{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T05:08:30Z","timestamp":1761541710141,"version":"3.41.2"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,11,22]],"date-time":"2024-11-22T00:00:00Z","timestamp":1732233600000},"content-version":"vor","delay-in-days":326,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Botswana, like the rest of the world, has been significantly impacted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In December 2022, we detected a monophyletic cluster of genomes comprising a sublineage of the Omicron variant of concern (VOC) designated as B.1.1.529.5.3.1.1.1.1.1.1.74.1 (alias FN.1, clade 22E). These genomes were sourced from both epidemiologically linked and unlinked samples collected in three close locations within the district of Greater Gaborone. In this study, we assessed the worldwide prevalence of the FN.1 lineage, evaluated its mutational profile, and conducted a phylogeographic analysis to reveal its global dispersal dynamics. Among approximately 16 million publicly available SARS-CoV-2 sequences generated by 30 September 2023, only 87 were of the FN.1 lineage, including 22 from Botswana, 6 from South Africa, and 59 from the UK. The estimated time to the most recent common ancestor of the 87 FN.1 sequences was 22 October 2022 [95% highest posterior density: 2 September 2022\u201424 November 2022], with the earliest of the 22 Botswana sequences having been sampled on 7 December 2022. Discrete trait reconstruction of FN.1 identified Botswana as the most probable place of origin. The FN.1 lineage is derived from the BQ.1.1 lineage and carries two missense variants in the spike protein, S:K182E in NTD and S:T478R in RDB. Among the over 90 SARS-CoV-2 lineages circulating in Botswana between September 2020 and July 2023, FN.1 was most closely related to BQ.1.1.74 based on maximum likelihood phylogenetic inference, differing only by the S:K182E mutation found in FN.1. Given the early detection of numerous novel variants from Botswana and its neighbouring countries, our study underscores the necessity of continuous surveillance to monitor the emergence of potential VOCs, integrating molecular and spatial data to identify dissemination patterns enhancing preparedness efforts.<\/jats:p>","DOI":"10.1093\/ve\/veae095","type":"journal-article","created":{"date-parts":[[2024,11,22]],"date-time":"2024-11-22T13:24:49Z","timestamp":1732281889000},"source":"Crossref","is-referenced-by-count":3,"title":["Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana"],"prefix":"10.1093","volume":"10","author":[{"given":"Wonderful T","family":"Choga","sequence":"first","affiliation":[{"name":"Research Laboratory, Botswana Harvard Health Partnership , Gaborone, Private Bag BO 320,","place":["Botswana"]},{"name":"Faculty of Health Sciences, School of Allied Health Sciences , Gaborone, Private Bag UB 0022,","place":["Botswana"]},{"name":"Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University , Stellenbosch 7600,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emanuele","family":"Gustani-Buss","sequence":"additional","affiliation":[{"name":"Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven , Leuven 3000,","place":["Belgium"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7102-8540","authenticated-orcid":false,"given":"Houriiyah","family":"Tegally","sequence":"additional","affiliation":[{"name":"Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University , Stellenbosch 7600,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2587-8904","authenticated-orcid":false,"given":"Dorcas","family":"Maruapula","sequence":"additional","affiliation":[{"name":"Research Laboratory, Botswana Harvard Health Partnership , Gaborone, Private Bag BO 320,","place":["Botswana"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoyu","family":"Yu","sequence":"additional","affiliation":[{"name":"Institute of Evolutionary Biology, University of Edinburgh , Edinburgh EH9 3FL, ,","place":["Scotland UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monika","family":"Moir","sequence":"additional","affiliation":[{"name":"Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University , Stellenbosch 7600,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Boitumelo J L","family":"Zuze","sequence":"additional","affiliation":[{"name":"Research Laboratory, Botswana Harvard Health Partnership , Gaborone, Private Bag BO 320,","place":["Botswana"]},{"name":"Faculty of Health Sciences, School of Allied Health Sciences , Gaborone, Private Bag UB 0022,","place":["Botswana"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5736-664X","authenticated-orcid":false,"given":"San Emmanuel","family":"James","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory. 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