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Choga WT, Kurusa Gasenna GK, San JE, Ookame T, Gobe I, Chand M, Phafane B, Seru K, Matshosi P, Zuze B, Ndlovu N, Matsuru T, Maruapula D, Bareng OT, Macheke K, Kuate-Lere L, Tlale L, Lesetedi O, Tau M, Mbulawa MB, Smith-Lawrence P, Matshaba M, Shapiro R, Makhema J, Martin DP, de Oliveira T, Lessells RJ, Lockman S, Gaseitsiwe S, Moyo S. Rapid dynamic changes of FL.2 variant: A case report of COVID-19 breakthrough infection. Int J Infect Dis 2024; 138:91-96. [PMID: 37952911 PMCID: PMC10719116 DOI: 10.1016/j.ijid.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/23/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023] Open
Abstract
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.
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Affiliation(s)
- Wonderful T Choga
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | | | - James Emmanuel San
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory. Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Irene Gobe
- School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana
| | - Mohammed Chand
- Diagnofirm Medical Laboratories, Plot 12583, Nyerere Drive MiddleStar, Gaborone, Botswana
| | - Badisa Phafane
- Diagnofirm Medical Laboratories, Plot 12583, Nyerere Drive MiddleStar, Gaborone, Botswana
| | - Kedumetse Seru
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Boitumelo Zuze
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Teko Matsuru
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Ontlametse T Bareng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana
| | | | | | | | | | - Modiri Tau
- National Health laboratory, Gaborone, Botswana
| | | | | | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana; Department of Pediatrics, Baylor College of Medicine, Houston, USA
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, Division of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory. Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Global Health, University of Washington, Seattle, USA
| | - Richard J Lessells
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory. Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA; School of Health Systems and Public Health, University of Pretoria, South Africa; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
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