{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T20:43:09Z","timestamp":1789159389083,"version":"build-2803163510"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T00:00:00Z","timestamp":1771545600000},"content-version":"vor","delay-in-days":50,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The SARS-CoV-2 Omicron subvariant BA.3.2 descends from BA.3. It emerged two years after BA.3 ceased to circulate and differs by 39 spike mutations from BA.3. Similar to BA.2.86, which circulated at low levels before giving rise to JN.1, BA.3.2 shows a low but persistent circulation globally. Here, we characterize the phylogenetic origin, infection in cell culture, and neutralization of BA.3.2 using live virus and blood plasma samples collected in South Africa at different stages of the Covid-19 pandemic. Like the Omicron BA.2.86 subvariant, we find that BA.3.2 likely emerged in Southern Africa. We also find that an 871 bp deletion removed ORF7 and ORF8. In H1299-ACE2 cells, BA.3.2 has lower cytotoxicity measured as plaque area compared to ancestral SARS-CoV-2 but similar to the co-circulating LP.8.1 Omicron subvariant with which it also shares similar replication and infection focus size. BA.3.2 and LP.8.1 exhibit complete escape from neutralization from pre-Omicron collected plasma samples, have low levels of neutralization by plasma collected in 2024, and higher neutralization by plasma collected in 2025, with BA.3.2 showing moderately lower neutralization than LP.8.1. The emergence of long branch subvariants like BA.3.2 without intermediates likely indicates that unmonitored persistent infections continue to drive large evolutionary shifts in this virus.<\/jats:p>","DOI":"10.1093\/ve\/veag011","type":"journal-article","created":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T12:26:04Z","timestamp":1771331164000},"source":"Crossref","is-referenced-by-count":12,"title":["Evolution and viral properties of the SARS-CoV-2 BA.3.2 subvariant"],"prefix":"10.1093","volume":"12","author":[{"given":"Zesuliwe","family":"Jule","sequence":"first","affiliation":[{"name":"Africa Health Research Institute and University of KwaZulu-Natal, Nelson R. Mandela School of Medicine , 719 Umbilo Road, Durban 4001, KwaZulu-Natal ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cornelius","family":"R\u00f6mer","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel , Spitalstrasse 41, 4053 Basel ,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics , Spitalstrasse 41, 4053 Basel ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taskeen","family":"Hossen","sequence":"additional","affiliation":[{"name":"Africa Health Research Institute and University of KwaZulu-Natal, Nelson R. Mandela School of Medicine , 719 Umbilo Road, Durban 4001, KwaZulu-Natal ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria","family":"Sviridchik","sequence":"additional","affiliation":[{"name":"The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, Hebrew University of Jerusalem , Jerusalem 91120 ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kajal","family":"Reedoy","sequence":"additional","affiliation":[{"name":"Africa Health Research Institute and University of KwaZulu-Natal, Nelson R. Mandela School of Medicine , 719 Umbilo Road, Durban 4001, KwaZulu-Natal ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yashica","family":"Ganga","sequence":"additional","affiliation":[{"name":"Africa Health Research Institute and University of KwaZulu-Natal, Nelson R. Mandela School of Medicine , 719 Umbilo Road, Durban 4001, KwaZulu-Natal ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siphokazi","family":"Silangwe","sequence":"additional","affiliation":[{"name":"Africa Health Research Institute and University of KwaZulu-Natal, Nelson R. Mandela School of Medicine , 719 Umbilo Road, Durban 4001, KwaZulu-Natal ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurelle","family":"Jackson","sequence":"additional","affiliation":[{"name":"Africa Health Research Institute and University of KwaZulu-Natal, Nelson R. Mandela School of Medicine , 719 Umbilo Road, Durban 4001, KwaZulu-Natal ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Norman","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Boston University , Boston, MA 