novel immune evasive strategy of Theilovirus.
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Affiliation(s)
- Masahiko Miyamoto
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Toshiki Himeda
- Department of Microbiology, Kanazawa Medical University School of Medicine, Ishikawa, Japan
| | - Kazuki Ishihara
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Takako Okuwa
- Department of Microbiology, Kanazawa Medical University School of Medicine, Ishikawa, Japan
| | - Daiki Kobayashi
- Omics Unit, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masaaki Nameta
- Electron Microscope Core Facility, Niigata University, Niigata, Japan
| | - Yu Karasawa
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Benyapa Chunhaphinyokul
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Yutaka Yoshida
- Department of Structural Pathology, Kidney Research Center, Niigata University, Niigata, Japan; and
| | - Nobuyuki Tanaka
- Division of Tumor Immunology, Miyagi Cancer Center Research Institute, Medeshima-Shiode, Natori, Miyagi, Japan
| | - Masaya Higuchi
- Department of Microbiology, Kanazawa Medical University School of Medicine, Ishikawa, Japan
| | - Akihiko Komuro
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
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84
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Whole-genome characterization of avian picornaviruses from diarrheic broiler chickens co-infected with multiple picornaviruses in Iran. Virus Genes 2023; 59:79-90. [PMID: 36239871 DOI: 10.1007/s11262-022-01938-0] [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: 06/19/2022] [Accepted: 09/25/2022] [Indexed: 01/13/2023]
Abstract
Gastrointestinal symptoms in poultry are caused by several factors, such as infecting viruses. Several avian picornaviruses can cause diarrhea in these valuable animals. Poultry flocks in Iran suffer from gastrointestinal diseases, and information on picornaviruses is limited. In this study, two genera of avian picornaviruses were isolated from poultry and identified by the viral metagenomics. Fecal samples were collected from broiler chicken flocks affected with diarrhea from Gilan province Iran. The results showed that Eastern chicken flocks carried two genera of picornaviridae belonging to Sicinivirus A (SiV A) and Megrivirus C (MeV C). The Western chicken flocks carried SiV A based on whole-genome sequencing data. SiV A had type II IRES and MeV C contained a type IVB IRES 5'UTR. Phylogenetic results showed that all these three picornaviruses were similar to the Hungarian isolates. Interestingly, two different picornavirus genera were simultaneously co-infected with Eastern flocks. This phenomenon could increase and facilitate the recombination and evolution rate of picornaviruses and consequently cause this diversity of gastrointestinal diseases in poultry. This is the first report and complete genome sequencing of Sicinivirus and Megrivirus in Iran. Further studies are needed to evaluate the pathogenic potential of these picornaviruses.
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85
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Hill SC, François S, Thézé J, Smith AL, Simmonds P, Perrins CM, van der Hoek L, Pybus OG. Impact of host age on viral and bacterial communities in a waterbird population. THE ISME JOURNAL 2023; 17:215-226. [PMID: 36319706 PMCID: PMC9860062 DOI: 10.1038/s41396-022-01334-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Abstract
Wildlife harbour pathogens that can harm human or livestock health and are the source of most emerging infectious diseases. It is rarely considered how changes in wildlife population age-structures or how age-stratified behaviours might alter the level of pathogen detection within a species, or risk of spillover to other species. Micro-organisms that occur in healthy animals can be an important model for understanding and predicting the dynamics of pathogens of greater health concern, which are hard to study in wild populations due to their relative rarity. We therefore used a metagenomic approach to jointly characterise viral and prokaryotic carriage in faeces collected from a healthy wild bird population (Cygnus olor; mute swan) that has been subject to long-term study. Using 223 samples from known individuals allowed us to compare differences in prokaryotic and eukaryotic viral carriage between adults and juveniles at an unprecedented level of detail. We discovered and characterised 77 novel virus species, of which 21% belong putatively to bird-infecting families, and described the core prokaryotic microbiome of C. olor. Whilst no difference in microbiota diversity was observed between juveniles and adult individuals, 50% (4/8) of bird-infecting virus families (picornaviruses, astroviruses, adenoviruses and bornaviruses) and 3.4% (9/267) of prokaryotic families (including Helicobacteraceae, Spirochaetaceae and Flavobacteriaceae families) were differentially abundant and/or prevalent between juveniles and adults. This indicates that perturbations that affect population age-structures of wildlife could alter circulation dynamics and spillover risk of microbes, potentially including pathogens.
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Affiliation(s)
- Sarah C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
- Department of Biology, University of Oxford, Oxford, UK.
| | - Sarah François
- Department of Biology, University of Oxford, Oxford, UK.
| | - Julien Thézé
- Department of Biology, University of Oxford, Oxford, UK
- UMR EPIA, Université Clermont Auvergne, INRAE, VetAgro Sup, Saint-Genès-Champanelle, France
| | - Adrian L Smith
- Department of Biology, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, UK
| | | | - Lia van der Hoek
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Oliver G Pybus
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
- Department of Biology, University of Oxford, Oxford, UK.
