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Klangprapan J, Sudjarwo WAA, Lieberzeit PA, Choowongkomon K. Synthesis and characterization of molecularly imprinted polymer nanoparticles against porcine circovirus type 2 viral-like particles. Anal Bioanal Chem 2024; 416:7357-7368. [PMID: 39392505 PMCID: PMC11584434 DOI: 10.1007/s00216-024-05576-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 09/26/2024] [Accepted: 09/30/2024] [Indexed: 10/12/2024]
Abstract
PCV2 is a significant epidemic agricultural pathogen that causes a variety of swine diseases. PCV2 infections have significant economic impact on the swine industry, making effective strategies for rapid detection of PCV2 in pigs essential. Herein, we report on the synthesis of the so-called nano-MIPs which can be utilized for molecular recognition of PCV2. The morphology and structure of nano-MIPs were characterized using scanning electron microscopy (SEM). Nano-MIPs are spherical with sizes around 120-150 nm. Binding experiments demonstrate that the fluorescence intensity of PCV2 samples decreases proportionally to increasing the concentration of nano-MIPs due to quenching, while non-imprinted polymer nanoparticles (nano-NIPs) do not affect the signal. The Stern-Volmer constant of nano-MIPs binding to PCV2 was 1.3 × 10-3 mL/µg, whereas nano-NIPs led to 7 × 10-5 mL/µg, i.e., 1.8 orders of magnitude lower. The detection limit for binding MIP particles to PCV2 by fluorescence measurements is 47 µg/mL. This affinity test allows for designing both direct and competitive quartz crystal microbalance (QCM) assays for PCV2 leading to QCM measurements. The QCM results show nano-MIPs binding to PCV2 immobilized on the sensor surface with appreciable reproducibility. QCM sensor characteristics reveal signal saturation above around 200 µg/mL at a response of - 354 Hz and an LOD of approximately 35 µg/mL. Nano-MIPs also show selectivity factors of 2-5 for CSFV and PRRSV probably because the three viruses have similar diameters around 50 nm.
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Affiliation(s)
- Jutapak Klangprapan
- Genetic Engineering Interdisciplinary Program, Graduate School, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
- Department of Research Affairs, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wisnu Arfian A Sudjarwo
- University of Vienna, Faculty for Chemistry, Department of Physical Chemistry, Waehringer Strasse 42, A-1090, Wien, Austria
- Research Center for Polymer Technology, National Research and Innovation Agency, Republic of Indonesia (BRIN), Serpong, Tangerang Selatan, 15314, Indonesia
| | - Peter A Lieberzeit
- University of Vienna, Faculty for Chemistry, Department of Physical Chemistry, Waehringer Strasse 42, A-1090, Wien, Austria.
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand.
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Dei Giudici S, Mura L, Bonelli P, Hawko S, Angioi PP, Sechi AM, Denti S, Sulas A, Burrai GP, Madrau MP, Antuofermo E, Oggiano A. Evidence of Porcine Circovirus Type 2 (PCV2) Genetic Shift from PCV2b to PCV2d Genotype in Sardinia, Italy. Viruses 2023; 15:2157. [PMID: 38005836 PMCID: PMC10674684 DOI: 10.3390/v15112157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Porcine Circovirus type 2 (PCV2) is the etiological agent of a disease syndrome named Porcine Circovirus disease (PCVD), representing an important threat for the pig industry. The increasing international trade of live animals and the development of intensive pig farming seem to have sustained the spreading of PCVD on a global scale. Recent classification criteria allowed the identification of nine different PCV2 genotypes (PCV2a-i). PCV2a was the first genotype detected with the highest frequency from the late 1990s to 2000, which was then superseded by PCV2b (first genotype shift). An ongoing genotype shift is now determining increasing prevalence rates of PCV2d, in replacement of PCV2b. In Italy, a complete genotype replacement was not evidenced yet. The present study was carried out on 369 samples originating from domestic pigs, free-ranging pigs, and wild boars collected in Sardinia between 2020 and 2022, with the aim to update the last survey performed on samples collected during 2009-2013. Fifty-seven complete ORF2 sequences were obtained, and the phylogenetic and network analyses evidenced that 56 out of 57 strains belong to the PCV2d genotype and only one strain to PCV2b, thus showing the occurrence of a genotype shift from PCV2b to PCV2d in Sardinia.
