Optimising RNA structure to develop flexible influenza virus vector backbones for co-vaccination

This is a BBSRC-AstraZeneca-iCASE funded PhD position for the 2021 programme in the lab of David LV Bauer at the Crick, in collaboration with Oliver Dibben at AstraZeneca.

Project background and description

The Live Attenuated Influenza Vaccine (LAIV), marketed as FluMist/Fluenz by AstraZeneca forms the backbone of the United Kingdom’s childhood influenza vaccination programme and is given as a nasal spray annually to all 2-12 year-olds. Unlike inactivated vaccines, LAIVs are unique in generating significant mucosal immunity (Barría et al., J Infect Dis, 2013), offering the possibility of pre-empting virus spread from the upper to lower respiratory tract and consequent risk of severe disease.

This project aims to understand how the genome segments of LAIVs are assembled in order to develop a next-generation of LAIVs suitable as flexible vectors for all seasonal or pandemic influenza strains and co-vaccination against viruses such as SARS-CoV-2 — to which we have no vaccine that confers mucosal immunity. Such a vaccine would be invaluable, especially if SARS-CoV-2 required routine vaccination against ongoing variants or vaccine escape mutants.

This project builds on a successful 2-year collaboration between the Bauer lab and the team of Oliver Dibben at AstraZeneca. The student involved in this project will spend the majority of their time at the Crick. However, to learn the necessary LAIV virology techniques, and collaborate with AZ scientists on related projects, the student would be expected to spend a period of at least 3 months in the Flu-BPD labs, distributed over the course of the project.

Like all natural influenza viruses, LAIV strains must efficiently package one copy of each of their eight genome segments into each new virus particle in order to produce infectious progeny. This process is driven by inter-segment RNA:RNA interactions during virus replication, guiding genome assembly (Dadonaite et al., Nat Microbiol, 2019), though the exact mechanisms of the process remain unknown. Crucially, this process also underpins influenza virus “reassortment”, a process analogous to viral sexual reproduction in which genome segments from one virus “mix and match” with those from another virus that has infected the same cell. In nature, this process of reassortment can give rise to new pandemic strains of influenza to which there is little existing immunity in the human population. In the lab, the same process is exploited to generate a new LAIV strain, which is a reassortant between six segments from an attenuated “Master Donor Virus” (MDV) and two segments (HA and NA) from circulating influenza viruses.

In the 2013-14 and 2015-16 influenza seasons, low vaccine effectiveness was observed for the H1N1 component of FluMist in the USA, attributed to decreased LAIV replication in human nasal epithelial cells (Hawksworth et al., Vaccine, 2020), rather than decreased HA antigen stability (Parker et al., Vaccine 2019). One potential contributing factor to this reduced fitness was a decrease in the production of infectious virus particles carrying all eight genome segments. Observations also suggest that the ability of the historic MDV genome to incorporate HA and NA genes from different, contemporary influenza A viruses can vary, resulting in LAIV strains with unexpected replicative differences.

This project aims to (1) map RNA:RNA interactions that drive assembly of LAIV strains and (2) to use this knowledge to develop a flexible MDV backbone enabling efficient generation of either seasonal or pandemic LAIV, that (3) can also act as a vector for co-vaccination of influenza along with other respiratory pathogens, such as SARS-CoV-2.

Candidate background

This project would suit candidates with a strong background in molecular biology, virology, or RNA biochemistry, who have a strong interest in translational potential of their work. Applications from those who have significant laboratory-based experience (e.g. Masters’ project, ‘year in industry’, time spent working following degree) are encouraged. As part of this project, students will work closely with the Influenza Biopharmaceuticals Development (Flu-BPD) group at AstraZeneca (Liverpool, UK), and the project would suit candidates interested in spending part of their research time in an industrial setting.


1.         Barría, M.I., Garrido, J.L., Stein, C., Scher, E., Ge, Y., Engel, S.M., . . . Moran, T.M. (2013)

            Localized mucosal response to intranasal live attenuated influenza vaccine in adults.

            Journal of Infectious Diseases 207: 115-124. PubMed abstract

2.         Dadonaite, B., Gilbertson, B., Knight, M.L., Trifkovic, S., Rockman, S., Laederach, A., . . . Bauer, D.L.V. (2019)

            The structure of the influenza A virus genome.

            Nature Microbiology 4: 1781-1789. PubMed abstract

3.         Ferhadian, D., Contrant, M., Printz-Schweigert, A., Smyth, R.P., Paillart, J.-C. and Marquet, R. (2018)

            Structural and functional motifs in influenza virus RNAs.

            Frontiers in Microbiology 9: 559. PubMed abstract

4.         Hawksworth, A., Lockhart, R., Crowe, J., Maeso, R., Ritter, L., Dibben, O. and Bright, H. (2020)

            Replication of live attenuated influenza vaccine viruses in human nasal epithelial cells is associated with H1N1 vaccine effectiveness.

            Vaccine 38: 4209-4218. PubMed abstract

5.         Parker, L., Ritter, L., Wu, W., Maeso, R., Bright, H. and Dibben, O. (2019)

            Haemagglutinin stability was not the primary cause of the reduced effectiveness of live attenuated influenza vaccine against A/H1N1pdm09 viruses in the 2013-2014 and 2015-2016 seasons.

            Vaccine 37: 4543-4550. PubMed abstract