The role of UAE in supporting COVID-19 genomic surveillance across the EMRO for complex emergency countries

Abstract

Introduction The Eastern Mediterranean region was highly exposed to COVID-19 due to diverse challenges and lack of laboratory resources and relevant expertise in these countries limited the quality of detection and surveillance of circulating strains. UAE, through the Reference Laboratory for Infectious Disease-Abu Dhabi (RLID-AD), played a central role in providing genomic support to these countries. Methods SARS-CoV-2 samples were transported to RLID-AD with support from WHO/EMRO, then sequenced primarily using the Midnight workflow and GridION from Oxford Nanopore Technology and the data were analysed using the CLC platform from Qiagen, and lineages assigned using Pangolin. Results Between April 2021 and March 2022, RLID-AD received 170 COVID-19 samples from Syria, Yemen and Lebanon for genomic analysis. Of these , 159 were successfully sequenced (93.5%) with >90% coverage and 30x depth, with lineages being successfully assigned through Pangolin. The lineages discovered were predominantly alpha, beta, and delta variants, largely consistent with the global waves at the time. Turnaround time from receipt at the lab to result sharing with member states was 2-3 weeks. Conclusion The implementation of a hub-and-spoke model for sequencing support was a key aspect to the COVID-19 response in the EMRO region. UAE played a critical role in supporting genomics surveillance in the region, despite the logistic challenges faced with transport and importing of samples to UAE. The challenges faced during COVID19 pandemic clearly demonstrates the need for implementation of national-level sequencing laboratories that contribute data to the region, with hubs acting in technical and emergency support.