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1.
Viruses ; 14(2)2022 02 17.
Article in English | MEDLINE | ID: covidwho-1786043

ABSTRACT

Various adenoviruses are being used as viral vectors for the generation of vaccines against chronic and emerging diseases (e.g., AIDS, COVID-19). Here, we report the improved capsid structure for one of these vectors, human adenovirus D26 (HAdV-D26), at 3.4 Å resolution, by reprocessing the previous cryo-electron microscopy dataset and obtaining a refined model. In addition to overall improvements in the model, the highlights of the structure include (1) locating a segment of the processed peptide of VIII that was previously believed to be released from the mature virions, (2) reorientation of the helical appendage domain (APD) of IIIa situated underneath the vertex region relative to its counterpart observed in the cleavage defective (ts1) mutant of HAdV-C5 that resulted in the loss of interactions between the APD and hexon bases, and (3) the revised conformation of the cleaved N-terminal segments of pre-protein VI (pVIn), located in the hexon cavities, is highly conserved, with notable stacking interactions between the conserved His13 and Phe18 residues. Taken together, the improved model of HAdV-D26 capsid provides a better understanding of protein-protein interactions in HAdV capsids and facilitates the efforts to modify and/or design adenoviral vectors with altered properties. Last but not least, we provide some insights into clotting factors (e.g., FX and PF4) binding to AdV vectors.


Subject(s)
Adenoviruses, Human/chemistry , Capsid/chemistry , Capsid/ultrastructure , Cryoelectron Microscopy/methods , Adenoviruses, Human/genetics , Capsid Proteins/genetics , Humans , Models, Molecular , Protein Conformation , Protein Interaction Domains and Motifs , Virus Assembly , Virus Internalization
2.
J Virol ; 96(2): e0106021, 2022 01 26.
Article in English | MEDLINE | ID: covidwho-1759286

ABSTRACT

Rhinoviruses (RVs) cause recurrent infections of the nasal and pulmonary tracts, life-threatening conditions in chronic respiratory illness patients, predisposition of children to asthmatic exacerbation, and large economic cost. RVs are difficult to treat. They rapidly evolve resistance and are genetically diverse. Here, we provide insight into RV drug resistance mechanisms against chemical compounds neutralizing low pH in endolysosomes. Serial passaging of RV-A16 in the presence of the vacuolar proton ATPase inhibitor bafilomycin A1 (BafA1) or the endolysosomotropic agent ammonium chloride (NH4Cl) promoted the emergence of resistant virus populations. We found two reproducible point mutations in viral proteins 1 and 3 (VP1 and VP3), A2526G (serine 66 to asparagine [S66N]), and G2274U (cysteine 220 to phenylalanine [C220F]), respectively. Both mutations conferred cross-resistance to BafA1, NH4Cl, and the protonophore niclosamide, as identified by massive parallel sequencing and reverse genetics, but not the double mutation, which we could not rescue. Both VP1-S66 and VP3-C220 locate at the interprotomeric face, and their mutations increase the sensitivity of virions to low pH, elevated temperature, and soluble intercellular adhesion molecule 1 receptor. These results indicate that the ability of RV to uncoat at low endosomal pH confers virion resistance to extracellular stress. The data endorse endosomal acidification inhibitors as a viable strategy against RVs, especially if inhibitors are directly applied to the airways. IMPORTANCE Rhinoviruses (RVs) are the predominant agents causing the common cold. Anti-RV drugs and vaccines are not available, largely due to rapid evolutionary adaptation of RVs giving rise to resistant mutants and an immense diversity of antigens in more than 160 different RV types. In this study, we obtained insight into the cell biology of RVs by harnessing the ability of RVs to evolve resistance against host-targeting small chemical compounds neutralizing endosomal pH, an important cue for uncoating of normal RVs. We show that RVs grown in cells treated with inhibitors of endolysosomal acidification evolved capsid mutations yielding reduced virion stability against elevated temperature, low pH, and incubation with recombinant soluble receptor fragments. This fitness cost makes it unlikely that RV mutants adapted to neutral pH become prevalent in nature. The data support the concept of host-directed drug development against respiratory viruses in general, notably at low risk of gain-of-function mutations.