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Bero DM, da Silva EE, Júnior IPDS, Nhassengo SA, Machado RS, Bauhofer AFL, Chilaúle JJ, Munlela B, Guimarães E, Cossa-Moiane I, Sambo J, Anapakala E, Cassocera M, Coutinho-Manhique L, Chissaque A, Langa JS, Burlandy F, de Deus N. Enterovirus detection in stool samples from Mozambican children with acute gastroenteritis. Acta Trop 2023; 238:106755. [PMID: 36379257 DOI: 10.1016/j.actatropica.2022.106755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/15/2022]
Abstract
Enteroviruses (EV) are predominantly enteric viruses, present in all parts of the world causing disease in humans with a broad spectrum of clinical presentations. The purpose of this study was to identify non-polio enteroviruses (NPEV) in stool samples collected from children with acute gastroenteritis (AGE) symptoms of unknown etiology in four provinces (Maputo, Nampula, Sofala and Zambézia) of Mozambique. From June 2014 to March 2018, 327 stool samples were collected from children hospitalized with AGE in health care units. NPEVs were detected in 52 samples (52/327; 15.9%) and were more frequent in children under 5 years of age. The age group from 12 to 23 months was the most affected and showed more severity of disease. We also identified 26 different EV-types with the following detection pattern EV-B>EV-C>EV-A. The major EV-types were EV-A119 (9/52; 17.3%) and EV-C99 (8/52; 15.4%), accounting for 32.7% of the total. In addition to EV-A119, other uncommon EV-types were also identified, such as EV-B75, EV-B97 and EV-C113. The current study shows a high heterogeneity of EV types circulating in children with AGE in Mozambique as well as the identification of rarely described enteroviruses.
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Affiliation(s)
- Diocreciano Matias Bero
- Instituto Nacional de Saúde, Vila de Marracuene, EN1, Parcela N° 3943, Província de Maputo, Moçambique.
| | - Edson Elias da Silva
- Enterovirus Laboratory, Oswaldo Cruz Institute, Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ CEP 21040-360, Brazil
| | - Ivanildo Pedro de Sousa Júnior
- Enterovirus Laboratory, Oswaldo Cruz Institute, Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ CEP 21040-360, Brazil
| | - Sheila António Nhassengo
- Instituto Nacional de Saúde, Vila de Marracuene, EN1, Parcela N° 3943, Província de Maputo, Moçambique
| | - Raiana Scerni Machado
- Enterovirus Laboratory, Oswaldo Cruz Institute, Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ CEP 21040-360, Brazil
| | - Adilson Fernando Loforte Bauhofer
- Instituto Nacional de Saúde, Vila de Marracuene, EN1, Parcela N° 3943, Província de Maputo, Moçambique; Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Jorfélia José Chilaúle
- Instituto Nacional de Saúde, Vila de Marracuene, EN1, Parcela N° 3943, Província de Maputo, Moçambique
| | - Benilde Munlela
- Instituto Nacional de Saúde, Vila de Marracuene, EN1, Parcela N° 3943, Província de Maputo, Moçambique
| | - Esperança Guimarães
- Instituto Nacional de Saúde, Vila de Marracuene, EN1, Parcela N° 3943, Província de Maputo, Moçambique; Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Idalécia Cossa-Moiane
- Instituto Nacional de Saúde, Vila de Marracuene, EN1, Parcela N° 3943, Província de Maputo, Moçambique; Institute of Tropical Medicine, Antwerp, Belgium
| | - Júlia Sambo
- Instituto Nacional de Saúde, Vila de Marracuene, EN1, Parcela N° 3943, Província de Maputo, Moçambique; Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Elda Anapakala
- Instituto Nacional de Saúde, Vila de Marracuene, EN1, Parcela N° 3943, Província de Maputo, Moçambique
| | - Marta Cassocera
- Instituto Nacional de Saúde, Vila de Marracuene, EN1, Parcela N° 3943, Província de Maputo, Moçambique; Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Lena Coutinho-Manhique
- Instituto Nacional de Saúde, Vila de Marracuene, EN1, Parcela N° 3943, Província de Maputo, Moçambique
| | - Assucênio Chissaque
- Instituto Nacional de Saúde, Vila de Marracuene, EN1, Parcela N° 3943, Província de Maputo, Moçambique; Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Jerónimo S Langa
- Instituto Nacional de Saúde, Vila de Marracuene, EN1, Parcela N° 3943, Província de Maputo, Moçambique
| | - Fernanda Burlandy
- Enterovirus Laboratory, Oswaldo Cruz Institute, Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ CEP 21040-360, Brazil
| | - Nilsa de Deus
- Instituto Nacional de Saúde, Vila de Marracuene, EN1, Parcela N° 3943, Província de Maputo, Moçambique
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87
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Bouin A, Vu MN, Al-Hakeem A, Tran GP, Nguyen JHC, Semler BL. Enterovirus-Cardiomyocyte Interactions: Impact of Terminally Deleted Genomic RNAs on Viral and Host Functions. J Virol 2023; 97:e0142622. [PMID: 36475766 PMCID: PMC9888282 DOI: 10.1128/jvi.01426-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
Group B enteroviruses, including coxsackievirus B3 (CVB3), can persistently infect cardiac tissue and cause dilated cardiomyopathy. Persistence is linked to 5' terminal deletions of viral genomic RNAs that have been detected together with minor populations of full-length genomes in human infections. In this study, we explored the functions and interactions of the different viral RNA forms found in persistently infected patients and their putative role(s) in pathogenesis. Since enterovirus cardiac pathogenesis is linked to the viral proteinase 2A, we investigated the effect of different terminal genomic RNA deletions on 2A activity. We discovered that 5' terminal deletions in CVB3 genomic RNAs decreased the levels of 2A proteinase activity but could not abrogate it. Using newly generated viral reporters encoding nano-luciferase, we found that 5' terminal deletions resulted in decreased levels of viral protein and RNA synthesis in singly transfected cardiomyocyte cultures. Unexpectedly, when full-length and terminally deleted forms were cotransfected into cardiomyocytes, a cooperative interaction was observed, leading to increased viral RNA and protein production. However, when viral infections were carried out in cells harboring 5' terminally deleted CVB3 RNAs, a decrease in infectious particle production was observed. Our results provide a possible