{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T06:11:53Z","timestamp":1776060713900,"version":"3.50.1"},"reference-count":59,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T00:00:00Z","timestamp":1762128000000},"content-version":"vor","delay-in-days":306,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100016962","name":"South African Department of Science and Innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016962","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Department of Science and Innovation"},{"name":"Centers for Disease Control and Prevention (CDC) and the COVID International Task Force"},{"name":"UK Department of Health and Social Care\u2019s Fleming Fund"},{"name":"UK Foreign, Commonwealth and Development Office and Wellcome","award":["221003\/Z\/20\/Z"],"award-info":[{"award-number":["221003\/Z\/20\/Z"]}]},{"name":"African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention","award":["INV-050051"],"award-info":[{"award-number":["INV-050051"]}]},{"name":"African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention","award":["INV-049272"],"award-info":[{"award-number":["INV-049272"]}]},{"name":"African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention","award":["INV-018978"],"award-info":[{"award-number":["INV-018978"]}]},{"DOI":"10.13039\/501100001322","name":"South African Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001322","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institute for Communicable Diseases of the National Health Laboratory Service and the United States Centers for Disease Control and Prevention","award":["NU51IP000930"],"award-info":[{"award-number":["NU51IP000930"]}]},{"name":"National Institute for Communicable Diseases of the National Health Laboratory Service and the United States Centers for Disease Control and Prevention","award":["U01IP001048"],"award-info":[{"award-number":["U01IP001048"]}]},{"name":"South African National Department of Health"},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["D43TW011255"],"award-info":[{"award-number":["D43TW011255"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The emergence of various SARS-CoV-2 lineages with adaptive mutations is of significant concern worldwide, especially when these mutations enhance the virus\u2019s ability to either evade immune responses or transmit more efficiently. Between September and December 2023, a highly diverged BA.2-related lineage, designated BA.2.87.1, was detected through diagnostic testing, syndromic surveillance, and wastewater surveillance in the Limpopo, Mpumalanga, Western Cape, Eastern Cape, and Gauteng provinces of South Africa. This lineage harbours 20 amino acid substitutions in Spike protein relative to baseline BA.2, including at antigenic sites of the receptor-binding domain (including N417T, K444N, V445G, L452M, N460K, K478T, N481K, and R493Q) and, most strikingly, large deletions of the N-terminal domain (NTD) residues 15\u201326 and 136\u2013146. Such large NTD deletions have never been observed in circulating lineages but do sometimes occur in highly mutated sequences originating in chronic infections. Phylodynamic analysis supports the possibility that the BA.2.87.1 lineage originated in a chronic infection in that the nearest known ancestor of this lineage last circulated at least 18\u00a0months prior to its first detection. Although BA.2.87.1 had immune evasion and\/or transmission potential, its detection was not associated with a surge of infections and it was displaced by the globally dominant BA.2.86 lineage, JN.1, in the last few weeks of 2023. Our findings further strengthen the case for genomic surveillance through clinical and wastewater surveillance systems. SARS-CoV-2 continues to circulate and evolve within the global population. Multiple divergent Omicron lineages such as BA.1, BA.2, BA.3, BA.4, and BA.5 that have emerged from the southern African region have had a major impact on the epidemiology of the virus worldwide. This is likely driven by the large population of immunocompromised individuals due to the high burden of HIV\/AIDS and TB in the region that facilitates long-term chronic infections. This article provides insights into the emergence of the BA.2.87.1 lineage, which briefly circulated in South Africa. The lineage displayed a unique mutational profile, including major substitutions in the receptor-binding domain and N-terminal domain deletions. The study also highlights the critical role of syndromic and wastewater surveillance in monitoring the circulation and evolution of SARS-CoV-2.