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Background & Aims: The final goal in hepatitis B therapy is eradication of the hepatitis B virus (HBV) replication template, the so-called covalently closed circular DNA (cccDNA).
During DNA replication, template nucleotides that have been chemically modified or lack a base altogether frequently block advancement of the replication fork, and can even cause fork collapse.
HCV genome is an ssRNA that functions as both an mRNA and a replication template so that destruction of HCV RNA could eliminate not only virally directed protein synthesis, but also viral replication.
During DNA replication, single-stranded DNA can form a secondary structure by allowing base pairing between inverted L1 and Alu pairs, which may predispose DNA polymerase to slip on the replication template, leading to the deletion of some genomic regions.
This generates an HJ-like structure with a recombinogenic double-stranded DNA end homologous to the replication template upstream of the RF.
The replication template (negative-stranded RNA) was also positive in ICD patients, but was weaker than the virus template, suggesting that virus replication occurred at a slow rate.
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Evidence suggests that QPs mutate by a replication template-switch whereby one copy of the inverted repeat templates synthesis of the other.
The diluted epigenome is mostly restored within one cell cycle using the epigenome on the parental DNA and nucleosomes as replication templates.
We hypothesize that unlinkase activity is usurped by the virus to distinguish templates for translation versus those destined to become replication templates or to be encapsidated.
Due to VPg retention on nascent RNA strands and replication templates, but not on viral mRNA, we hypothesize that picornaviruses utilize unlinkase activity as a means of controlling the ratio of viral RNAs that are translated versus those that either serve as RNA replication templates or are encapsidated.
An explanation for how picornaviruses protect RNA replication templates and full-length genomes for encapsidation from VPg removal from virion RNA is via coupling RNA replication and encapsidation, as these viral processes have been demonstrated to be coupled in vitro [32], [50], [52], [53], [54]; it is feasible that the capsid proteins shield the nascent viral genomic RNA from unlinkase activity.
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