RNA Sequence Features Are at the Core of Influenza A Virus Genome Packaging

Abstract

The influenza A virus (IAV), a respiratory pathogen for humans, poses serious medical and economic challenges to global healthcare systems. The IAV genome, consisting of eight single-stranded viral RNA segments, is incorporated into virions by a complex process known as genome packaging. Specific RNA sequences within the viral RNA segments serve as signals that are necessary for genome packaging. Although efficient packaging is a prerequisite for viral infectivity, many of the mechanistic details about this process are still missing. In this review, we discuss the recent advances toward the understanding of IAV genome packaging and focus on the RNA features that play a role in this process.

Keywords: genome packaging; influenza virus; reassortment.

Figure 1.. Structure of IAV vRNPs and vRNAs.

(A) Diagram showing the”7 + 1”arrangement of vRNPs inside a virion (left side). A schematic representation of a vRNP complex is shown with a tripartite viral polymerase complex at the top of the vRNP where it binds the panhandle structure formed by 5’ and 3’ UTRs (right side). Rest of the vRNA (black) is covered with multiple nucleoproteins (blue). (B) Schematic diagram showing the positions of packaging signals on a vRNA. The viral ORF is depicted as a rectangle that is flanked by UTRs, which are shown as lines. Typical packaging signals (violet) are situated at both ends of the vRNA consisting of UTRs and ends of the ORF.

Figure 2.. A model for vRNA-vRNA interactions and their consequence on IAV genome packaging.

Different vRNA segments are shown here as lines of different colors (red, green and yellow). Regions of vRNA that are not bound to nucleoprotein may form RNA structures, which mediate inter-vRNA interactions. It is also possible that vRNPs interact with each other by a still unknown mechanism, which is depicted here as a question mark. Closely related IAV strains have compatible vRNA-vRNA interaction profiles resulting in efficient genome packaging (left). For divergent IAV strains, dissimilarity in nucleotide sequences results in formation of RNA features that are not compatible for RNA-RNA interactions, and thus reduce genome packaging efficiency (right).

Figure 3.. A hierarchical model for IAV genome packaging during trafficking through the cytoplasm.

Here, eight different vRNPs are shown in different colors. Upon export from the nucleus, multiple vRNPs may interact with each other to form a “core complex” for packaging. However, the identity of the initial “core complex” and the sequence of vRNP association are not clear. Three different models for vRNP transport and bundling through the cytoplasm are shown here as A, B and C. In model A, multiple “core complex” form after exit from the nucleus and these clusters associate with each other as they move towards the plasma membrane. In model B, one major type of core-complex forms after nuclear exit. As the vRNPs move towards the plasma membrane rest of the vRNPs associate with the core complex one by one before being released as progeny virions. In model C, multiple vRNP pre-complex that are formed after nuclear exit can interact with each other and exchange vRNPs among themselves.