Next-generation mass spectrometry diagnostics to guide patient management post-SARS-CoV-2 infection
- Supervisors: Dr Ed Emmott Dr Anna Smielewska Prof P McNamara Dr Jordan Skittrall
Applications will be reviewed until a suitable candidate is appointed.
The COVID-19 pandemic continues to contribute to extensive morbidity and mortality worldwide. A myriad of diagnostic assays are available. However, none of these offer a robust measure of pathogen infectivity. This is of particular importance in the immunosenescent and immunosuppressed including those in whom prolonged shedding of respiratory viruses has been extensively demonstrated, and where vaccines may not prevent infection or re-infection. Repeated long-term SARS-CoV-2 positivity results in unnecessary use of isolation beds, delays to essential treatment and staff absence due to isolation. Therefore, there is an urgent need for a reliable diagnostic test to determine whether these groups of patients and staff should be considered infectious to inform both treatment and infection control precautions.
In this project you will develop LC-MS/MS assays for absolute quantification of viral proteins and degradation products from patient samples and benchmark these assays against current best clinical and research assays for monitoring SARS-CoV-2 viral load and infectivity (cell culture). You will have use of a biobank of over 3000 clinical respiratory virus samples.
This project covers both ‘wet-lab’ and computational training. You will receive training in mass spectrometry including absolute quantification using QconCATS, data analysis in Matlab or R, and standard cell culture and virological methods for handling SARS-CoV-2-infected patient samples.
This is a collaborative project between Dr Ed Emmott (Centre for Proteome Research, University of Liverpool), Dr Anna Smielewska (Liverpool Clinical Laboratories), Prof. Paul McNamara (ICMS University of Liverpool) and Dr Jordan Skitrall (University of Cambridge). A successful Student will be based within the Centre for Proteome Research. The project is suited to a student with at least a good B.Sc. Upper Second in Biological or Life Sciences (particularly Biochemistry or Virology).
Please email Dr Ed Emmott (email@example.com, emmottllab.org) for more details.
Open to students worldwide
The project is open to both European/UK and International students. It is UNFUNDED and applicants are encouraged to contact the Principal Supervisor directly to discuss their application and the project.
Assistance will be given to those who are applying to international funding schemes.
The successful applicant will be expected to provide the funding for tuition fees and living expenses as well as research costs of £5000 per year.
A fee bursary may be available for well qualified and motivated applicants.
Details of costs can be found on the University website: View Website
1. Johnson et al. (2021) Construction of à la carte QconCAT protein standards for multiplexed quantification of user-specified target proteins. BMC Biology. https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01135-9
2. Meyer et al. (2022) Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential. Nature Communications. https://www.nature.com/articles/s41467-021-25796-w
3. Cardozo et al. (2020) Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts. Nature Communications. https://www.nature.com/articles/s41467-020-19925-0