SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection

Hannah Goldswain¹, Rebekah Penrice-Randal¹, I’ah Donovan-Banfield¹, Craig W. Duffy¹, Xiaofeng Dong¹, Nadine Randle¹, Yan Ryan¹, Alex Rzeszutek², Jack Pilgrim², Emma Keyser³, Simon A. Weller³, Emma J. Hutley⁴, Catherine Hartley¹, Tessa Prince¹, Alistair C. Darby¹, Niall Aye Maung⁵, Henry Nwume³, Julian A. Hiscox^1,6, and Stevan R. Emmett³.

¹Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, UK.
²Centre for Genomic Research, University of Liverpool, UK.
³Defence Science Technology Laboratory, Porton Down, UK.
⁴Centre for Defence Pathology, OCT Centre, Royal Centre for Defence Medicine, Birmingham, B15 2WB.
⁵British Army, Hunter House, St Omer Barracks, Aldershot, Hampshire, GU11 2BG
⁶ASTAR Infectious Diseases Laboratories (ASTAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore. \

Sequencing of longitudinal nasopharyngeal swab samples from immunocompetent participants in an isolated geographical location

1. 50 participant samples sequenced via NimaGen-Illumina sequencing (Coolen et al., 2021).
2. EasySeq pipeline used to analyse data (https://github.com/JordyCoolen/easyseq_covid19).
3. Sequences filtered at 85% coverage across the genome.
4. Further downstream analysis using DiversiTools (https://josephhughes.github.io/DiversiTools/tutorial.html), Pangolin (https://github.com/cov-lineages/pangolin), Snipit (https://github.com/aineniamh/snipit) and Nextclade (https://clades.nextstrain.org/).
5. Plotting of outputs using custom R scripts in this repository.

Scripts included in repository

heatmap_updated_paper.R # developed by HG/IDB
letrs_paper.R # developed by HG
nonsyn_lineplot_paper.R # developed by HG/IDB
prop_diff_colours_paper.R # developed by HG/IDB
top_sndaa_paper.R # developed by HG/IDB 

Contributors: XD- Xiaofeng Dong, RPR- Rebekah Penrice-Randal, IDB- I'ah Donovan Banfield, HG- Hannah Goldswain

Example data included in repository

The example data includes files used in the R scripts and generated by the Syn_NonSyn_parse_aa_V3.pl script:

1. Participant01_S1.final_AA_parse.txt
2. Participant01_S1.final_AA.txt
3. Participant01_S1.final_entropy.txt

Raw data availability

Raw fastq files have been deposited in the National Center for Biotechnology Information (NCBI) Short Read Archive (SRA) under the bioproject: PRJNA1012698. Accessible here: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1012698

Contact us

Hannah Goldswain at [email protected], Julian Hiscox at [email protected].