GenomeBits insight into omicron and delta variants of coronavirus pathogen

Canessa, Enrique; Tenze, Livio

doi:10.1371/journal.pone.0271039

Cited by 3 publications

(8 citation statements)

References 18 publications

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“…A study of GenomeBits into the most recent delta and omicron variants of the coronavirus pathogen can be found in Ref. [ 13 ] (see also [ 14 ]). The GenomeBits method focuses on single-nucleotide structures and may also provide useful information to study the evolution of the MPXV outbreak via simple statistical analysis.…”

Section: Discussionmentioning

confidence: 99%

GenomeBits Characterization of MPXV

Canessa

2022

Genes

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Genome sequences of the monkeypox virus (MPXV) causing the current outbreak are being reported from an increasing number of countries. We present a letter-to-numerical sequence study via GenomeBits signal mapping in order to characterize the evolution of the MPXV via simple statistical analysis. Histograms, empirical and theoretical cumulative distribution curves and the resulting scatter plots for the base nucleotides A and C versus their complementary base nucleotides T and G are discussed. GenomeBits may help the surveillance of emergent infectious diseases.

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Section: Discussionmentioning

confidence: 99%

GenomeBits Characterization of MPXV

Canessa

2022

Genes

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“…The GenomeBits Eq. (1) can also reveal another interesting underlying genomics feature of coronavirus variants, namely, an 'order-disorder' transition [5]. In Fig.…”

Section: 'Order-disorder' Transitionmentioning

confidence: 99%

“…The results obtained for a 'Order-disorder' transition are for each sequences of A,C,G and T nucleotide of the coronavirus Delta and Omicron variants from Spain (a different sequence was used in Ref. [5]). In Ref.…”

Section: Final Remarks and Future Directionsmentioning

confidence: 99%

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Physics-Based Signal Analysis of Genome Sequences: An Overview of GenomeBits

Canessa

2023

Microorganisms

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A comprehensive overview of the recent physics-inspired genome analysis tool, GenomeBits, is presented. This is based on traditional signal processing methods such as discrete Fourier transform (DFT). GenomeBits can be used to extract underlying genomics features from the distribution of nucleotides, and can be further used to analyze the mutation patterns in viral genomes. Examples of the main GenomeBits findings outlining the intrinsic signal organization of genomics sequences for different SARS-CoV-2 variants along the pandemic years 2020–2022 and Monkeypox cases in 2021 are presented to show the usefulness of GenomeBits. GenomeBits results for DFT of SARS-CoV-2 genomes in different geographical regions are discussed, together with the GenomeBits analysis of complete genome sequences for the first coronavirus variants reported: Alpha, Beta, Gamma, Epsilon and Eta. Interesting features of the Delta and Omicron variants in the form of a unique ‘order–disorder’ transition are uncovered from these samples, as well as from their cumulative distribution function and scatter plots. This class of transitions might reveal the cumulative outcome of mutations on the spike protein. A salient feature of GenomeBits is the mapping of the nucleotide bases (A,T,C,G) into an alternating spin-like numerical sequence via a series having binary (0,1) indicators for each A,T,C,G. This leads to the derivation of a set of statistical distribution curves. Furthermore, the quantum-based extension of the GenomeBits model to an analogous probability measure is shown to identify properties of genome sequences as wavefunctions via a superposition of states. An association of the integral of the GenomeBits coding and a binding-like energy can, in principle, also be established. The relevance of these different results in bioinformatics is analyzed.

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“…Among other proteins, the SARS-CoV-2 spike (S) protein is a key target for the induction of neutralizing antibodies and the development of T-cell responses during infection. With next-generation sequencing techniques, it is now known that after the Wuhan variant, the viral spike protein has undergone several modifications throughout the course of months of alterations, increasing the virus’s ability to infect and elude the immune system at a much faster pace than we could follow. − The exceptional and unanticipated genome flexibility of SARS-CoV-2 is frequently linked to the faster rate of mutational adaptation of the viral genome . While evolution is normally a slow time scale phenomenon, such a faster mutational pace of SARS-CoV-2 allows researchers to assort a good collection of mutational data in a relatively less time frame.…”

Section: Introductionmentioning

confidence: 99%

Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective

2023

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Novel coronavirus (SARS-CoV-2) enters its host cell through a surface spike protein. The viral spike protein has undergone several modifications/mutations at the genomic level, through which it modulated its structure−function and passed through several variants of concern. Recent advances in high-resolution structure determination and multiscale imaging techniques, cost-effective next-generation sequencing, and development of new computational methods (including information theory, statistical methods, machine learning, and many other artificial intelligence-based techniques) have hugely contributed to the characterization of sequence, structure, function of spike proteins, and its different variants to understand viral pathogenesis, evolutions, and transmission. Laying on the foundation of the sequence−structure−function paradigm, this review summarizes not only the important findings on structure/function but also the structural dynamics of different spike components, highlighting the effects of mutations on them. As dynamic fluctuations of three-dimensional spike structure often provide important clues for functional modulation, quantifying time-dependent fluctuations of mutational events over spike structure and its genetic/amino acidic sequence helps identify alarming functional transitions having implications for enhanced fusogenicity and pathogenicity of the virus. Although these dynamic events are more difficult to capture than quantifying a static, average property, this review encompasses those challenging aspects of characterizing the evolutionary dynamics of spike sequence and structure and their implications for functions.

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GenomeBits insight into omicron and delta variants of coronavirus pathogen

Cited by 3 publications

References 18 publications

GenomeBits Characterization of MPXV

GenomeBits Characterization of MPXV

Physics-Based Signal Analysis of Genome Sequences: An Overview of GenomeBits

Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective

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