The structure of the influenza A virus genome


Influenza A viruses (IAVs) constitute a major threat to human health. The IAV genome consists of eight single-stranded viral RNA segments contained in separate viral ribonucleoprotein (vRNP) complexes that are packaged together into a single virus particle. The structure of viral RNA is believed to play a role in assembling the different vRNPs into budding virions1,2,3,4,5,6,7,8 and in directing reassortment between IAVs9. Reassortment between established human IAVs and IAVs harboured in the animal reservoir can lead to the emergence of pandemic influenza strains to which there is little pre-existing immunity in the human population10,11. While previous studies have revealed the overall organization of the proteins within vRNPs, characterization of viral RNA structure using conventional structural methods is hampered by limited resolution and an inability to resolve dynamic components12,13. Here, we employ multiple high-throughput sequencing approaches to generate a global high-resolution structure of the IAV genome. We show that different IAV genome segments acquire distinct RNA conformations and form both intra- and intersegment RNA interactions inside influenza virions. We use our detailed map of IAV genome structure to provide direct evidence for how intersegment RNA interactions drive vRNP cosegregation during reassortment between different IAV strains. The work presented here is a roadmap both for the development of improved vaccine strains and for the creation of a framework to ‘risk assess’ reassortment potential to better predict the emergence of new pandemic influenza strains.

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Fig. 1: Analysis of the IAV genome structure using SHAPE-MaP.
Fig. 2: Intersegment RNA interactions in the IAV genome.
Fig. 3: RNA interactions form a redundant, plastic network to accommodate variation and reassortment.
Fig. 4: Intersegment RNA interactions drive IAV segment cosegregation during reassortment.

Data availability

All sequencing data have been deposited with the Sequence Read Archive (accession numbers: SRP127020, SRP126994, SRP150669, SRP150677 and SRP212811); the processed SHAPE-MaP reactivities are available in SNRNASM format as Supplementary Table 1 and processed SPLASH data as Supplementary Table 2.


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We thank G.G. Brownlee and J. Kenyon for helpful discussions, J. Kenyon, J.G. Aw, and Y. Wan for sharing protocols, J. Robertson for making the 1M7 reagent, J. Sharps for technical assistance and St Jude Children’s Research Hospital for providing the pHW2000 plasmid. This work was supported by a Wellcome Trust studentship (no. 105399/Z/14/Z to B.D.), a UK Biotechnology and Biological Sciences Research Council studentship (no. BB/M011224/1 to M.L.K.), grants from the National Institutes of Health (nos. HL111527, GM101237 and HG008133 to A.L.), a National Health and Medical Research Council of Australia programme grant (no. ID1071916 to L.E.B.), UK Medical Research Council programme grants (nos. MR/K000241/1 and MR/R009945/1 to E.F.) and a Sir Edward Penley Abraham Cephalosporin Junior Research Fellowship to D.L.V.B.

Author information

B.D. designed, performed and analysed the SHAPE-MaP and SPLASH experiments and associated virus replication and purification work. M.L.K. performed and analysed the SPLASH experiments on reassortant viruses and associated virus replication and purification experiments. D.L.V.B. designed the SPLASH experiments and analysed the resulting data. B.G. designed and performed the competitive reassortant virus rescue experiments, created the reassortant viruses and analysed the data. S.T. and B.G. performed the viral replication experiments with the reassortant viruses. S.R., A.L., L.E.B., E.F. and D.L.V.B. supervised the work. B.D., B.G. and D.L.V.B. wrote the paper with contributions from the other authors.

Correspondence to Lorena E. Brown or Ervin Fodor or David L. V. Bauer.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–11.

Reporting Summary

Supplementary Table 1

Complete SHAPE-MaP data in SNRNASM format.

Supplementary Table 2

Complete SPLASH data and reference genome sequences.

Supplementary Table 3

Sequences of primers used.

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