scholarly journals SARS COV-2: Exploring the Virus of the Century

2021 ◽  
Vol 8 (8) ◽  
pp. 459-467
Author(s):  
Arpita Saxena ◽  
Sukanya Gangopadhyay ◽  
Shilpa Suneja
Keyword(s):  
Nucleocapsid Protein ◽  
Matrix Protein ◽  
Large Family ◽  
Surface Glycoprotein ◽  
Structural Proteins ◽  
Virus Particles ◽  
Genomic Knowledge ◽  
Intestinal Infections ◽  
Recent Outbreak ◽  
Intracellular Virus

Coronaviruses comprise a large family of viruses that cause respiratory and intestinal infections in animals and humans. This recent outbreak of unusual respiratory disease plaguing the entire world has been named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the basis of phylogenetic analysis of related coronaviruses. Its transmission occurs mainly through airborn, fomite and other modes. Structurally, it is similar to other coronaviruses and has four major structural proteins; the spike surface glycoprotein (S), small envelope protein (E), matrix protein (M) and nucleocapsid protein (N). The M protein is most abundant and is responsible for intracellular formation of virus particles. S protein induces antibody generation and is involved in intracellular virus entry. Drug combinations are being tried on the basis of structural and genomic knowledge of the virus. Various researchers have found that the SARS CoV2 has many strains among which L type is most pathogenic and D614 type is most infective. All this information has been collected in this review to understand the virus behind this calamity in depth and to make it handy for the researchers to search literature related to SARS COV2. Keywords: SARS COV2, spike glycoprotein, L type strain, D614 strain.

scholarly journals SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins

2020 ◽  
Author(s):  
Martí Cortey ◽  
Yanli Li ◽  
Ivan Díaz ◽  
Hepzibar Clilverd ◽  
Laila Darwich ◽  
...  
Keyword(s):  
Amino Acid ◽  
Viral Genome ◽  
Nucleocapsid Protein ◽  
Human Population ◽  
Matrix Protein ◽  
Structural Proteins ◽  
Virus Population ◽  
The Matrix ◽  
Amino Acid Mutations ◽  
The Moment

AbstractThe Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic offers a unique opportunity to study the introduction and evolution of a pathogen into a completely naïve human population. We identified and analysed the amino acid mutations that gained prominence worldwide in the early months of the pandemic. Eight mutations have been identified along the viral genome, mostly located in conserved segments of the structural proteins and showing low variability among coronavirus, which indicated that they might have a functional impact. At the moment of writing this paper, these mutations present a varied success in the SARS-CoV-2 virus population; ranging from a change in the spike protein that becomes absolutely prevalent, two mutations in the nucleocapsid protein showing frequencies around 25%, to a mutation in the matrix protein that nearly fades out after reaching a frequency of 20%.

scholarly journals Sequence Analysis and Amino Acid Variations of Structural Proteins Deduced From Novel Coronavirus SARS-CoV-2 Strains, Isolated in Different Countries

2020 ◽  
Author(s):  
Tarlan Mamedov ◽  
Inanc Soylu ◽  
Gunay Mammadova ◽  
Gulnara Hasanova
Keyword(s):  
Amino Acid ◽  
Sequence Analysis ◽  
Nucleocapsid Protein ◽  
Matrix Protein ◽  
Structural Proteins ◽  
Therapeutic Drug ◽  
E Proteins ◽  
Multiple Sequence ◽  
Highly Pathogenic ◽  
Novel Coronavirus

SARS-CoV-2 is a novel and highly pathogenic coronavirus, which was first diagnosed in Wuhan city, China, in 2019, and spread to 185 countries and territories, and as of April 29, 2020, more than 3.11 million cases were recorded, and more than 217,000 people were killed. Despite all worldwide efforts, there is currently no vaccine, any drugs available to protect people against deadly SARS-CoV-2 coronavirus. The world urgently needs a SARS-CoV-2 coronavirus vaccine or effective antiviral drugs to relieve the human suffering associated with the pandemic that kills thousands of people every day. The SARS-CoV-2 genome encode a non-structural proteins named as ORF1a/b, and structural proteins such as spike (S) glycoprotein, nucleocapsid protein (N), small envelop protein (E) and matrix protein (M). A number of studies have been shown that CoV spike (S) glycoprotein and nucleocapsid protein (N) could be promising targets for vaccine, antibodies and therapeutic drug development to combat with deadly, pandemic SARS-CoV-2. Purposes of the present paper is the sequence analysis and amino acid variations of structural proteins deduced from novel coronavirus SARS-CoV-2 strains, isolated in different countries. Multiple sequence alignment of S, N and E proteins from four different coronavirus species, are also described. It is expected that the data from these studies will be very useful for the the designing and development of vaccines, antibodies and therapeutic agents that can be used to combat with the highly pathogenic SARS-CoV-2 coronavirus worldwide.