02215 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Farina","family":"Karim","sequence":"additional","affiliation":[{"name":"Khalifa University of Science and Technology , P.O. Box 127788, Abu Dhabi ,","place":["United Arab Emirates"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dikeledi","family":"Kekana","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service , 1 Modderfontein Road, Johannesburg 2192, Gauteng ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boitshoko","family":"Mahlangu","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service , 1 Modderfontein Road, Johannesburg 2192, Gauteng ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anele","family":"Mnguni","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service , 1 Modderfontein Road, Johannesburg 2192, Gauteng ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayanda","family":"Nzimande","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service , 1 Modderfontein Road, Johannesburg 2192, Gauteng ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadine","family":"Stock","sequence":"additional","affiliation":[{"name":"Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service , 1 Modderfontein Road, Johannesburg 2192, Gauteng ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7498-2391","authenticated-orcid":false,"given":"Mallory","family":"Bernstein","sequence":"additional","affiliation":[{"name":"Africa Health Research Institute and University of KwaZulu-Natal, Nelson R. Mandela School of Medicine , 719 Umbilo Road, Durban 4001, KwaZulu-Natal ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernadett I","family":"Gosnell","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal , Durban 4001, KwaZulu-Natal ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6191-4023","authenticated-orcid":false,"given":"Mahomed-Yunus S","family":"Moosa","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal , Durban 4001, KwaZulu-Natal ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"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, a Division of the National Health Laboratory Service , 1 Modderfontein Road, Johannesburg 2192, Gauteng ,","place":["South Africa"]},{"name":"School of Pathology, University of the Witwatersrand , 7 York Road, Johannesburg 2193, Gauteng ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khadija","family":"Khan","sequence":"additional","affiliation":[{"name":"Africa Health Research Institute and University of KwaZulu-Natal, Nelson R. Mandela School of Medicine , 719 Umbilo Road, Durban 4001, KwaZulu-Natal ,","place":["South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2525-1407","authenticated-orcid":false,"given":"Richard A","family":"Neher","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel , Spitalstrasse 41, 4053 Basel ,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics , Spitalstrasse 41, 4053 Basel ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8571-2004","authenticated-orcid":false,"given":"Alex","family":"Sigal","sequence":"additional","affiliation":[{"name":"Africa Health Research Institute and University of KwaZulu-Natal, Nelson R. Mandela School of Medicine , 719 Umbilo Road, Durban 4001, KwaZulu-Natal ,","place":["South Africa"]},{"name":"The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, Hebrew University of Jerusalem , Jerusalem 91120 ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,2,20]]},"reference":[{"key":"2026032411032439700_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":"2026032411032439700_ref2","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1093\/emph\/eoac010","article-title":"Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution","volume":"10","author":"Amicone","year":"2022","journal-title":"Evol Med Public Health"},{"key":"2026032411032439700_ref3","doi-asserted-by":"publisher","first-page":"15","DOI":"10.3390\/v15040871","article-title":"A rapidly evolving immune and viral modulator in covid-19","volume":"15","author":"Arduini","year":"2023","journal-title":"Viruses"},{"key":"2026032411032439700_ref4","doi-asserted-by":"publisher","first-page":"1901","DOI":"10.1016\/j.cell.2020.10.049","article-title":"Case study: prolonged infectious SARS-CoV-2 shedding from an asymptomatic