Tracing SARS-CoV-2 Evolution in Algeria: Insights from 2020 to 2023

Genomic surveillance is a cornerstone of pandemic response; it has helped guide public health interventions worldwide. However, North Africa stands between limited surveillance resources and efforts to address the data gap in this strategic geographic region that links sub-Saharan Africa and Europe. In this study, we present the first comprehensive evolutionary investigation of Algerian SARS-CoV-2 genomes, revealing their phylogeny, continuous phylogeography within the country, mutation analysis, and a super-spreading event through haplotype network analysis. We characterized the genetic diversity and unique mutation pattern of 449 Algerian sequences, revealing multiple independent introductions into the country since the first reported case on the 25th of February 2020 followed by numerous local transmissions that facilitated the virus's rapid propagation. This study highlights both the importance of molecular epidemiology and equitable access to resources in implementing genomic epidemiology and in increasing sequencing efforts to strengthen pandemic preparedness.