explanation for the necessity of full-length viral genomes during persistent infection, as they would stimulate efficient viral replication compared to that of the deleted genomes alone. To avoid high levels of viral particle production that would trigger cellular immune activation and host cell death, the terminally deleted RNA forms act to limit the production of viral particles, possibly as trans-dominant inhibitors. IMPORTANCE Enteroviruses like coxsackievirus B3 are able to initiate acute infections of cardiac tissue and, in some cases, to establish a long-term persistent infection that can lead to serious disease sequelae, including dilated cardiomyopathy. Previous studies have demonstrated the presence of 5' terminally deleted forms of enterovirus RNAs in heart tissues derived from patients with dilated cardiomyopathy. These deleted RNAs are found in association with very low levels of full-length enterovirus genomic RNAs, an interaction that may facilitate continued persistence while limiting virus particle production. Even in the absence of detectable infectious virus particle production, these deleted viral RNA forms express viral proteinases at levels capable of causing viral pathology. Our studies provide mechanistic insights into how full-length and deleted forms of enterovirus RNA cooperate to stimulate viral protein and RNA synthesis without stimulating infectious viral particle production. They also highlight the importance of targeting enteroviral proteinases to inhibit viral replication while at the same time limiting the long-term pathologies they trigger.
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Affiliation(s)
- Alexis Bouin
- Department of Microbiology & Molecular Genetics, School of Medicine and Center for Virus Research, University of California, Irvine, California, USA
| | - Michelle N. Vu
- Department of Microbiology & Molecular Genetics, School of Medicine and Center for Virus Research, University of California, Irvine, California, USA
| | - Ali Al-Hakeem
- Department of Microbiology & Molecular Genetics, School of Medicine and Center for Virus Research, University of California, Irvine, California, USA
| | - Genevieve P. Tran
- Department of Microbiology & Molecular Genetics, School of Medicine and Center for Virus Research, University of California, Irvine, California, USA
| | - Joseph H. C. Nguyen
- Department of Microbiology & Molecular Genetics, School of Medicine and Center for Virus Research, University of California, Irvine, California, USA
| | - Bert L. Semler
- Department of Microbiology & Molecular Genetics, School of Medicine and Center for Virus Research, University of California, Irvine, California, USA
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88
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Patterns and Temporal Dynamics of Natural Recombination in Noroviruses. Viruses 2023; 15:v15020372. [PMID: 36851586 PMCID: PMC9961210 DOI: 10.3390/v15020372] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Noroviruses infect a wide range of mammals and are the major cause of gastroenteritis in humans. Recombination at the junction of ORF1 encoding nonstructural proteins and ORF2 encoding major capsid protein VP1 is a well-known feature of noroviruses. Using all available complete norovirus sequences, we systematically analyzed patterns of natural recombination in the genus Norovirus both throughout the genome and across the genogroups. Recombination events between nonstructural (ORF1) and structural genomic regions (ORF2 and ORF3) were found in all analyzed genogroups of noroviruses, although recombination was most prominent between members of GII, the most common genogroup that infects humans. The half-life times of recombinant forms (clades without evidence of recombination) of human GI and GII noroviruses were 10.4 and 8.4-11.3 years, respectively. There was evidence of many recent recombination events, and most noroviruses that differed by more than 18% of nucleotide sequence were recombinant relative to each other. However, there were no distinct recombination events between viruses that differed by over 42% in ORF2/3, consistent with the absence of systematic recombination between different genogroups. The few inter-genogroup recombination events most likely occurred between ancient viruses before they diverged into contemporary genogroups. The recombination events within ORF1 or between ORF2/3 were generally rare. Thus, noroviruses routinely exchange full structural and nonstructural blocks of the genome, providing a modular evolution.
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89
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Jaramillo-Mesa H, Rakotondrafara AM. All eggs in one basket: How potyvirus infection is controlled at a single cap-independent translation event. Semin Cell Dev Biol 2023; 148-149:51-61. [PMID: 36608998 DOI: 10.1016/j.semcdb.2022.12.011] [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: 10/27/2022] [Revised: 12/28/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023]
Abstract
Regulation of protein synthesis is a strong determinant of potyviral pathogenicity. The Potyviridae family is the largest family of plant-infecting positive sense RNA viruses. Similar to the animal-infecting Picornaviridae family, the potyviral RNA genome lacks a 5' cap, and instead has a viral protein (VPg) linked to its 5' end. Potyviral genomes are mainly translated into one large polyprotein relying on a single translation event to express all their protein repertoire. In the absence of the 5' cap, the Potyviridae family depends on cis-acting elements in their 5' untranslated regions (UTR) to recruit the translation machinery. In this review, we summarize the diverse 5'UTR-driven, cap-independent translation mechanisms employed by the Potyviridae family including scanning-dependent mechanism, internal initiation, and the stimulatory role of the VPg. These mechanisms have direct implications on potyviral pathogenicity, including host range specificity and resistance. Finally, we discuss how these viral strategies could not only inform new avenues for engineering and/or breeding for crop resistance but would also provide opportunities for the development of biotechnological tools for large-scale protein production in plant systems.
