A Quantitative Genomic View of the Coronaviruses: SARS-COV2

Abstract

In 2020, the pandemic caused by the Coronaviruses (CoV) that are a large family of viruses that cause illness ranging from the common cold to more severe diseases such as Middle East Respiratory Syndrome (MERS-CoV) and Severe Acute Respiratory Syndrome (SARS-CoV2). The Coronavirus disease (COVID-19) is a new strain that was discovered in 2019 and has not been previously identified in humans. It is the high time to investigate the quantitative and/or qualitative genomic informations of the virus SARS-CoV2 in order to strengthen the healthcare facility to fight against this viral disease. In this article, a through quantitative understanding of the purine and pyrimidine spatial distribution/organization of all 89 complete sequences of SARS-CoV (available as on date in the NCBI virus database, is made using different parameters such as fractal dimension, Hurst exponent, Shannon entropy and GC content of the nucleotide sequences of the genome of SARS-CoV2. Also a cluster among all the the SARS-CoV sequences of nucleotide have been made based on their phylogeny made through their closeness (Hamming distance) based on respective purine-pyrimidine distribution.

Molecular conservation and Differential mutation on ORF3a gene in Indian SARS-CoV2 genomes

“…In order to determine the molecular level conservations and descriptions of the ORF3a genes across different hosts as mentioned, some methods are discussed [24,25,26,27,28,29], which would be subsequently used.…”

“…where p si = 3ki l ; k i represents the number of occurrences of an amino acid s i in the given sequence. In addition to the different conservation SEs, some basic derivative features such as nucleotide frequency and density, frequency of all possible sixteen dimers, frequency of codon usages, frequency of amino acids in the protein sequence encoded by the ORF3a gene, GC content, pyrimidine density are obtained for a given ORF3a gene sequence [24,26]. It is worth noting that the first positive frame has been considered to determine codons and double nucleotides over a given gene.…”

On spatial molecular arrangements of SARS-CoV2 genomes of Indian patients

“…. , n In addition to these two parameters Shannon entropy and Hurst exponent, some basic derivative features such as nucleotide frequency (Freq), double nucleotide frequency, codon usage frequency, GC content, purine-pyrimidine density are obtained for a given nucleotide sequence [29,31]. Also 90 based on nucleotide densities, a decreasing order (density order) is obtained for a given sequence.…”

Spatial Distribution of Amino Acids of the SARS-CoV2 Proteins

“…Also frequency analysis of the amino acids over the proteins have been chalked out. It is noted that authors have done similar analysis for the 89 genomes of SARS-CoV2 [27].…”