Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens.

The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry (MS) based proteomics for the detection of SARS-CoV-2 proteins in both research samples and clinical specimens. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) MS in infected Vero E6 cells. For tryptic peptides of Nucleocapsid protein, the limit of detection was estimated to be in the mid-attomole range (9E-13 g). Next, this PRM methodology was applied to the detection of viral proteins in various COVID-19 patient clinical specimens, such as sputum and nasopharyngeal swabs. SARS-CoV-2 proteins were detected in these samples with high sensitivity in all specimens with PCR Ct values <24 and in several samples with higher CT values. A clear relationship was observed between summed MS peak intensities for SARS-CoV-2 proteins and Ct values reflecting the abundance of viral RNA. Taken together, these results suggest that targeted MS based proteomics may have the potential to be used as an additional tool in COVID-19 diagnostics.

Cryo-EM structure reveals cylindrical nucleocapsids from two polydnaviruses.

Bracovirus is one of the two polydnavirus genera. Here, we used a cryo-EM analysis to reveal the near-native morphology of two nucleocapsid-containing model bracoviruses: Microplitis bicoloratus bracovirus (MbBV) and Microplitis mediator bracovirus (MmBV). MbBV and MmBV nucleocapsids have discernable cap structures in two distal regions with relatively high electron density. Adjacent to the end-cap structures are two electron-lucent rings. Some nucleocapsids were uniformly electron-dense and had a distinctive "helix-tail-like structure". Cryo-EM revealed inconsistent nucleocapsid diameters of 34-69.9 nm in MbBV and 46-69.9 nm in MmBV, and the largest observed cylindrical area length was expanded to 126 nm.

Quantification of RNA Content in Reconstituted Ebola Virus Nucleocapsids by Immunoprecipitation.

Immunoprecipitations are commonly used to isolate proteins or protein complexes and assess protein-protein interactions; however, they can also be used to assess protein-RNA complexes. Here we describe an adapted RNA immunoprecipitation technique that permits the quantification of RNA content in Ebola virus nucleocapsids that have been reconstituted in vitro by transient transfection.

Development of a novel hepatitis B virus encapsidation detection assay by viral nucleocapsid-captured quantitative RT-PCR.

After encapsidation, where pregenomic RNA (pgRNA) is packaged into viral nucleocapsids, hepatitis B virus (HBV) uses the pgRNA as a template to replicate its DNA genome by reverse transcription. To date, there are only two encapsidation detection methods for evaluating the amount of pgRNA packaged into nucleocapsids: (i) the RNase protection assay and (ii) the native agarose gel electrophoresis assay. However, these methods are complex and laborious because they require multiple pgRNA purification steps followed by detection via an isotope-labeled probe. Moreover, both assays are unsuitable for evaluating a large number of antiviral agents in a dose-dependent manner. To overcome these limitations, we devised a novel HBV encapsidation assay in a 96-well plate format using nucleocapsid capture plates coated with an anti-HBV core (HBc) antibody, usually employed in enzyme-linked immunosorbent assays, to immobilize viral nucleocapsids. Viral pgRNA is then detected by quantitative RT-PCR (RT-qPCR). This strategy allows fast, convenient, and quantitative analysis of multiple viral RNA samples to evaluate encapsidation inhibitors. Furthermore, our protocol is potentially suitable for high-throughput screening (HTS) of compounds targeting HBV pgRNA encapsidation.

Isolation of herpes simplex virus nucleocapsid DNA.

As an inanimate virus, herpes simplex virus type 1 (HSV-1) necessarily encodes all of its functions in its DNA. Isolation of pure viral DNA allows multiple downstream applications, including the creation of recombinant HSV strains, cloning of selected regions, and sequencing of viral DNA. The term nucleocapsid refers to the combination of the viral genome with the enclosing capsid; these viral genomes are necessarily linear and have been packaged for egress, even if they are not yet released from the cell. In contrast, viral DNA that is not associated with capsids may include episomal or concatenated forms and may have modifications such as histones that are added within cells. During this protocol, the viral capsid protects the HSV genome from reagents that strip away and destroy most cellular contaminants. This procedure describes the isolation of viral nucleocapsids and their subsequent dissolution to purify clean, linear HSV DNA.

