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.

scholarly journals Two amino acid residues in the matrix protein M1 contribute to the virulence difference of H5N1 avian influenza viruses in mice

Virology ◽  
2009 ◽  
Vol 384 (1) ◽  
pp. 28-32 ◽  
Author(s):  
Shufang Fan ◽  
Guohua Deng ◽  
Jiasheng Song ◽  
Guobin Tian ◽  
Yongbing Suo ◽  
...  
Keyword(s):  
Amino Acid ◽  
Avian Influenza ◽  
Matrix Protein ◽  
Influenza Viruses ◽  
Amino Acid Residues ◽  
Avian Influenza Viruses ◽  
H5n1 Avian Influenza ◽  
The Matrix ◽  
Matrix Protein M1

scholarly journals Matrix and Envelope Coevolution Revealed in a Patient Monitored since Primary Infection with Human Immunodeficiency Virus Type 1

2009 ◽  
Vol 83 (19) ◽  
pp. 9875-9889 ◽  
Author(s):  
Elodie Beaumont ◽  
Daniela Vendrame ◽  
Bernard Verrier ◽  
Emmanuelle Roch ◽  
François Biron ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Amino Acid ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Matrix Protein ◽  
Immunodeficiency Virus ◽  
The Matrix ◽  
Hiv 1

ABSTRACT Lentiviruses, including human immunodeficiency virus type 1 (HIV-1), typically encode envelope glycoproteins (Env) with long cytoplasmic tails (CTs). The strong conservation of CT length in primary isolates of HIV-1 suggests that this factor plays a key role in viral replication and persistence in infected patients. However, we report here the emergence and dominance of a primary HIV-1 variant carrying a natural 20-amino-acid truncation of the CT in vivo. We demonstrated that this truncation was deleterious for viral replication in cell culture. We then identified a compensatory amino acid substitution in the matrix protein that reversed the negative effects of CT truncation. The loss or rescue of infectivity depended on the level of Env incorporation into virus particles. Interestingly, we found that a virus mutant with defective Env incorporation was able to spread by cell-to-cell transfer. The effects on viral infectivity of compensation between the CT and the matrix protein have been suggested by in vitro studies based on T-cell laboratory-adapted virus mutants, but we provide here the first demonstration of the natural occurrence of similar mechanisms in an infected patient. Our findings provide insight into the potential of HIV-1 to evolve in vivo and its ability to overcome major structural alterations.

scholarly journals Transmembrane communication in cells chronically infected with measles virus.

1979 ◽  
Vol 81 (2) ◽  
pp. 396-402 ◽  
Author(s):  
D L Tyrrell ◽  
A Ehrnst
Keyword(s):  
Nucleocapsid Protein ◽  
Measles Virus ◽  
Matrix Protein ◽  
Cytochalasin B ◽  
Viral Proteins ◽  
Surface Proteins ◽  
Nucleocapsid Proteins ◽  
Viral Antigens ◽  
The Matrix ◽  
Viral Inclusions

The transmembrane association of the measles virus hemagglutinin and hemolysin surface proteins with intracellular viral antigens was studied. Rabbit antisera monospecific for measles virus matrix and nucleocapsid proteins and a human antiserum containing specificities for both the hemagglutinin and hemolysin proteins were used to study the co-capping of these proteins in human Lu 106 cell-line, chronically infected with measles virus. Capping of the surface-associated envelope components was accompanied by co-capping of the matrix and nucleocapsid proteins, the latter being localized mainly within the inclusions. This demonstrated transmembrane communication between surface-associated envelope components and the intracellular measles virus matrix and nucleocapsid proteins. The results demonstrated the existence of a linkage between viral inclusions and viral proteins associated with cell membranes. In the presence of cytochalasin B (1--2 micrograms/ml), co-capping of the matrix protein was unchanged or slightly enhanced, whereas co-capping of the nucleocapsid protein decreased, indicating that actin filaments may mediate the communication between viral nucleocapsids and the cell membrane.

scholarly journals QUASISPECIES FEATURE IN SARS-CoV-2

2021 ◽  
Vol 9 (5) ◽  
pp. 591-597
Author(s):  
Bramhadev Pattnaik ◽  
◽  
Kuralayanapalya Puttahonnappa Suresh ◽  
Rajangam Sridevi ◽  
Mahendra P. Yadav ◽  
...  
Keyword(s):  
Genetic Heterogeneity ◽  
Viral Genome ◽  
Neutralizing Antibodies ◽  
Human Population ◽  
Rna Virus ◽  
Base Population ◽  
Virus Population ◽  
Control Programs ◽  
Positive Sense ◽  
Selection Of

Since the identification of the SARS-CoV-2, genus Beta- Coronavirus, in January 2020, the virus quickly spread in less than 3 months to all continents with a susceptible human population of about a 7.9billion, and still in active circulation. In the process, it has accumulated mutations leading to genetic diversity. Regular emergence of variants of concern/significance in different ecology shows genetic heterogeneity in the base population of SARS-CoV-2 that is continuously expanding with the passage of the virus in the vast susceptible human population. Natural selection of mutant occurs frequently in a positive sense (+) single-stranded (ss) RNA virus upon replication in the host. The Pressure of sub-optimal levels of virus-neutralizing antibodies and also innate immunity influence the process of genetic/ antigenic selection. The fittest of the mutants, that could be more than one, propagate and emerge as variants. The existence of different lineages, clades, and strains, as well as genetic heterogeneity of plaque purified virus population, justifies SARS-CoV-2 as ‘Quasispecies’ that refers to swarms of mutant sequences generated during replication of the viral genome, and all mutant sequences may not lead to virion. Viruses having a quasispecies nature may end up with progressive antigenic changes leading to antigenic plurality that is driven by ecology, and this phenomenon challenges vaccination-based control programs.

Association of the nucleocapsid protein N of vesicular stomatitis virus with phospholipids vesicles containing the matrix protein M

1984 ◽  
Vol 62 (11) ◽  
pp. 1174-1180 ◽  
Author(s):  
John Capone ◽  
Hara P. Ghosh
Keyword(s):  
Vesicular Stomatitis Virus ◽  
Nucleocapsid Protein ◽  
Matrix Protein ◽  
Lipid Vesicles ◽  
Viral Envelope ◽  
M Protein ◽  
Phospholipid Vesicles ◽  
N Protein ◽  
The Matrix ◽  
Vesicular Stomatitis

The matrix protein M and the nucleocapsid protein N were isolated from vesicular stomatitis virus and reconstituted into artificial phospholipid vesicles. While the M protein could be reconstituted into phospholipid vesicles, the N protein had no affinity for lipid vesicles. The N protein could, however, associate with phospholipid vesicles in the presence of M protein. Identical results were also obtained when an in vitro system synthesizing M and N proteins was used for reconstitution. The results suggest that M protein is involved in virus maturation by interacting with the viral envelope and the N protein of the nucleoprotein core.

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