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

Publication date: Feb 28, 2024

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

Concepts Keywords
40centre Africa
Botswana Ba
Canada Based
Influenza Berlin
Cov
International
Laboratory
Medrxiv
Pasteur
Pcr
Preprint
Sars
South
Spread
Variant

Semantics

Type Source Name
disease VO effectiveness
disease MESH COVID-19
disease VO time
drug DRUGBANK Flunarizine
disease IDO country
disease MESH Influenza
disease MESH AIDS
drug DRUGBANK Diethylstilbestrol
disease MESH Infection
disease MESH Infectious Diseases
disease VO USA
disease VO Canada

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