immunocompromised individual with cancer","volume":"183","author":"Avanzato","year":"2020","journal-title":"Cell"},{"key":"2026032411032439700_ref5","doi-asserted-by":"publisher","first-page":"EMBJ2020106267","DOI":"10.15252\/embj.2020106267","article-title":"Syncytia formation by SARS-CoV-2-infected cells","volume":"39","author":"Buchrieser","year":"2020","journal-title":"EMBO J"},{"key":"2026032411032439700_ref6","doi-asserted-by":"publisher","first-page":"S111","DOI":"10.1093\/cid\/ciy045","article-title":"Persistent high burden of advanced HIV disease among patients seeking care in South Africa\u2019s national HIV program: data from a nationwide laboratory cohort","volume":"66","author":"Carmona","year":"2018","journal-title":"Clin Infect Dis"},{"key":"2026032411032439700_ref7","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1038\/s41586-021-03471-w","article-title":"Escape of SARS-CoV-2 501y.V2 from neutralization by convalescent plasma","volume":"593","author":"Cele","year":"2021","journal-title":"Nature"},{"key":"2026032411032439700_ref8","doi-asserted-by":"publisher","first-page":"654","DOI":"10.1038\/s41586-021-04387-1","article-title":"Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization","volume":"602","author":"Cele","year":"2022","journal-title":"Nature"},{"key":"2026032411032439700_ref9","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":"2026032411032439700_ref10","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":"2026032411032439700_ref11","doi-asserted-by":"publisher","first-page":"15","DOI":"10.3390\/v15010167","article-title":"A detailed overview of SARS-CoV-2 Omicron: its sub-variants, mutations and pathophysiology, clinical characteristics, immunological landscape, immune escape, and therapies","volume":"15","author":"Chatterjee","year":"2023","journal-title":"Viruses"},{"key":"2026032411032439700_ref12","doi-asserted-by":"publisher","first-page":"2291","DOI":"10.1056\/NEJMc2031364","article-title":"Persistence and evolution of SARS-CoV-2 in an immunocompromised host","volume":"383","author":"Choi","year":"2020","journal-title":"N Engl J Med"},{"key":"2026032411032439700_ref13","author":"covSPECTRUM","year":"2025"},{"key":"2026032411032439700_ref14","doi-asserted-by":"publisher","first-page":"4631","DOI":"10.1038\/s41598-022-08780-2","article-title":"Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing","volume":"12","author":"DeRonde","year":"2022","journal-title":"Sci Rep"},{"key":"2026032411032439700_ref15","doi-asserted-by":"publisher","first-page":"1808","DOI":"10.1002\/jmv.27601","article-title":"Emergence of Omicron third lineage BA.3 and its importance","volume":"94","author":"Desingu","year":"2022","journal-title":"J Med Virol"},{"key":"2026032411032439700_ref16","doi-asserted-by":"publisher","DOI":"10.64898\/2025.12.19.25342658","article-title":"Identification and genomic characterisation of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa","author":"Dor","year":"2025","journal-title":"medRxiv"},{"key":"2026032411032439700_ref17","doi-asserted-by":"publisher","first-page":"4937","DOI":"10.1038\/s41467-025-60081-0","article-title":"Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa","volume":"16","author":"Dor","year":"2025","journal-title":"Nat Commun"},{"key":"2026032411032439700_ref18","doi-asserted-by":"publisher","first-page":"930086","DOI":"10.3389\/fimmu.2023.930086","article-title":"Interferon regulatory factor 3 mediates effective antiviral responses to human coronavirus 229e and oc43 infection","volume":"14","author":"Duncan","year":"2023","journal-title":"Front Immunol"},{"key":"2026032411032439700_ref19","doi-asserted-by":"publisher","DOI":"10.1093\/biomethods\/bpaa014","article-title":"Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200\u2009bp tiled amplicons and oxford nanopore rapid barcoding","volume":"5","author":"Freed","journal-title":"Biol Methods Protoc"},{"key":"2026032411032439700_ref20","doi-asserted-by":"publisher","first-page":"e1009130","DOI":"10.1371\/journal.ppat.1009130","article-title":"Infection of human nasal epithelial cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles","volume":"16","author":"Gamage","year":"2020","journal-title":"PLoS