Periodic Structure in the Matrix Protein of an Insect Virus

1982 ◽  
Vol 40 ◽  
pp. 302-303
Author(s):  
H.M. Mazzone ◽  
W.F. Engler ◽  
R. Zerillo ◽  
G.F. Bahr
Keyword(s):  
Inclusion Body ◽  
Periodic Structure ◽  
Matrix Protein ◽  
Malacosoma Disstria ◽  
Insect Virus ◽  
Virus Particles ◽  
The Matrix ◽  
Nucleopolyhedrosis Virus

The nucleopolyhedrosis virus (NPV) of the forest tent cater - pillar (Malacosoma disstria Hubner) has been analyzed in our laboratories. As a representative of the Baculovirus class, the NPV has virus particles enclosed with in a proteinaceous structure, the inclusion body.

Exposure of protein VP7 on the surface of bluetongue virus

1990 ◽  
Vol 48 (3) ◽  
pp. 600-601
Author(s):  
A.D. Hyatt
Keyword(s):  
Bluetongue Virus ◽  
Structural Proteins ◽  
Major Constituent ◽  
Outer Coat ◽  
Virus Particles ◽  
Antibody Recognition ◽  
The Core ◽  
The Family ◽  
Electron Microscopical ◽  
Physical Accessibility

Bluetongue virus (BTV) is the type species os the genus orbivirus in the family Reoviridae. The virus has a fibrillar outer coat containing two major structural proteins VP2 and VP5 which surround an icosahedral core. The core contains two major proteins VP3 and VP7 and three minor proteins VP1, VP4 and VP6. Recent evidence has indicated that the core comprises a neucleoprotein center which is surrounded by two protein layers; VP7, a major constituent of capsomeres comprises the outer and VP3 the inner layer of the core . Antibodies to VP7 are currently used in enzyme-linked immunosorbant assays and immuno-electron microscopical (JEM) tests for the detection of BTV. The tests involve the antibody recognition of VP7 on virus particles. In an attempt to understand how complete viruses can interact with antibodies to VP7 various antibody types and methodologies were utilized to determine the physical accessibility of the core to the external environment.

scholarly journals Protease Inhibitors as Antiviral Agents

1998 ◽  
Vol 11 (4) ◽  
pp. 614-627 ◽  
Author(s):  
A. K. Patick ◽  
K. E. Potts
Keyword(s):  
Protease Inhibitors ◽  
Viral Infections ◽  
Critical Role ◽  
Antiviral Agents ◽  
Antiviral Agent ◽  
Structural Proteins ◽  
Viral Protease ◽  
Virus Particles ◽  
Viral Proteases ◽  
Viral Polyprotein

SUMMARY Currently, there are a number of approved antiviral agents for use in the treatment of viral infections. However, many instances exist in which the use of a second antiviral agent would be beneficial because it would allow the option of either an alternative or a combination therapeutic approach. Accordingly, virus-encoded proteases have emerged as new targets for antiviral intervention. Molecular studies have indicated that viral proteases play a critical role in the life cycle of many viruses by effecting the cleavage of high-molecular-weight viral polyprotein precursors to yield functional products or by catalyzing the processing of the structural proteins necessary for assembly and morphogenesis of virus particles. This review summarizes some of the important general features of virus-encoded proteases and highlights new advances and/or specific challenges that are associated with the research and development of viral protease inhibitors. Specifically, the viral proteases encoded by the herpesvirus, retrovirus, hepatitis C virus, and human rhinovirus families are discussed.

scholarly journals C-Terminal DxD-Containing Sequences within Paramyxovirus Nucleocapsid Proteins Determine Matrix Protein Compatibility and Can Direct Foreign Proteins into Budding Particles

2016 ◽  
Vol 90 (7) ◽  
pp. 3650-3660 ◽  
Author(s):  
Greeshma Ray ◽  
Phuong Tieu Schmitt ◽  
Anthony P. Schmitt
Keyword(s):  
Nucleocapsid Protein ◽  
Matrix Protein ◽  
Nipah Virus ◽  
Mumps Virus ◽  
Foreign Protein ◽  
Efficient Production ◽  
Nucleocapsid Proteins ◽  
Virus Like Particles ◽  
Ribonucleoprotein Complexes ◽  
M Proteins

