Genomic and Epidemiological Insights into the 2022-23 Dengue outbreak in Oman

Objective: Recognised as a neglected tropical disease, dengue continues to pose substantial public health challenges in both endemic and emerging regions.Oman, previously considered a low-risk country, has recently reported an increase in local transmission.This study aimed to characterise the genomic diversity of circulating DENV lineages during the 2022-2023 outbreak. Methods: We analysed 162 DENV-positive patient samples from the Sultan Qaboos University Hospital.Near-complete genomes were obtained via long-read amplicon sequencing and phylogenetically compared with global reference genomes.Results: DENV-2 genotype II-F1.1 predominated comprising 95.68% of the total samples.DENV-1 and DENV-3 were detected in Oman for the first time.Five of the six DENV-1 genotype III-A and one DENV-3 genotype I-A2 case suggested possible local transmission.Phylogenetic reconstruction revealed distinct monophyletic clades for Omani DENV-1 and DENV-2 sequences, suggesting potential localised transmission within the study cohort.DENV-1 clustered with Pakistani lineages, suggesting probable importation, whereas two divergent DENV-2 cases aligned with Indian isolates, consistent with their travel history.Conclusion: This first full-length DENV genomic study from the Middle East and North Africa (MENA) region documents diverse lineages identified in this cohort and provides evidence suggestive of local transmission in Oman, underscoring the importance of real-time genomic surveillance for dengue control.