Molecular mechanisms of SARS-CoV-2 recombination

Key information

Application close date
05 October 2023, 11:59 BST
Hours per week
36 (full time)
Application guidance
Posted 25 August 2023
Background texture taken from the lab imagery.

This sandwich placement will be based in the lab of David LV Bauer. 

Project background and description

Coronaviruses (CoVs) are present in a wide number of hosts, and are occasionally able to “jump” from one host to another in a process termed zoonosis [1]. In addition to the gradual accumulation of individual point mutations (SNPs), coronavirus evolution is driven by frequent RNA recombination: a process in which two different RNA molecules are joined together, which may cause sudden alterations in the ability to infect different hosts and/or evade host immunity. Remarkably, many SARS-CoV-2 recombinant variants have been detected in humans, most notably the Omicron “XBB” variant, which has been responsible for most COVID cases in the UK since February 2023.

The accepted model of recombination is a “copy-choice” mechanism, where the CoV RNA-dependent RNA polymerase (RdRp) initiates transcription, then switches to a new template, where it resumes transcription, generating a recombinant RNA molecule [2]. (This process is analogous to the common laboratory technique of Overlap Extension PCR.) However, for coronaviruses, the processes that drive template-switching remain undefined: what viral factors (e.g. proteins, mutations, RNA sequences) and what host factors (e.g. RNA chaperones) control this process?

To dissect the molecular mechanism of recombination, we will use a safe (Containment Level 2) in vitro setup, based on a SARS-CoV-2 “replicon”, and synthetic biology tools: split T7 RNA polymerase (T7pol) and a fluorescent reporter. When recombination occurs, T7pol will be generated and express Green Fluorescent Protein (GFP) under the control of a T7 promotor, allowing us to use flow cytometry and fluorescence-activated cell sorting (FACS) of cells, plus Illumina & nanopore sequencing to understand how and when recombination occurs.

This work will advance the understanding of fundamental and conserved mechanisms driving viral evolution. Ultimately, the generated knowledge may improve the preventive monitoring of viruses with zoonotic potential and refine public health measures to limit viral evolution during an outbreak.

Candidate background

The post holder should embody and demonstrate the Crick ethos and ways of working: bold, open and collegial. The candidate must be registered at a UK Higher Education Institution, studying in the UK and must have completed a minimum of two years’ undergraduate study in a relevant discipline, and on track to receive a final degree grade of 2:1 or 1. In addition, they should be able demonstrate the following experience and key competencies:

  • This project would suit a candidate studying molecular biology or biochemistry, with interest in virology
  • Good knowledge in relevant scientific area(s)
  • Good written and spoken communication skills
  • Ability to work independently and also capable of interacting within a group


diagram of biological mechanisms


1.        Graham, R.L. and Baric, R.S. (2010)

            Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission.

            Journal of Virology 84: 3134-3146. PubMed abstract

2.         Bentley, K. and Evans, D.J. (2018)

            Mechanisms and consequences of positive-strand RNA virus recombination.

            Journal of General Virology 99: 1345-1356. PubMed abstract