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Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.

Raquel VianaSikhulile MoyoDaniel Gyamfi AmoakoHouriiyah TegallyCathrine ScheepersChristian L AlthausUgochukwu J AnyanejiPhillip A BesterMaciej F BoniMohammed ChandWonderful T ChogaRachel ColquhounMichaela DavidsKoen DeforcheDeelan DoolabhLouis du PlessisSusan EngelbrechtJosie EverattJennifer GiandhariMarta GiovanettiDiana HardieVerity HillNei-Yuan HsiaoArash IranzadehArshad IsmailCharity JosephRageema JosephLegodile KoopileSergei L Kosakovsky PondMoritz U G KraemerLesego Kuate-LereOluwakemi Laguda-AkingbaOnalethatha Lesetedi-MafokoRichard J LessellsShahin LockmanAlexander G LucaciArisha MaharajBoitshoko MahlanguTongai MapongaKamela MahlakwaneZinhle MakatiniGert MaraisDorcas MaruapulaKereng MasupuMogomotsi MatshabaSimnikiwe MayaphiNokuzola MbheleMpaphi B MbulawaAdriano MendesKoleka MlisanaAnele MnguniThabo MohaleMonika MoirKgomotso MoruisiMosepele MosepeleGerald MotsatsiModisa S MotswalediThongbotho MphoyakgosiNokukhanya MsomiPeter N MwangiYeshnee NaidooNoxolo NtuliMartin NyagaLucier OlubayoSureshnee PillayBotshelo RadibeYajna RamphalUpasana RamphalJames E SanLesley ScottRoger ShapiroLavanya SinghPamela Smith-LawrenceWendy StevensAmy StrydomKathleen SubramoneyNaume TebeilaDerek TshiabuilaJoseph TsuiStephanie van WykSteven WeaverConstantinos K WibmerEduan WilkinsonNicole WolterAlexander E ZarebskiBoitumelo ZuzeDominique GoedhalsWolfgang PreiserFlorette TreurnichtMarietje VenterCarolyn WilliamsonOliver George PybusJinal N BhimanAllison GlassDarren P MartinAndrew RambautSimani GaseitsiweAnne von GottbergTulio de Oliveira
Published in: Nature (2022)
The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively 1-3 . In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function 4 . Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.
Keyphrases
  • sars cov
  • south africa
  • respiratory syndrome coronavirus
  • hiv positive
  • copy number
  • genome wide
  • hiv infected