<\/jats:p>","DOI":"10.1093\/ve\/veaf083","type":"journal-article","created":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T13:12:32Z","timestamp":1761916352000},"source":"Crossref","is-referenced-by-count":2,"title":["Emergence of the BA.2.87.1 lineage of SARS-CoV-2 in South Africa, a highly diverged BA.2-related lineage"],"prefix":"10.1093","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2295-2099","authenticated-orcid":false,"given":"Dikeledi","family":"Kekana","sequence":"first","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service , 1 Modderfontein Road, Sandringham, Johannesburg, 2192 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-9951-4433","authenticated-orcid":false,"given":"Buhle","family":"Ntozini","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service , 1 Modderfontein Road, Sandringham, Johannesburg, 2192 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ryan","family":"Hisner","sequence":"additional","affiliation":[{"name":"Department of Integrative Biomedical Sciences, Division of Computational Biology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Observatory , Cape Town, 7925 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mukhlid","family":"Yousif","sequence":"additional","affiliation":[{"name":"Centre for Vaccines and Immunology, National Institute for Communicable Diseases of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham , Johannesburg, 2192 ,","place":["South Africa"]},{"name":"School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , 7 York Road, Parktown, Johannesburg, 2193 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Phindile","family":"Ntuli","sequence":"additional","affiliation":[{"name":"Centre for Vaccines and Immunology, National Institute for Communicable Diseases of the National Health Laboratory Service , 1 Modderfontein Road, Sandringham, Johannesburg, 2192 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nkosenhle","family":"Ndlovu","sequence":"additional","affiliation":[{"name":"Centre for Vaccines and Immunology, National Institute for Communicable Diseases of the National Health Laboratory Service , 1 Modderfontein Road, Sandringham, Johannesburg, 2192 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kerrigan","family":"McCarthy","sequence":"additional","affiliation":[{"name":"Centre for Vaccines and Immunology, National Institute for Communicable Diseases of the National Health Laboratory Service , 1 Modderfontein Road, Sandringham, Johannesburg, 2192 ,","place":["South Africa"]},{"name":"School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , 7 York Road, Parktown, Johannesburg, 2193 ,","place":["South Africa"]},{"name":"School of Public Health, Faculty of Health Sciences, University of the Witwatersrand , 7 York Road, Parktown, Johannesburg, 2193 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anele","family":"Mnguni","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service , 1 Modderfontein Road, Sandringham, Johannesburg, 2192 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Boitshoko","family":"Mahlangu","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service , 1 Modderfontein Road, Sandringham, Johannesburg, 2192 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ayanda","family":"Nzimande","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service , 1 Modderfontein Road, Sandringham, Johannesburg, 2192 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nadine","family":"Stock","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service , 1 Modderfontein Road, Sandringham, Johannesburg, 2192 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7102-8540","authenticated-orcid":false,"given":"Houriiyah","family":"Tegally","sequence":"additional","affiliation":[{"name":"School for Data Science and Computational Thinking, Stellenbosch University, Centre for Vaccines and Immunology , 44 Banghoek Road, Stellenbosch, 7599 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mary-Ann","family":"Davis","sequence":"additional","affiliation":[{"name":"Western Cape Government Health and Wellness and School of Public Health, University of Cape Town , Robert Sobukwe Road, Bellville, Cape Town, 7535 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monika","family":"Moir","sequence":"additional","affiliation":[{"name":"School for Data Science and Computational Thinking, Stellenbosch University, Centre for Vaccines and Immunology , 44 Banghoek Road, Stellenbosch, 7599 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eduan","family":"Wilkinson","sequence":"additional","affiliation":[{"name":"School for Data Science and Computational Thinking, Stellenbosch University, Centre for Vaccines and Immunology , 44 Banghoek Road, Stellenbosch, 7599 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheryl","family":"Baxter","sequence":"additional","affiliation":[{"name":"School for Data Science and Computational Thinking, Stellenbosch University, Centre for Vaccines and Immunology , 44 Banghoek Road, Stellenbosch, 7599 