Zika virus recombination
Zika virus is an emerging mosquito-transmitted flavivirus related to important human pathogens such as dengue, West Nile and Yellow Fever. Zika virus infection is generally asymptomatic, but may cause birth defects if transmitted during pregnancy from mother to foetus. Zika virus has an RNA genome and an error-prone polymerase and, like other RNA viruses, evolves rapidly. Distinct South American and Asian strains of Zika virus exist.
In addition to polymerase-driven variation, RNA viruses also exhibit high levels of recombination – the formation of hybrid viruses created in cells infected by two different parental viruses. Recombinant viruses may exhibit changes in tropism (the ability to infect different hosts or tissues) and can cause increased pathogenesis. Understanding the mechanism and consequences of recombination is important at both fundamental and applied levels; if we understand how it happens we can develop strategies to detect or prevent it, and if we understand the consequences we will be better prepared to deal with the novel viruses the process generates.
Using poliovirus as a model system we have developed novel strategies to study viral recombination (Lowry et al., 2014). These have provided important insights into the process. We have demonstrated the process is biphasic. An initial sequence-independent crossover event generates a new virus genome that undergoes successive rounds of replication and increases in fitness. We have additionally shown that the fidelity (accuracy) of the virus polymerase is an important influence on the frequency of recombination. As a consequence of this recombination can be prevented by defined mutations that increase polymerase fidelity (Woodman et. al., 2016). This is relevant to the design of new live-attenuated vaccines for humans and animals. Our studies additionally show that there are distinct replication-dependent and –independent recombination mechanisms. These recent studies have provided a new paradigm for our understanding of this important evolutionary mechanism. Kym Lowry and Andrew Woodman were both PhD students in our laboratory when these studies on poliovirus recombination were conducted.
This new PhD project extends these studies from poliovirus into the flaviviruses, using Zika virus as a model system. We have identified a cellular protein involved in recombination using our poliovirus system and have excellent evidence that Zika, and possibly other flaviviruses, interact with this protein. The consequences of this interaction for recombination in flaviviruses are not yet known. Evidence suggests that additional cellular proteins – as yet unindentified – also contribute to the process. By extension, differences in these cellular proteins – for example between mammalian and insect cells – may influence whether recombination occurs at all, the rate at which is happens and the types of hybrid viruses generated.
The aims of this project are to study recombination in Zika virus, to investigate the role of several cellular proteins in the process, to determine whether recombination can occur in both mammalian and insect hosts, and to characterise the resulting recombinant viruses.
The project will provide excellent training in molecular virology using a combination of reverse genetics, cell biology, proteomics and 3rd generation sequencing. Techniques to be used will include cloning, sequencing (Sanger and NGS), RNAi gene knockdown, CRISPR-CAS gene editing, mammalian and insect cell culture, virus infection, quantification and characterisation by plaque assay and single-step growth.
The successful applicant will join a large, well-funded group occupying excellent laboratories in the Biomedical Sciences Research Complex (BSRC). The BSRC has state-of-the-art proteomic and imaging facilities, dedicated high containment laboratories and a supportive and collegiate environment.
Informal enquiries to Professor David Evans (email@example.com) or by telephone +44 (0)1334 463396. Further details about the Evans group research interests, activities and publications can be found on our website httpw://www.evanslab.org.uk/. Interested students are strongly encouraged to make informal contact before submitting an application. Those local to St. Andrews/Scotland are particularly encouraged to – by arrangement – visit to meet the group, to see the excellent facilities we have and to discover St. Andrews.
Funding is provided for 3.5 years to cover home fees and stipend.
Woodman, A, Arnold, J, Cameron, C & Evans, DJ 2016, ‘Biochemical and genetic analysis of the role of the viral polymerase in enterovirus recombination’ Nucleic Acids Research, 44, 6883-6895. DOI: 10.1093/nar/gkw567
Lowry, K, Woodman, A, Cook, J & Evans, DJ 2014, ‘Recombination in enteroviruses is a biphasic replicative process involving the generation of greater-than genome length ‘imprecise’ intermediates’ PLoS Pathogens, 10, e1004191. DOI: 10.1371/journal.ppat.1004191
Additional references can be found on our lab webpages.