Maturation-associated destabilization of hepatitis B virus nucleocapsid.

The mature nucleocapsid (NC) of hepatitis B virus containing the relaxed circular (RC) DNA genome can be secreted extracellularly as virions after envelopment with the viral surface proteins or, alternatively, can be disassembled to release RC DNA (i.e., uncoating) into the host cell nucleus to form the covalently closed circular (CCC) DNA, which sustains viral replication and persistence. In contrast, immature NCs containing the viral single-stranded DNA or the pregenomic RNA are incompetent for either envelopment or uncoating. Little is currently known about how mature NCs, and not the immature ones, are specifically selected for these processes. Here, we have carried out a biochemical analysis of the different NC populations upon their separation through sucrose gradient centrifugation. We have found that the maturation of NCs is associated with their destabilization, manifested as increased protease and nuclease sensitivity, altered sedimentation during sucrose gradient centrifugation, and retarded mobility during native agarose gel electrophoresis. Also, three distinct populations of intracellular mature NCs could be differentiated based on these characteristics. Furthermore, mature NCs generated in vitro under cell-free conditions acquired similar properties. These results have thus revealed significant structural changes associated with NC maturation that likely play a role in the selective uncoating of the mature NC for CCC DNA formation and/or its preferential envelopment for virion secretion.

Rescue of infectious particles from preassembled alphavirus nucleocapsid cores.

Alphaviruses are small, spherical, enveloped, positive-sense, single-stranded, RNA viruses responsible for considerable human and animal disease. Using microinjection of preassembled cores as a tool, a system has been established to study the assembly and budding process of Sindbis virus, the type member of the alphaviruses. We demonstrate the release of infectious virus-like particles from cells expressing Sindbis virus envelope glycoproteins following microinjection of Sindbis virus nucleocapsids purified from the cytoplasm of infected cells. Furthermore, it is shown that nucleocapsids assembled in vitro mimic those isolated in the cytoplasm of infected cells with respect to their ability to be incorporated into enveloped virions following microinjection. This system allows for the study of the alphavirus budding process independent of an authentic infection and provides a platform to study viral and host requirements for budding.

Label free detection of white spot syndrome virus using lead magnesium niobate-lead titanate piezoelectric microcantilever sensors.

We have investigated rapid, label free detection of white spot syndrome virus (WSSV) using the first longitudinal extension resonance peak of five lead-magnesium niobate-lead titanate (PMN-PT) piezoelectric microcantilever sensors (PEMS) 1050-700 µm long and 850-485 µm wide constructed from 8 µm thick PMN-PT freestanding films. The PMN-PT PEMS were encapsulated with a 3-mercaptopropyltrimethoxysilane (MPS) insulation layer and further coated with anti-VP28 and anti-VP664 antibodies to target the WSSV virions and nucleocapsids, respectively. By inserting the antibody coated PEMS in a flowing virion or nucleocapsid suspension, label free detection of the virions and nucleocapsids were respectively achieved by monitoring the PEMS resonance frequency shift. We showed that positive label free detection of both the virion and the nucleocapsid could be achieved at a concentration of 100virions(nucleocapsids)/ml or 10 virions(nucleocapsids)/100 µl, comparable to the detection sensitivity of polymerase chain reaction (PCR). However, in contrast to PCR, PEMS detection was label free, in situ and rapid (less than 30 min), potentially requiring minimal or no sample preparation.

Structure of a Venezuelan equine encephalitis virus assembly intermediate isolated from infected cells.

Venezuelan equine encephalitis virus (VEEV) is a prototypical enveloped ssRNA virus of the family Togaviridae. To better understand alphavirus assembly, we analyzed newly formed nucleocapsid particles (termed pre-viral nucleocapsids) isolated from infected cells. These particles were intermediates along the virus assembly pathway, and ultimately bind membrane-associated viral glycoproteins to bud as mature infectious virus. Purified pre-viral nucleocapsids were spherical with a unimodal diameter distribution. The structure of one class of pre-viral nucleocapsids was determined with single particle reconstruction of cryo-electron microscopy images. These studies showed that pre-viral nucleocapsids assembled into an icosahedral structure with a capsid stoichiometry similar to the mature nucleocapsid. However, the individual capsomers were organized significantly differently within the pre-viral and mature nucleocapsids. The pre-viral nucleocapsid structure implies that nucleocapsids are highly plastic and undergo glycoprotein and/or lipid-driven rearrangements during virus self-assembly. This mechanism of self-assembly may be general for other enveloped viruses.