ABSTRACTParamyxovirus particles are formed by a budding process coordinated by viral matrix (M) proteins. M proteins coalesce at sites underlying infected cell membranes and induce other viral components, including viral glycoproteins and viral ribonucleoprotein complexes (vRNPs), to assemble at these locations from which particles bud. M proteins interact with the nucleocapsid (NP or N) components of vRNPs, and these interactions enable production of infectious, genome-containing virions. For the paramyxoviruses parainfluenza virus 5 (PIV5) and mumps virus, M-NP interaction also contributes to efficient production of virus-like particles (VLPs) in transfected cells. A DLD sequence near the C-terminal end of PIV5 NP protein was previously found to be necessary for M-NP interaction and efficient VLP production. Here, we demonstrate that 15-residue-long, DLD-containing sequences derived from either the PIV5 or Nipah virus nucleocapsid protein C-terminal ends are sufficient to direct packaging of a foreign protein,Renillaluciferase, into budding VLPs. Mumps virus NP protein harbors DWD in place of the DLD sequence found in PIV5 NP protein, and consequently, PIV5 NP protein is incompatible with mumps virus M protein. A single amino acid change converting DLD to DWD within PIV5 NP protein induced compatibility between these proteins and allowed efficient production of mumps VLPs. Our data suggest a model in which paramyxoviruses share an overall common strategy for directing M-NP interactions but with important variations contained within DLD-like sequences that play key roles in defining M/NP protein compatibilities.IMPORTANCEParamyxoviruses are responsible for a wide range of diseases that affect both humans and animals. Paramyxovirus pathogens include measles virus, mumps virus, human respiratory syncytial virus, and the zoonotic paramyxoviruses Nipah virus and Hendra virus. Infectivity of paramyxovirus particles depends on matrix-nucleocapsid protein interactions which enable efficient packaging of encapsidated viral RNA genomes into budding virions. In this study, we have defined regions near the C-terminal ends of paramyxovirus nucleocapsid proteins that are important for matrix protein interaction and that are sufficient to direct a foreign protein into budding particles. These results advance our basic understanding of paramyxovirus genome packaging interactions and also have implications for the potential use of virus-like particles as protein delivery tools.

scholarly journals Investigation of orf virus structure and morphogenesis using recombinants expressing FLAG-tagged envelope structural proteins: evidence for wrapped virus particles and egress from infected cells

2009 ◽  
Vol 90 (3) ◽  
pp. 614-625 ◽  
Author(s):  
Joanne L. Tan ◽  
Norihito Ueda ◽  
Andrew A. Mercer ◽  
Stephen B. Fleming
Keyword(s):  
Fluorescent Microscopy ◽  
Cellular Membrane ◽  
Immunogold Labelling ◽  
Orf Virus ◽  
Structural Proteins ◽  
Post Translational Modification ◽  
Virus Particles ◽  
Viral Egress ◽  
Infected Cells ◽  
Almost All

Orf virus (ORFV) is the type species of the genus Parapoxvirus, but little is known about the structure or morphogenesis of the virus. In contrast, the structure and morphogenesis of vaccinia virus (VACV) has been extensively studied. VACV has two main infectious forms, mature virion (MV) and extracellular virion (EV). The MV is wrapped by two additional membranes derived from the trans-Golgi to produce a wrapped virion (WV), the outermost of which is lost by cellular membrane fusion during viral egress to form the EV. Genome sequencing of ORFV has revealed that it has homologues of almost all of the VACV structural genes. Notable exceptions are A36R, K2L, A56R and B5R, which are associated with WV and EV envelopes. This study investigated the morphogenesis and structure of ORFV by fusing FLAG peptide to the structural proteins 10 kDa, F1L and ORF-110 to form recombinant viruses. 10 kDa and F1L are homologues of VACV A27L and H3L MV membrane proteins, whilst ORF-110 is homologous to VACV A34R, an EV membrane protein. Immunogold labelling of FLAG proteins on virus particles isolated from lysed cells showed that FLAG–F1L and FLAG–10 kDa were displayed on the surface of infectious particles, whereas ORF-110–FLAG could not be detected. Western blot analysis of solubilized recombinant ORF-110–FLAG particles revealed that ORF-110–FLAG was abundant and undergoes post-translational modification indicative of endoplasmic reticulum trafficking. Fluorescent microscopy confirmed the prediction that ORF-110–FLAG localized to the Golgi in virus-infected cells. Finally, immunogold labelling of EVs showed that ORF-110–FLAG became exposed on the surface of EV-like particles as a result of egress from the cell.

