Research Article
Volume 13 Issue 7 - 2021
Spread of SARS-CoV-2 Genomes on Genomic Index Maps of Hierarchy - Compared with B.1.1.7 Lineage on BLAST
Jeffrey Zheng1,2*, Yang Zhou3, Minghan Zhu3, Mu Qiao3 and Zhigang Zhang4
1Key Laboratory of Quantum Information of Yunnan, China
2Key Laboratory of Software Engineering of Yunnan, Yunnan University, Kunming, China
3Yunnan University, Kunming, China
4School of Life Sciences and Technology, Yunnan University, Kunming, China
*Corresponding Author: Jeffrey Zheng, Key Laboratory of Quantum Information of Yunnan and Key Laboratory of Software Engineering of Yunnan, Yunnan University, Kunming, China.
Received: April 20, 2021; Published: June 22, 2021




Abstract

COVID-19 patients worldwide are conveniently described by position in-formation to collect samples, and modern GIS maps are useful to show influenced flows and numbers of patients on various regions of a pandemic. 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. How-ever, there are structural difficulties in projecting phylogenetic information into 2D distributions as GIS maps naturally.

Considering advanced generating schemes of phylogenetic trees, information entropy provides ultra optimal properties in the minimum computational complexity, superior flexibility, better stability, improved reliability and higher quality on global constructions. This super technology may play a key role in future development of advanced neurology, neuroscience and brain researches.

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. Applied diversity measure to a given set of genomes, equivalent clusters and complementary visual effects are provided between genomic index maps and phylogenetic trees. Sample genomes of three UK new lineages are aligned by BLAST as a basis on both RNA-dependent RNA polymerase RDRP segments and whole genomes. Selected regions and various projections show spread effects of five thousand SARS-CoV-2 genomes in 72 countries on both RDRP and whole genomes, and six special countries/regions are selected on genomic index maps.

Based on genomic index maps, one SNV of two genomes on B.1.1.7 lineage can be identified from a unit of 10-4 probability measure to a unit of 10-6 difference for genomic indexes on a special ‘G’ projection to extract the finest variation.

Further exploration on optimal classification and phylogenetic analysis of genomic index maps and phylogenetic trees on SARS-CoV-2 genomes worldwide are dis-cussed.

Keywords: Genomic Index; Visual Maps; Phylogeny; Projection; Information Entropy; Diversity Measure; Global Invariant; Hierarchical Projection; Optimization

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