Subject(s)
Capsid/chemistry , Mutation/drug effects , Rhinovirus/physiology , Virus Uncoating/physiology , Antiviral Agents/pharmacology , Capsid/drug effects , Capsid Proteins/genetics , Capsid Proteins/metabolism , Drug Resistance, Viral/drug effects , Drug Resistance, Viral/genetics , Endosomes/chemistry , Endosomes/drug effects , Endosomes/metabolism , HeLa Cells , Humans , Hydrogen-Ion Concentration , Intercellular Adhesion Molecule-1/metabolism , Protein Conformation , Rhinovirus/chemistry , Rhinovirus/drug effects , Rhinovirus/genetics , Virion/chemistry , Virion/genetics , Virion/metabolism , Virus Internalization/drug effects , Virus Uncoating/drug effects , Virus Uncoating/genetics
3.
Viruses ; 14(2)2022 02 10.
Article in English | MEDLINE | ID: covidwho-1715772

ABSTRACT

Enterovirus genus has over one hundred genotypes and could cause several kinds of severe animal and human diseases. Understanding the role of conserved residues in the VP1 capsid protein among the enterovirus genus may lead to anti-enteroviral drug development. The highly conserved residues were found to be located at the loop and ß-barrel intersections. To elucidate the role of these VP1 residues among the enterovirus genus, alanine substitution reverse genetics (rg) variants were generated, and virus properties were investigated for their impact. Six highly conserved residues were identified as located near the inside of the canyon, and four of them were close to the ß-barrel and loop intersection. The variants rgVP1-R86A, rgVP1-P193A, rgVP1-G231A, and rgVP1-K256A were unable to be obtained, which may be due to disruption in the virus replication process. In contrast, rgVP1-E134A and rgVP1-P157A replicated well and rgVP1-P157A showed smaller plaque size, lower viral growth kinetics, and thermal instability at 39.5°C when compared to the rg wild type virus. These findings showed that the conserved residues located at the ß-barrel and loop junction play roles in modulating viral replication, which may provide a pivotal role for pan-enteroviral inhibitor candidate.


Subject(s)
Capsid Proteins/chemistry , Enterovirus/physiology , Virus Replication , Amino Acid Sequence , Antiviral Agents/chemistry , Capsid Proteins/genetics , Cell Line, Tumor , Conserved Sequence , Humans , Mutation , Protein Conformation , Protein Stability , RNA, Viral/metabolism , Small Molecule Libraries/chemistry , Temperature , Viral Load
4.
Viruses ; 14(1)2022 01 13.
Article in English | MEDLINE | ID: covidwho-1625824

ABSTRACT

Infection with enterovirus D68 (EV-D68) has been linked with severe neurological disease such as acute flaccid myelitis (AFM) in recent years. However, active surveillance for EV-D68 is lacking, which makes full assessment of this association difficult. Although a high number of EV-D68 infections were expected in 2020 based on the EV-D68's known biannual circulation patterns, no apparent increase in EV-D68 detections or AFM cases was observed during 2020. We describe an upsurge of EV-D68 detections in wastewater samples from the United Kingdom between July and November 2021 mirroring the recently reported rise in EV-D68 detections in clinical samples from various European countries. We provide the first publicly available 2021 EV-D68 sequences showing co-circulation of EV-D68 strains from genetic clade D and sub-clade B3 as in previous years. Our results show the value of environmental surveillance (ES) for the early detection of circulating and clinically relevant human viruses. The use of a next-generation sequencing (NGS) approach helped us to estimate the prevalence of EV-D68 viruses among EV strains from other EV serotypes and to detect EV-D68 minor variants. The utility of ES at reducing gaps in virus surveillance for EV-D68 and the possible impact of nonpharmaceutical interventions introduced to control the COVID-19 pandemic on EV-D68 transmission dynamics are discussed.


Subject(s)
Enterovirus D, Human/isolation & purification , Waste Water/virology , COVID-19/epidemiology , COVID-19/prevention & control , Capsid Proteins/genetics , Enterovirus D, Human/classification , Enterovirus D, Human/genetics , Humans , Phylogeny , RNA, Viral/genetics , SARS-CoV-2 , Sequence Analysis, DNA , United Kingdom/epidemiology , Wastewater-Based Epidemiological Monitoring , Water Microbiology
5.
Cell ; 184(25): 6037-6051.e14, 2021 12 09.
Article in English | MEDLINE | ID: covidwho-1520752

ABSTRACT

RNA viruses generate defective viral genomes (DVGs) that can interfere with replication of the parental wild-type virus. To examine their therapeutic potential, we created a DVG by deleting the capsid-coding region of poliovirus. Strikingly, intraperitoneal or intranasal administration of this genome, which we termed eTIP1, elicits an antiviral response, inhibits replication, and protects mice from several RNA viruses, including enteroviruses, influenza, and SARS-CoV-2. While eTIP1 replication following intranasal administration is limited to the nasal cavity, its antiviral action extends non-cell-autonomously to the lungs. eTIP1 broad-spectrum antiviral effects are mediated by both local and distal type I interferon responses. Importantly, while a single eTIP1 dose protects animals from SARS-CoV-2 infection, it also stimulates production of SARS-CoV-2 neutralizing antibodies that afford long-lasting protection from SARS-CoV-2 reinfection. Thus, eTIP1 is a safe and effective broad-spectrum antiviral generating short- and long-term protection against SARS-CoV-2 and other respiratory infections in animal models.


