Dengue fever represents a significant public health challenge in Saudi Arabia, yet comprehensive molecular characterization of circulating serotypes remains limited. This study combines epidemiological and phylogenetic analyses to understand dengue virus (DENV) dynamics in the Kingdom. A systematic review and meta-analysis of dengue epidemiological data from Saudi Arabia (1992–2026) was the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. All available DENV envelope (E) gene sequences from Saudi human cases (1992–2023) were retrieved from GenBank and Global Initiative on Sharing All Influenza Data (GISAID). Phylogenetic trees were constructed using maximum likelihood with 1000 bootstrap replicates and best-fit models. Selection pressure was analyzed using SLAC, FEL, FUBAR, and MEME methods, while glycosylation sites were predicted with NetNGlyc and NetOGlyc. The pooled seroprevalence from 25 studies (n = 32,393) was 40.71% (95% CI: 26.96–56.10%). DENV-2 predominated (80.25%), followed by DENV-1 and DENV-3, with DENV-4 remaining rare (0.42%). Males (67–78%) and adults aged 25–44 years were most affected. Phylogenetic analysis of 50 Saudi isolates showed DENV-1 strains clustered within American–African (1994) and Asian (2004–2011) genotypes, all DENV-2 within the Cosmopolitan genotype, and all DENV-3 within Genotype III (bootstrap support 99–100%). Selection pressure analysis indicated pervasive positive selection in DENV-2, episodic selection across serotypes, and strong purifying selection in the E gene. Several amino acid substitutions with potential functional importance were identified. No DENV-4 E gene sequences from Saudi Arabia are publicly available. Dengue in western Saudi Arabia is characterized by DENV-2 predominance, co-circulation of three serotypes, and multiple introductions. The absence of DENV-4 sequences highlights critical surveillance gaps. Sustained molecular surveillance, expanded genomic sequencing, and data sharing are essential for effective prevention and vaccine preparedness.

Rift Valley fever virus (RVFV) is a mosquito-borne zoonotic pathogen that causes severe disease in livestock and humans, with epidemic potential and a capacity for geographic expansion beyond its African endemic range. The 2000–2001 outbreak in Saudi Arabia represented the first confirmed introduction of RVFV outside Africa, yet comprehensive multi-segment genomic characterization of the circulating strains has remained incomplete. Here, we performed an integrated evolutionary and molecular analysis of the three complete-genome Saudi RVFV strains (Saudi 2000-10911, Saudi 200010901, and SA01-1322) using publicly available sequences. Whole-genome comparisons revealed substantial nucleotide and amino acid diversity, with the L segment exhibiting the highest mutation burden (182 nucleotide substitutions, 17 amino acid changes), while the NSs region of the S segment accumulated 52 nucleotide and 11 amino acid mutations compared to the highly conserved nucleocapsid domain. Maximum-likelihood phylogenetic analyses of all three segments consistently placed the Saudi strains within Lineage C (bootstrap = 100/100), clustering with East African strains from Kenya (2006–2007), Tanzania (2007), and South Africa (2008–2010), with congruent topologies across segments confirming the absence of reassortment. Bayesian phylogeographic analysis of 118 L-segment sequences estimated a mean substitution rate of 1.697 × 10⁻⁴ substitutions/site/year (95% HPD: 1.5–1.9 × 10⁻⁴) and a time to the most recent common ancestor of approximately 1857 (95% HPD: 1835–1876). Selection-pressure analyses using four complementary methods (MEME, FEL, FUBAR, and SLAC) demonstrated pervasive purifying selection across all three segments, with only sporadic episodic positive selection detected at a limited number of codons (six in L, seven in M, and one in S). In silico glycosylation prediction identified conserved N- and O-glycosylation sites on the M segment, with the Saudi strains displaying a Lineage C-typical profile lacking geographically restricted markers. However, the absence of canonical signal peptides in all sequences warrants cautious interpretation of these predictions. Collectively, our findings are consistent with a single introduction of Lineage C RVFV from East Africa among the sampled strains, with no subsequent reassortment, and that the virus has evolved under strong functional constraints with only rare, lineage-restricted episodes of positive selection. The identified Saudi-specific and lineage-defining mutations provide molecular markers for surveillance, while the high conservation of core proteins supports the feasibility of broadly protective vaccines.