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6354-4003","authenticated-orcid":false,"given":"Jinal","family":"Bhiman","sequence":"additional","affiliation":[{"name":"SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand , 7 York Road, Parktown, Johannesburg, 2193 ,","place":["South Africa"]},{"name":"Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service , 1 Modderfontein Road, Sandringham, Johannesburg, 2192 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0376-2302","authenticated-orcid":false,"given":"Cheryl","family":"Cohen","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service , 1 Modderfontein Road, Sandringham, Johannesburg, 2192 ,","place":["South Africa"]},{"name":"School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , 7 York Road, Parktown, Johannesburg, 2193 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7588-2480","authenticated-orcid":false,"given":"Sibongile","family":"Walaza","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service , 1 Modderfontein Road, Sandringham, Johannesburg, 2192 ,","place":["South Africa"]},{"name":"School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , 7 York Road, Parktown, Johannesburg, 2193 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0243-7455","authenticated-orcid":false,"given":"Anne","family":"von Gottberg","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service , 1 Modderfontein Road, Sandringham, Johannesburg, 2192 ,","place":["South Africa"]},{"name":"School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , 7 York Road, Parktown, Johannesburg, 2193 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3027-5254","authenticated-orcid":false,"given":"Tulio","family":"de Oliveira","sequence":"additional","affiliation":[{"name":"School for Data Science and Computational Thinking, Stellenbosch University, Centre for Vaccines and Immunology , 44 Banghoek Road, Stellenbosch, 7599 ,","place":["South Africa"]},{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of Kwa-Zulu Natal , 719 Umbilo Road, Durban, 4001 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9526-0133","authenticated-orcid":false,"given":"Nicole","family":"Wolter","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service , 1 Modderfontein Road, Sandringham, Johannesburg, 2192 ,","place":["South Africa"]},{"name":"School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , 7 York Road, Parktown, Johannesburg, 2193 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8785-0870","authenticated-orcid":false,"given":"Darren","family":"Martin","sequence":"additional","affiliation":[{"name":"Department of Integrative Biomedical Sciences, Division of Computational Biology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Observatory , Cape Town, 7925 ,","place":["South Africa"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,11,3]]},"reference":[{"key":"2025112410120894600_ref1","doi-asserted-by":"publisher","first-page":"3773","DOI":"10.21105\/joss.03773","article-title":"Nextclade: Clade assignment, mutation calling and quality control for viral genomes","volume":"6","author":"Aksamentov","year":"2021","journal-title":"J Open Source Softw"},{"key":"2025112410120894600_ref2","doi-asserted-by":"publisher","first-page":"4597","DOI":"10.1016\/j.cell.2023.08.026","article-title":"SARS-CoV-2 variants evolve convergent strategies to remodel the host response","volume":"186","author":"Bouhaddou","year":"2023","journal-title":"Cell"},{"key":"2025112410120894600_ref3","doi-asserted-by":"publisher","DOI":"10.15252\/embr.202154322","article-title":"Evolutionary remodelling of N-terminal domain loops fine-tunes SARS-CoV-2 spike","volume":"23","author":"Cantoni","year":"2022","journal-title":"EMBO Rep"},{"key":"2025112410120894600_ref4","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1016\/j.chom.2022.01.005","article-title":"SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape","volume":"30","author":"Cele","year":"2022","journal-title":"Cell Host Microbe"},{"key":"2025112410120894600_ref5","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1016\/j.chom.2021.03.005","article-title":"Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite","volume":"29","author":"Cerutti","year":"2021","journal-title":"Cell Host Microbe"},{"key":"2025112410120894600_ref6","doi-asserted-by":"publisher","first-page":"100943","DOI":"10.1016\/j.xcrm.2023.100943","article-title":"Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection","volume":"4","author":"Chaguza","year":"2023","journal-title":"Cell Rep Med"},{"key":"2025112410120894600_ref7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2148-7-214\/TABLES\/1","article-title":"BEAST: Bayesian evolutionary analysis by sampling trees","volume":"7","author":"Drummond","year":"2007","journal-title":"BMC Evol Biol"},{"key":"2025112410120894600_ref8","doi-asserted-by":"publisher","DOI":"10.7189\/jogh.12.03067","article-title":"Is long COVID the next global