Subject(s)
Capsid Proteins/genetics , Virus Replication/drug effects , Administration, Intranasal , Animals , Antiviral Agents/pharmacology , Broadly Neutralizing Antibodies/immunology , Broadly Neutralizing Antibodies/pharmacology , COVID-19 , Capsid Proteins/metabolism , Cell Line , Disease Models, Animal , Genome, Viral/genetics , Humans , Influenza, Human , Interferons/metabolism , Male , Mice , Mice, Inbred C57BL , Poliovirus/genetics , Poliovirus/metabolism , Respiratory Tract Infections/virology , SARS-CoV-2/drug effects , SARS-CoV-2/pathogenicity
6.
Viruses ; 13(10)2021 10 13.
Article in English | MEDLINE | ID: covidwho-1481011

ABSTRACT

Human noroviruses are a common pathogen causing acute gastroenteritis worldwide. Among all norovirus genotypes, GII.3 is particularly prevalent in the pediatric population. Here we report the identification of two distinct blockade antibody epitopes on the GII.3 capsid. We generated a panel of monoclonal antibodies (mAbs) from mice immunized with virus-like particle (VLP) of a GII.3 cluster 3 strain. Two of these mAbs, namely 8C7 and 8D1, specifically bound the parental GII.3 VLP but not VLPs of GII.4, GII.17, or GI.1. In addition, 8C7 and 8D1 efficiently blocked GII.3 VLP binding with its ligand, histo-blood group antigens (HBGA). These data demonstrate that 8C7 and 8D1 are GII.3-specific blockade antibodies. By using a series of chimeric VLPs, we mapped the epitopes of 8C7 and 8D1 to residues 385-400 and 401-420 of the VP1 capsid protein, respectively. These two blockade antibody epitopes are highly conserved among GII.3 cluster 3 strains. Structural modeling shows that the 8C7 epitope partially overlaps with the HBGA binding site (HBS) while the 8D1 epitope is spatially adjacent to HBS. These findings may enhance our understanding of the immunology and evolution of GII.3 noroviruses.


Subject(s)
Norovirus/genetics , Norovirus/immunology , Amino Acid Sequence , Animals , Antibodies, Blocking/immunology , Antibodies, Monoclonal/immunology , Antibodies, Viral/immunology , Binding Sites/genetics , Blood Group Antigens/genetics , Caliciviridae Infections/genetics , Capsid/immunology , Capsid Proteins/genetics , Capsid Proteins/immunology , Epitopes/genetics , Epitopes/immunology , Gastroenteritis/virology , Genotype , Humans , Mice , Protein Binding/genetics , Protein Binding/immunology , Protein Domains/genetics
7.
Viruses ; 13(2)2021 01 21.
Article in English | MEDLINE | ID: covidwho-1456346

ABSTRACT

Rubella virus (RuV) is the infectious agent of a series of birth defect diseases termed congenital rubella syndrome, which is a major public health concern all around the world. RNA interference (RNAi) is a crucial antiviral defense mechanism in eukaryotes, and numerous viruses have been found to encode viral suppressors of RNAi (VSRs) to evade antiviral RNAi response. However, there is little knowledge about whether and how RuV antagonizes RNAi. In this study, we identified that the RuV capsid protein is a potent VSR that can efficiently suppress shRNA- and siRNA-induced RNAi in mammalian cells. Moreover, the VSR activity of the RuV capsid is dependent on its dimerization and double-stranded RNA (dsRNA)-binding activity. In addition, ectopic expression of the RuV capsid can effectively rescue the replication defect of a VSR-deficient virus or replicon, implying that the RuV capsid can act as a VSR in the context of viral infection. Together, our findings uncover that RuV encodes a VSR to evade antiviral RNAi response, which expands our understanding of RuV-host interaction and sheds light on the potential therapeutic target against RuV.