A new rod-shaped virus from parasitic wasp Diachasmimorpha longicaudata (Hymenoptera: Braconidae).

A new rod-shaped nucleocapsids (NCs) was found inadvertently in Diachasmimorpha longicaudata accessory gland filaments (AGFs). The NCs were 30 nm in diameter and nearly 900 nm in length. They replicated in a small cell type of the AGFs in D. longicaudata, and following oviposition, invaded and proliferated in the hemocytes of a parasitized host Bactrocera dorsalis Hendel. This finding of a completely new virus in the AGF indicate that different geographical populations (subspecies) of D. longicaudata may carry different sybionts. This is the first report showing that the same wasp species, but from a different geographical populations, can carry an entirely different virus.

Detection of antibodies against SARS-Coronavirus using recombinant truncated nucleocapsid proteins by ELISA.

Severe acute respiratory syndrome (SARS) is a lifethreatening emerging respiratory disease caused by the coronavirus, SARS-CoV. The nucleocapsid (N) protein of SARS-CoV is highly antigenic and may be a suitable candidate for diagnostic applications. We constructed truncated recombinant N proteins (N1 [1-422 aa], N2 [1- 109 aa], and N3 [110-422 aa]) and determined their antigenicity by Western blotting using convalescent SARS serum. The recombinants containing N1 and N3 reacted with convalescent SARS serum in Western blotting. However, the recombinant with N2 did not. In ELISA using N1 or N3 as the antigens, positive results were observed in 10 of 10 (100%) SARS-CoV-positive human sera. None of 50 healthy sera gave positive results in either assay. These data indicate that the ELISA using N1 or N3 has high sensitivity and specificity. These results suggest that the middle or C-terminal region of the SARS N protein is important for eliciting antibodies against SARS-CoV during the immune response, and ELISA reactions using N1 or N3 may be a valuable tool for SARS diagnosis.

Expression, purification and characterization of full-length RNA-free hepatitis B core particles.

The nucleocapsid or core particle of the hepatitis B virus has become one of the favourite recombinant vaccine carriers for foreign peptides, proteins and stimulatory oligonucleotides. The core protein consists of three regions: an N-terminal, a central and a C-terminal region that can accommodate the addition or insertion of the foreign sequences. The protamine-like C-terminal region that binds host RNA randomly during recombinant particle formation is often truncated. It is commonly thought that these truncations do not affect particle assembly. Recent studies have demonstrated that the C-terminal domains mediate a glycosaminoglycan-dependent attachment of nucleocapsids to the plasma membranes of host cells. This interaction might well contribute to the immunogenicity of nucleocapsids. Testing the hypothesis that full-length particles might be safer and superior for the induction of an immune response against the nucleocapsids and inserted sequences, requires the availability of purified particles. In this report, we detail a novel method for the synthesis and purification of full-length core particles essentially free of RNA from Escherichia coli.

[First detection of human metapneumovirus in a child with respiratory syndrome in Hungary]. / Humán metapneumovírus elso hazai kimutatása gyermekkori légúti fertozésbol.

INTRODUCTION: Human metapneumovirus was identified in 2001 as a respiratory-tract pathogen that has been classified as a new genera in family Paramyxoviridae. AIMS: Molecular detection of human metapneumovirus in Hungary. MATERIALS AND METHODS: Human metapneumovirus was identified in nasopharyngeal aspirate amplification of the viral fusion and nucleocapsid genes by reverse transcription-polymerase chain reaction followed by sequencing and phylogenetic analysis. RESULTS: A 4 years-old girl with chronic respiratory syndrome chronically treated with anti-asthma drugs was admitted to hospital in November 2005 with acute respiratory syndrome and atelectasis. Nasopharyngeal aspirate was negative for common bacteria by culture and for influenza and coronavirus by reverse transcription-polymerase chain reaction. By contrast, specimen was positive by reverse transcription-polymerase chain reaction and was confirmed by sequencing both genes (nucleocapsid and fusion) of human metapneumovirus. Human metapneumovirus (HUN 05-L20) clustered into the subgroup B1 has the closest nucleotide similarity (98%) to JPS03-194 (AY530094) detected in Japan. CONCLUSIONS: Human metapneumovirus contributes as an etiological agent of acute lower and upper respiratory tract infection especially in winter season in children with bronchiolitis, pneumonia or episodes of asthma exacerbation in Hungary, too.