health crisis?","volume":"12","author":"Faghy","year":"2022","journal-title":"J Glob Health"},{"key":"2025112410120894600_ref9","doi-asserted-by":"publisher","first-page":"e1010636","DOI":"10.1371\/journal.ppat.1010636","article-title":"Genetic diversity and evolutionary convergence of cryptic SARS- CoV-2 lineages detected via wastewater sequencing","volume":"18","author":"Gregory","year":"2022","journal-title":"PLoS Pathog"},{"key":"2025112410120894600_ref10","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1038\/s41588-023-01622-5","article-title":"The ongoing evolution of UShER during the SARS-CoV-2 pandemic","volume":"56","author":"Hinrichs","year":"2023","journal-title":"Nat Genet"},{"key":"2025112410120894600_ref11","volume-title":"Repeated Loss of ORF8 Expression in Circulating SARS-CoV-2 Lineages","author":"Hisner","year":"2023. ."},{"key":"2025112410120894600_ref12","doi-asserted-by":"publisher","first-page":"165817","DOI":"10.1016\/j.scitotenv.2023.165817","article-title":"The role of wastewater-based epidemiology for SARS-CoV-2 in developing countries: Cumulative evidence from South Africa supports sentinel site surveillance to guide public health decision-making","volume":"903","author":"Iwu-Jaja","year":"2023","journal-title":"Sci Total Environ"},{"key":"2025112410120894600_ref13","doi-asserted-by":"publisher","first-page":"2126","DOI":"10.1016\/S0140-6736(21)02758-6","article-title":"Omicron SARS-CoV-2 variant: A new chapter in the COVID-19 pandemic","volume":"398","author":"Karim","year":"2021","journal-title":"Lancet"},{"key":"2025112410120894600_ref14","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2025112410120894600_ref15","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1038\/s41586-021-03291-y","article-title":"SARS-CoV-2 evolution during treatment of chronic infection","volume":"592","author":"Kemp","year":"2021","journal-title":"Nature"},{"key":"2025112410120894600_ref16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-023-43703-3","article-title":"Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant","volume":"14","author":"Khan","year":"2023","journal-title":"Nat Commun"},{"key":"2025112410120894600_ref17","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.03448-22","article-title":"Intra-host evolution provides for the continuous emergence of SARS-CoV-2 variants","volume":"14","author":"Landis","year":"2023","journal-title":"MBio"},{"key":"2025112410120894600_ref18","doi-asserted-by":"publisher","first-page":"3276","DOI":"10.1093\/BIOINFORMATICS\/BTU531","article-title":"AliView: A fast and lightweight alignment viewer and editor for large datasets","volume":"30","author":"Larsson","year":"2014","journal-title":"Bioinformatics"},{"key":"2025112410120894600_ref19","doi-asserted-by":"publisher","first-page":"2952","DOI":"10.1016\/j.cell.2022.06.023","article-title":"Structural basis of human ACE2 higher binding affinity to currently circulating omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1","volume":"185","author":"Li","year":"2022","journal-title":"Cell"},{"key":"2025112410120894600_ref20","doi-asserted-by":"publisher","first-page":"e0243505","DOI":"10.1371\/journal.pone.0243505","article-title":"Survival of MS2 and \u03a66 viruses in droplets as a function of relative humidity, pH, and salt, protein, and surfactant concentrations","volume":"15","author":"Lin","year":"2020","journal-title":"PLoS One"},{"key":"2025112410120894600_ref21","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1038\/s41579-023-00878-2","article-title":"The evolution of SARS-CoV-2","volume":"21","author":"Markov","year":"2023","journal-title":"Nat Rev Microbiol"},{"key":"2025112410120894600_ref22","doi-asserted-by":"publisher","first-page":"e1012883","DOI":"10.1371\/journal.ppat.1012883","article-title":"Evolution of SARS-CoV-2 in white-tailed deer in Pennsylvania 2021-2024","volume":"21","author":"Marques","year":"2025","journal-title":"PLoS Pathog"},{"key":"2025112410120894600_ref23","doi-asserted-by":"publisher","first-page":"veaa087","DOI":"10.1093\/ve\/veaa087","article-title":"RDP5: A computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets","volume":"7","author":"Martin","year":"2021","journal-title":"Virus Evol"},{"key":"2025112410120894600_ref24","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1126\/science.abi7994","article-title":"SARS-CoV-2 immune evasion by the B.1.427\/B.1.429 variant of concern","volume":"373","author":"McCallum","year":"2021","journal-title":"Science"},{"key":"2025112410120894600_ref25","doi-asserted-by":"publisher","first-page":"2332","DOI":"10.1016\/j.cell.2021.03.028","article-title":"N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2","volume":"184","author":"McCallum","year":"2021","journal-title":"Cell"},{"key":"2025112410120894600_ref26","doi-asserted-by":"publisher","first-page":"1139","DOI":"10.1126\/science.abf6950","article-title":"Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape","volume":"371","author":"McCarthy","year":"2021","journal-title":"Science"},{"key":"2025112410120894600_ref27","doi-asserted-by":"publisher","first-page":"e229","DOI":"10.1016\/S2666-5247(20)30116-6","article-title":"A