Subject(s)
Capsid Proteins/metabolism , Host-Pathogen Interactions , RNA Interference , Rubella virus/pathogenicity , Animals , Capsid , Capsid Proteins/genetics , Chlorocebus aethiops , HEK293 Cells , Humans , RNA, Double-Stranded , RNA, Small Interfering , Rubella virus/genetics , Vero Cells , Virion , Virus Replication
8.
Viruses ; 13(7)2021 06 24.
Article in English | MEDLINE | ID: covidwho-1389547

ABSTRACT

Adenovirus vector-based genetic vaccines have emerged as a powerful strategy against the SARS-CoV-2 health crisis. This success is not unexpected because adenoviruses combine many desirable features of a genetic vaccine. They are highly immunogenic and have a low and well characterized pathogenic profile paired with technological approachability. Ongoing efforts to improve adenovirus-vaccine vectors include the use of rare serotypes and non-human adenoviruses. In this review, we focus on the viral capsid and how the choice of genotypes influences the uptake and subsequent subcellular sorting. We describe how understanding capsid properties, such as stability during the entry process, can change the fate of the entering particles and how this translates into differences in immunity outcomes. We discuss in detail how mutating the membrane lytic capsid protein VI affects species C viruses' post-entry sorting and briefly discuss if such approaches could have a wider implication in vaccine and/or vector development.


Subject(s)
Adenoviruses, Human/immunology , Adenoviruses, Human/physiology , Capsid/metabolism , Genetic Vectors , Viral Vaccines/immunology , Virus Internalization , Adaptive Immunity , Adenoviruses, Human/genetics , Animals , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/immunology , Capsid/immunology , Capsid Proteins/genetics , Capsid Proteins/immunology , Capsid Proteins/metabolism , Clinical Trials as Topic , Humans , Immunity, Innate , Mice , SARS-CoV-2/immunology
9.
Viruses ; 13(1)2021 Jan 07.
Article in English | MEDLINE | ID: covidwho-1389524

ABSTRACT

We describe the complete capsid of a genotype C1-like Enterovirus A71 variant recovered from wastewater in a neighborhood in the greater Tempe, Arizona area (Southwest United States) in May 2020 using a pan-enterovirus amplicon-based high-throughput sequencing strategy. The variant seems to have been circulating for over two years, but its sequence has not been documented in that period. As the SARS-CoV-2 pandemic has resulted in changes in health-seeking behavior and overwhelmed pathogen diagnostics, our findings highlight the importance of wastewater-based epidemiology (WBE ) as an early warning system for virus surveillance.


Subject(s)
Capsid Proteins/genetics , Enterovirus A, Human/genetics , Enterovirus A, Human/isolation & purification , High-Throughput Nucleotide Sequencing/methods , Waste Water/virology , Wastewater-Based Epidemiological Monitoring , Arizona/epidemiology , Capsid/chemistry , Enterovirus Infections/epidemiology , Enterovirus Infections/virology , Humans , Molecular Epidemiology , Pandemics , Phylogeny
10.
Int J Mol Sci ; 22(5)2021 Feb 28.
Article in English | MEDLINE | ID: covidwho-1120219

ABSTRACT

Adenovirus-based gene transfer vectors are the most frequently used vector type in gene therapy clinical trials to date, and they play an important role as genetic vaccine candidates during the ongoing SARS-CoV-2 pandemic. Immediately upon delivery, adenovirus-based vectors exhibit multiple complex vector-host interactions and induce innate and adaptive immune responses. This can severely limit their safety and efficacy, particularly after delivery through the blood stream. In this review article we summarize two strategies to modulate Ad vector-induced immune responses: extensive genomic and chemical capsid modifications. Both strategies have shown beneficial effects in a number of preclinical studies while potential synergistic effects warrant further investigations.


Subject(s)
Adenoviridae/genetics , Adenoviridae/immunology , Capsid/immunology , Genetic Vectors/genetics , Genetic Vectors/immunology , Animals , COVID-19 , COVID-19 Vaccines/immunology , Capsid Proteins/genetics , Humans , Immunity , Immunogenicity, Vaccine , SARS-CoV-2/genetics , SARS-CoV-2/immunology
11.
Ann Diagn Pathol ; 50: 151645, 2021 Feb.
Article in English | MEDLINE | ID: covidwho-1064802