Pathog"},{"key":"2026032411032439700_ref21","doi-asserted-by":"publisher","first-page":"e1008690","DOI":"10.1371\/journal.ppat.1008690","article-title":"Inhibition of anti-viral stress granule formation by coronavirus endoribonuclease nsp15 ensures efficient virus replication","volume":"17","author":"Gao","year":"2021","journal-title":"PLoS Pathog"},{"key":"2026032411032439700_ref22","doi-asserted-by":"publisher","first-page":"e374","DOI":"10.1016\/S1473-3099(25)00308-1","article-title":"Antigenic and virological characteristics of SARS-CoV-2 variants BA.3.2, xfg, and NB.1.8.1","volume":"25","author":"Guo","year":"2025","journal-title":"Lancet Infect Dis"},{"key":"2026032411032439700_ref23","volume-title":"Virus Watch: Covid-19, Influenza and RSV Epidemiology Report \u2014 Week 34, 2025. Government of Western Australia, Department of Health","author":"Health WADo","year":"2025"},{"key":"2026032411032439700_ref24","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.00002-21","article-title":"SARS-CoV-2 and SARS-CoV spike-mediated cell-cell fusion differ in their requirements for receptor expression and proteolytic activation","volume":"95","author":"H\u00f6rnich","journal-title":"J Virol"},{"key":"2026032411032439700_ref25","doi-asserted-by":"publisher","first-page":"e67397","DOI":"10.7554\/eLife.67397","article-title":"HIV status alters disease severity and immune cell responses in Beta variant SARS-CoV-2 infection wave","volume":"10","author":"Karim","year":"2021","journal-title":"eLife"},{"key":"2026032411032439700_ref26","doi-asserted-by":"publisher","first-page":"2360","DOI":"10.1038\/s41467-024-46673-2","article-title":"Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-art initiation","volume":"15","author":"Karim","year":"2024","journal-title":"Nat Commun"},{"key":"2026032411032439700_ref27","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":"2026032411032439700_ref28","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1038\/s41586-022-04830-x","article-title":"Omicron infection enhances Delta antibody immunity in vaccinated persons","volume":"607","author":"Khan","year":"2022","journal-title":"Nature"},{"key":"2026032411032439700_ref29","doi-asserted-by":"publisher","first-page":"8078","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":"2026032411032439700_ref30","doi-asserted-by":"publisher","first-page":"e427","DOI":"10.1016\/S2352-3018(18)30104-8","article-title":"Community-based HIV prevalence in Kwazulu-Natal, South Africa: results of a cross-sectional household survey","volume":"5","author":"Kharsany","year":"2018","journal-title":"Lancet HIV"},{"key":"2026032411032439700_ref31","doi-asserted-by":"publisher","first-page":"3992","DOI":"10.1016\/j.cell.2022.09.018","article-title":"Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5","volume":"185","author":"Kimura","year":"2022","journal-title":"Cell"},{"key":"2026032411032439700_ref32","doi-asserted-by":"publisher","first-page":"1055","DOI":"10.3201\/eid2805.220278","article-title":"Sars-cov-2 seroprevalence after third wave of infections, South Africa","volume":"28","author":"Kleynhans","year":"2022","journal-title":"Emerg Infect Dis"},{"key":"2026032411032439700_ref33","doi-asserted-by":"publisher","first-page":"198074","DOI":"10.1016\/j.virusres.2020.198074","article-title":"The orf6, orf8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway","volume":"286","author":"Li","year":"2020","journal-title":"Virus Res"},{"key":"2026032411032439700_ref34","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1093\/ve\/vead075","article-title":"SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations","volume":"10","author":"Lustig","year":"2024","journal-title":"Virus Evol"},{"key":"2026032411032439700_ref35","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/j.omtn.2016.12.007","article-title":"Type I interferons impede short hairpin RNA-mediated RNAi via inhibition of dicer-mediated processing to small interfering RNA","volume":"6","author":"Machitani","year":"2017","journal-title":"Mol Ther Nucleic Acids"},{"key":"2026032411032439700_ref36","doi-asserted-by":"publisher","first-page":"e453","DOI":"10.1016\/S1473-3099(23)00815-0","article-title":"Persistent SARS-CoV-2 infection: significance and implications","volume":"24","author":"Machkovech","year":"2024","journal-title":"Lancet