The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.
Houriiyah TegallyJames Emmanuel SanMatthew CottenMonika MoirBryan TegomohGerald MboowaDarren P MartinCheryl BaxterArnold W LambisiaAmadou DialloDaniel Gyamfi AmoakoMoussa M DiagneAbay SisayAbdel Rahman N ZekriAbdou Salam GueyeAbdoul K SangareAbdoul-Salam OuedraogoAbdourahmane SowAbdualmoniem O MusaAbdul K SesayAbe G AbiasAdam I ElzagheidAdamou LagareAdedotun-Sulaiman KemiAden Elmi AbarAdeniji A JohnsonAdeola FowotadeOluwapelumi Olufemi AdeyemiAdrienne Amuri AzizaAgnes JuruAhmed M KandeilAhmed MostafaAhmed E O OumaAhmed SayedAkano KazeemAladje BaldeSarel MalanAlexander J TrotterAllan CampbellAlpha K KeitaAmadou KoneAmal BouzidAmal SouissiAmbrose AgweyuAmel NaguibAna V GutierrezAnatole NkeshimanaAndrew J PageAnges YadouletonAnika VinzeAnise N HappiAnissa ChouikhaArash IranzadehArisha MaharajArmel L Batchi-BouyouArshad IsmailAugustina Angelina AnnanAugustine GobaAyoade FemiAyotunde E SijuwolaMarycelin Mandu BabaBabatunde L SalakoBamidele S OderindeBankole BolajokoBassirou DiarraBelinda L HerringBenjamin TsofaJean-Bernard Lekana-DoukiBernard MvulaBerthe-Marie Njanpop-LafourcadeBlessing T MaronderaBouh Abdi KhairehBourema KouribaBright AduBrigitte PoolBronwyn L MacInnisCara E BrookCarolyn WilliamsonCassien NduwimanaCatherine AnscombeCatherine B PrattCathrine ScheepersChantal G Akoua-KoffiCharles N AgotiChastel M MapanguyCheikh LoucoubarChika Kingsley OnwuamahChikwe IhekweazuChristian N MalakaChristophe PeyrefitteChukwa GraceChukwuma E OmoruyiClotaire D RafaïCollins Misita Morang'aCyril Oshomah EramehDaniel Lule BugembeDaniel J BridgesDaniel Mukadi-BamulekaDaniel J ParkDavid A RasmussenDavid BakerDavid James NokesDeogratius SsemwangaDerek TshiabuilaDominic Selorm Yao AmuzuDominique GoedhalsDonald S GrantDonwilliams O OmuoyoDorcas MaruapulaDorcas W WanjohiEbenezer Foster-NyarkoEddy Kinganda LusamakiEdgar SimulunduEdidah M Ong'eraEdith N NgabanaEdward O AbworoEdward OtienoEdwin ShumbaEdwine W BarasaEl Bara AhmedElhadi A AhmedEmmanuel LokiloEnatha MukantwariEromon PhilomenaEssia BelarbiEtienne Simon-LoriereEtilé A AnohEusebio ManuelFabian LeendertzFahn M TawehWasfi FaresFatma AbdelmoulaFaustinos T TakawiraFawzi DerrarFehintola V AjogbasileFlorette TreurnichtOnikepe A FolarinFrancine NtoumiFrancisca M MuyembeFrank E Z RagomzingbaFred A DratibiFred-Akintunwa IyanuGabriel K MbunsuGaetan J A ThilliezGemma L KayGeorge O AkpedeGert U van ZylGordon A AwandareGrace S KpeliGrit SchubertGugu P MaphalalaHafaliana C RanaivosonHannah E OmunakweHarris OnyweraHaruka AbeHela H KarrayHellen NansumbaHenda TrikiHerve Albéric Adje KadjoHesham ElghazalyHlanai GumboHota MathieuHugo Kavunga-MemboIbtihel SmetiIdowu B OlawoyeIfedayo M O AdetifaIkponmwosa OdiaIlhem Boutiba Ben BoubakerIluoreh Ahmed MuhammadIsaac SsewanyanaIsatta WurieIyaloo S KonstantinusJacqueline Wemboo Afiwa HalatokoJames AyeiJanaki SonooJean-Claude Makangara CigoloJean-Jacques M TamfumJean Michel HeraudJeffrey G ShafferJennifer GiandhariJennifer MusyokiJerome NkurunzizaJessica N UwanibeJinal N BhimanJiro YasudaJoana F M de MoraisJocelyn KiconcoJohn D SandiJohn HuddlestonJohn K OdoomJohn Mwita MorobeJohn O GyapongJohn T KayiwaJohnson C OkolieJoicymara S XavierJones GyamfiJoseph F WamalaJoseph H K BonneyJoseph NyandwiJosie EverattJoweria