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Affiliation(s)
- Helena Jaramillo-Mesa
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53704, USA
| | - Aurélie M Rakotondrafara
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53704, USA.
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90
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Gadir M, Azimi SM, Harzandi N, Hemati B, Eskandarzade N. Molecular detection, genetic diversity, and phylogenetic analysis of foot-and-mouth disease virus (FMDV) type O in Iran during 2015-2016. IRANIAN JOURNAL OF VETERINARY RESEARCH 2023; 24:30-36. [PMID: 37378387 PMCID: PMC10291526 DOI: 10.22099/ijvr.2022.43156.6284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 09/11/2022] [Accepted: 11/07/2022] [Indexed: 06/29/2023]
Abstract
Background The major challenge of foot-and-mouth disease (FMD) control is attributed to the rapid mutations in the FMDV RNA genome, resulting in continuous antigenic changes of circulating strains. Despite widespread vaccination of livestock populations, the incidence of the FMDV serotype O outbreaks in Iran during 2015-2016 raised concerns about the emergence of new strains. Aims The aim of this study is the genetic and antigenic evaluation of FMDV type O isolates from different outbreak areas including Alborz, Tehran, Isfahan, Markazi, Zahedan, and Qom provinces. Methods For this purpose, 71 FMD-infected samples were collected from six provinces of Iran, of which 12 serotype O positive were selected for genetic analysis. Results All samples were in ME-SA topotypes/OPanAsia2 lineage, and the overall mean of genetic diversities at the 1D gene level was about 5% between the sequences. Blasting 1D gene sequences of isolated viruses showed more than 90% genetic identity with sequences registered from neighboring countries; therefore, it could be concluded that they had a common origin. Six isolates showed the highest genetic diversity (6% to 11%) with the OPanAsia2 vaccine strain (JN676146), which three of them (Qom, Alborz, and Zahedan isolates), had less than 30% antigenic homology with the OPanAsia2 virus (JN676146). Conclusion Results of this study suggested OPanAsia2 vaccine had no enough coverage with some circulating strains in outbreak areas in Qom, Alborz, and Zahedan provinces, and the necessity of OPanAsia2 replacement with a new vaccine strain in Iran.
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Affiliation(s)
- M Gadir
- Ph.D. Student in Microbiology, Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - S. M Azimi
- Foot and Mouth Disease Reference Laboratory, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - N Harzandi
- Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - B Hemati
- Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - N Eskandarzade
- Department of Basic Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
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91
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Wang Y, Zou W, Niu Y, Wang S, Chen B, Xiong R, Zhang P, Luo Z, Wu Y, Fan C, Zhong Z, Xu P, Peng Y. Phosphorylation of enteroviral 2A pro at Ser/Thr125 benefits its proteolytic activity and viral pathogenesis. J Med Virol 2023; 95:e28400. [PMID: 36511115 PMCID: PMC10107306 DOI: 10.1002/jmv.28400] [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: 09/18/2022] [Revised: 11/19/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
Enteroviral 2A proteinase (2Apro ), a well-established and important viral functional protein, plays a key role in shutting down cellular cap-dependent translation, mainly via its proteolytic activity, and creating optimal conditions for Enterovirus survival. Accumulated data show that viruses take advantage of various signaling cascades for their life cycle; studies performed by us and others have demonstrated that the extracellular signal-regulated kinase (ERK) pathway is essential for enterovirus A71 (EV-A71) and other viruses replication. We recently showed that ERK1/2 is required for the proteolytic activity of viral 2Apro ; however, the mechanism underlying the regulation of 2Apro remains unknown. Here, we demonstrated that the 125th residue Ser125 of EV-A71 2Apro or Thr125 of coxsackievirus B3 2Apro , which is highly conserved in the Enterovirus, was phosphorylated by ERK1/2. Importantly, 2Apro with phosphor-Ser/Thr125 had much stronger proteolytic activity toward eukaryotic initiation factor 4GI and rendered the virus more efficient for multiplication and pathogenesis in hSCARB2 knock-in mice than that in nonphospho-Ser/Thr125A (S/T125A) mutants. Notably, phosphorylation-mimic mutations caused deleterious changes in 2Apro catalytic function (S/T125D/E) and in viral propagation (S125D). Crystal structure simulation analysis showed that Ser125 phosphorylation in EV-A71 2Apro enabled catalytic Cys to adopt an optimal conformation in the catalytic triad His-Asp-Cys, which enhances 2Apro proteolysis. Therefore, we are the first to report Ser/Thr125 phosphorylation of 2Apro increases enteroviral adaptation to the host to ensure enteroviral multiplication, causing pathogenicity. Additionally, weakened viruses containing a S/T125A mutation could be a general strategy to develop attenuated Enterovirus vaccines.