ABSTRACT

The objective of this study was to elucidate the pathophysiology that underlies severe COVID-19 by assessing the histopathology and the in situ detection of infectious SARS-CoV-2 and viral capsid proteins along with the cellular target(s) and host response from twelve autopsies. There were three key findings: 1) high copy infectious virus was limited mostly to the alveolar macrophages and endothelial cells of the septal capillaries; 2) viral spike protein without viral RNA localized to ACE2+ endothelial cells in microvessels that were most abundant in the subcutaneous fat and brain; 3) although both infectious virus and docked viral spike protein was associated with complement activation, only the endocytosed pseudovirions induced a marked up-regulation of the key COVID-19 associated proteins IL6, TNF alpha, IL1 beta, p38, IL8, and caspase 3. Importantly, this microvasculitis was associated with characteristic findings on hematoxylin and eosin examination that included endothelial degeneration and resultant basement membrane zone disruption and reduplication. It is concluded that serious COVID-19 infection has two distinct mechanisms: 1) a microangiopathy of pulmonary capillaries associated with a high infectious viral load where endothelial cell death releases pseudovirions into the circulation, and 2) the pseudovirions dock on ACE2+ endothelial cells most prevalent in the skin/subcutaneous fat and brain that activates the complement pathway/coagulation cascade resulting in a systemic procoagulant state as well as the expression of cytokines that produce the cytokine storm. The data predicts a favorable response to therapies based on either removal of circulating viral proteins and/or blunting of the endothelial-induced response.


Subject(s)
COVID-19/physiopathology , Capsid Proteins/metabolism , SARS-CoV-2/pathogenicity , Spike Glycoprotein, Coronavirus/metabolism , Thrombotic Microangiopathies/physiopathology , Vascular Diseases/physiopathology , Adult , Aged , Aged, 80 and over , Angiotensin-Converting Enzyme 2/metabolism , Autopsy , COVID-19/virology , Capsid Proteins/genetics , Endothelial Cells/enzymology , Endothelial Cells/virology , Female , Humans , Lung/physiopathology , Lung/virology , Male , Microvessels/physiopathology , Microvessels/virology , Middle Aged , RNA, Viral/genetics , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Thrombotic Microangiopathies/virology , Vascular Diseases/virology , Virion
12.
Proc Natl Acad Sci U S A ; 118(3)2021 01 19.
Article in English | MEDLINE | ID: covidwho-1003394

ABSTRACT

Human adenovirus species D (HAdV-D) types are currently being explored as vaccine vectors for coronavirus disease 2019 (COVID-19) and other severe infectious diseases. The efficacy of such vector-based vaccines depends on functional interactions with receptors on host cells. Adenoviruses of different species are assumed to enter host cells mainly by interactions between the knob domain of the protruding fiber capsid protein and cellular receptors. Using a cell-based receptor-screening assay, we identified CD46 as a receptor for HAdV-D56. The function of CD46 was validated in infection experiments using cells lacking and overexpressing CD46, and by competition infection experiments using soluble CD46. Remarkably, unlike HAdV-B types that engage CD46 through interactions with the knob domain of the fiber protein, HAdV-D types infect host cells through a direct interaction between CD46 and the hexon protein. Soluble hexon proteins (but not fiber knob) inhibited HAdV-D56 infection, and surface plasmon analyses demonstrated that CD46 binds to HAdV-D hexon (but not fiber knob) proteins. Cryoelectron microscopy analysis of the HAdV-D56 virion-CD46 complex confirmed the interaction and showed that CD46 binds to the central cavity of hexon trimers. Finally, soluble CD46 inhibited infection by 16 out of 17 investigated HAdV-D types, suggesting that CD46 is an important receptor for a large group of adenoviruses. In conclusion, this study identifies a noncanonical entry mechanism used by human adenoviruses, which adds to the knowledge of adenovirus biology and can also be useful for development of adenovirus-based vaccine vectors.


Subject(s)
Adenoviruses, Human , COVID-19 Vaccines , Capsid Proteins , Gene Expression Regulation, Viral , SARS-CoV-2/genetics , Virus Internalization , Adenoviruses, Human/genetics , Adenoviruses, Human/metabolism , COVID-19 Vaccines/genetics , COVID-19 Vaccines/metabolism , Capsid Proteins/biosynthesis , Capsid Proteins/genetics , Cell Line , Humans
13.
Mikrochim Acta ; 187(11): 624, 2020 10 23.
Article in English | MEDLINE | ID: covidwho-888208

