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The Evolution of Virus Topology

Principal Supervisor: Dr Craig ThompsonLink opens in a new window

Co-supervisor: Prof Sascha Ott, Dr Nicole Robb

PhD project title: The Evolution of Virus Topology

University of Registration: University of Warwick

Project outline:

Zoonotic diseases by definition move from animal reservoirs into humans. Once circulating in humans, they adapt to their new environment. A well-defined change leading to adaptation in influenza is the PB2 E627K mutation. This enhances transcription in human cells [1]. However, one element that has not been fully explored is the effect that unadapted 5’ and 3’UTR as well as Kozak sequences of viral genes have on the expression of proteins, such as the viral surface glycoproteins haemagglutinin (HA) and neuraminidase (NA).

Influenza has approximately 300-400 HA and 40-50 NA proteins on its surface. The amount of protein on the surface of the virion will be affected by the capacity of the HA and NA viral genomic fragments to express their downstream sequences. In pandemic strains, these promoters are unlikely to be optimised for expression in their new host organism, reducing the amount of HA on the surface of the virion. Once circulating in humans, epitopes of limited variability in HA and NA proteins also appear to constrain the diversity of influenza and cycle between a limited number of conformations, potentially effecting the abundance and distribution of HA and NA [2,3]. The distribution of NA and HA on the surface of the virion is also not evenly distributed, with NA forming clusters between sections of HA (Figure 1). Finally, it is also unclear, whether these NA clusters change or disappear as the virus evolves.

The aim of this project is to determine if HA and NA distribution changes as a virus moves from a zoonotic reservoir into human circulation. It will involve using an array of techniques. Cross-linking, mass spectrometry and super resolution microscopy in addition to qRT-PCR will be used to determine how the distribution of these proteins changes over time in relation to virus genome copy number [4]. Sialic acid binding assays will be used to determine how the affinity of HA and NA proteins change as influenza moves host and evolves. Phenotypic changes will be bioinformatically related to sequence change via the use of association studies.

This is an almost unexplored field of virology but it is also critically important as it directly impacts our understanding of pandemic potential and influenza vaccine design, in addition to answering fundamental question about virus evolution, pathogenesis and virulence.



1. Ari et al (2016) PLOS Pathogen 12(4):e1005583. 2. Thompson et al (2018), Nat Commun9, 3859. 3. Bolton et al (2021) Vaccines 9 (6), 657-673. 4. Robb NC (2022) Biochimica et Biophysica Acta 1868 (4), 166347.

BBSRC Strategic Research Priority: Understanding the rules of life Systems Biology, Structural Biology,
Immunology, and Microbiology, Sustainable Agriculture and Food - Animal Health and Welfare, and Integrated Understanding of Health - Pharmaceuticals, and Diet and Health.


Techniques that will be undertaken during the project:

- CL2 and CL3 virus culture

- Bioinformatics

- Molecular Biology (e.g. cloning, PCR, plasmid digestion, western blotting, qRT-PCR, RNA synthesis, protein cross-linking)

- Mass spectroscopy

- Super-resolution imaging

Contact: Dr Craig Thompson