scholarly journals Mutation patterns of human SARS-COV-2 and bat RaTG13 coronaviruses genomes are strongly biased towards C>U indicating rapid evolution in their hosts

2020 ◽  
Author(s):  
Roman Matyasek ◽  
Ales Kovarik
Keyword(s):  
World Wide ◽  
Genome Structure ◽  
Rapid Evolution ◽  
Protein Domain ◽  
Spike Protein ◽  
Single Nucleotide ◽  
The World ◽  
Cpg Dinucleotide ◽  
Rhinolophus Affinis ◽  
Contact Domain

Abstract Background: The world pandemy caused by SARS-CoV-2 spreading has raised considerable interest about its evolutionary origin and genome structure. Here we analysed mutation patterns in 13 human SARS-COV-2 isolates and a closely related RaTG13 isolated from Rhinolophus affinis bat. We also evaluated the CpG dinucleotide contents in SARS-COV-2 and other human and animal coronavirus genomes. Results: Out of 1107 single nucleotide differences (c. 4% divergence) between human SARS-COV-2 and bat RaTG13, 672 (61%) can be attributed to C>U and U>T substitutions significantly (P<0.001) exceeding other types of SNPs. A similar trend was observed among the 13 sequenced SARS-COV-2 genomes. Accumulation of C>U mutations was also observed in a highly variable subregion encoding the ACE2 receptor contact domain. Contrast to most other coronaviruses both SARS-COV-2 and RaTG13 exhibited CpG depletion in their genomes. Conclusion: The data support that the C-to-U conversion played a significant role in the evolution of pathogenic RNA coronaviruses including SARS-COV-2. These mutations apparently also influenced amino acid composition of the SARS-Cov-2 spike protein domain receptor implicated in virus pathogenicity. We propose that SARS-COV-2 was evolving relatively long in humans following the transfer from animals before spreading world-wide.

scholarly journals Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 761 ◽  
Author(s):  
Roman Matyášek ◽  
Aleš Kovařík
Keyword(s):  
High Frequency ◽  
Genome Structure ◽  
Rapid Evolution ◽  
Single Nucleotide ◽  
Hydrophobic Amino Acids ◽  
Cpg Dinucleotide ◽  
Single Nucleotide Variations ◽  
Horseshoe Bat ◽  
Adaptation Processes ◽  
Virus Adaptation

The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated from Rhinolophus affinis (a horseshoe bat). We also evaluated the CpG dinucleotide contents in SARS-CoV-2 and other human and animal coronavirus genomes. Out of 1136 single nucleotide variations (~4% divergence) between human SARS-CoV-2 and bat RaTG13, 682 (60%) can be attributed to C>U and U>C substitutions, far exceeding other types of substitutions. An accumulation of C>U mutations was also observed in SARS-CoV2 variants that arose within the human population. Globally, the C>U substitutions increased the frequency of codons for hydrophobic amino acids in SARS-CoV-2 peptides, while U>C substitutions decreased it. In contrast to most other coronaviruses, both SARS-CoV-2 and RaTG13 exhibited CpG depletion in their genomes. The data suggest that C-to-U conversion mediated by C deamination played a significant role in the evolution of the SARS-CoV-2 coronavirus. We hypothesize that the high frequency C>U transitions reflect virus adaptation processes in their hosts, and that SARS-CoV-2 could have been evolving for a relatively long period in humans following the transfer from animals before spreading worldwide.

scholarly journals Geographic and Genomic Distribution of SARS-CoV-2 Mutations

2020 ◽  
Author(s):  
Daniele Mercatelli ◽  
Federico Manuel Giorgi
Keyword(s):  
Spike Protein ◽  
The Novel ◽  
Single Nucleotide ◽  
Genomic Distribution ◽  
Genomic Variability ◽  
The World ◽  
The Status ◽  
Novel Virus ◽  
Initial Interaction ◽  
Local Modulation

The novel respiratory disease COVID-19 has reached the status of worldwide pandemic and large efforts are currently being undertaken in molecularly characterizing the virus causing it, SARS-CoV-2. The genomic variability of SARS-CoV-2 specimens scattered across the globe can underly geographically specific etiological effects. In the present study, we gather the 10,014 SARS-CoV-2 complete genomes currently available thanks to the collection endeavor of the GISAID consortium and thousands of contributing laboratories. We analyze and annotate all SARS-CoV-2 mutations compared with the reference Wuhan genome NC_045512.2. Our analysis shows the prevalence of single nucleotide transitions as the major mutational type across the world. There exist at least three clades characterized by geographic and genomic specificity. In particular, the clade G, prevalent in Europe, carries a D614G mutation in the Spike protein, which is responsible for the initial interaction of the virus with the host human cell. Our analysis may drive local modulation of antiviral strategies based on the molecular specificities of this novel virus.

scholarly journals Origin, Phylogeny, Variability and Epitope Conservation of SARS-CoV-2 Worldwide

