Viral particles must assemble swiftly and efficiently from their components during an infection in order to compete in a molecular arms race with the host’s immune system. A particular challenge lies in the formation of the viral capsid, a protein container that packages the viral genome and provides protection for it between infection cycles. In the case of Hepatitis B virus (HBV), the principal cause of liver cancer worldwide, its nucleocapsid also acts like a test tube in which the viral pre-genomic RNA is reverse-transcribed into DNA. HBV must simultaneously assemble a symmetrical, closed spherical container around its RNA genome, whilst ensuring that reverse transcription can still occur.

In our joint research programme, we have shown that a wide range of single-stranded RNA viruses from different viral families that infect a wide range of hosts including humans, make use of multiple dispersed sequence-structure motifs in their genomes, called packaging signals (PSs), to code for efficient capsid assembly. These PSs recruit cognate capsid proteins, directing capsid assembly along the most energetically favourable pathways, and simultaneously aid the compaction of the viral genome for ease of packaging. PSs occur in both coding and non-coding regions of genomes and they function to provide a self-assembly instruction manual for viruses.

The existence of such multiple dispersed PSs in the viral genomes had been obscure for decades. The first hint of their existence came from studies with the bacteriophage MS2, where we showed that RNA stem-loops are used as allosteric effectors to set the quasi-equivalent conformations of coat protein dimers in its T=3 shell. Up to sixty such conformational switches are needed to define capsid geometry and we developed an interdisciplinary approach, with our colleagues, to identify them and characterize their functional role(s). Having established this elegant assembly mechanism the question was whether it was unique to MS2 or used more widely. It appears to be widespread, including in major human pathogens like the parechoviruses.  

The ubiquity of PS-mediated assembly suggests that it confers significant selective advantages on the evolution of these viruses.. HBV is classed as a DNA virus, but packages its genome as pre-genomic RNA into its nucleocapsid. We wondered if this RNA packaging strategy hints at evolutionary descent from an RNA virus, and that this ‘modern’ DNA virus still relies on an assembly mechanism inherited from its RNA ancestors. Using our unique highly interdisciplinary approach we identified PS-like sites in HBV and demonstrated that they promote efficient formation of a nucleocapsid of the correct geometry. In contrast to the RNA viruses, however, HBV pre-genomic RNA has fewer PSs, consistent with the requirement for the packaged pre-genome to remain readily accessible for transcription into the DNA copy.

Although there is an excellent recombinant vaccine for HBV, there is no curative treatment for the >250 million people worldwide who suffer chronic infection. The discovery of PS-mediated assembly in HBV could thus pave the way for developments of new drug treatments for the infection, targeting the beneficial effects of PS-coat protein binding with inhibitors.

The paper in Nature Microbiology is here: http://go.nature.com/2sed2j0