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Affiliation(s)
- Silvia Dei Giudici
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (L.M.); (P.B.); (P.P.A.); (A.M.S.); (S.D.); (A.S.); (M.P.M.); (A.O.)
| | - Lorena Mura
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (L.M.); (P.B.); (P.P.A.); (A.M.S.); (S.D.); (A.S.); (M.P.M.); (A.O.)
| | - Piero Bonelli
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (L.M.); (P.B.); (P.P.A.); (A.M.S.); (S.D.); (A.S.); (M.P.M.); (A.O.)
| | - Salwa Hawko
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (S.H.); (G.P.B.); (E.A.)
| | - Pier Paolo Angioi
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (L.M.); (P.B.); (P.P.A.); (A.M.S.); (S.D.); (A.S.); (M.P.M.); (A.O.)
| | - Anna Maria Sechi
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (L.M.); (P.B.); (P.P.A.); (A.M.S.); (S.D.); (A.S.); (M.P.M.); (A.O.)
| | - Stefano Denti
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (L.M.); (P.B.); (P.P.A.); (A.M.S.); (S.D.); (A.S.); (M.P.M.); (A.O.)
| | - Antonella Sulas
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (L.M.); (P.B.); (P.P.A.); (A.M.S.); (S.D.); (A.S.); (M.P.M.); (A.O.)
| | - Giovanni Pietro Burrai
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (S.H.); (G.P.B.); (E.A.)
| | - Maria Paola Madrau
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (L.M.); (P.B.); (P.P.A.); (A.M.S.); (S.D.); (A.S.); (M.P.M.); (A.O.)
| | - Elisabetta Antuofermo
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (S.H.); (G.P.B.); (E.A.)
| | - Annalisa Oggiano
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (L.M.); (P.B.); (P.P.A.); (A.M.S.); (S.D.); (A.S.); (M.P.M.); (A.O.)
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Li J, Liu F, Ren Z, Fu G, Shi J, Zhao N, Huang Y, Su J. Generation of a monoclonal antibody against duck circovirus capsid protein and its potential application for native viral antigen detection. Front Microbiol 2023; 14:1206038. [PMID: 37426000 PMCID: PMC10326623 DOI: 10.3389/fmicb.2023.1206038] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/05/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction Duck circovirus (DuCV) infection is currently recognized as an important immunosuppressive disease in commercial duck flocks in China. Specific antibodies against DuCV viral proteins are required to improve diagnostic assays and understand the pathogenesis of DuCV infection. Methods and results To generate DuCV-specific monoclonal antibodies (mAbs), a recombinant DuCV capsid protein without the first 36 N-terminal amino acids was produced in Escherichia coli. Using the recombinant protein as an immunogen, a mAb was developed that reacted specifically with the DuCV capsid protein, expressed in E. coli and baculovirus systems. Using homology modeling and recombinant truncated capsid proteins, the antibody-binding epitope was mapped within the region of 144IDKDGQIV151, which is exposed to solvent in the virion capsid model structure. To assess the applicability of the mAb to probe the native virus antigen, the murine macrophage cell line RAW267.4 was tested for DuCV replicative permissiveness. Immunofluorescence and Western blot analysis revealed that the mAb recognized the virus in infected cells and the viral antigen in tissue samples collected from clinically infected ducks. Discussion This mAb, combined with the in vitro culturing method, would have widespread applications in diagnosing and investigating DuCV pathogenesis.