genomics network established to respond rapidly to public health threats in South Africa","volume":"1","author":"Msomi","year":"2020","journal-title":"Lancet Microbe"},{"key":"2025112410120894600_ref28","doi-asserted-by":"publisher","DOI":"10.1101\/2023.09.14.23295379","volume-title":"A Highly Divergent SARS-CoV-2 Lineage B.1.1 Sample in a Patient with Long-Term COVID-19","author":"Nabieva","year":"2023.09.14.23295379"},{"key":"2025112410120894600_ref29","doi-asserted-by":"publisher","first-page":"e83685","DOI":"10.7554\/eLife.83685","article-title":"Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis","volume":"12","author":"Naderi","year":"2023","journal-title":"elife"},{"key":"2025112410120894600_ref30","volume-title":"Weekly Respiratory Pathogens Surveillance Report","author":"National Health Laboratory Service","year":"2023"},{"key":"2025112410120894600_ref31","volume-title":"Weekly Respiratory Pathogens Surveillance Report","author":"National Health Laboratory Service","year":"2024"},{"key":"2025112410120894600_ref32","doi-asserted-by":"publisher","first-page":"veab064","DOI":"10.1093\/ve\/veab064","article-title":"Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool","volume":"7","author":"O\u2019Toole","year":"2021","journal-title":"Virus Evol"},{"key":"2025112410120894600_ref33","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1038\/s42003-022-03565-9","article-title":"Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7\/alpha variant infections","volume":"5","author":"Parker","year":"2022","journal-title":"Commun Biol"},{"key":"2025112410120894600_ref34","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1152\/PHYSIOLGENOMICS.00089.2020","article-title":"The COVID-19 pandemic: A global health crisis","volume":"52","author":"Pollard","year":"2020","journal-title":"Physiol Genomics"},{"key":"2025112410120894600_ref35","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01590-21","article-title":"Dynamics of SARS-CoV-2 spike proteins in cell entry: Control elements in the amino-terminal domains","volume":"12","author":"Qing","year":"2021","journal-title":"MBio"},{"key":"2025112410120894600_ref36","doi-asserted-by":"publisher","first-page":"vew007","DOI":"10.1093\/VE\/VEW007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly path-O-gen)","volume":"2","author":"Rambaut","year":"2016","journal-title":"Virus Evol"},{"key":"2025112410120894600_ref37","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior summarization in Bayesian phylogenetics using tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Syst Biol"},{"key":"2025112410120894600_ref38","doi-asserted-by":"publisher","first-page":"1952","DOI":"10.1038\/s41564-023-01504-w","article-title":"SARS-CoV-2 evolution in the omicron era","volume":"8","author":"Roemer","year":"2023","journal-title":"Nat Microbiol"},{"key":"2025112410120894600_ref39","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1038\/s41586-023-06649-6","article-title":"A molnupiravir-associated mutational signature in global SARS-CoV-2 genomes","volume":"623","author":"Sanderson","year":"2023","journal-title":"Nature"},{"key":"2025112410120894600_ref40","doi-asserted-by":"publisher","first-page":"e15990","DOI":"10.7717\/peerj.15990","article-title":"The evolution of SARS-CoV-2 and the COVID-19 pandemic","volume":"11","author":"Si","year":"2023","journal-title":"PeerJ"},{"key":"2025112410120894600_ref41","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1038\/s41467-022-28246-3","article-title":"Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater","volume":"13","author":"Smyth","year":"2022","journal-title":"Nat Commun"},{"key":"2025112410120894600_ref42","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1016\/J.IJSU.2020.02.034","article-title":"World Health Organization declares global emergency: A review of the 2019 novel coronavirus (COVID-19)","volume":"76","author":"Sohrabi","year":"2020","journal-title":"Int J Surg (London, England)"},{"key":"2025112410120894600_ref43","doi-asserted-by":"publisher","first-page":"2506","DOI":"10.1128\/jvi.79.4.2506-2516.2005","article-title":"Role of nucleotides immediately flanking the transcription-regulating sequence Core in coronavirus subgenomic mRNA synthesis","volume":"79","author":"Sola","year":"2005","journal-title":"J Virol"},{"key":"2025112410120894600_ref44","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1146\/annurev-virology-100114-055218","article-title":"Continuous and discontinuous RNA synthesis in