ABSTRACT

A label-free electrochemical strategy is proposed combining equivalent substitution effect with AuNPs-assisted signal amplification. According to the differences of S1 protein in various infectious bronchitis virus (IBV) strains, a target DNA sequence that can specifically recognize H120 RNA forming a DNA-RNA hybridized double-strand structure has been designed. Then, the residual single-stranded target DNA is hydrolyzed by S1 nuclease. Therefore, the content of target DNA becomes equal to the content of virus RNA. After equivalent coronavirus, the target DNA is separated from DNA-RNA hybridized double strand by heating, which can partly hybridize with probe 2 modified on the electrode surface and probe 1 on AuNPs' surface. Thus, AuNPs are pulled to the surface of the electrode and the abundant DNA on AuNPs' surface could adsorb a large amount of hexaammineruthenium (III) chloride (RuHex) molecules, which produce a remarkably amplified electrochemical response. The voltammetric signal of RuHex with a peak near - 0.28 V vs. Ag/AgCl is used as the signal output. The proposed method shows a detection range of 1.56e-9 to 1.56e-6 µM with the detection limit of 2.96e-10 µM for IBV H120 strain selective quantification detection, exhibiting good accuracy, stability, and simplicity, which shows a great potential for IBV detection in vaccine research and avian infectious bronchitis diagnosis. Graphical abstract.


Subject(s)
Biosensing Techniques/methods , Coronavirus Infections/virology , Coronavirus/isolation & purification , Electrochemical Techniques/methods , Infectious bronchitis virus/isolation & purification , Spike Glycoprotein, Coronavirus/chemistry , Animals , Biosensing Techniques/standards , Capsid Proteins/genetics , Chickens , Coronavirus/genetics , DNA Probes , Gold , In Situ Hybridization , Infectious bronchitis virus/genetics , Limit of Detection , Metal Nanoparticles/chemistry , RNA, Viral/genetics , RNA, Viral/isolation & purification , Species Specificity
14.
Transbound Emerg Dis ; 67(3): 1284-1294, 2020 May.
Article in English | MEDLINE | ID: covidwho-832791

ABSTRACT

In recent years, reports indicated that PCV3 may be involved in porcine dermatitis and nephropathy syndrome (PDNS)-like disease similar to that linked to PCV2. A total of 2,125 porcine samples from 910 cases were collected during 2016-2018 and tested for presence of PCV3 and PCV2 by real-time PCR assays. Results showed high prevalence of PCV3 and PCV2: 28.4% samples from 41.2% cases were PCV3 positive and 16.4% samples from 16.7% cases were PCV2 positive. The overall coinfection rate was 5.4% and 8.4% at the sample and case level, respectively. Temporal analysis indicated that PCV3 positive case rate increased from 31.6% in 2016, 40.9% in 2017, to 55.6% in 2018. Although its prevalence was lower, PCV2-positive case rate in 2018 (28.8%) doubled that in 2017 (14.4%). The coinfection case rate also increased from 3.4% in 2016, 8.0% in 2017 to 16.1% in 2018. The high positive rate of PCV3 (56.9%) and PCV2 (33.8%) in oral fluids, PCV3 in foetuses (57.1%) and PCV2 in tonsils (54.8%) implied viral transmission route and tissue tropism. In phylogenetic analysis, two small PCV3 clusters (1 and 2) were separated but others were clustered with low bootstrapping values indicating overall low genetic diversity. Genotypes, PCV2a-h, were confirmed by analysing 2,944 strains, with a new genotype proposed as PCV2i. In this study, 61 PCV3 unique whole genomes were sequenced; 12 belonged to a separate cluster that were characterized by five consistent amino acid changes in the capsid protein (24V, 27K, 56D, 98R and 168K) and may be associated with potential differences in immunogenicity. Among the 43 unique PCV2 whole genomes sequenced, 31 belonged to PCV2d, 7 to PCV2a and 5 to PCV2b. Thus, our study demonstrates that PCV2d is the predominant genotype and PCV3 is widely circulating in the Midwest of the USA.


Subject(s)
Circoviridae Infections/virology , Circovirus/genetics , Genetic Variation , Swine Diseases/virology , Animals , Capsid Proteins/genetics , Circovirus/classification , Coinfection , Genotype , Midwestern United States/epidemiology , Phylogeny , Prevalence , Swine , Swine Diseases/epidemiology
15.
J Virol Methods ; 279: 113842, 2020 05.
Article in English | MEDLINE | ID: covidwho-832023

