Conserved features of an RNA promoter for RNA polymerase II determined from sequence heterogeneity of a hepatitis delta virus population

Abstract

The right terminal domain of genomic hepatitis delta virus (HDV) RNA is involved in viral replication by recruiting host RNA polymerase II. To identify conserved features of this region, we performed high-throughput 454 sequencing of an HDV population actively replicating in cells. We generated 473,139 sequences representing 2351 new HDV variants of this region and investigated nucleotide conservation and positions of covariation in the population. We found that the sequence is heterogeneous and the rod-like conformation is conserved for both polarities of the HDV RNA genome at this location. Additionally, we identified conserved nucleotides near the previously reported initiation site of transcription, and corroborated our finding with sequences from HDV variants isolated in various hosts. Our analysis highlights the importance of both a conserved sequence at the tip of the rod-like structure and the RNA secondary structure upstream of the tip, which are likely important for HDV replication.

Genetic diversity and worldwide distribution of the deltavirus genus: A study of 2,152 clinical strains

“…Putative promoter regions have been identified on the HDV RNA sequence, mainly by chromatography affinity experiments . According to these studies, a terminal region of the pseudo–double‐stranded structure spanning nucleotides –1683 to 80 was compared for the 265 full‐length HDV genomes.…”

“…The main posttranslational modification positions are indicated. At the top of the figure, a schematic representation of the HDV genome according to Beeharry et al is drawn. Red box highlights the studied region.…”

Hepatitis delta virus: From biological and medical aspects to current and investigational therapeutic options

“…It seems to be the case for HDV mRNA (27), and a recent study has suggested that the 5'-end region of the HDAg mRNA, which coincides with one extremity of the rod-like genomic RNA and displays a complex secondary structure, may play an important role in HDV replication (80).…”

Evidence of an Exponential Decay Pattern of the Hepatitis Delta Virus Evolution Rate and Fluctuations in Quasispecies Complexity in Long-Term Studies of Chronic Delta Infection

“…HDV circulates as a “cloud” of virions that are different from each other but highly related, known as a quasispecies [ 11 , 12 ]. Study of viral quasispecies has been traditionally based on cloning and sequencing, and more recently on a more sensitive and reproducible method known as next-generation sequencing (NGS) [ 13 – 15 ].…”

“…Study of viral quasispecies has been traditionally based on cloning and sequencing, and more recently on a more sensitive and reproducible method known as next-generation sequencing (NGS) [ 13 – 15 ]. In HDV, this method has been used in samples derived from cell cultures [ 12 ], but never in clinical samples. The RNA evolution rate, defined as the rate at which RNA substitutions occur, is a useful parameter to understand viral adaptation to the host.…”