2021 ◽  
Author(s):  
Filipa F Vale ◽  
Jorge M.B. Vítor ◽  
Andreia T. Marques ◽  
José Miguel Azevedo-Pereira ◽  
Elsa Anes ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Rna Virus ◽  
Spike Protein ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Single Nucleotide ◽  
Genomic Variability ◽  
Spike Gene ◽  
The World ◽  
Structure Of Proteins

The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenges include understanding what triggered SARS-CoV-2 emergence, how this RNA virus is evolving or how the genomic variability may impact the primary structure of proteins that are targets for vaccine. We analyzed 19471 SARS-CoV-2 genomes and 199,984 spike glycoprotein sequences available at the GISAID database from all over the world and 3335 genomes of other Coronoviridae family members available at Genbank, collecting SARS-CoV-2 high-quality genomes and distinct Coronoviridae family genomes. Here, we identify a SARS-CoV-2 emerging cluster containing 13 closely related genomes isolated from bat and pangolin that showed evidence of recombination, which may have contributed to the emergence of SARS-CoV-2. The analyzed SARS-CoV-2 genomes presented 9632 single nucleotide polymorphisms (SNPs) corresponding to a variant density of 0.3 over the genome, and a clear geographic distribution. SNPs are unevenly distributed throughout the genome and hotspots for mutations were found for the spike gene and ORF 1ab. We describe a set of predicted spike protein epitopes whose variability is negligible. All predicted epitopes for the structural E, M and N proteins are highly conserved. This result favors the continuous efficacy of the available vaccines.

Rotational Characteristics of the Green Solar Corona: 1947-1991

1994 ◽  
Vol 144 ◽  
pp. 139-141 ◽  
Author(s):  
J. Rybák ◽  
V. Rušin ◽  
M. Rybanský
Keyword(s):  
Solar Corona ◽  
World Wide ◽  
Rotation Period ◽  
Original Data ◽  
Coronal Emission ◽  
Time Intervals ◽  
Data Set ◽  
The World ◽  
Coronal Emission Line ◽  
Homogeneous Data

AbstractFe XIV 530.3 nm coronal emission line observations have been used for the estimation of the green solar corona rotation. A homogeneous data set, created from measurements of the world-wide coronagraphic network, has been examined with a help of correlation analysis to reveal the averaged synodic rotation period as a function of latitude and time over the epoch from 1947 to 1991.The values of the synodic rotation period obtained for this epoch for the whole range of latitudes and a latitude band ±30° are 27.52±0.12 days and 26.95±0.21 days, resp. A differential rotation of green solar corona, with local period maxima around ±60° and minimum of the rotation period at the equator, was confirmed. No clear cyclic variation of the rotation has been found for examinated epoch but some monotonic trends for some time intervals are presented.A detailed investigation of the original data and their correlation functions has shown that an existence of sufficiently reliable tracers is not evident for the whole set of examinated data. This should be taken into account in future more precise estimations of the green corona rotation period.

Dancing Across the World Wide Web: Advocacy in the 21st Century

2009 ◽  
Author(s):  
Blair Williams Cronin ◽  
Ty Tedmon-Jones ◽  
Lora Wilson Mau
Keyword(s):  
World Wide Web ◽  
21St Century ◽  
World Wide ◽  
The World

Biodiesel production from non-edible oils: A review

2020 ◽  
pp. 149-159
Author(s):  
Jatinder Kataria ◽  
Saroj Kumar Mohapatra ◽  
Amit Pal
Keyword(s):  
Environmental Impact ◽  
Energy Demand ◽  
Fossil Fuels ◽  
World Wide ◽  
Edible Oils ◽  
Control Measure ◽  
Biodiesel Production ◽  
Pollution Level ◽  
Animal Fats ◽  
The World

The limited fossil reserves, spiraling price and environmental impact due to usage of fossil fuels leads the world wide researchers’ interest in using alternative renewable and environment safe fuels that can meet the energy demand. Biodiesel is an emerging renewable alternative fuel to conventional diesel which can be produced from both edible and non-edible oils, animal fats, algae etc. The society is in dire need of using renewable fuels as an immediate control measure to mitigate the pollution level. In this work an attempt is made to review the requisite and access the capability of the biodiesel in improving the environmental degradation.

THE EUROPEAN UNION FORUM ON KIDS' SAFETY IN INTERNET SIF 2019

2019 ◽  
pp. 3-6
Author(s):  
D. A. Bogdanova
Keyword(s):  
European Union ◽  
World Wide Web ◽  
World Wide ◽  
The European Union ◽  
Internet Forum ◽  
The World

The article provides an overview of the activities of the European Union Forum on kids' safety in Internet — Safer Internet Forum (SIF) 2019, which was held in Brussels, Belgium, in November 2019. The current Internet risks addressed by the World Wide Web users, especially children, are described.

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