Uncovering Signals from the Coronavirus Genome

Abstract

A signal analysis of the complete genome sequenced for coronavirus variants of concern—B.1.1.7 (Alpha), B.1.135 (Beta) and P1 (Gamma)—and coronavirus variants of interest—B.1.429–B.1.427 (Epsilon) and B.1.525 (Eta)—is presented using open GISAID data. We deal with a certain new type of finite alternating sum series having independently distributed terms associated with binary (0,1) indicators for the nucleotide bases. Our method provides additional information to conventional similarity comparisons via alignment methods and Fourier Power Spectrum approaches. It leads to uncover distinctive patterns regarding the intrinsic data organization of complete genomics sequences according to its progression along the nucleotide bases position. The present new method could be useful for the bioinformatics surveillance and dynamics of coronavirus genome variants.

GenomeBits insight into omicron and delta variants of coronavirus pathogen

“…In the plot, we verified multiple deviations of both delta and omicron variants against one of the first Wuhan-China sequences identified over a year ago (MN908947) [8]. Multiple deviations from the delta variants from Spain (EPI ISL 7900475 and 7951710) against several omicron variants from Spain, plus the delta variant from Spain EPI ISL 8179449 against different omicron variants from the USA are also show in Fig 1 . For the calculations we used "lalign36" sequence comparison software (via the Waterman-Eggert algorithm at github.com/wrpearson/fasta36) [4].…”

“…GenomeBits is a user-friendly Graphics User Interface (GUI) to the present signal analysis method of genome sequences according to its progression along the nucleotide bp [4]. It runs under Linux Ubuntu O.S.…”

“…• Visual compare the GenomeBits GUI curves versus bp for (up to six) given variants/species and (up to two) selected Countries, with those results from the original paper in [4].…”

“…Genome sequence comparisons can be studied using the new GenomeBits method [4,5]. This is a statistical algorithm based on a finite alternating sum series having independently distributed terms associated with (0,1) binary indicators for the nucleotide bases.…”

Adenoviral vector‐based platforms for developing effective vaccines to combat respiratory viral infections

“…161 The Oxford/AstraZeneca vaccine demonstrated about 74% efficacy against the alpha variant versus 84% with the original strain; however, it showed a reduced neutralisation activity against the alpha variant. 162 , 163 Currently, the delta variant is of the greatest concern globally.…”