RETRACTED: Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa

Fischer, Carlo; Maponga, Tongai; Yadouléton, Anges; Abílio, Nuro; Aboce, Emmanuel; Adewumi, Praise; Afonso, Pedro; Akorli, Jewelna; Andriamandimby, Soa Fy; Anga, Latifa; Ashong, Yvonne; Beloufa, Mohamed Amine; Bensalem, Aïcha; Birtles, Richard; Boumba, Anicet Luc Magloire; Bwanga, Freddie; Chaponda, Mike; Chibukira, Paradzai; Chico, R Matthew; Chileshe, Justin; Chongwe, Gershom; Cissé, Assana; D’Alessandro, Umberto; Lamballerie, Xavier de; Morais, Joana; Derrar, Fawzi; Dia, Ndongo; Diarra, Youssouf; Doumbia, Lassina; Drosten, Christian; Dussart, Philippe; Echodu, Richard; Eggers, Yannik; Eloualid, Abdelmajid; Faye, Ousmane; Feldt, Torsten; Frühauf, Anna; Halatoko, Afiwa; Ilouga, Pauliana-Vanessa; Ismael, Nália; Jambou, Ronan; Jarju, Sheikh; Kamprad, Antje; Katowa, Ben; Kayiwa, John; Kingwara, Leonard; Koïta, Ousmane; Lacoste, Vincent; Lagaré, Adamou; Landt, Olfert; Lekana-Douki, Sonia Etenna; Lékana-Douki, Jean Bernard; Iipumbu, Etuhole; Loemba, Hugues; Lutwama, Julius J.; Mamadou, Santou; Maman, Issaka; Manyisa, Brendon; Martı́nez, Pedro; Matoba, Japhet; Mhuulu, Lusia; Moreira-Soto, Andrés; Mwangi, Judy; Dilimabaka, Nadine N; Nassuna, Charity Angella; Ndiath, Mamadou Ousmane; Nepolo, Emmanuel; Njouom, Richard; Nourlil, Jalal; Nyanjom, Steven Ger; Odari, Eddy Okoth; Okeng, Alfred; Ouoba, Jean Bienvenue; Owusu, Michael; Donkor, Irene Owusu; Phadu, Karabo Kristen; Phillips, Richard Odame; Preiser, Wolfgang; Ruhanya, Vurayai; Salah, Fortune; Salifou, Sourakatou; Sall, Amadou Alpha; Sylverken, Augustina Angelina; Tagnouokam-Ngoupo, Paul Alain; Tarnagda, Zékiba; Tchikaya, Francis Olivier; Tufa, Tafese Beyene; Drexler, Jan Felix

doi:10.1126/science.add8737

Cited by 9 publications

(7 citation statements)

References 40 publications

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“…The largest COVID wave our university community experienced was caused by the Omicron lineage. The Omicron lineage spread rapidly after its first detection in southern Africa in November 2021 (11,103); the >30 amino acid substitutions in Spike enabled Omicron to bind ACE2 with higher affinity, as well as escape the anti-Spike antibody response elicited by either natural infection or vaccination with pre-Omicron lineages or vaccines (104)(105)(106). The immunoevasive properties of Omicron are consistent with its causing a COVID wave in our community after vaccine mandates had been established.…”

Section: Discussionsupporting

confidence: 52%

The emergence of SARS-CoV-2 lineages and associated antibody responses among asymptomatic individuals in a large university community

Merling

Williams

Mahfooz

et al. 2023

Preprint

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SARS-CoV-2 (CoV2) infected, asymptomatic individuals are an important contributor to COVID transmission. CoV2-specific immunoglobulin (Ig), as generated by the immune system following infection or vaccination, has helped limit CoV2 transmission from asymptomatic individuals to susceptible populations (e.g. elderly). Here, we describe the relationships between COVID incidence and CoV2 lineage, viral load, saliva Ig levels (CoV2-specific IgM, IgA and IgG) and inhibitory capacity in asymptomatic individuals between Jan 2021 and May 2022. These data were generated as part of a large university COVID monitoring program and demonstrate that COVID incidence among asymptomatic individuals occurred in waves which mirrored those in surrounding regions, with saliva CoV2 viral loads becoming progressively higher in our community until vaccine mandates were established. Among the unvaccinated, infection with each CoV2 lineage (pre-Omicron) resulted in saliva Spike-specific IgM, IgA and IgG responses, the latter increasing significantly post-infection and being more pronounced than N-specific IgG responses. Vaccination resulted in significantly higher Spike-specific IgG levels compared to unvaccinated infected individuals, and uninfected vaccinees saliva was more capable of inhibiting Spike function. Vaccinees with breakthrough Delta infections had Spike-specific IgG levels comparable to those of uninfected vaccinees; however, their ability to inhibit Spike binding was diminished. These data demonstrate that COVID vaccines achieved hoped-for effects in our community, including the generation of mucosal antibodies that inhibit Spike and lower community viral loads, and suggest breakthrough Delta infections were not due to an absence of vaccine-elicited Ig, but instead limited Spike binding activity in the face of high community viral loads.