coronaviruses","volume":"2","author":"Sola","year":"2015","journal-title":"Annu Rev Virol"},{"key":"2025112410120894600_ref45","doi-asserted-by":"publisher","first-page":"2800","DOI":"10.1038\/s41467-023-38435-3","article-title":"Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two omicron subvariants","volume":"14","author":"Tamura","year":"2023","journal-title":"Nat Commun"},{"key":"2025112410120894600_ref46","doi-asserted-by":"publisher","first-page":"1785","DOI":"10.1038\/s41591-022-01911-2","article-title":"Emergence of SARS-CoV-2 omicron lineages BA.4 and BA.5 in South Africa","volume":"28","author":"Tegally","year":"2022","journal-title":"Nat Med"},{"key":"2025112410120894600_ref47","doi-asserted-by":"publisher","first-page":"7315","DOI":"10.3390\/ijms23137315","article-title":"Omicron BA.2 lineage, the \u201cstealth\u201d variant: Is it truly a silent epidemic? A literature review","volume":"23","author":"Tiecco","year":"2022","journal-title":"Int J Mol Sci"},{"key":"2025112410120894600_ref48","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1038\/s41579-020-00468-6","article-title":"Coronavirus biology and replication: Implications for SARS-CoV-2","volume":"19","author":"V\u2019kovski","year":"2021","journal-title":"Nat Rev Microbiol"},{"key":"2025112410120894600_ref49","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1038\/s41586-022-04411-y","article-title":"Rapid epidemic expansion of the SARS-CoV-2 omicron variant in southern Africa","volume":"603","author":"Viana","year":"2022","journal-title":"Nature"},{"key":"2025112410120894600_ref50","doi-asserted-by":"publisher","first-page":"358","DOI":"10.3390\/jpm14040358","article-title":"Delta variant in the COVID-19 pandemic: A comparative study on clinical outcomes based on vaccination status","volume":"14","author":"Vulturar","year":"2024","journal-title":"J Pers Med"},{"key":"2025112410120894600_ref51","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/j.cytogfr.2023.03.001","article-title":"Immune evasion of neutralizing antibodies by SARS-CoV-2 omicron","volume":"70","author":"Wang","year":"2023","journal-title":"Cytokine Growth Factor Rev"},{"key":"2025112410120894600_ref52","doi-asserted-by":"publisher","DOI":"10.1038\/s41392-024-01849-6","article-title":"Robust neutralization of SARS-CoV-2 variants including JN.1 and BA.2.87.1 by trivalent XBB vaccine-induced antibodies","volume":"9","author":"Wang","year":"2024","journal-title":"Sig Transduct Target Ther"},{"key":"2025112410120894600_ref53","volume-title":"One Year since the Emergence of COVID-19 Virus Variant Omicron","author":"World Health Organization (WHO)","year":"2022"},{"key":"2025112410120894600_ref54","volume-title":"Tracking SARS-CoV-2 Variants","author":"World Health Organization (WHO)","year":"2024"},{"key":"2025112410120894600_ref55","doi-asserted-by":"publisher","DOI":"10.1038\/s41392-024-01849-6","article-title":"Antigenicity assessment of SARS-CoV-2 saltation variant BA.2.87.1","volume":"13","author":"Yang","year":"2024"},{"key":"2025112410120894600_ref56","doi-asserted-by":"publisher","DOI":"10.1590\/1678-4685-gmb-2021-0309","article-title":"Evolutionary history of the SARS-CoV-2 gamma variant of concern (P.1): A perfect storm","volume":"45","author":"Y\u00e9pez","year":"2022","journal-title":"Genet Mol Biol"},{"key":"2025112410120894600_ref57","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"Ggtree: An r package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol Evol"},{"key":"2025112410120894600_ref58","doi-asserted-by":"publisher","first-page":"e1011308","DOI":"10.1371\/journal.ppat.1011308","article-title":"Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike","volume":"19","author":"Yu","year":"2023","journal-title":"PLoS Pathog"},{"key":"2025112410120894600_ref59","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/s41256-020-00135-6","article-title":"The novel coronavirus outbreak in Wuhan, China","volume":"5","author":"Zhu","year":"2020","journal-title":"Glob Health Res Policy"}],"container-title":["Virus Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ve\/advance-article-pdf\/doi\/10.1093\/ve\/veaf083\/65130389\/veaf083.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/11\/1\/veaf083\/65130389\/veaf083.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/11\/1\/veaf083\/65130389\/veaf083.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,24]],"date-time":"2025-11-24T15:12:15Z","timestamp":1763997135000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ve\/article\/doi\/10.1093\/ve\/veaf083\/8313344"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":59,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,1,9]]}},"URL":"https:\/\/doi.org\/10.1093\/ve\/veaf083","relation":{},"ISSN":["2057-1577"],"issn-type":[{"value":"2057-1577","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2025]]},"article-number":"veaf083"}}