Rapid dynamic changes of FL.2 variant : a case report of COVID-19 breakthrough infection

dc.contributor.authorChoga, Wonderful T.
dc.contributor.authorKurusa (Gasenna), Gobuiwang Khilly
dc.contributor.authorSan, James Emmanuel
dc.contributor.authorOokame, Tidimalo
dc.contributor.authorGobe, Irene
dc.contributor.authorChand, Mohammed
dc.contributor.authorPhafane, Badisa
dc.contributor.authorSeru, Kedumetse
dc.contributor.authorMatshosi, Patience
dc.contributor.authorZuze, Boitumelo
dc.contributor.authorNdlovu, Nokuthula
dc.contributor.authorMatsuru, Teko
dc.contributor.authorMaruapula, Dorcas
dc.contributor.authorBareng, Ontlametse T.
dc.contributor.authorMacheke, Kutlo
dc.contributor.authorKuate-Lere, Lesego
dc.contributor.authorTlale, Labapotswe
dc.contributor.authorLesetedi, Onalethata
dc.contributor.authorTau, Modiri
dc.contributor.authorMbulawa, Mpaphi B.
dc.contributor.authorSmith-Lawrence, Pamela
dc.contributor.authorMatshaba, Mogomotsi
dc.contributor.authorShapiro, Roger
dc.contributor.authorMakhema, Joseph
dc.contributor.authorMartin, Darren P.
dc.contributor.authorDe Oliveira, Tulio
dc.contributor.authorLessells, Richard
dc.contributor.authorLockman, Shahin
dc.contributor.authorGaseitsiwe, Simani
dc.contributor.authorMoyo, Sikhulile
dc.date.accessioned2024-08-01T07:45:06Z
dc.date.available2024-08-01T07:45:06Z
dc.date.issued2024-01
dc.descriptionAVAILABILITY 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].en_US
dc.description.abstractWe 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.en_US
dc.description.departmentSchool of Health Systems and Public Health (SHSPH)en_US
dc.description.librarianhj2024en_US
dc.description.sdgSDG-03:Good heatlh and well-beingen_US
dc.description.sponsorshipSupported 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.en_US
dc.description.urihttp://www.elsevier.com/locate/ijiden_US
dc.identifier.citationChoga, W.T., Kurusa (Gasenna), G.K., San, J.E. et al. 2024, 'Rapid dynamic changes of FL.2 variant : a case report of COVID-19 breakthrough infection', International Journal of Infectious Diseases, vol. 138, pp. 91-96, doi : 10.1016/j.ijid.2023.11.011.en_US
dc.identifier.issn1201-9712 (print)
dc.identifier.issn1878-3511 (online)
dc.identifier.other10.1016/j.ijid.2023.11.011
dc.identifier.urihttp://hdl.handle.net/2263/97387
dc.language.isoenen_US
dc.publisherElsevieren_US
dc.rights© 2023 The Authors. Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).en_US
dc.subjectSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2)en_US
dc.subjectEvolutionen_US
dc.subjectPango lineage FL.2en_US
dc.subjectImmunocompromiseden_US
dc.subjectBotswanaen_US
dc.subjectFL.2en_US
dc.subjectSDG-03: Good health and well-beingen_US
dc.titleRapid dynamic changes of FL.2 variant : a case report of COVID-19 breakthrough infectionen_US
dc.typeArticleen_US

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