ABSTRACT

Infectious bovine viral diarrhea virus (BVDV) cDNA clones have been used for the expression of classical swine fever virus (CSFV) genes for immune prevention and control. However, can it be used for the expression of an allogenetic fragment? To answer this question, a BVDV chimeric virus expressing the spike (S) antigen fragment of porcine epidemic diarrhea virus (PEDV) was constructed. Antigen S499-602 was inserted into pig-derived BVDV-2 infectious cDNA clone pASH28 in tandem by overlapping PCR, located between the seventh and eighth amino acids at the N-terminus of the capsid (C) protein of BVDV. Indirect immunofluorescence assay confirmed that the chimeric virus vASH-dS312 containing double S499-602 sequences was successfully assembled, which could react with the monoclonal antibody (MAb) against BVDV E2 and PEDV S proteins. Further western blot analysis confirmed that the exogenous S499-602 double protein could be stably expressed. Next, the chimeric virus vASH-dS312 was administered to BALB/C mice either orally or by intramuscular injection. The immunized mice were healthy and showed no signs of toxicity. IgG against BVDV and PEDV antibodies could be detected in the mice administered vASH-dS312 by intramuscular injection, which had neutralization activity against BVDV and PEDV. Thus, this study reported a new insertion site in the BVDV infectious cDNA clone that could successfully express an allogenetic antigen.


Subject(s)
Antigens, Viral/genetics , Capsid Proteins/genetics , Diarrhea Virus 2, Bovine Viral/genetics , Porcine epidemic diarrhea virus/genetics , Viral Vaccines/immunology , Animals , Antibodies, Viral/blood , Diarrhea Virus 2, Bovine Viral/growth & development , Genetic Vectors , Homologous Recombination , Immunogenicity, Vaccine , Mice , Mice, Inbred BALB C , Swine , Viral Vaccines/genetics
16.
Vet Microbiol ; 251: 108878, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-808435

ABSTRACT

Canine chaphamaparvovirus (CaChPV) is a newly recognised parvovirus discovered by metagenomic analysis during an outbreak of diarrhoea in dogs in Colorado, USA, in 2017 and more recently detected in diarrhoeic dogs in China. Whether the virus plays a role as canine pathogen and whether it is distributed elsewhere, in other geographical areas, is not known. We performed a case-control study to investigate the possible association of CaChPV with enteritis in dogs. CaChPV DNA was detected both in the stools of diarrhoeic dogs (1.9 %, 3/155) and of healthy animals (1.6 %, 2/120). All the CaChPV-infected dogs with diarrhea were mixed infected with other enteric viruses such as canine parvovirus (formerly CPV-2), canine bufavirus (CBuV) and canine coronavirus (CCoV), whilst none of the asymptomatic CaChPV positive animals resulted co-infected. The nearly full-length genome and the partial capsid protein (VP) gene of three canine strains, Te/36OVUD/19/ITA, Te/37OVUD/19/ITA and Te/70OVUD/19/ITA, were reconstructed. Upon phylogenetic analyses based on the NS1 and VP aa sequences, the Italian CaChPV strains tightly clustered with the American reference viruses. Distinctive residues could be mapped to the deduced variable regions of the VP of canine and feline chaphamaparvoviruses, considered as important markers of host range and pathogenicity for parvoviruses.


Subject(s)
Diarrhea/veterinary , Dog Diseases/virology , Genome, Viral , Parvoviridae Infections/veterinary , Parvovirus, Canine/classification , Animals , Capsid Proteins/genetics , Case-Control Studies , Diarrhea/virology , Dogs/virology , Feces/virology , Host Specificity , Italy , Parvoviridae Infections/diagnosis , Parvoviridae Infections/virology , Parvovirus, Canine/isolation & purification , Pets/virology , Phylogeny , Viral Nonstructural Proteins/genetics
17.
Infect Genet Evol ; 85: 104489, 2020 11.
Article in English | MEDLINE | ID: covidwho-692494

ABSTRACT

The current SARS-CoV-2 pandemic has imposed new challenges and demands for health systems, especially in the development of new vaccine strategies. Vaccines for many pathogens were developed based on the display of foreign epitopes in the variable regions of the human adenovirus (HAdV) major capsid proteins (hexon, penton and fiber). The humoral immune response against the HAdV major capsid proteins was demonstrated to play a role in the development of an immune response against the epitopes in display. Through the immunoinformatic profiling of the major capsid proteins of HAdVs from different species, we developed a modular concept that can be used in the development of vaccines based on HAdV vectors. Our data suggests that different immunomodulatory potentials can be observed in the conserved regions, present in the hexon and penton proteins, from different species. Using this modular approach, we developed a HAdV-5 based vaccine strategy for SARS-CoV-2, constructed through the display of SARS-CoV-2 epitopes indicated by our prediction analysis as immunologically relevant. The sequences of the HAdV vector major capsid proteins were also edited to enhance the IFN-gamma induction and antigen presenting cells activation. This is the first study proposing a modular HAdV platform developed to aid the design of new vaccines by inducing an immune response more suited for the epitopes in display.