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Affiliation(s)
- Yuya Wang
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Wenjia Zou
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yan Niu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, China
| | - Sanyuan Wang
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Bangtao Chen
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Rui Xiong
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Peng Zhang
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Zhijun Luo
- Jiangxi Provincial Key Laboratory of Tumor Pathogens and Molecular Pathology, Queen Mary School, Nanchang University Jiangxi Medical College, Nanchang, China
| | - Yong Wu
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control, Beijing, China
| | - Changfa Fan
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control, Beijing, China
| | - Zhaohua Zhong
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Ping Xu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, China
| | - Yihong Peng
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
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92
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Wu X, Cui L, Bai Y, Bian L, Liang Z. Pseudotyped Viruses for Enterovirus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1407:209-228. [PMID: 36920699 DOI: 10.1007/978-981-99-0113-5_11] [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: 03/16/2023]
Abstract
Using a non-pathogenic pseudotyped virus as a surrogate for a wide-type virus in scientific research complies with the recent requirements for biosafety. Enterovirus (EV) contains many species of viruses, which are a type of nonenveloped virus. The preparation of its corresponding pseudotyped virus often needs customized construction compared to some enveloped viruses. This article describes the procedures and challenges in the construction of pseudotyped virus for enterovirus (pseudotyped enterovirus, EVpv) and also introduces the application of EVpv in basic virological research, serological monitoring, and the detection of neutralizing antibody (NtAb).
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Affiliation(s)
- Xing Wu
- Division of Hepatitis Virus & Enterovirus Vaccines, Institute for Biological Products, National Institutes for Food and Drug Control, Beijing, China
- WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Lisha Cui
- Minhai biotechnology Co. Ltd, Beijing, China
| | - Yu Bai
- Division of Hepatitis Virus & Enterovirus Vaccines, Institute for Biological Products, National Institutes for Food and Drug Control, Beijing, China
- WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Lianlian Bian
- Division of Hepatitis Virus & Enterovirus Vaccines, Institute for Biological Products, National Institutes for Food and Drug Control, Beijing, China
- WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
| | - Zhenglun Liang
- Division of Hepatitis Virus & Enterovirus Vaccines, Institute for Biological Products, National Institutes for Food and Drug Control, Beijing, China
- WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, China
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93
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Guo Q, Zhao H, Zhang Y, Wang X, Yu Q, Tan Z, Lu H, Xiao J, Ji T, Zhu S, Wang D, Yang Q, Han Z, Xu W, Yan D. Genetic characterization and molecular epidemiology of Coxsackievirus A12 from mainland China during 2010-2019. Front Microbiol 2022; 13:988538. [PMID: 36620057 PMCID: PMC9811122 DOI: 10.3389/fmicb.2022.988538] [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: 07/07/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Coxsackievirus A12 (CVA12) is an enterovirus that has been isolated in many countries in recent years. However, studies on CVA12 are limited, and its effective population size, evolutionary dynamics and recombination patterns have not been clarified now. In this study, we described the phylogenetic characteristics of 16 CVA12 strains isolated from pediatric HFMD patients in mainland China from 2010 to 2019. Comparison of the nucleotide sequences and amino acid sequences with the CVA12 prototype strain revealed that the 16 CVA12 strains are identical in 78.8-79% and 94-94.2%, respectively. A phylodynamic analysis based on the 16 full-length VP1 sequences from this study and 21 sequences obtained from GenBank revealed a mean substitution rate of 6.61 × 10-3 substitutions/site/year (95% HPD: 5.16-8.20 × 10-3), dating the time to most recent common ancestor (tMRCA) of CVA12 back to 1946 (95% HPD: 1942-1947). The Bayesian skyline plot showed that the effective population size has experienced twice dynamic fluctuations since 2007. Phylogeographic analysis identified two significant migration pathways, indicating the existence of cross-provincial transmission of CVA12 in mainland China. Recombination analysis revealed two recombination patterns between 16 CVA12 strains and other EV-A, suggesting that there may be extensive genetic exchange between CVA12 and other enteroviruses. In summary, a total of 16 full-length CVA12 strains were reported in this study, providing valuable references for further studies of CVA12 worldwide.
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Affiliation(s)
- Qin Guo
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China,Da Zhou Vocational College of Chinese Medicine, Dazhou, China
| | - Hehe Zhao
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Yong Zhang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Shandong, China
| | - Qiuli Yu
- Hebei Center for Disease Control and Prevention, Shijiazhuang, China
| | - Zhaolin Tan
- Tianjin Center for Disease Control and Prevention, Tianjin, China
| | - Huanhuan Lu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Jinbo Xiao
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Tianjiao Ji
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Shuangli Zhu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Dongyan Wang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Qian Yang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Zhenzhi Han
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Wenbo Xu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Dongmei Yan
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China,*Correspondence: Dongmei Yan,
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94
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Warsaba R, Salcedo-Porras N, Flibotte S, Jan E. Expansion of viral genomes with viral protein genome linked copies. Virology 2022; 577:174-184. [PMID: 36395539 DOI: 10.1016/j.virol.2022.10.012] [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: 10/05/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022]
Abstract
Virus protein-linked genome (VPg) proteins are required for replication. VPgs are duplicated in a subset of RNA viruses however their roles are not fully understood and the extent of viral genomes containing VPg copies has not been investigated in detail. Here, we generated a novel bioinformatics approach to identify VPg sequences in viral genomes using hidden Markov models (HMM) based on alignments of dicistrovirus VPg sequences. From metagenomic datasets of dicistrovirus genomes, we identified 717 dicistrovirus genomes containing VPgs ranging from a single copy to 8 tandem copies. The VPgs are classified into nine distinct types based on their sequence and length. The VPg types but not VPg numbers per viral genome followed specific virus clades, thus suggesting VPgs co-evolved with viral genomes. We also identified VPg duplications in aquamavirus and mosavirus genomes. This study greatly expands the number of viral genomes that contain VPg copies and indicates that duplicated viral sequences are more widespread than anticipated.
