The influenza A virus genome packaging network — complex, flexible and yet unsolved

Abstract

The genome of influenza A virus (IAV) consists of eight unique viral RNA segments. This genome organization allows genetic reassortment between co-infecting IAV strains, whereby new IAVs with altered genome segment compositions emerge. While it is known that reassortment events can create pandemic IAVs, it remains impossible to anticipate reassortment outcomes with pandemic prospects. Recent research indicates that reassortment is promoted by a viral genome packaging mechanism that delivers the eight genome segments as a supramolecular complex into the virus particle. This finding holds promise of predicting pandemic IAVs by understanding the intermolecular interactions governing this genome packaging mechanism. Here, we critically review the prevailing mechanistic model postulating that IAV genome packaging is orchestrated by a network of intersegmental RNA–RNA interactions. Although we find supporting evidence, including segment-specific packaging signals and experimentally proposed RNA–RNA interaction networks, this mechanistic model remains debatable due to a current shortage of functionally validated intersegmental RNA–RNA interactions. We speculate that identifying such functional intersegmental RNA–RNA contacts might be hampered by limitations of the utilized probing techniques and the inherent complexity of the genome packaging mechanism. Nevertheless, we anticipate that improved probing strategies combined with a mutagenesis-based validation could facilitate their discovery.

In vivo secondary structural analysis of Influenza A virus genomic RNA

“…In conclusion, since RNA structure constraints appear to suppress sequence variation, RNA motifs of high structural and sequential conservation, such as 79–93, 2301–2311 (vRNA2, Table 4 ); 1527–1550 (vRNA5, Table 5 ); 788–809, and 995–1004 (vRNA7, Table 6 ) have great functional potential. These motifs are all located in regions identified as terminal packaging signals for IAV genome assembly (reviewed in [ 87 ]).…”

“…In our structural study, we found several small hairpins and motifs within this region but these have rather low base-pairing probability as well as structural conservation. It is worth noting that this may be a result of evolutionary pressure to preserve intersegmental interactions, especially since the 40–260 nt region has been shown in previous research to be a 5ʹ end packaging signal [ 19 , 87 ]. Two regions 40–255 and 1340–1405 nt of vRNA3 were identified as taking part in vRNA-vRNA interactions in A/WSN/1933 [ 17 ].…”

B‐cell lymphoma‐2 family proteins‐activated proteases as potential therapeutic targets for influenza A virus and severe acute respiratory syndrome coronavirus‐2: Killing two birds with one stone?

“…It consists of 8 gene segments enclosed in an enveloped virion which is 100 nm in diameter. 29 , 30 Haemagglutinin (HA), matrix (M), neuraminidase (NA), nucleoprotein (NP), non‐structural protein (NS1), polymerase acidic protein (PA), polymerase basic protein 1 (PB1), and polymerase basic protein 2 (PB2) are the eight IAV gene segments which encode protein(s) with specific functions. 31 , 32 The segmented genome of IAV has important implications in virus evolution and immune escape.…”

“…IAV is a segmented negative‐sense single‐stranded RNA (ssRNA) virus belonging to the Orthomyxoviridae family. It consists of 8 gene segments enclosed in an enveloped virion which is 100 nm in diameter 29,30 . Haemagglutinin (HA), matrix (M), neuraminidase (NA), nucleoprotein (NP), non‐structural protein (NS1), polymerase acidic protein (PA), polymerase basic protein 1 (PB1), and polymerase basic protein 2 (PB2) are the eight IAV gene segments which encode protein(s) with specific functions 31,32 .…”

High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing

“…These signals, accountable for direct vRNA–vRNA interactions, display segment and subtype specificity and have been mapped throughout the entire length of the vRNAs ( 9 – 19 ). Hence, the current model for vRNA packaging, which also relies on structural ( 20 ) and genetic data ( 21 – 25 ), is that vRNA–vRNA interactions between adjacent packaging signals control the bundling of the eight viral segments and their copackaging into virions with a conserved “7 + 1” pattern, with one central segment surrounded by seven others ( 16 , 26 , 27 ). Direct contacts between segments have been observed by electron tomography ( 10 , 28 ).…”