Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa.
Carlo FischerTongai Gibson MapongaAnges YadouletonNuro AbílioEmmanuel AbocePraise AdewumiPedro AfonsoJewelna AkorliSoa Fy AndriamandimbyLatifa AngaYvonne AshongMohamed Amine BeloufaAicha BensalemRichard BirtlesAnicet Luc Magloire BoumbaFreddie BwangaMike ChapondaParadzai ChibukiraR Matthew ChicoJustin ChilesheGershom ChongweAssana CisséUmberto D AlessandroXavier Nicolas de LamballerieJoana F M de MoraisFawzi DerrarNdongo DiaYoussouf DiarraLassina DoumbiaChristian DrostenPhilippe DussartRichard EchoduYannik EggersAbdelmajid EloualidOusmane FayeTorsten FeldtAnna FrühaufAfiwa HalatokoPauliana-Vanessa IlougaNalia IsmaelRonan JambouSheikh JarjuAntje KampradBen KatowaJohn KayiwaLeonard King'waraOusmane KoitaVincent LacosteAdamou LagareOlfert LandtSonia Etenna Lekana-DoukiJean-Bernard Lekana-DoukiEtuhole IipumbuHugues LoembaJulius Julian LutwamaSantou MamadouIssaka MamanBrendon ManyisaPedro A MartinezJaphet MatobaLusia MhuuluAndres Moreira-SotoJudy MwangiNadine N DilimabakaCharity Angella NassunaMamadou Ousmane NdiathEmmanuel NepoloRichard NjouomJalal NourlilSteven Ger NyanjomEddy Okoth OdariAlfred OkengJean Bienvenue OuobaMichael OwusuIrene Owusu DonkorKarabo Kristen PhaduRichard Odame PhillipsWolfgang PreiserVurayai RuhanyaFortune SalahSourakatou SalifouAmadou Alpha SallAugustina Angelina AnnanPaul Alain Tagnouokam NgoupoZekiba TarnagdaFrancis Olivier TchikayaTafese Beyene TufaJan Felix DrexlerPublished in: Science (New York, N.Y.) (2022)
The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection.