Evolution patterns of SARS-CoV-2: Snapshot on its genome variants

@article{Giovanetti2020EvolutionPO,
  title={Evolution patterns of SARS-CoV-2: Snapshot on its genome variants},
  author={Marta Giovanetti and Francesca Benedetti and Giovanni Campisi and Alessandra Ciccozzi and Silvia Fabris and Giancarlo Ceccarelli and Vittoradolfo Tambone and Arnaldo Caruso and Silvia Angeletti and Davide Zella and Massimo Ciccozzi},
  journal={Biochemical and Biophysical Research Communications},
  year={2020},
  volume={538},
  pages={88 - 91}
}
An acute respiratory syndrome (COVID-19), caused by a novel coronavirus (SARS-CoV-2) with a high rate of morbidity and elevate mortality, has emerged as one of the most important threats to humankind in the last centuries. Rigorous determination of SARS-CoV-2 infectivity is very difficult owing to the continuous evolution of the virus, with its single nucleotide polymorphism (SNP) variants and many lineages. However, it is urgently necessary to study the virus in depth, to understand the… 

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References

SHOWING 1-10 OF 29 REFERENCES
A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual
TLDR
The SARS-CoV-2 GZ69 strain, isolated in May from an asymptomatic healthcare worker, showed an unprecedented capability of replication in Vero E6 cells in the absence of any evident cytopathic effect.
Genetic diversity and evolution of SARS-CoV-2
  • T. Phan
  • Biology, Medicine
    Infection, Genetics and Evolution
  • 2020
TLDR
Genetic analyses of eighty-six complete or near-complete genomes of SARS-CoV-2 revealed many mutations and deletions on coding and non-coding regions that provided evidence of the genetic diversity and rapid evolution of this novel coronavirus.
Genomic characterization of a novel SARS-CoV-2
TLDR
The genomic signature analysis demonstrates that a strong association between the time of sample collection, location of sample and accumulation of genetic diversity is found and heavily supports an intense requirement for additional prompt, inclusive investigations that combine genomic detail, epidemiological information and graph records of the clinical features of patients with COVID-19.
Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1
TLDR
Modelling analysis of a newly identified deletion of 3 amino acids of SARS-CoV-2 nsp1 suggests that this deletion could affect the structure of the C-terminal region of the protein, important for regulation of viral replication and negative effect on host’s gene expression.
The proximal origin of SARS-CoV-2
TLDR
It is shown that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus, and scenarios by which they could have arisen are discussed.
Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity
TLDR
The present method of genome annotation employed at this early pandemic stage could be a promising tool for monitoring and tracking the continuously evolving pandemic situation, the associated genetic variants, and their implications for the development of effective control and prophylaxis strategies.
Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant
TLDR
The findings suggest that the virus is evolving and European, North American and Asian strains might coexist, each of them characterized by a different mutation pattern.
Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2
TLDR
The mutation Spike D614G is of urgent concern; it began spreading in Europe in early February, and when introduced to new regions it rapidly becomes the dominant form, indicative of multiple strain infections.
Identification of Residues of SARS-CoV nsp1 That Differentially Affect Inhibition of Gene Expression and Antiviral Signaling
TLDR
Six classes of mutants were identified that abolished, attenuated or increased nsp1 inhibition of host gene expression and/or antiviral signaling, suggesting that coronaviruses could evolve a greater ability to evade the host response through mutations of such residues.
Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan
TLDR
Binformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection.
...
1
2
3
...