Publication date: Feb 01, 2025

In mid-November, 2021, the SARS-CoV-2 omicron variant (B. 1.1. 529; BA. 1 sublineage) was detected in southern Africa, prompting international travel restrictions. We aimed to investigate the spread of omicron BA. 1 in Africa. In this observational study, samples from patients infected with SARS-CoV-2 from 27 laboratories in 24 African countries, collected between June 1, 2021 and April 14, 2022, were tested for omicron BA. 1 and delta (B. 1.617. 2) variants using real-time RT-PCR. Samples that tested positive for BA. 1 by RT-PCR and were collected before estimated BA. 1 emergence according to epidemiological properties were excluded from downstream analyses. The diagnostic precision of the assays was evaluated by high-throughput sequencing of samples from four countries. The observed spread of BA. 1 was compared with mobility-based mathematical simulations and entries for SARS-CoV-2 in the Global Initiative on Sharing All Influenza Data (GISAID) genomic database. We estimated the effective reproduction number (R) at the country level considering the BA. 1 fraction and the reported numbers of infections. Phylogeographical analyses were done in a Bayesian framework. Through testing of 13 294 samples from patients infected with SARS-CoV-2, we established that, by November-December, 2021, omicron BA. 1 had replaced the delta variant of SARS-CoV-2 in all African subregions, following a south-north gradient, with a median R of 2.60 (95% CI 2.46-2.71). This south-north spread, established on the basis of PCR data, was substantiated by phylogeographical reconstructions, ancestral state reconstructions, and GISAID data. PCR-based reconstructions of country-level BA. 1 predominance and the availability of BA. 1 genomic sequences in GISAID correlated significantly in time (p=0.0002, r=0.78). The first detections of BA. 1 in high-income settings beyond Africa were predicted accurately in time by mobility-based mathematical simulations (p

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