The bioinformatics of the finding that the hepatitis delta virus RNA editing mechanism by a conformational switch exists in genotype 7 in addition to genotype 3.

Abstract

Hepatitis delta virus (HDV) is geographically classified according to eight known genotypes. The combined hepatitis B-hepatitis D (HEPB-HEPD) disease is the severest form of chronic viral hepatitis in humans and is characterized by mortality rates of ~20%. Hepatitis delta virus has no FDA approved therapy and its only available vaccine is the one for HEPB. Because it is the smallest RNA virus known to infect humans, RNA folding predictions by energy minimization of the whole genome can reveal important information on functional RNA secondary structure elements within the genome. A public HDV database (HDVdb) contains 512 HDV strains on which various bioinformatics methods can be applied, aiming to detect strains that could perform RNA editing via conformational switching. Up to date, only one such strain from HDVdb was known to perform that, in HDV genotype 3. Our goal was to locate more such strains, both in genotype 3 and in other possible HDV genotypes. In past work, by an eigenvalue mathematical analysis, we made an initial prediction that this peculiar RNA editing mechanism also exists in HDV genotype 7. We hereby extend our earlier findings and present newly discovered HDV strains from multiple genotypes for further analysis of RNA editing sites within the virus. The relevant strains taken from HDVdb are from both genotype 3 of Peru and genotype 7 of Cameroon. Additionally, the new strains have a variety of optional RNA editing sites that we report, many of which are unknown to date.