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Affiliation(s)
- Jinxin Li
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Fengli Liu
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhihao Ren
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guanghua Fu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jizhen Shi
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Naiyu Zhao
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yu Huang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jingliang Su
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Butkovic A, Kraberger S, Smeele Z, Martin DP, Schmidlin K, Fontenele RS, Shero MR, Beltran RS, Kirkham AL, Aleamotu’a M, Burns JM, Koonin EV, Varsani A, Krupovic M. Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein. Virus Evol 2023; 9:vead035. [PMID: 37325085 PMCID: PMC10266747 DOI: 10.1093/ve/vead035] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Anelloviruses are highly prevalent in diverse mammals, including humans, but so far have not been linked to any disease and are considered to be part of the 'healthy virome'. These viruses have small circular single-stranded DNA (ssDNA) genomes and encode several proteins with no detectable sequence similarity to proteins of other known viruses. Thus, anelloviruses are the only family of eukaryotic ssDNA viruses currently not included in the realm Monodnaviria. To gain insights into the provenance of these enigmatic viruses, we sequenced more than 250 complete genomes of anelloviruses from nasal and vaginal swab samples of Weddell seal (Leptonychotes weddellii) from Antarctica and a fecal sample of grizzly bear (Ursus arctos horribilis) from the USA and performed a comprehensive family-wide analysis of the signature anellovirus protein ORF1. Using state-of-the-art remote sequence similarity detection approaches and structural modeling with AlphaFold2, we show that ORF1 orthologs from all Anelloviridae genera adopt a jelly-roll fold typical of viral capsid proteins (CPs), establishing an evolutionary link to other eukaryotic ssDNA viruses, specifically, circoviruses. However, unlike CPs of other ssDNA viruses, ORF1 encoded by anelloviruses from different genera display remarkable variation in size, due to insertions into the jelly-roll domain. In particular, the insertion between β-strands H and I forms a projection domain predicted to face away from the capsid surface and function at the interface of virus-host interactions. Consistent with this prediction and supported by recent experimental evidence, the outermost region of the projection domain is a mutational hotspot, where rapid evolution was likely precipitated by the host immune system. Collectively, our findings further expand the known diversity of anelloviruses and explain how anellovirus ORF1 proteins likely diverged from canonical jelly-roll CPs through gradual augmentation of the projection domain. We suggest assigning Anelloviridae to a new phylum, 'Commensaviricota', and including it into the kingdom Shotokuvirae (realm Monodnaviria), alongside Cressdnaviricota and Cossaviricota.
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Affiliation(s)
- Anamarija Butkovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, Paris 75015, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Zoe Smeele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Darren P Martin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Michelle R Shero
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Rd, Woods Hole, MA 02543, USA
| | - Roxanne S Beltran
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Amy L Kirkham
- U.S. Fish and Wildlife Service, Marine Mammals Management, 1011 E, Tudor Road, Anchorage, AK 99503, USA
| | - Maketalena Aleamotu’a
- School of Environmental and Life Sciences, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Jennifer M Burns
- Department of Biological Sciences, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, 1 Anzio Road, Cape Town 7925, South Africa
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, Paris 75015, France
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Ouyang Y, Nauwynck HJ. PCV2 Uptake by Porcine Monocytes Is Strain-Dependent and Is Associated with Amino Acid Characteristics on the Capsid Surface. Microbiol Spectr 2023; 11:e0380522. [PMID: 36719220 PMCID: PMC10100887 DOI: 10.1128/spectrum.03805-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/13/2023] [Indexed: 02/01/2023] Open
Abstract
Porcine circovirus type 2 (PCV2) is associated with several economically important diseases that are described as PCV2-associated diseases (PCVADs). PCV2 is replicating in lymphoblasts, and PCV2 particles are taken up by monocytes without effective replication or complete degradation. Glycosaminoglycans (GAGs) have been demonstrated to be important receptors for PCV2 binding and entry in T-lymphocytes and continuous cell lines. The objective of this study was to determine whether differences exist in viral uptake and outcome among six PCV2 strains from different disease outbreaks in primary porcine monocytes: Stoon-1010 (PCV2a; PMWS), 1121 (PCV2a; abortion), 1147 (PCV2b; PDNS), 09V448 (PCV2d-1; PCVAD with high viral load in lymphoid tissues [PCVADhigh]), DE222-13 (PCV2d-2; PCVADhigh), and 19V245 (PCV2d-2; PCVADhigh). The uptake of PCV2 in peripheral blood monocytes was different among the PCV2 strains. A large number of PCV2 particles were found in the monocytes for Stoon-1010, DE222-13, and 19V245, while a low number was found for 1121, 1147, and 09V448. Competition with, and removal of GAGs on the cell surface, demonstrated an important role of chondroitin sulfate (CS) and dermatan sulfate (DS) in PCV2 entry into monocytes. The mapping of positively/negatively charged amino acids exposed on the surface of PCV2 capsids revealed that their number and distribution could have an impact on the binding of the capsids to GAGs, and the internalization into monocytes. Based on the distribution of positively charged amino acids on PCV2 capsids, phosphacan was hypothesized, and further demonstrated, as an effective candidate to mediate virus attachment to, and internalization in, monocytes. IMPORTANCE PCV2 is present on almost every pig farm in the world and is associated with a high number of diseases (PCV2-associated diseases [PCVADs]). It causes severe economic losses. Although vaccination is successfully applied in the field, there are still a lot of unanswered questions on the pathogenesis of PCV2 infections. This article reports on the uptake difference of various PCV2 strains by peripheral blood monocytes, and reveals the mechanism of the strong viral uptake ability of monocytes of Piétrain pigs. We further demonstrated that: (i) GAGs mediate the uptake of PCV2 particles by monocytes, (ii) positively charged three-wings-windmill-like amino acid patterns on the capsid outer surface are activating PCV2 uptake, and (iii) phosphacan is one of the potential candidates for PCV2 internalization. These results provide new insights into the mechanisms involved in PCVAD and contribute to a better understanding of PCV2 evolution. This may lead to the development of resistant pigs.
