Title of PhD project / theme
Investigating the within-host diversity of SARS-CoV-2 and its implications for transmission dynamics
Damien Tully (Lead) Damien.Tully@lshtm.ac.uk
Stéphane Hué Stephane.Hue@lshtm.ac.uk
Shingo Inoue email@example.com
Nabeshima Takeshi firstname.lastname@example.org
Chris Smith Christopher.Smith@lshtm.ac.uk
Brief description of project / theme
The ongoing COVID-19 pandemic has witnessed the generation of over 150,000 genomes of the causative agent, the virus SARS-CoV-2, across the globe. To date, the focus of most genomic studies has been at the population level, i.e. on genetic changes observed in the viral consensus genome which represent the dominant variation within infected individuals. Although such data has been key to understanding the spread and evolution of the virus , the intra-host evolutionary dynamics of SARS-CoV-2 remain poorly understood .
The aim of this PhD project is to utilize publicly-available raw sequencing datasets (Amplicon and RNA-Sequencing data) to understand the full underlying within-host diversity of the virus and its potential impact on transmission, pathogenesis and vaccine design. Specifically, this project will use phylogenetic methods to evaluate (1) whether SARS-CoV-2 within-host diversity can provide further resolution for identifying transmission clusters and (2) whether any inferences on the direction of transmission can be made with high statistical support, as is done for other viruses . To gain further insights into how SARS-CoV-2 within-host dynamics affects which viral variants are transmitted, we will search for genomic signatures of transmission from known households  and outbreaks  and explore whether factors such as host’s age, sex, geographical location, infection status (asymptomatic, symptomatic) and clinical outcome are related to viral genetic diversity.
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The role of LSHTM and NU in this collaborative project
The LSHTM have extensive experience in viral genomic studies, next-generation sequencing and phylogenetic analyses. With professional supervision from researchers at NU the student will gain the expertise of epidemiological, clinical tropical medicine and virology research that will be needed to meet the objectives of the project. The PhD student will spend time in the UK and in Japan and both institutions will work together on study design, analysis and dissemination of findings.
Particular prior educational requirements for a student undertaking this project
The ideal candidate will hold a masters or undergraduate (minimum) degree.
Prior experience with viral sequence data, bioinformatics and a knowledge of molecular evolution is preferred. Technical expertise with at least one computer coding language (ideally python or R) is also highly desirable. Verbal and written English proficiency are required.
Since this project is at the forefront of research on the use of phylogenetics for a newly emerged viral pathogen, a high degree of personal motivation is essential.
Skills we expect a student to develop/acquire whilst pursuing this project
The student is expected to develop a number of key skills including the handling and analysis of high-throughput viral genetic data, the analysis of viral molecular evolution and phylogenetic reconstruction. In addition, the student will build skills in epidemiology, programming, big data analyses, scientific communication (written and oral) and grant writing.