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1.
Carlo Fischer; Tongai Gibson Maponga; Anges Yadouleton; Nuro Abilio; Emmanuel Aboce; Praise Adewumi; Pedro Afonso; Jewelna Akorli; Soa Fy Andriamandimby; Latifa Anga; Yvonne Ashong; Mohamed Amine Beloufa; Aicha Bensalem; Richard Birtles; Anicet Luc Magloire Boumba; Freddie Bwanga; Mike Chaponda; Paradzai Chibukira; R Matthew Chico; Justin Chileshe; Wonderful Choga; Gershom Chongwe; Assana Cisse; Fatoumata Cisse; Umberto D Alessandro; Xavier de Lamballerie; Joana F.M. de Morais; Fawzi Derrar; Ndongo Dia; Youssouf Diarra; Lassina Doumbia; Christian Drosten; Philippe Dussart; Richard Echodu; Tom Luedde; Abdelmajid Eloualid; Ousmane Faye; Torsten Feldt; Anna Fruehauf; Simani Gaseitsiwe; Afiwa Halatoko; Pauliana-Vanessa Ilouga; Nalia Ismael; Ronan Jambou; Sheikh Jarju; Antje Kamprad; Ben Katowa; John Kayiwa; Leonard Kingwara; Ousmane Koita; Vincent Lacoste; Adamou Lagare; Olfert Landt; Sonia Etenna Lekana-Douki; Jean-Bernard Lekana-Douki; Etuhole Iipumbu; Hugues Loemba; Julius Lutwama; Santou Mamadou; Issaka Maman; Brendon Manyisa; Pedro A. Martinez; Japhet Matoba; Lusia Mhuulu; Andres Moreira-Soto; Sikhulile Moyo; Judy Mwangi; Nadine Ndilimabaka; Charity Angella Nassuna; Mamadou Ousmane Ndiath; Emmanuel Nepolo; Richard Njouom; Jalal Nourlil; Steven Ger Nyanjom; Eddy Okoth Odari; Alfred Okeng; Jean Bienvenue Ouoba; Michael Owusu; Irene Owusu Donkor; Karabo Kristen Phadu; Richard Odame Phillips; Wolfgang Preiser; Pierre Roques; Vurayai Ruhanya; Fortune Salah; Sourakatou Salifou; Amadou Alpha Sall; Augustina Angelina Sylverken; Paul Alain Tagnouokam-Ngoupo; Zekiba Tarnagda; Francis Olivier Tchikaya; Noel Tordo; Tafese Beyene Tufa; Jan Felix Drexler.
medrxiv; 2024.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2024.02.27.24303356

ABSTRACT

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.


Subject(s)
COVID-19
2.
medrxiv; 2022.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2022.03.08.22272087

ABSTRACT

Background. Sparse data documenting the impact of COVID-19 in Africa has fostered the belief that COVID-19 skipped Africa. We previously published results from a systematic postmortem surveillance at a busy inner-city morgue in Lusaka, Zambia. Between June-October 2021, we detected COVID-19 in 15-19% of all deaths and concentrated in community settings where testing for COVID-19 was absent. Yet these conclusions rested on a small cohort of 70 COVID-19+ individuals. Subsequently, we conducted a longer and far larger follow-on survey using the same methodology. Methods We obtained a nasopharyngeal swab from each enrolled decedent and tested these using reverse transcriptase quantitative PCR (RT-qPCR). A subset of samples with a PCR cycle threshold <30 underwent genotyping to identify viral variants. We weighted our results to adjust for enrolment ratios and stratified them by setting (facility vs. community), time of year, age, and location. Results From 1,118 enrolled decedents, COVID-19 was detected among 32.0% (358/1,116). We observed three waves of transmission that peaked in July 2020, January 2021, and ~June 2021 (end of surveillance). These were dominated by viral variants AE.1, Beta, and Delta, respectively. During peak transmission, COVID-19 was detected in ~90% of all deaths. COVID-19 deaths clustered in Lusakas poorest city wards. Roughly four COVID-19 deaths occurred in the community for every facility death. Antemortem testing occurred for 52.6% (302/574) of facility deaths but only 1.8% (10/544) of community deaths; overall, only ~10% of COVID-19+ deaths were identified in life. Conclusions COVID-19 had a devastating impact in Lusaka. COVID-19+ deaths occurred in all age groups and was the leading cause of death during peak transmission periods. Testing was rarely done for the vast majority of COVID-19 deaths that occurred in the community, yielding a substantial undercount. If typical, these findings contradict assertions that Africa was spared from the COVID-19 pandemic.


Subject(s)
COVID-19 , Death
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