scholarly journals Complete nucleotide sequence of avian paramyxovirus type 6 isolated from ducks

2001 ◽  
Vol 82 (9) ◽  
pp. 2157-2168 ◽  
Author(s):  
P.-C. Chang ◽  
M.-L. Hsieh ◽  
J.-H. Shien ◽  
D. A. Graham ◽  
M.-S. Lee ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Nucleocapsid Protein ◽  
Matrix Protein ◽  
New Genus ◽  
Simian Virus ◽  
Avian Paramyxovirus ◽  
V Protein ◽  
Small Hydrophobic

There are nine serotypes of avian paramyxovirus (APMV). Only the genome of APMV type 1 (APMV-1), also called Newcastle disease virus (NDV), has been completely sequenced. In this study, the complete nucleotide sequence of an APMV-6 serotype isolated from ducks is reported. The 16236 nt genome encodes eight proteins, nucleocapsid protein (NP), phosphoprotein (P), V protein, matrix protein (M), fusion protein (F), small hydrophobic (SH) protein, haemagglutinin–neuraminidase (HN) protein and large (L) protein, which are flanked by a 55 nt leader sequence and a 54 nt trailer sequence. Sequence comparison reveals that the protein sequences of APMV-6 are most closely related to those of APMV-1 (NDV) and -2, with sequence identities ranging from 22 to 44%. However, APMV-6 contains a gene that might encode the SH protein, which is absent in APMV-1, but present in the rubulaviruses simian virus type 5 and mumps virus. The presence of an SH gene in APMV-6 might provide a link between the evolution of APMV and rubulaviruses. Phylogenetic analysis demonstrates that APMV-6, -1, -2 (only the F and HN sequences were available for analysis) and -4 (only the HN sequences were available for analysis) all cluster into a single lineage that is distinct from other paramyxoviruses. This result suggests that APMV should constitute a new genus within the subfamily Paramyxovirinae.

scholarly journals Atomic Force Microscopy Investigation of Human Immunodeficiency Virus (HIV) and HIV-Infected Lymphocytes

2003 ◽  
Vol 77 (22) ◽  
pp. 11896-11909 ◽  
Author(s):  
Y. G. Kuznetsov ◽  
J. G. Victoria ◽  
W. E. Robinson ◽  
A. McPherson
Keyword(s):  
Human Immunodeficiency Virus ◽  
Atomic Force Microscopy ◽  
Nucleic Acid ◽  
Matrix Protein ◽  
Human Lymphocytes ◽  
Tween 20 ◽  
Force Microscopy ◽  
Virus Particles ◽  
Atomic Force ◽  
Immunodeficiency Virus

ABSTRACT Isolated human immunodeficiency virus (HIV) and HIV-infected human lymphocytes in culture have been imaged for the first time by atomic force microscopy (AFM). Purified virus particles spread on glass substrates are roughly spherical, reasonably uniform, though pleomorphic in appearance, and have diameters of about 120 nm. Similar particles are also seen on infected cell surfaces, but morphologies and sizes are considerably more varied, possibly a reflection of the budding process. The surfaces of HIV particles exhibit “tufts” of protein, presumably gp120, which do not physically resemble spikes. The protein tufts, which number about 100 per particle, have average diameters of about 200 Å, but with a large variance. They likely consist of arbitrary associations of small numbers of gp120 monomers on the surface. In examining several hundred virus particles, we found no evidence that the gp120 monomers form threefold symmetric trimers. Although >95% of HIV-infected H9 lymphocytic cells were producing HIV antigens by immunofluorescent assay, most lymphocytes displayed few or no virus on their surfaces, while others were almost covered by a hundred or more viruses, suggesting a dependence on cell cycle or physiology. HIV-infected cells treated with a viral protease inhibitor and their progeny viruses were also imaged by AFM and were indistinguishable from untreated virions. Isolated HIV virions were disrupted by exposure to mild neutral detergents (Tween 20 and CHAPS) at concentrations from 0.25 to 2.0%. Among the products observed were intact virions, the remnants of completely degraded virions, and partially disrupted particles that lacked sectors of surface proteins as well as virions that were split or broken open to reveal their empty interiors. Capsids containing nucleic acid were not seen, suggesting that the capsids were even more fragile than the envelope and were totally degraded and lost. From these images, a good estimate of the thickness of the envelope protein-membrane-matrix protein outer shell of the virion was obtained. Treatment with even low concentrations (<0.1%) of sodium dodecyl sulfate completely destroyed all virions but produced many interesting products, including aggregates of viral proteins with strands of nucleic acid.

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