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Section: Discussionsupporting

confidence: 52%

The emergence of SARS-CoV-2 lineages and associated antibody responses among asymptomatic individuals in a large university community

Merling

Williams

Mahfooz

et al. 2023

Preprint

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“…In this regard, the chances for saltations lineages that emerged after intrahost evolution in IC patients (i.e. in the absence of RBD immune escape) seem minimal: accordingly, despite the initial hypothesis of intrahost evolution to explain the saltation seen with the emergence of Omicron, recent evidence suggests that Omicron ancestors circulated undetected long before the exponential spread [27].…”

Section: Convergent Evolutionmentioning

confidence: 99%

Convergent evolution in SARS-CoV-2 Spike creates a variant soup that causes new COVID-19 waves

Focosi¹,

Quiroga

McConnell

et al. 2022

Preprint

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The first 2 years of the COVID-19 pandemic were mainly characterized by convergent evolution of mutations of SARS-CoV-2 Spike protein at residues K417, L452, E484, N501 and P681 across different variants of concern (Alpha, Beta, Gamma, and Delta). Since Spring 2022 and the third year of the pandemic, with the advent of Omicron and its sublineages, convergent evolution has led to the observation of different lineages acquiring an additional group of mutations at different amino acid residues, namely R346, K444, N450, N460, F486, F490, Q493, and S494. Mutations at these residues have become increasingly prevalent during Summer and Autumn 2022, with combinations showing increased fitness. The most likely reason for this convergence is the selective pressure exerted by previous infection- or vaccine-elicited immunity. Such accelerated evolution has caused failure of all anti-Spike monoclonal antibodies, including bebtelovimab and cilgavimab. While we are learning how fast coronaviruses can mutate and recombine, we should reconsider opportunities for economically sustainable escape-proof combination therapies, and reevaluate the potential for polyclonal therapies (such as COVID19 convalescent plasma) in immunocompromised patients.

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“…33 samples collected before November 2021 in Benin, Ghana, Mali, Niger, and Uganda were tested positive for BA.1 but could not be validated by full genome sequencing due to exhaustion of clinical materials and potential contamination during sample or library preparation prior to HTS. 21 Although nearparallel detection of BA.1 marker-positive samples in five African countries may hypothetically represent emergence of ancestral SARS-CoV-2 strains prior to BA.1 emergence, those samples were excluded from downstream analyses to minimize the impact of potentially false-positive samples. Moreover, data were analyzed based on time points when BA.1 became dominant and modelled early cases backwards to further increase the robustness of downstream epidemiological analyses.…”

Section: Across African Countries Ba1 Replaced Delta As the Predomina...mentioning

confidence: 99%

Ineffectiveness of international travel restrictions to contain spread of the SARS-CoV-2 Omicron BA.1 variant: a continent-wide laboratory-based observational study from Africa

Fischer,

Maponga,

Yadouleton

et al. 2024

Preprint

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Background: In mid-November 2021, the SARS-CoV-2 Omicron BA.1 variant was detected in Southern Africa, prompting international travel restrictions of unclear effectiveness that exacted a substantial economic toll. Methods: Amidst the BA.1 wave, we tested 13,294 COVID-19 patients in 24 African countries between mid-2021 to early 2022 for BA.1 and Delta variants using real-time reverse transcription-PCR tests. The diagnostic precision of the assays was evaluated by high-throughput sequencing in four countries. The observed BA.1 spread was compared to mobility-based mathematical simulations. Findings: By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a median Rt of 2.4 up to 30 days before BA.1 became predominant. PCR-based South-North spread was in agreement with phylogeographic reconstructions relying on 939 SARS-CoV-2 genomes from GISAID. PCR-based reconstructions of country-level BA.1 predominance correlated significantly in time with the emergence of BA.1 genomic sequences on GISAID (p=0.0035, cor=0.70). First BA.1 detections in affluent settings beyond Africa were predicted adequately in time by mobility-based mathematical simulations (p<0.0001). BA.1-infected inbound travelers departing from five continents were identified in five Western countries and one Northern African country by late November/early December 2021, highlighting fast global BA.1 spread aided by international travel. Interpretation: Unilateral travel bans were poorly effective because by the time they came into effect, BA.1 was already widespread in Africa and beyond. PCR-based variant typing combined with mobility-based mathematical modelling can inform rapidly and cost-efficiently on Rt, spread to inform non-pharmaceutical interventions.

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RETRACTED: Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa

Cited by 9 publications

References 40 publications

The emergence of SARS-CoV-2 lineages and associated antibody responses among asymptomatic individuals in a large university community

The emergence of SARS-CoV-2 lineages and associated antibody responses among asymptomatic individuals in a large university community

Convergent evolution in SARS-CoV-2 Spike creates a variant soup that causes new COVID-19 waves

Ineffectiveness of international travel restrictions to contain spread of the SARS-CoV-2 Omicron BA.1 variant: a continent-wide laboratory-based observational study from Africa

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