Genomic Epidemiology of SARS-CoV-2 in East Anglia (PAGE_Q22MMB)

Applications Close: 17 January 2022

Salary: MRC stipend

Contract Length: 4 years

The UK is a world leader in SARS-CoV-2 genome sequencing thanks to the COVID-19 Genomics UK Consortium (COG-UK). The Quadram Institute, in particular the Page group, has been at the forefront of sequencing SARS-CoV-2 genomes with over 60,000 sequenced in 18 months. Through our efforts to assist with the pandemic response, Norfolk is the most densely sequenced region of England. This PhD project focuses on looking more deeply at how the pandemic unfolded within one region to gain a deep understanding of genomic epidemiology and will help to inform future management of infectious diseases. Using genomics, we want to find answers to questions like: how did the Alpha variant spread within the region, what happened during hospital outbreaks, did different aged people spread the virus in different ways, were sampled from closed environments like prisons linked to the local community, did trends from random community surveillance match up with trends seen in hospitals? This builds upon existing research that looked at the early days of the pandemic. You will learn SARS-CoV-2 genomics, bioinformatics, genomic epidemiology, phylogenetics, how to work with Big Data, amplicon sequencing, as well as how to undertake large scale analyses on the Quadram Cloud which is run by the Page Group.

You will join a large group of bioinformaticians and molecular biologists who are experts in the field of SARS-CoV-2 and microbial bioinformatics, who have built many bioinformatics methods that are widespread use around the world. Our podcast is a major source of information for the latest in microbial bioinformatics.

The Microbes, Microbiomes and Bioinformatics (MMB) Doctoral Training Partnership (DTP) is open to the UK and international candidates with an undergraduate degree relevant to the scope of the programme for entry in October 2022 and offers postgraduates the opportunity to undertake a 4-year PhD research project funded by the UKRI Medical Research Council to advance the training of students in microbiology, with an emphasis on microbial bioinformatics.

The distinctive training offered by the programme aims to ensure that students feel comfortable running sophisticated computer analyses alongside laboratory work whilst enhancing problem-based learning in microbial bioinformatics and professional development and research skills through a comprehensive training programme. All students will undertake a Professional Placement lasting up to 12 weeks.

This project has been shortlisted for funding by the MMB DTP programme. Interviews for shortlisted candidates will take place on Tuesday 15 February or Wednesday 16 February 2022.

This MMB DTP is committed to equality, diversity, widening participation and inclusion in all areas of the programme. We encourage enquiries and applications from all sections of the community, regardless of gender, ethnicity, disability, age, sexual orientation, and transgender status. We value an aptitude for computer-based analysis, curiosity, and independence of thought, plus a commitment to work across the boundaries between the laboratory and bioinformatics to deliver high-impact research. We welcome applicants from low- and middle-income countries.

You can find more information on eligibility and how to apply on the Partnerships in doctoral training page.

Primary Supervisor: Dr Andrew Page (QIB) –
Secondary Supervisor: Prof Rob Kingsley (QIB)

Entry Requirements

At least UK equivalence Bachelors (Honours) 2:1 or UK equivalence Master’s degree. English Language requirement (Faculty of Medicine and Health equivalent: IELTS 6.5 overall, 6 in each category).


This project is awarded with a 4-year Microbes, Microbiomes and Bioinformatics (MMB) Doctoral Training Partnership (DTP) PhD studentship. Studentships include support for:

•    A maintenance stipend, provided over four years, and funded according to the MRC stipend scale;
•    Full tuition fees which will be paid directly to the University;
•    Research and training costs.

Studentship funding will not normally cover costs associated with visa or health surcharges, or additional costs associated with entry to, and living in the UK.