Subject(s)
Capsid Proteins/chemistry , Computational Biology/methods , Epitopes, B-Lymphocyte/immunology , Viral Vaccines/immunology , Antigen Presentation , Capsid Proteins/genetics , Capsid Proteins/immunology , Computer Simulation , Dependovirus/immunology , Drug Design , Epitopes, B-Lymphocyte/genetics , Humans , Immunity, Humoral , Interferon-gamma/metabolism , SARS-CoV-2/drug effects , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Viral Vaccines/genetics
18.
Viral Immunol ; 33(6): 434-443, 2020.
Article in English | MEDLINE | ID: covidwho-165137

ABSTRACT

Canine parvovirus type 2 (CPV2) is a highly contagious cause of serious and often fatal disease in young dogs. Despite the widespread availability of attenuated vaccines, safer, more stable, and more effective CPV2 vaccine candidates are still under exploration. Vaccinia virus (VV) has already been proved to be a safe, stable, and effective vaccine vector. In this study, we generated a VV-based CPV2 vaccine candidate (VV-CPV-VP2) and then evaluated its immunogenicity in mice and dogs. The exogenous vp2 gene of CPV2, which replaced the major virulence gene hemagglutinin (ha) of VV, expressed efficiently and stably in vitro. Subsequently, intramuscular immunization of mice induced robust and lasting systemic immune responses, including neutralizing antibody against both CPV2a and CPV2b, and CPV2-VP2-specific interferon gamma (IFN-γ) secreting T cell. In addition, administration with a high-dose of VV-CPV-VP2 did not cause significant side effects for mice, thus indicating marked safety of this vaccine candidate. Most importantly, a single-dose vaccination of VV-CPV2-VP2 elicited substantial antibody responses and provided comparable protection for dogs with attenuated CPV2 vaccine. Collectively, this study demonstrated that VV-CPV2-VP2 could be used as a promising vaccine candidate preventing CPV2 from infection for dogs.


Subject(s)
Capsid Proteins/immunology , Parvoviridae Infections/prevention & control , Parvoviridae Infections/veterinary , Parvovirus, Canine/genetics , Vaccinia virus/genetics , Viral Vaccines/immunology , Animals , Antibodies, Neutralizing/blood , Antibodies, Viral/blood , Antibodies, Viral/immunology , Capsid Proteins/genetics , Chlorocebus aethiops , Dog Diseases/prevention & control , Dog Diseases/virology , Dogs , Female , Male , Mice , Mice, Inbred BALB C , Parvovirus, Canine/immunology , Vaccines, Synthetic/administration & dosage , Vaccines, Synthetic/immunology , Vaccinia virus/immunology , Vero Cells , Viral Vaccines/administration & dosage , Viral Vaccines/genetics
19.
J Infect ; 81(1): e24-e27, 2020 07.
Article in English | MEDLINE | ID: covidwho-47836

ABSTRACT

BACKGROUND: SARS-CoV-2 is a new coronavirus that has spread globally, infecting more than 150000 people, and being declared pandemic by the WHO. We provide here bio-informatic, evolutionary analysis of 351 available sequences of its genome with the aim of mapping genome structural variations and the patterns of selection. METHODS: A Maximum likelihood tree has been built and selective pressure has been investigated in order to find any mutation developed during the SARS-CoV-2 epidemic that could potentially affect clinical evolution of the infection. FINDING: We have found in more recent isolates the presence of two mutations affecting the Non-Structural Protein 6 (NSP6) and the Open Reding Frame10 (ORF 10) adjacent regions. Amino acidic change stability analysis suggests both mutations could confer lower stability of the protein structures. INTERPRETATION: One of the two mutations, likely developed within the genome during virus spread, could affect virus intracellular survival. Genome follow-up of SARS-CoV-2 spread is urgently needed in order to identify mutations that could significantly modify virus pathogenicity.


Subject(s)
Betacoronavirus/genetics , Capsid Proteins/genetics , Coronavirus Infections/virology , Mutation , Pneumonia, Viral/virology , Autophagy , COVID-19 , Coronavirus Nucleocapsid Proteins , Evolution, Molecular , Gene Expression Regulation, Viral , Genome, Viral , Humans , Likelihood Functions , Models, Molecular , Open Reading Frames , Pandemics , Protein Conformation , SARS-CoV-2
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