Structural difference recognized by a monoclonal antibody #404-11 between the rabies virus nucleocapsid (NC) produced in virus infected cells and the NC-like structures produced in the nucleoprotein (N) cDNA-transfected cells.

We investigated structural changes in the rabies virus (HEP-Flury strain) nucleocapsid (NC) during the virus replication, for which we used two anti-nucleoprotein (N) monoclonal antibodies (mAbs), #404-11 (specific for a conformation-dependently exposed linear epitope) and #1-7-11 (specific for a conformational epitope which is exposed after the nucleocapsid formation). Both mAbs recognized the N protein of the viral NC, but not of the RNA-free N-P complex. The 1-7-11 and 404-11 epitopes could be mapped to the N-terminal and the C-terminal regions of N protein, respectively. Immunoprecipitation studies demonstrated that treatment of the NC either with the alkaline phosphatase or sodium deoxycholate (DOC) resulted in dissociation of most P proteins from the NC and in the reduced reactivity to mAb #404-11, but not to mAb #1-7-11. NC-like structures produced in the N cDNA-transfected cells displayed strong reactivity to mAb #1-7-11; however, reactivity to mAb #404-11 was very weak. And, coexpression with viral phosphoprotein (P) resulted in little increase in reactivity to mAb #404-11 of the NC-like structures, while the reactivity was significantly increased by cotransfection with P and the viral minigenome whose 3'- and 5'-end structures were derived from the viral genome. From these results, we assume that, although the 404-11 epitope is a linear one, the epitope-containing region is exposed only when N proteins encapsidate properly the viral RNA in collaboration with the P protein. Further, exposure of the 404-11 epitope region might be function-related, and be regulated by association and dissociation of the P protein.

Stability of intracellular influenza virus nucleocapsid protein oligomers.

Stability of A/Duck/Ukrainae/63 (H3N8) influenza virus intracellular NP oligomers was studied using reducing agents, denaturants, detergents, salts, various pH and a range of temperatures. The results obtained indicate that influenza virus NP oligomers are noncovalently stabilized, and NP subunits are not linked by disulfide bonds. NP oligomers are thermostable and SDS resistant. Urea and high ionic strength also do not dissociate avian influenza virus intracellular NP oligomers. However, NP oligomers are completely dissociated at pH < 5. The data obtained suggest that hydrophobic bonds together with the electrostatic interactions take part in the stabilization of compact conformation of influenza virus NP oligomers. It was also shown that intrachain disulfides revealed in nascent NPs are reduced in NP subunits of NP oligomers, and this probably contributes to the stability and compactness of the oligomers.

Selection and characterization of peptides specifically binding to HIV-1 psi (psi) RNA.

The packaging of HIV genomic RNA is mediated by a specific interaction between a nucleocapsid (NC) protein and packaging signal (psi, psi) RNA sequence. However, this interaction can be inhibited by the presence of peptides or proteins that specifically bind to the psi sequence. The 125-base-long psi RNA comprises a specific secondary structure that can be recognized by certain peptide sequences. Accordingly, the current study presents a method for selecting such peptides from a phage-displayed peptide library and characterization of resulting peptides in vitro. The RNA was covalently immobilized in a Covalink module using a carbodiimide condensation reaction at its 5'-end, leaving the proper secondary structure exposed and readily accessible. A phage display random peptide library was then screened against the RNA structure, and after five rounds of biopanning, enriched peptide sequences and conserved amino acid frames appeared. One of the enriched peptides was tested and shown to bind to psi RNA in a dose-dependent manner, plus it competed effectively with the NC protein as regards binding with the target RNA.

The phosphorylation of NS protein of wheat rosette stunt virus.