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Affiliation(s)
- Yueling Ouyang
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Hans J. Nauwynck
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
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Payne S. Other small DNA viruses. Viruses 2023. [DOI: 10.1016/b978-0-323-90385-1.00035-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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Sun X, Xing S, Wang S, Zhang X, Yu Y, Wang L. In vitro assembly of chimeric virus-like particles composed of a porcine circovirus 2b capsid protein and a B-cell epitope of infectious bursal disease virus. Biotechnol Lett 2022; 44:429-438. [PMID: 35199255 DOI: 10.1007/s10529-022-03237-y] [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: 09/25/2021] [Accepted: 02/11/2022] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To develop a method for in vitro assembly of recombinant proteins expressed in E. coli into chimeric virus-like particles (cVLPs). RESULTS A fusion protein (Bepi-Cap-A) between capsid protein (Cap) of PCV2b and B cell epitope (Bepi) of IBDV was expressed in E. Coli, and purified. For assembling them into cVLPs (Bepi-Cap-VLP), the Bepi-Cap-A was suspended in buffer C [0.03% ("%" stands for "v/v" unless otherwise indicated) polyethylene glycol, 0.4 M Tris, 10 mM β-mercaptoethanol, 5% glycerol, 0.02% (w/v) gellan gum, 0.1 M glycine, 0.03% Tween 80, 500 mM NaCl], and incubated. After centrifugation, the pellet was resuspended in buffer D [50 mM Na2HPO4, 50 mM NaH2PO4, 0.01% (w/v) gellan gum, 0.05 mM EDTA, 500 mM NaCl, 0.03% Tween 80, pH 6.5], and then dialyzed against dialysis buffer (50 mM Na2HPO4, 50 mM NaH2PO4, 500 mM NaCl, 0.03% Tween 80, pH 6.5). The procedure resulted in typical and immunogenic Bepi-Cap-VLP. CONCLUSIONS The data provide a method which is feasible for in vitro assembly of recombinant proteins into chimeric virus-like particles.
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Affiliation(s)
- Xiaomeng Sun
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, 130021, People's Republic of China
- Department of Immunology, School of Changchun Medical College, Changchun, Jilin, 130031, People's Republic of China
| | - Shiyu Xing
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, 130021, People's Republic of China
| | - Shengnan Wang
- Department of Molecular Biology, College of Basic Medical Sciences and Institute of Pediatrics in the First Hospital of Jilin University, Jilin University, Changchun, Jilin, 130021, People's Republic of China
| | - Xian Zhang
- Department of Molecular Biology, College of Basic Medical Sciences and Institute of Pediatrics in the First Hospital of Jilin University, Jilin University, Changchun, Jilin, 130021, People's Republic of China
| | - Yongli Yu
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, 130021, People's Republic of China.
| | - Liying Wang
- Department of Molecular Biology, College of Basic Medical Sciences and Institute of Pediatrics in the First Hospital of Jilin University, Jilin University, Changchun, Jilin, 130021, People's Republic of China.
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Tarasova E, Okimoto N, Feng S, Nerukh D, Khayat R, Taiji M. Constant pH molecular dynamics of porcine circovirus 2 capsid protein reveals a mechanism for capsid assembly. Phys Chem Chem Phys 2021; 23:24617-24626. [PMID: 34726674 PMCID: PMC8705882 DOI: 10.1039/d1cp02874j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Spatiotemporal regulation of viral capsid assembly ensures the selection of the viral genome for encapsidation. The porcine circovirus 2 is the smallest autonomously replicating pathogenic virus, yet how PCV2 capsid assembly is regulated to occur within the nucleus remains unknown. We report that pure PCV2 capsid proteins, in the absence of nucleic acids, require acidic conditions to assemble into empty capsids in vitro. By employing constant pH replica exchange molecular dynamics, we unveil the atomistic mechanism of pH-dependency for capsid assembly. The results show that an appropriate protonation configuration for a cluster of acidic amino acids is necessary to appropriately position the GH-loop for driving the capsid assembly. We demonstrate that assembly is prohibited at neutral pH because deprotonation of these residues results in their electrostatic repulsion, shifting the GH-loop to a position incompatible with capsid assembly. We propose that encapsulation of nucleic acids overcomes this repulsion to suitably position the GH-loop. Our findings provide the first atomic resolution mechanism of capsid assembly regulation. These findings are useful for the development of therapeutics that inhibit PCV2 self-assembly.
