Functional characterisation of the molecular interactome of emerging viral haemorrhagic fever arenaviruses

The recent Ebola and Lassa fever epidemics highlight the immense impact human viral haemorrhagic fevers (VHFs) have on human health and on the socio-economic status of the developing world. Arenaviruses are the largest family of VHF-causing viruses; they have worldwide distribution and are endemic in South America and West Africa, mainly in Sierra Leone, Liberia and Nigeria. The current outbreak by the most common arenavirus, Lassa, in Nigeria, makes it imperative to understand the molecular basis of viral pathogenesis and immune evasion, to identify factors that drive viral emergence and to identify drug targets.

The Arenaviridae family is divided into Old World (OW - endemic in West Africa) and New World (NW - endemic in South America) viruses based on their phylogeny, geographical distribution and serological cross reactivity. Arenaviruses cause persistent infections in their natural rodent hosts and viral transmission to humans occurs through direct contact with infectious materials or exposure to rodent urine/faeces. Fatality rates are extremely high; there is no vaccine and the few therapeutic options are ineffective. The overarching aim is to map the complex pathways that are responsible for potentiating and antagonising arenavirus infection and, importantly, explore the molecular basis of host adaptation.
Despite possessing a small genome and encoding for only 4 proteins, arenaviruses have developed strategies to maintain high levels of replication and avoid host immune responses, implying multiple viral and host protein interactions. Thus far, few host cell protein interactions have been identified.
Current knowledge of the modulation of immune factors is restricted to the viral nucleoprotein (NP) and matrix protein (Z) and their inhibition of type I interferon (IFN) induction. Given, the involvement of these proteins in early to late steps of the viral life cycle, it is unlikely that their immunosuppressive function is exclusively limited to this mechanism. Furthermore, they possess structural characteristics that could be fundamental to their ability to modulate different viral processes central to viral spread.

In order to unravel the arenavirus interactome and the differential mechanisms between OW and NW viruses, the student will aim to:
1) develop proteomic screens for the identification of novel interacting partners of NP and Z. Developing these methods will reveal novel co-factors that define pathogenicity differences. Mutational analysis of NP and Z will inform experiments that can delineate differential mechanisms used by pathogenic and non-pathogenic viral strains. Validation of identified protein interactors will involve CRISPR/Cas9 knockout and CAT4 virus assays conducted via collaboration in Marburg. Linked to this will be the use of structural methods, i.e. X-ray crystallography and NMR, to
2) elucidate the molecular details of the interactions of NP and Z with host factors; exploiting these interactions is key in the application of this research to the design of therapeutics. Structural information will define the molecular details of novel host interactions and will inform the future design of effective therapeutics. NP and Z are highly amenable for structural studies and interactions revealed in Aim 1 will be exploited to obtain protein complex structures.
References to learn more:
1. Zapata, J.C.; Salvato, M.S. (2013) Arenavirus Variations Due to Host-Specific Adaptation. Viruses 5, 241-278.
2. Yun, N.E.; Walker, D.H. (2012) Pathogenesis of Lassa Fever. Viruses 4, 2031-2048