Infect Dis"},{"key":"2026032411032439700_ref37","doi-asserted-by":"publisher","first-page":"e522","DOI":"10.1093\/cid\/ciac548","article-title":"Persistent severe acute respiratory syndrome coronavirus 2 infection with accumulation of mutations in a patient with poorly controlled human immunodeficiency virus infection","volume":"76","author":"Maponga","year":"2023","journal-title":"Clin Infect Dis"},{"key":"2026032411032439700_ref38","doi-asserted-by":"publisher","first-page":"7001","DOI":"10.1073\/pnas.2002589117","article-title":"Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells","volume":"117","author":"Matsuyama","year":"2020","journal-title":"Proc Natl Acad Sci"},{"key":"2026032411032439700_ref39","doi-asserted-by":"publisher","first-page":"S25","DOI":"10.1016\/j.ijid.2021.12.060","article-title":"Prolonged shedding of SARS-CoV-2 at high viral loads amongst hospitalised immunocompromised persons living with HIV, South Africa","volume":"116","author":"Meiring","year":"2022","journal-title":"Clin Infect Dis"},{"key":"2026032411032439700_ref40","doi-asserted-by":"publisher","first-page":"706","DOI":"10.1038\/s41586-022-04474-x","article-title":"Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity","volume":"603","author":"Meng","year":"2022","journal-title":"Nature"},{"key":"2026032411032439700_ref41","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"Iq-tree 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2026032411032439700_ref42","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1038\/s41586-021-03944-y","article-title":"SARS-CoV-2 b.1.617.2 Delta variant replication and immune evasion","volume":"599","author":"Mlcochova","year":"2021","journal-title":"Nature"},{"key":"2026032411032439700_ref43","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1093\/ve\/veac113","article-title":"Contributions of adaptation and purifying selection to SARS-CoV-2 evolution","volume":"8","author":"Neher","year":"2022","journal-title":"Virus Evol"},{"key":"2026032411032439700_ref44","doi-asserted-by":"publisher","first-page":"3143","DOI":"10.1038\/s41467-019-11048-5","article-title":"BRCA2 abrogation triggers innate immune responses potentiated by treatment with parp inhibitors","volume":"10","author":"Reisl\u00e4nder","year":"2019","journal-title":"Nat Commun"},{"key":"2026032411032439700_ref45","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1093\/ve\/vex042","article-title":"Treetime: maximum-likelihood phylodynamic analysis","volume":"4","author":"Sagulenko","year":"2018","journal-title":"Virus Evol"},{"key":"2026032411032439700_ref46","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1038\/s41586-021-04266-9","article-title":"Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation","volume":"602","author":"Saito","year":"2022","journal-title":"Nature"},{"key":"2026032411032439700_ref47","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.Es.2017.22.13.30494","article-title":"Gisaid: global initiative on sharing all influenza data - from vision to reality","volume":"22","author":"Shu","journal-title":"Euro Surveill"},{"key":"2026032411032439700_ref48","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1038\/s41577-022-00720-5","article-title":"Estimating disease severity of Omicron and Delta SARS-CoV-2 infections","volume":"22","author":"Sigal","year":"2022","journal-title":"Nat Rev Immunol"},{"key":"2026032411032439700_ref49","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1038\/s41579-024-01125-y","article-title":"The consequences of SARS-CoV-2 within-host persistence","volume":"23","author":"Sigal","year":"2024","journal-title":"Nat Rev Microbiol"},{"key":"2026032411032439700_ref50","doi-asserted-by":"publisher","first-page":"e01610-20","DOI":"10.1128\/mBio.01610-20","article-title":"Discovery and genomic characterization of a 382-nucleotide deletion in ORF7b and ORF8 during the early evolution of SARS-CoV-2","volume":"11","author":"Su","year":"2020","journal-title":"mBio"},{"key":"2026032411032439700_ref51","doi-asserted-by":"publisher","first-page":"700","DOI":"10.1038\/s41586-022-04462-1","article-title":"Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant","volume":"603","author":"Suzuki","year":"2022","journal-title":"Nature"},{"key":"2026032411032439700_ref52","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":"2026032411032439700_ref53","doi-asserted-by":"publisher","first-page":"e03129","DOI":"10.1128\/mbio.03129-23","article-title":"Comparison