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Affiliation(s)
- Elvira Tarasova
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York, USA.
| | - Noriaki Okimoto
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Shanshan Feng
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York, USA.
| | - Dmitry Nerukh
- Department of Mathematics, Aston University, Birmingham, UK
| | - Reza Khayat
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York, USA.
| | - Makoto Taiji
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
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Bhattacharjee U, Sen A, Sharma I. A retrospective study reveals the Porcine circovirus-2f genotype predominant in the indigenous pig population of North-eastern India. INFECTION GENETICS AND EVOLUTION 2021; 96:105100. [PMID: 34619393 DOI: 10.1016/j.meegid.2021.105100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/26/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022]
Abstract
Porcine circovirus-2 (PCV2) is a widespread virus and presents sub-clinically in most of the swineherd. Globally, eight genotypes of PCV2 have been identified that is PCV2a to 2h. To determine the region-wide genotype distribution of PCV2 infection, with additional reference to indigenous breeds, a total of 1314 pig's clinical samples from the eight states of North-eastern India between 2011 and 2014; were analyzed. The overall prevalence rate of PCV2 in this region was 28.2% (370/1314) by PCR. The state-wise PCR based PCV2 prevalence rate was: Tripura (20.8%), Nagaland (25.0%), Meghalaya (25.8%), Assam (32.1%), Sikkim (32.6%), Manipur (33.3%), Mizoram (36.7%) and Arunachal Pradesh (42.3%). Subsequently, a total of 29 complete genomes of PCV2 were amplified and sequenced from these PCV2 positive samples. The phylogenetic tree represents that the 29 PCV2 isolates of this study were divided into four distinct genetic groups; PCV2a, PCV2b, PCV2d, and PCV2f. Among these, 14 PCV2 strains were classified as PCV2f, 13 classified as PCV2d, and one isolate of each classified as PCV2a and PCV2b. All the 14 PCV2f strains appeared from indigenous pigs of this region. Based on the date of collection, the present study further describes that the PCV2f genotypes circulate in the indigenous pigs' population back in 2011. The amino acid residues and the atomic coordinate structure (3D model) of PCV2f capsid protein represents similarity to PCV2d capsid protein support the efficacy of the existing PCV2 vaccine against the PCV2f. The observation of this study helps to understand the genotype distribution of PCV2 and stands as a reference for future molecular epidemiological studies in North-eastern India.
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Affiliation(s)
- Uttaran Bhattacharjee
- Department of Microbiology, Assam University, Silchar, Assam, India; Division of Animal Health, Indian Council of Agricultural Research-Research Complex for North-Eastern Hill Region (ICAR-RC for NEH Region), Umiam, Barapani, Meghalaya, India
| | - Arnab Sen
- Division of Animal Health, Indian Council of Agricultural Research-Research Complex for North-Eastern Hill Region (ICAR-RC for NEH Region), Umiam, Barapani, Meghalaya, India
| | - Indu Sharma
- Department of Microbiology, Assam University, Silchar, Assam, India.
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Structural insight into the type-specific epitope of porcine circovirus type 3. Biosci Rep 2021; 40:225017. [PMID: 32458997 PMCID: PMC7295619 DOI: 10.1042/bsr20201109] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 01/12/2023] Open
Abstract
The recently identified pathogenic Porcine circovirus type 3 (PCV3) may threaten to reduce the pig population dramatically worldwide. In our previous study, a PCV3-specific monoclonal antibody (mAb-1H11) was successfully applied in immune-histochemistry staining and ELISA, which specifically recognize PCV3 capsid protein in PCV3-positive pig tissues. In the present study, we expressed and purified the soluble sole capsid protein of PCV3. The purified capsid protein was capable of self-assembly into virus-like-particles (VLPs), which is validated by transmission electron microscopy and dynamic light scattering assays. Moreover, the epitope of mAb-1H11 was identified in the CD-loop region (a.a. 72-79) on the VLP surface, which is confirmed by PCV2-PCV3 epitope swapping assay. For the first time, we determined the cryo-EM structure of PCV3-VLP at 8.5 Å resolution that reveals the detailed structural information of PCV3-VLP. In our cryo-EM structure, PCV3-VLP is composed of 60 capsid protein subunits assembled with T = 1 icosahedral symmetry. Consistent to our bio-dot Western blot assay, the structural comparison between PCV3 and PCV2 revealed significant structural differences in the surface-exposed loops, including the CD-loop (a.a. 72-79) and the EF-loop (a.a. 109-131). Our work provides a structural framework for engineering future PCV3 vaccine and diagnosis kits development.
