AVAILABILITY OF DATA AND MATERIALS :
The figures and tables of the study are included in the manuscript. The FASTA files are deposited in the Global Initiative on Sharing All Influenza Data (GISAID) database https://doi.org/10.55876/gis8.230821xh
: Day-08 is EPI_ISL_17601323[hCoV-19/Botswana/BHP_0123017470/2023], and Day-21 is EPI_ISL_17601322[hCoV-19/Botswana/BHP_1100219671/2023].We investigated intra-host genetic evolution using two SARS-CoV-2 isolates from a fully vaccinated (primary schedule x2 doses of AstraZeneca plus a booster of Pfizer), >70-year-old woman with a history of lymphoma and hypertension who presented a SARS-CoV-2 infection for 3 weeks prior to death due to COVID-19. Two full genome sequences were determined from samples taken 13 days apart with both belonging to Pango lineage FL.2: the first detection of this Omicron sub-variant in Botswana. FL.2 is a sub-lineage of XBB.1.9.1. The repertoire of mutations and minority variants in the Spike protein differed between the two time points. Notably, we also observed deletions within the ORF1a and Membrane proteins; both regions are associated with high T-cell epitope density. The internal milieu of immune-suppressed individuals may accelerate SARS-CoV-2 evolution; hence, close monitoring is warranted.Supported by the Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE) which is funded by the Science for Africa Foundation to the Developing Excellence in Leadership, Training and Science in Africa (DELTAS Africa) programme [Del-22-007] with support from Wellcome Trust and the UK Foreign, Commonwealth & Development Office and is part of the EDCPT2 programme supported by the European Union; the Bill & Melinda Gates Foundation [INV-033558]; and Gilead Sciences Inc., [19275]. This work was also supported by the National Institutes of Health NIH Fogarty International Center K43 TW012350. Sequencing was supported by funding from the Foundation for Innovation in Diagnostics, the Bill and Melinda Gates Foundation, the National Institutes of Health Fogarty International Centre, the HHS/NIH/National Institute of Allergy and Infectious Diseases (NIAID) and the Africa Centers of Disease Control through the Pathogen Genomics Initiative.http://www.elsevier.com/locate/ijidhj2024School of Health Systems and Public Health (SHSPH)SDG-03:Good heatlh and well-bein
