A Mathematical Analysis of HDV Genotypes: From Molecules to Cells

Rami Zakh, Alexander Churkin, Franziska Totzeck, Marina Parr, Tamir Tuller, Ohad Etzion, Harel Dahari, Michael Roggendorf, Dmitrij Frishman and Danny Barash
Additional contact information
Rami Zakh: Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel
Alexander Churkin: Department of Software Engineering, Sami Shamoon College of Engineering, Beer-Sheva 8410501, Israel
Franziska Totzeck: Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
Marina Parr: Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
Tamir Tuller: Department of Biomedical Engineering, Tel-Aviv University, Tel-Aviv 6997801, Israel
Ohad Etzion: Soroka University Medical Center, Ben-Gurion University, Beer-Sheva 8410501, Israel
Harel Dahari: Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
Michael Roggendorf: Institute of Virology, Technische Universität München, 81675 Munich, Germany
Dmitrij Frishman: Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
Danny Barash: Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel

Mathematics, 2021, vol. 9, issue 17, 1-16

Abstract: Hepatitis D virus (HDV) is classified according to eight genotypes. The various genotypes are included in the HDVdb database, where each HDV sequence is specified by its genotype. In this contribution, a mathematical analysis is performed on RNA sequences in HDVdb. The RNA folding predicted structures of the Genbank HDV genome sequences in HDVdb are classified according to their coarse-grain tree-graph representation. The analysis allows discarding in a simple and efficient way the vast majority of the sequences that exhibit a rod-like structure, which is important for the virus replication, to attempt to discover other biological functions by structure consideration. After the filtering, there remain only a small number of sequences that can be checked for their additional stem-loops besides the main one that is known to be responsible for virus replication. It is found that a few sequences contain an additional stem-loop that is responsible for RNA editing or other possible functions. These few sequences are grouped into two main classes, one that is well-known experimentally belonging to genotype 3 for patients from South America associated with RNA editing, and the other that is not known at present belonging to genotype 7 for patients from Cameroon. The possibility that another function besides virus replication reminiscent of the editing mechanism in HDV genotype 3 exists in HDV genotype 7 has not been explored before and is predicted by eigenvalue analysis. Finally, when comparing native and shuffled sequences, it is shown that HDV sequences belonging to all genotypes are accentuated in their mutational robustness and thermodynamic stability as compared to other viruses that were subjected to such an analysis.

Keywords: RNA graph representation; Laplacian eigenvalues; viral kinetic models; hepatitis delta virus genotypes; folding energy; mutational robustness (search for similar items in EconPapers)
JEL-codes: C (search for similar items in EconPapers)
Date: 2021
References: View complete reference list from CitEc
Citations: View citations in EconPapers (1)

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