Genomic epidemiology of SARS-CoV-2 in Sudan: A retrospective analysis 2020-2022
Author:
Mburu Maureen W.ORCID, Lambisia Arnold W.ORCID, Elnegoumi MusabORCID, Nour Eman O. M., Khair Osama M. M., Abualas ElaminORCID, Elhassan Rehab M, Adam Muatsim A. M.ORCID, Mohammed Khadija SaidORCID, Morobe John M.ORCID, Ndwiga LeonardORCID, Moraa Edidah O., Makori Timothy O.ORCID, Murunga NicksonORCID, Katama Esther Nyadzua, Waruguru Dorcas W., Mwangi Sarah, Tessema Sofonias K.ORCID, Adam Mawahib H. E., Mahmoud Iman, Mohamed Hanan SalmanBabikir, Mustafa Yousif A. A., Mohamed Mohamedtaha M. A., Ahmed Rasheeda H.A., Mohamed Nuha Y.I., Ali Rahma H., Ebraheem Rasha S.M., Ahmed Huda H.H., Abdalla Hamadelniel E., Mukhtar Izdihar, Alla Abdalkhalig E. M. W., Elsheikh Omer H. A., Musa Abdualmoniem O., Faki Mahmoud Taha, Ahmed Gada Mustfa, Ahmed Thoyba E. R., Abdalla Mohammed A. O., Mohamed Mujtaba O. K., Ahmed Rayan A. A., AwadElkarim Samah M. M., Ahmed Basamat A. E. M., Shumo Zainab A. I., Ahmed Eiman N. A., Rushwan Samia S. A., Bejon PhillipORCID, Nokes D. JamesORCID, Ochola-Oyier Lynette IsabellaORCID, Agoti Charles N.ORCID, Githinji GeorgeORCID, Bedri Shahinaz A.
Abstract
AbstractSARS-CoV-2 was first detected in Sudan on 13thMarch 2020. Here, we describe the genomic epidemiology of SARS-CoV-2 in Sudan between May 2020 and April 2022 to understand the introduction and transmission of SARS-CoV-2 variants in the country. A total of 667 SARS-CoV-2 positive samples were successfully sequenced using the nCoV-19 Artic protocol on the Oxford Nanopore Technology (≥70% genome completeness). The genomes were compared with a select contemporaneous global dataset to determine genetic relatedness and estimate import/export events. The genomes were classified into 37 Pango lineages within theancestral strain(107 isolates across 13 Pango lineages),Eta variant of interest (VOI)(78 isolates in 1 lineage),Alpha variant of concern (VOC)(10 isolates in 2 lineages),Beta VOC(26 isolates in 1 lineage),Delta VOC(171 isolates across 8 lineages) andOmicron VOC(242 isolates across 12 lineages). We estimated a total of 144 introductions of the observed variants from different countries across the globe. Multiple introductions of the Eta VOI, Beta VOC and Omicron VOC were observed in Sudan mainly from Europe and Africa. These findings suggest a need for continuous genomic surveillance of SARS-CoV-2 to monitor their introduction and spread consequently inform public health measures to combat SARS-CoV-2 transmission.
Publisher
Cold Spring Harbor Laboratory
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