of SARS-CoV-2 variants of concern in primary human nasal cultures demonstrates Delta as most cytopathic and Omicron as fastest replicating","volume":"15","author":"Tanneti","year":"2024","journal-title":"MBio"},{"key":"2026032411032439700_ref54","doi-asserted-by":"publisher","first-page":"3207","DOI":"10.1038\/s41467-024-47599-5","article-title":"Positive selection underlies repeated knockout of orf8 in SARS-CoV-2 evolution","volume":"15","author":"Wagner","year":"2024","journal-title":"Nat Commun"},{"key":"2026032411032439700_ref55","doi-asserted-by":"publisher","first-page":"veac050","DOI":"10.1093\/ve\/veac050","article-title":"Recurrent SARS-CoV-2 mutations in immunodeficient patients","volume":"8","author":"Wilkinson","year":"2022","journal-title":"Virus Evol"},{"key":"2026032411032439700_ref56","doi-asserted-by":"publisher","first-page":"1161","DOI":"10.1038\/s41564-022-01143-7","article-title":"SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway","volume":"7","author":"Willett","year":"2022","journal-title":"Nat Microbiol"},{"key":"2026032411032439700_ref57","doi-asserted-by":"publisher","first-page":"e70","DOI":"10.1016\/s1473-3099(23)00744-2","article-title":"Fast evolution of SARS-CoV-2 BA.2.86 to jn.1 under heavy immune pressure","volume":"24","author":"Yang","year":"2024","journal-title":"Lancet Infect Dis"},{"key":"2026032411032439700_ref58","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1016\/s0140-6736(20)31757-8","article-title":"Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study","volume":"396","author":"Young","year":"2020","journal-title":"Lancet"},{"key":"2026032411032439700_ref59","doi-asserted-by":"publisher","first-page":"e2111400119","DOI":"10.1073\/pnas.2111400119","article-title":"SARS-CoV-2 spreads through cell-to-cell transmission","volume":"119","author":"Zeng","year":"2022","journal-title":"Proc Natl Acad Sci"},{"key":"2026032411032439700_ref60","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1038\/s41392-021-00604-5","article-title":"The interferon-stimulated exosomal hace2 potently inhibits SARS-CoV-2 replication through competitively blocking the virus entry","volume":"6","author":"Zhang","year":"2021","journal-title":"Signal Transduct Target Ther"},{"key":"2026032411032439700_ref61","doi-asserted-by":"publisher","first-page":"101165","DOI":"10.1016\/j.lanmic.2025.101165","article-title":"Host cell entry and neutralisation sensitivity of SARS-CoV-2 BA.3.2","volume":"6","author":"Zhang","year":"2025","journal-title":"Lancet Microbe"},{"key":"2026032411032439700_ref62","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2024202118","article-title":"The ORF8 protein of SARS-CoV-2 mediates immune evasion through down-regulating mhc-\u03b9","volume":"118","author":"Zhang","journal-title":"Proc Natl Acad Sci U S A."},{"key":"2026032411032439700_ref63","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1080\/22221751.2021.2023329","article-title":"SARS-CoV-2 Omicron variant shows less efficient replication and fusion activity when compared with Delta variant in tmprss2-expressed cells","volume":"11","author":"Zhao","year":"2022","journal-title":"Emerg Microbes Infect"}],"container-title":["Virus Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ve\/advance-article-pdf\/doi\/10.1093\/ve\/veag011\/66994680\/veag011.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/12\/1\/veag011\/66994680\/veag011.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/12\/1\/veag011\/66994680\/veag011.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T15:03:29Z","timestamp":1774364609000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ve\/article\/doi\/10.1093\/ve\/veag011\/8490867"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":63,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,19]]}},"URL":"https:\/\/doi.org\/10.1093\/ve\/veag011","relation":{},"ISSN":["2057-1577"],"issn-type":[{"value":"2057-1577","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026]]},"published":{"date-parts":[[2026]]},"article-number":"veag011"}}