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Affiliation(s)
- Reid Warsaba
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Nicolas Salcedo-Porras
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Stephane Flibotte
- Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; UBC/LSI Bioinformatics Facility, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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95
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Yang Y, Abi K, Li Y, Yang C, Yang F. First detection and molecular characteristics of bopivirus from goats in China. Front Vet Sci 2022; 9:1033011. [PMID: 36532341 PMCID: PMC9753977 DOI: 10.3389/fvets.2022.1033011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/14/2022] [Indexed: 10/13/2023] Open
Abstract
A metavirome analysis was performed and detected bopivirus in the diarrhoeal fecal samples of goats in China. A total of 136 fecal samples were collected from yeanlings between the dates of June 2021 and January 2022 in Sichuan province, China. Moreover, "Bopivirus B" strains were detected by a specific RT-PCR targeting the 3D gene of the virus. The results showed that the overall detection rate of "Bopivirus B" was 19.12% (26/136). Additionally, there was a higher detection rate (24.05%, 19/79) in the fecal samples collected from yeanlings with diarrhea compared to those from asymptomatic animals (12.28%, 7/57). In these samples, no other common diarrhea-causing pathogens were detected except for three enteric viruses, namely caprine enterovirus, caprine kobuvirus and caprine hunnivirus (with detection rates of 13.97, 13.97, and 8.82%, respectively). Subsequently, full-length VP4, VP2, VP3, and VP1 genes from "Bopivirus B"-positive samples were amplified, cloned, sequenced, and analyzed. The phylogenetic analysis performed on the VP1 genes revealed that the identified bopivirus belonged to genotype B1 (seven strains) and B2 (three strains) and presented a high genetic diversity. Furthermore, a complete genome sequence of a "Bopivirus B" strain (SWUN/B1/2022) was obtained using PCR from fecal sample of a diarrhoeal yeanling. The complete genome was 7,309 nucleotides in length with a standard picornavirus genome organization, and shares 93.10% and 91.10% nucleotide similarity with bopivirus B1 genotype strain ovine/TB14/2010-HUN and bopivirus B2 genotype strain goat/AGK16/2020-HUN, respectively. According to the species classification criteria put forward by the International Committee on Taxonomy of Viruses and VP1 genotype, the strain SWUN/B1/2022 belongs to the bopivirus B1. This strain has unique amino acid substitutions in the VP4, VP2, VP3, and VP1 genes. Moreover, genomic recombination analysis revealed that this strain may be a minor parental strain of bopivirus B1 ovine/TB14/2010-HUN. Evolutionary analysis based on the 2C and 3CD genes revealed that the new bopivirus B1 strain SWUN/B1/2022 presents a unique evolutionary pattern. This study provided evidence to suggest that "Bopivirus B" is circulating with substantial genetic diversity in goats in China at present, and the mixed infection of "Bopivirus B" with other enteric viruses should be considered to be a composite factor in the occurrence of viral diarrhea in goats.
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Affiliation(s)
- Youwen Yang
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Kehamo Abi
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Yanmin Li
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Chen Yang
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Falong Yang
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Chengdu, China
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96
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Hu J, Chang X, Wang R, Zhang Q, Zhang F, Zhang Z, Zhang F, Qian M, Wang X. Unveiling of the epidemiological patterns for caprine/ovine enterovirus infection in China. Front Vet Sci 2022; 9:1025916. [DOI: 10.3389/fvets.2022.1025916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/14/2022] [Indexed: 11/29/2022] Open
Abstract
Caprine/ovine enterovirus (CEV/OEV) infection is an emerging disease and remains largely unknown for its infection distribution, epidemic pattern, and the underlying contribution factors. Here, we report the investigation on CEV/OEV infection pattern and the underlying contribution factors by employing a sandwich ELISA kit for detection of CEV/OEV antigen. Epidemiological investigation revealed a wide range of infection rates of CEV/OEV from 19.80%−39.00% on goat/sheep farms in the major goat/sheep-raising provinces as such Henan, Shandong, Ningxia, Jilin, Inner Mongolia autonomous region, and Xinjiang autonomous region in China. Epidemic patterns and infection rates for CEV/OEV were affected by the breeds, raising mode, regions, and seasons. CEV/OEV infection rates were varied in different regions in China and significantly higher in the diarrheal herds (40.30%) than these in non-diarrheal herds (13.83%). Moreover, infection rate was higher in sheep (24.59%) than that in goats (9.84%), even dramatic difference among different breeds of goat or sheep. Out of different breeds of goat, Boer (20.13%) had the highest infection rate, followed by local breed (5.62%) and Saanen (2.61%). Among these breeds of sheep, higher infection rates were detected in local breed sheep (42.86%) and small-tailed Han sheep (35.91%) than these of Hu sheep (13.41%) and Dorper sheep (16.34%). Furthermore, raising modes were showed to contribute to the infection rate, where higher rates were detected among goats/sheep in captivity (27.10%) than these in free-range (12.27%) and semi-free range (19.24%). Additionally, CEV/OEV infection rate had obvious seasonality, while they increased from year 2015 to 2019. In summary, we investigated the CEV/OEV infection among the goat/sheep herds from different regions in China, revealed the epidemic pattern and the contribution factors to the infection, which provided the epidemiological data for future prevention and control of this emerging infection.
