| Abstract | During 2010, yellowing symptoms were fre- quently observed in cultivated squash fields in Egypt. A total of 717 symptomatic squash leaf samples were collected from four regions where squash cultivation is of economic importance for the country: Kafrelsheikh, El-Behira, El-Sharkia and El-Ismailia. Serological anal- ysis showed that 95.6% of the symptomatic squash samples were infected by Cucurbit aphid-borne yellows virus (CABYV), and visual estimation of the incidence of yellowing symptoms suggested a very high incidence of CABYV in the fields. Twelve CABYV isolates were characterized by sequencing two regions of the viral genome, open reading frame (ORF) 3 and ORFs 4/5. Overall, Egyptian isolates were very similar among them, and had higher similarity values with a French than with a Chinese isolate. The average nucleotide diversity for ORF 3 was significantly higher than for the other two regions, indicating that variability is not evenly distributed along the viral genome. The ratios between nucleotide diversity values in non-synonymous (dN) and synonymous (dS) positions (dN/dS) for each ORF showed that the three ORFs are evolving under different pressures, although predominantly under puri- fying selection. Phylogenetic analyses revealed that these Egyptian isolates, with only one exception, shared the same clade with a French isolate. Moreover, these analyses suggested that Egyptian isolates belong to the Mediterranean group described previously |