The genome of wheat rosette stunt virus (WRSV), a plant rhabdovirus, is a single negative strand RNA. It encodes five viral structural proteins: the glycoprotein (G), the matrix protein (M), the nucleocapsid protein (N), the large protein (L) and the non?structural protein (NS), which was later proved to be a viral structural protein too and existed in a variety of phosphorylation forms in case of vascular stomatitis virus (VSV). In this paper we demonstrated that NS protein of WRSV, either bound with the viral nucleocapsid or expressed in bacteria could be in vitro phosphorylated in presence of viral nucleocapsid. We concluded that the NS protein of WRSV was a phosphorylated protein and it might exist in both phosphorylated and dephosphorylated forms in virions. Our results excluded the possibility that the NS protein could be autophosphorylated. The L protein, the major component of viral RNA dependent RNA polymerase is associated with the protein kinase for phosphorylation of NS protein.

Identification of a novel protein associated with envelope of occlusion-derived virus in Spodoptera litura multicapsid nucleopolyhedrovirus.

Spodoptera litura multicapsid nucleopolyhedrovirus (SpltMNPV) ORF137 (Splt137) is one of 29 unique SpltMNPV ORFs. Splt137 has the potential to code for a polypeptide of 231 amino acid residues with predicted molecular weight of 27.5 kDa. Computer-assisted analysis of the predicted amino acid sequences of Splt137 protein showed 1 N-glycosylation site and 11 phosphorylation sites. For identification of Spit137, antibody was prepared by immunization of rabbits with purified Splt137 protein produced in Escherichia coli. This antibody was used to analyse Splt137 protein using Western blot. A 36-kDa protein was found both in the infected cells and envelope fractions of occlusion-derived virus (ODV) but could not be detected in the budded virus (BV). Tunicamycin treatment of SpltMNPV infected cells suggested that the 36-kDa protein had undergone N-glycosylation. Our data suggested that Splt137 protein was a novel envelope protein of ODV and might exist as a more complex form of 79-kDa protein in intact ODV. Further, transcriptional analysis with RT-PCR and 5' RACE analysis suggested that Splt137 might perform functions early and late in infection.

Isolation and characterisation of the rabies virus N degrees-P complex produced in insect cells.

When the nucleoprotein (N) of nonsegmented negative-strand RNA viruses is expressed in insect cells, it binds to cellular RNA and forms N-RNA complexes just like viral nucleocapsids. However, in virus-infected cells, N is prevented from binding to cellular RNA because a soluble complex is formed between N and the viral phosphoprotein (P), the N degrees -P complex. N is only released from this complex for binding to newly made viral or complementary RNA. We coexpressed rabies virus N and P proteins in insect cells and purified the N degrees -P complex. Characterisation by gel filtration, polyacrylamide gel electrophoresis, analytical ultracentrifugation, native mass spectroscopy, and electron microscopy showed that the complex consists of one N protein plus two P proteins, i.e., an N degrees -P(2) complex.

Structure of isolated nucleocapsids from venezuelan equine encephalitis virus and implications for assembly and disassembly of enveloped virus.

Venezuelan equine encephalitis virus (VEEV) is an important human and equine pathogen in the Americas, with widespread reoccurring epidemics extending from South America to the southern United States. Most troubling, VEEV has been made into a weapon by several countries and is currently restricted by the Centers for Disease Control and Prevention as a potential biological warfare and terrorism agent. To facilitate the development of antiviral compounds, the structure of the nucleocapsid isolated from VEEV has been determined by electron cryomicroscopy and image reconstruction and represents the first three-dimensional structure of a nucleocapsid isolated from a single-stranded enveloped RNA virus. The isolated VEEV nucleocapsid undergoes significant reorganization relative to its structure within VEEV. However, the isolated nucleocapsid clearly exhibits T=4 icosahedral symmetry, and its characteristic nucleocapsid hexons and pentons are preserved. The diameter of the isolated nucleocapsid is approximately 11.5% larger than that of the nucleocapsid within VEEV, with radial expansion being greatest near the hexons. Significantly, this is the first direct structural evidence showing that a simple enveloped virus undergoes large conformational changes during maturation, suggesting that the lipid bilayer and the transmembrane proteins of simple enveloped viruses provide the energy necessary to reorganize the nucleocapsid during maturation.