NakaseeguJoyce M NgoiJoyce NamulondoJudith Uche OguzieJulia C AndekoJulius Julian LutwamaJuma J H MoggaJustin O'GradyKatherine J SiddleKathleen VictoirKayode T AdeyemiKefentse A TumediKevin S CarvalhoKhadija Said MohammedKoussay DellagiKunda G MusondaKwabena Obeng DueduLamia Fki-BerrajahLavanya SinghLenora M KeplerLeon BiscornetLeonardo de Oliveira MartinsLucious ChabukaLuicer OlubayoLul Deng OjokLul Lojok DengLynette Isabella Ochola-OyierLynn TyersMadisa MineMagalutcheemee RamuthMaha MastouriMahmoud M ElhefnawiMaimouna MbanneMaitshwarelo I MatshekaMalebogo KebabonyeMamadou DiopMambu MomohMaria da Luz Lima MendonçaMarietjie VenterMarietou F PayeMartin FayeMartin M NyagaMathabo MarekaMatoke-Muhia DamarisMaureen W MburuMaximillian G MpinaMichael OwusuMichael R WileyMirabeau Y TatfengMitoha Ondo'o AyekabaMohamed AbouelhodaMohamed Amine BeloufaMohamed G SeadawyMohamed K KhalifaMooko Marethabile MatoboMouhamed KaneMounerou SalouMphaphi B MbulawaMwenda C MulengaMushal AllamMy V T PhanNabil AbidNadine RujeniNadir AbuzaidNalia IsmaelNancy ElguindyNdeye Marieme TopNdongo DiaNédio MabundaNei-Yuan HsiaoNelson Boricó SilochiNgiambudulu M FranciscoNgonda SaasaNicholas BbosaNickson MurungaNicksy GumedeNicole WolterNikita SitharamNnaemeka NdodoNnennaya A AjayiNoël TordoNokuzola MbheleNorosoa H RazanajatovoNosamiefan IguosadoloNwando MbaOjide C KingsleyOkogbenin SylvanusOladiji FemiMoses Olubusuyi AdewumiOlumade TestimonyOlusola A OgunsanyaOluwatosin FakayodeOnwe E OgahOpe-Ewe OludayoOusmane FayePamela Smith-LawrencePascale OndoaPatrice CombePatricia NabisubiPatrick SemandaPaul E OluniyiPaulo ArnaldoPeter Kojo QuashiePeter O OkokherePhilip BejonPhilippe DussartPhillip A BesterPlacide K MbalaPontiano KaleebuPriscilla AbechiRabeh El SheshenyRageema JosephRamy Karam AzizRené G EssombaReuben Ayivor-DjanieRichard NjouomRichard Odame PhillipsRichmond GormanRobert A KingsleyRosa Maria D E S A Neto RodriguesRosemary Ajuma AuduRosina A A CarrSaba GargouriSaber MasmoudiSacha BootsmaSafietou SankheSahra Isse MohamedSaibu FemiSalma MhallaSalome HoschSamar Kamal KassimSamar MethaSameh TrabelsiSara Hassan AgwaSarah Wambui MwangiOusmane A KoitaSheila Makiala-MandandaSherihane AryeeteyShymaa S AhmedSide Mohamed AhmedSiham ElhamoumiSikhulile MoyoSilvia LutucutaSimani GaseitsiweSimbirie JallohSoa Fy AndriamandimbySobajo OguntopeSolène GrayoSonia Etenna Lekana-DoukiSophie ProsolekSoumeya OuangraouaStephanie van WykStephen F SchaffnerStephen KanyereziSteve Ahuka-MundekeSteven RudderSureshnee PillaySusan NabaddaSylvie BehillilSylvie L BudiakiSylvie van der WerfTapfumanei MasheThabo MohaleThanh Le VietThirumalaisamy P VelavanTobias SchindlerTongai Gibson MapongaTrevor BedfordUgochukwu J AnyanejiChinedu A UgwuUpasana RamphalUwem Etop GeorgeVincent EnoufVishvanath NeneVivianne GorovaWael H RoshdyWasim Abdul KarimWilliam K AmpofoWolfgang PreiserWonderful T ChogaYahaya Ali AhmedYajna RamphalYaw BediakoYeshnee NaidooYvan ButeraZaydah R de Laurentnull nullAhmed E O OumaAnne von GottbergGeorge GithinjiMatshidiso MoetiOyewale TomoriPardis C SabetiAmadou A SallSamuel O OyolaYenew K TebejeSofonias K TessemaTulio de OliveiraChristian T HappiRichard J LessellsJohn NkengasongEduan WilkinsonPublished in: Science (New York, N.Y.) (2022)
Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.