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97
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Palombieri A, Fruci P, Di Profio F, Sarchese V, Robetto S, Martella V, Di Martino B. Detection and characterization of bopiviruses in domestic and wild ruminants. Transbound Emerg Dis 2022; 69:3972-3978. [PMID: 35933587 DOI: 10.1111/tbed.14676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/22/2022] [Accepted: 08/01/2022] [Indexed: 02/07/2023]
Abstract
Highly divergent picornaviruses (PVs) classified in the genus Bopivirus have been recently discovered on faecal samples from sheep and goats in Hungary and from fallow and red deer in Australia. In this study, we investigated the epidemiology of these novel viruses in domestic and wild ruminants from Northwestern Italian Alps by testing archival faecal samples collected from 128 sheep, 167 goats, 61 red deer (Cervus elaphus), 77 roe deer (Capreolus capreolus), 43 chamois (Rupicapra rupicapra) and 32 Alpine ibex (Capra ibex). Bopivirus RNA was detected in a total of 19 animals, including 14 sheep (10.9%), 2 red deer (3.3%), 1 roe deer (1.3%), 1 chamois (2.3 %) and 1 Alpine ibex (3.3 %), but not in goats. Upon sequence analysis of the 3DRdRp region, the sequences generated from chamois, roe deer, Alpine ibex and ovine faecal samples showed the highest nucleotide identity (96.8-100%) to bopiviruses detected in goats and sheep from Hungarian farms, whereas strains found in red deer displayed the closest relatedness (90.8%-91.2%) to bopiviruses identified in fallow and red deer in Australia. The nearly complete genome sequence of strains 12/2020/ITA (ON497046) and 14-73/2020/ITA (ON497047) detected in an Alpine ibex and in a sheep, respectively, was determined by combining a modified 3'-RACE protocol with Oxford Nanopore Technologies sequencing platform. On phylogenetic analysis based on the complete polyprotein, both strains segregated into the candidate species Bopivirus B along with ovine and caprine strains detected in Hungary (90.0-94.6% nucleotide and 94.6-98.0% amino acid identities). The findings of this study expand the host range of these novel viruses and hint to a possible virus circulation between domestic ruminants and wild animals.
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Affiliation(s)
- Andrea Palombieri
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Paola Fruci
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Federica Di Profio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Vittorio Sarchese
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Serena Robetto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, CeRMAS, Italy
| | - Vito Martella
- Department of Veterinary Medicine, Università Aldo Moro di Bari, Valenzano, Italy
| | - Barbara Di Martino
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
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98
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Asrani P, Seebohm G, Stoll R. Potassium viroporins as model systems for understanding eukaryotic ion channel behaviour. Virus Res 2022; 320:198903. [PMID: 36037849 DOI: 10.1016/j.virusres.2022.198903] [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: 03/14/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022]
Abstract
Ion channels are membrane proteins essential for a plethora of cellular functions including maintaining cell shape, ion homeostasis, cardiac rhythm and action potential in neurons. The complexity and often extensive structure of eukaryotic membrane proteins makes it difficult to understand their basic biological regulation. Therefore, this article suggests, viroporins - the miniature versions of eukaryotic protein homologs from viruses - might serve as model systems to provide insights into behaviour of eukaryotic ion channels in general. The structural requirements for correct assembly of the channel along with the basic functional properties of a K+ channel exist in the minimal design of the viral K+ channels from two viruses, Chlorella virus (Kcv) and Ectocarpus siliculosus virus (Kesv). These small viral proteins readily assemble into tetramers and they sort in cells to distinct target membranes. When these viruses-encoded channels are expressed into the mammalian cells, they utilise their protein machinery and hence can serve as excellent tools to study the cells protein sorting machinery. This combination of small size and robust function makes viral K+ channels a valuable model system for detection of basic structure-function correlations. It is believed that molecular and physiochemical analyses of these viroporins may serve as basis for the development of inhibitors or modulators to ion channel activity for targeting ion channel diseases - so called channelopathies. Therefore, it may provide a potential different scope for molecular pharmacology studies aiming at novel and innovative therapeutics associated with channel related diseases. This article reviews the structural and functional properties of Kcv and Kesv upon expression in mammalian cells and Xenopus oocytes. The mechanisms behind differential protein sorting in Kcv and Kesv are also thoroughly discussed.
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Affiliation(s)
- Purva Asrani
- Biomolecular Spectroscopy and RUBiospec|NMR, Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Bochum D-44780, Germany
| | - Guiscard Seebohm
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, Münster D-48149, Germany
| | - Raphael Stoll
- Biomolecular Spectroscopy and RUBiospec|NMR, Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Bochum D-44780, Germany.