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11
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Nath BK, Das S, Roby JA, Sarker S, Luque D, Raidal SR, Forwood JK. Structural Perspectives of Beak and Feather Disease Virus and Porcine Circovirus Proteins. Viral Immunol 2020; 34:49-59. [PMID: 33275868 DOI: 10.1089/vim.2020.0097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Circoviruses represent a rapidly expanding group of viruses that infect both vertebrate and invertebrate hosts. Members are responsible for diseases of veterinary and economic importance, including postweaning multisystemic wasting syndrome in pigs, and beak and feather disease (BFD) in birds. These viruses are associated with lymphoid depletion and immunosuppressive conditions in infected animals leading to systemic illness. Circoviruses are small nonenveloped DNA viruses containing a single-stranded circular genome, encoding two major proteins: the capsid-associated protein (Cap), comprising the entirety of the viral capsid, and the replication-associated protein (Rep). Cap is the only protein component of the virion and plays crucial roles throughout the virus replication cycle, including viral attachment, cell entry, genome uncoating, and packaging of newly formed viral particles. Rep mediates recognition of replication origin motifs in the viral genome sequence and is responsible for endonuclease activity enabling nicking of the circular DNA and initiation of rolling-circle replication (RCR). Porcine circovirus 2 (PCV2) was the first circovirus capsid structure to be solved at atomic resolution using X-ray crystallography. The structure revealed an assembly comprising 60 monomeric subunits to form virus-like particles. Each Cap monomer harbors a canonical viral jelly roll domain composed of two, four-stranded antiparallel β-sheets. Crystal structures of two distinct macromolecular assemblies from BFD virus Cap were also resolved at high resolution. In these structures, the exposure of the N-terminal arginine-rich motif, responsible for DNA binding and nuclear localization is reversed. Additional structural investigations have also elucidated a PCV2 type-specific neutralizing epitope, and interaction between the PCV2 capsid and polymers such as heparin. In this review, we provide a snapshot of the structural and functional aspects of circovirus proteins.
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Affiliation(s)
- Babu Kanti Nath
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Shubhagata Das
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Justin A Roby
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Daniel Luque
- Centro Nacional de Microbiología/ISCIII, Majadahonda, Madrid, Spain
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia
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12
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Opriessnig T, Karuppannan AK, Castro AMMG, Xiao CT. Porcine circoviruses: current status, knowledge gaps and challenges. Virus Res 2020; 286:198044. [PMID: 32502553 DOI: 10.1016/j.virusres.2020.198044] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 10/24/2022]
Abstract
Circoviruses (CV) include some of the smallest viruses known. They were named after their circularly arranged single-stranded DNA genome with a gene encoding a conserved replicase protein on the sense strand. Circoviruses are widely distributed in mammals, fish, avian species and even insects. In pigs, four different CVs have been identified and named with consecutive numbers based on the order of their discovery: Porcine circovirus 1 (PCV1), Porcine circovirus 2 (PCV2), Porcine circovirus 3 (PCV3) and most recently Porcine circovirus 4 (PCV4). PCVs are ubiquitous in global pig populations and uninfected herds are rarely found. It is generally accepted that PCV1 is non-pathogenic. In contrast, PCV2 is considered an important, economically challenging pathogen on a global scale with comprehensive vaccination schemes in place. The role of PCV3 is still controversial several years after its discovery. Propagation of PCV3 appears to be challenging and only one successful experimental infection model has been published to date. Similarly to PCV2, PCV3 is widespread and found in many pigs regardless of their health history, including high health herds. PCV4 has only recently been discovered and further information on this virus is required to understand its potential impact. This review summarizes current knowledge on CVs in pigs and aims to contrast and compare known facts on PCVs.
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Affiliation(s)
- Tanja Opriessnig
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK; Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA.
| | - Anbu K Karuppannan
- Vaccine Research Centre-Viral Vaccines, Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | | | - Chao-Ting Xiao
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, China
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