What type of study is this?

This is a Genome Sequencing study (also classified as: Serotyping, Phylogeographic Analysis).

September 10, 2025Open Access

Molecular Evolutionary Insights into the Repeated Introductions and Cryptic Transmission of Dengue Virus in Saudi Arabia

MBMuhammad Bashir BelloKing Saud bin Abdulaziz University for Health Sciences ZAZainab AliBushnell University NTNídia S. TrovãoNational Institutes of Health

Key Points

Phylogeographic analysis identifies at least five distinct introductions of DENV-2 from India, Sri Lanka, and Pakistan.
Serotyping revealed DENV-2 as the dominant serotype, with 20 full genomes sequenced across different serotypes.
Increased mass gatherings and labor migration are driving factors in the evolution of regional dengue transmission.
Strengthening genomic surveillance is critical for improving outbreak response to dengue virus spread.

Abstract

To investigate the genetic diversity, evolutionary dynamics, and phylogeography of DENV strains circulating in Saudi Arabia. We conducted serotyping, whole-genome sequencing, and phylogeographic analyses of DENV strains collected across Saudi Arabia between 2021 and 2023. A total of 20 full genomes were successfully obtained: DENV-1 (n = 2), DENV-2 (n = 10), and DENV-3 (n = 8). Serotyping revealed co-circulation of DENV-1, DENV-2, and DENV-3, with DENV-2 emerging as the predominant serotype. Phylogeographic analysis of whole genomes identified at least five distinct introductions of DENV-2 genotype II into Saudi Arabia, primarily originating from India, Sri Lanka and Pakistan. The earliest introduction was estimated around 13 June 1985 (95% HPD: 5 June 1983 to 11 September 1986). DENV-1 genotype III, undetected for over two decades, re-emerged in Jazan and was likely introduced from Djibouti (TMRCA: 27 July 2018; 95% HPD: 9 December 2017 to 21 March 2019). Two independent introductions of DENV-3 genotype III were identified, originating from Malaysia and India, with TMRCA estimates ranging from 2007 to 2011-indicating at least a decade of undetected circulation. Our findings highlight Saudi Arabia's evolving role as a regional hub for DENV transmission, driven by mass gatherings and labor migration. Strengthening genomic surveillance, enhancing vector control, and fostering regional data sharing are critical to improving outbreak response and preparedness. The 20 full genome sequences generated in this study have been deposited in GISAID under accession numbers EPIISL₁9825439-EPIISL₁9825458. Details of all DENV reference sequences used for phylogeographic and phylodynamic analyses-including strain names, accession numbers, sampling dates, geographic origins, and metadata-are provided in Supplementary Tables S2-S6. In compliance with GISAID's Terms of Use, the full set of reference sequences retrieved from GISAID is available through the following EPISETs: All contributing authors and laboratories are duly acknowledged in the Acknowledgments section.

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