Latent periodicity-2 in coronavirus SARS-CoV-2 genome: evolutionary implications

DOI10.1016/J.JTBI.2021.110604MaRDI QIDQ2659883zbMATH OpenOpenAlexFDO

Authors Changchuan Yin

Publication date 29 March 2021

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2006.00280

zbMATH Keywords

2019-nCoVCOVID-19dinucleotideevolution fitnessperiodicitySARS-CoV-2virulence

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Problems related to evolution (92D15)

Abstract: The ongoing global pandemic of infection disease COVID-19 caused by the 2019 novel coronavirus (SARS-COV-2, formerly 2019-nCoV) presents critical threats to public health and the economy since it was identified in China, December 2019. The genome of SARS-CoV-2 had been sequenced and structurally annotated, yet little is known of the intrinsic organization and evolution of the genome. To this end, we present a mathematical method for the genomic spectrum, a kind of barcode, of SARS-CoV-2 and common human coronaviruses. The genomic spectrum is constructed according to the periodic distributions of nucleotides, and therefore reflects the unique characteristics of the genome. The results demonstrate that coronavirus SARS-CoV-2 exhibits dinucleotide TT islands in the non-structural proteins 3, 4, 5, and 6. Further analysis of the dinucleotide regions suggests that the dinucleotide repeats are increased during evolution and may confer the evolutionary fitness of the virus. The special dinucleotide regions in the SARS-CoV-2 genome identified in this study may become diagnostic and pharmaceutical targets in monitoring and curing the COVID-19 disease.

Recommendations

• Inverted repeats in coronavirus SARS-CoV-2 genome manifest the evolution events
• Inverted repeats in coronavirus SARS-CoV-2 genome and implications in evolution
• Genome-wide covariation in SARS-CoV-2
• SARS-CoV-2 becoming more infectious as revealed by algebraic topology and deep learning
• Analysis of the genomic distance between bat coronavirus RaTG13 and SARS-CoV-2 reveals multiple origins of COVID-19

Cites work

• Identification of repeats in DNA sequences using nucleotide distribution uniformity
• Periodic power spectrum with applications in detection of latent periodicities in DNA sequences
• Smoothing and Interpolation with the State-Space Model

Cited in

(6)

• Electrostatic features for nucleocapsid proteins of SARS-CoV and SARS-CoV-2
• Genome-wide covariation in SARS-CoV-2
• Analysis of the genomic distance between bat coronavirus RaTG13 and SARS-CoV-2 reveals multiple origins of COVID-19
• Inverted repeats in coronavirus SARS-CoV-2 genome manifest the evolution events
• SARS-CoV-2 becoming more infectious as revealed by algebraic topology and deep learning
• Inverted repeats in coronavirus SARS-CoV-2 genome and implications in evolution

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Uses Software

• DNADU
• PPS

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