Genomic epidemiology reveals multiple introductions and local transmission of SARS-CoV-2 in Sudan from 2020 to 2022

Abstract

SARS-CoV-2 genomic epidemiology has been studied extensively. However, in Sudan, limited genomic analysis occurred during the pandemic of SARS-CoV-2 transmission and evolution. To address this gap, we analyzed genome sequences from 667 SARS-CoV-2 positive samples collected between May 2020 and April 2022. These data were combined with contemporaneous global SARS-CoV-2 sequences ( n = 1192) to evaluate genomic relatedness and estimate transmission dynamics. The Sudan sequences fell into 37 PANGO lineages with phylogeographic analysis suggesting multiple independent introductions into the country, primarily from other African nations but also Europe, the Asia-Pacific and Middle East regions. Notably, while the Alpha and Beta variants of concern (VOCs) were detected, they appeared to have been associated with limited outbreaks in Sudan. In contrast, the Delta ( n = 171, encompassing 24 estimated introduction events) and Omicron ( n = 242 sequences, encompassing 76 estimated introduction events) variants exhibited substantial genetic diversity and formed localized clusters, providing evidence for sustained local transmission following their introduction. Furthermore, spike protein mutations were identified within Delta B.1.617.2 genomes, including T95I, E484K and E484Q, associated elsewhere with reduced antibody neutralization. Our study provides insight into the genomic epidemiology of SARS-CoV-2 in Sudan and highlights the importance of genomic surveillance for tracking viral evolution, introductions, and transmission dynamics.