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Research Article
Spread of SARS-CoV-2 Genomes on Genomic Index Maps of Hierarchy
Jeffrey Zheng
Yunnan University
Corresponding Author
ORCiD: https://orcid.org/0000-0003-4225-7077
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Using visual technologies, COVID-19 patients worldwide are conveniently described by position information to collect samples, and modern GIS maps are useful to show influenced flows and numbers of patients on various regions of a pendamic. From an analysis viewpoint, it is more interesting to organize genomic information into a phylogenic tree with multiple branches and leaves in representations. Clusters of genomes are organized as phylogenic trees to represent intrinsic information of genomes. However, there are structural difficulties in projecting phylogenetic information into 2D distributions as GIS maps naturally. In this paper, a novel projection is proposed to arrange SARS-CoV-2 genomes by genomic indexes to make a structural organization as 2D GIS maps. For any genome, there is a unique invariant under certain conditions to provide an absolute position on a specific region. In this hierarchical framework, it is possible to use a visual tool to represent any selected region for clustering genomes on refined effects. Complementary visual effects are provided with phylogenetic tree technology. Sample regions and various projections show spread effects of five thousand SARS-CoV-2 genomes in 72 countries, and four special countries are selected on genomic index maps.
Keywords
genomic index, visual maps, phylogeny, projection, information entropy, global invariant, hierarchical projection
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Due to technical limitations, full-text HTML conversion of this manuscript could not be completed. However, the manuscript can be downloaded and accessed as a PDF.
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Jeffrey Zheng
commented on 16 September, 2020
A better version of the paper.
Jeffrey Zheng
commented on 02 October, 2020
The main supporting 21 papers for the preprint are accepted by EC Neurology in a special issue for fighting COVID-19 as ECNE SI.02 (2020). Some of them are already online, please check Latest Articles in https://www.ecronicon.com/neurology.php All the 21 preprints are on Research Square, their structures are organized in http://blog.sciencenet.cn/blog-629831-1251952.html In a convenience, the special issue has divided the 23 preprints and papers into six parts (I-VI) as an integrated organization, and each part contains 2-10 papers respectively. I Architecture of Metagenomic Analysis System 1-2 2 preprints II Genomic Index Maps on SARS-CoV-2 3-7 5 preprints III Clustering Projections and Integrations 8-9 2 preprints IV Global Projections for COVID-19 10-19 10 preprints V Machine Learning Approaches 20-21 2 preprints VI Whole Chinese Medicine 22-23 2 papers
Jeffrey Zheng
commented on 03 October, 2020
Research background of the preprint was shown in http://blog.sciencenet.cn/blog-629831-1251895.html
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This is a preprint. It has not completed peer review.
Research Article
Spread of SARS-CoV-2 Genomes on Genomic Index Maps of Hierarchy
Jeffrey Zheng
Yunnan University
Corresponding Author
ORCiD: https://orcid.org/0000-0003-4225-7077
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 3
Posted 16 Sep, 2020
Community comments: 3
Community comments: 1
Community comments: 4
Metrics
Comments: 3
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Using visual technologies, COVID-19 patients worldwide are conveniently described by position information to collect samples, and modern GIS maps are useful to show influenced flows and numbers of patients on various regions of a pendamic. From an analysis viewpoint, it is more interesting to organize genomic information into a phylogenic tree with multiple branches and leaves in representations. Clusters of genomes are organized as phylogenic trees to represent intrinsic information of genomes. However, there are structural difficulties in projecting phylogenetic information into 2D distributions as GIS maps naturally. In this paper, a novel projection is proposed to arrange SARS-CoV-2 genomes by genomic indexes to make a structural organization as 2D GIS maps. For any genome, there is a unique invariant under certain conditions to provide an absolute position on a specific region. In this hierarchical framework, it is possible to use a visual tool to represent any selected region for clustering genomes on refined effects. Complementary visual effects are provided with phylogenetic tree technology. Sample regions and various projections show spread effects of five thousand SARS-CoV-2 genomes in 72 countries, and four special countries are selected on genomic index maps.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Due to technical limitations, full-text HTML conversion of this manuscript could not be completed. However, the manuscript can be downloaded and accessed as a PDF.
Jeffrey Zheng
commented on 16 September, 2020
A better version of the paper.
Jeffrey Zheng
commented on 02 October, 2020
The main supporting 21 papers for the preprint are accepted by EC Neurology in a special issue for fighting COVID-19 as ECNE SI.02 (2020). Some of them are already online, please check Latest Articles in https://www.ecronicon.com/neurology.php All the 21 preprints are on Research Square, their structures are organized in http://blog.sciencenet.cn/blog-629831-1251952.html In a convenience, the special issue has divided the 23 preprints and papers into six parts (I-VI) as an integrated organization, and each part contains 2-10 papers respectively. I Architecture of Metagenomic Analysis System 1-2 2 preprints II Genomic Index Maps on SARS-CoV-2 3-7 5 preprints III Clustering Projections and Integrations 8-9 2 preprints IV Global Projections for COVID-19 10-19 10 preprints V Machine Learning Approaches 20-21 2 preprints VI Whole Chinese Medicine 22-23 2 papers
Jeffrey Zheng
commented on 03 October, 2020
Research background of the preprint was shown in http://blog.sciencenet.cn/blog-629831-1251895.html