Determining the frequency of SARS-CoV-2 coinfections during the UK epidemic

The SARS-CoV-2 pandemic has yielded an unprecedented amount of data, and yet we still have relatively little understanding of the role of within-host diversity in the evolution and spread of the virus. For this project you will analyse next generation sequencing data from over 50,000 samples in order to estimate the proportion of individuals coinfected with multiple variants as the UK epidemic unfolded, and the corresponding link with infection rates within the community. The project will involve modifying and then implementing methods to identify coinfections, analysing patterns through time, and writing up the project with a future publication in mind.

Length

6 – 12 weeks, depending on the availability of the candidate, starting in July 2022

Selection Criteria

The project would be suitable for an advanced undergraduate, or masters, student with basic programming skills. Experience in infectious disease epidemiology or pathogen genomics is desirable, but not necessary.