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99
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He X, Wang X, Fan G, Li F, Wu W, Wang Z, Fu M, Wei X, Ma S, Ma X. Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau. Sci Rep 2022; 12:17239. [PMID: 36241909 PMCID: PMC9562062 DOI: 10.1038/s41598-022-22134-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/10/2022] [Indexed: 01/06/2023] Open
Abstract
Rodents are natural reservoirs of diverse zoonotic viruses and widely distributed on the Tibetan Plateau. A comprehensive understanding of the virome in local rodent species could provide baseline of viral content and assist in efforts to reduce the risk for future emergence of rodent related zoonotic diseases. A total of 205 tissue and fecal samples from 41 wild Qinghai voles were collected. Metagenomic analyses were performed to outline the characteristics of the viromes, and phylogenetic analyses were used to identify the novel viral genomes. The virome distribution among five tissues (liver, lung, spleen, small intestine with content and feces) was also compared. We identified sequences related to 46 viral families. Novel viral genomes from distinct evolutionary lineages with known viruses were characterized for their genomic and evolutionary characteristics, including Hepatovirus, Hepacivirus, Rotavirus, and Picobirnavirus. Further analyses revealed that the core virome harbored by rodent internal tissues were quite different from the virome found in intestine and fecal samples. These findings provide an overview of the viromes in wild Qinghai voles, which are unique and the most common rodent species in the eastern Tibetan Plateau. A high diversity of viruses is likely present in rodent species in this area.
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Affiliation(s)
- Xiaozhou He
- grid.198530.60000 0000 8803 2373NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China ,grid.9227.e0000000119573309Chinese Center for Disease Control and Prevention - Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Xu Wang
- grid.508378.1National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, People’s Republic of China
| | - Guohao Fan
- grid.198530.60000 0000 8803 2373NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China ,grid.9227.e0000000119573309Chinese Center for Disease Control and Prevention - Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Fan Li
- grid.198530.60000 0000 8803 2373NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Weiping Wu
- grid.508378.1National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, People’s Republic of China
| | - Zhenghuan Wang
- grid.22069.3f0000 0004 0369 6365School of Life Sciences, East China Normal University, Shanghai, People’s Republic of China
| | - Meihua Fu
- grid.430328.eShanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
| | - Xu Wei
- grid.22069.3f0000 0004 0369 6365School of Life Sciences, East China Normal University, Shanghai, People’s Republic of China
| | - Shuo Ma
- grid.22069.3f0000 0004 0369 6365School of Life Sciences, East China Normal University, Shanghai, People’s Republic of China
| | - Xuejun Ma
- grid.198530.60000 0000 8803 2373NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China ,grid.9227.e0000000119573309Chinese Center for Disease Control and Prevention - Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
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100
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Han Z, Xiao J, Song Y, Zhao X, Sun Q, Lu H, Zhang K, Li J, Li J, Si F, Zhang G, Zhao H, Jia S, Zhou J, Wang D, Zhu S, Yan D, Xu W, Fu X, Zhang Y. Highly diverse ribonucleic acid viruses in the viromes of eukaryotic host species in Yunnan province, China. Front Microbiol 2022; 13:1019444. [PMID: 36312977 PMCID: PMC9606678 DOI: 10.3389/fmicb.2022.1019444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Background The diversity in currently documented viruses and their morphological characteristics indicates the need for understanding the evolutionary characteristics of viruses. Notably, further studies are needed to obtain a comprehensive landscape of virome, the virome of host species in Yunnan province, China. Materials and methods We implemented the metagenomic next-generation sequencing strategy to investigate the viral diversity, which involved in 465 specimens collected from bats, pangolins, monkeys, and other species. The diverse RNA viruses were analyzed, especially focusing on the genome organization, genetic divergence and phylogenetic relationships. Results In this study, we investigated the viral composition of eight libraries from bats, pangolins, monkeys, and other species, and found several diverse RNA viruses, including the Alphacoronavirus from bat specimens. By characterizing the genome organization, genetic divergence, and phylogenetic relationships, we identified five Alphacoronavirus strains, which shared phylogenetic association with Bat-CoV-HKU8-related strains. The pestivirus-like virus related to recently identified Dongyang pangolin virus (DYPV) strains from dead pangolin specimens, suggesting that these viruses are evolving. Some genomes showed higher divergence from known species (e.g., calicivirus CS9-Cali-YN-CHN-2020), and many showed evidence of recombination events with unknown or known strains (e.g., mamastroviruses BF2-astro-YN-CHN-2020 and EV-A122 AKM5-YN-CHN-2020). The newly identified viruses showed extensive changes and could be assigned as new species, or even genus (e.g., calicivirus CS9-Cali-YN-CHN-2020 and iflavirus Ifla-YN-CHN-2020). Moreover, we identified several highly divergent RNA viruses and estimated their evolutionary characteristics among different hosts, providing data for further examination of their evolutionary dynamics. Conclusion Overall, our study emphasizes the close association between emerging viruses and infectious diseases, and the need for more comprehensive surveys.
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Affiliation(s)
- Zhenzhi Han
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Jinbo Xiao
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Song
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaonan Zhao
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Qiang Sun
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huanhuan Lu
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Keyi Zhang
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jichen Li
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Junhan Li
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fenfen Si
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guoyan Zhang
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hehe Zhao
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Senquan Jia
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Jienan Zhou
- Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Dongyan Wang
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuangli Zhu
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongmei Yan
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenbo Xu
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Xiaoqing Fu
- Yunnan Center for Disease Control and Prevention, Kunming, China
- Xiaoqing Fu,
| | - Yong Zhang
- National Laboratory for Poliomyelitis, WHO Western Pacific Region Office (WPRO) Regional Polio Reference Laboratory, National Health Commission (NHC) Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Yong Zhang,
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