Despite, Egypt is started to be considered as an emerging endemic area for cystic echinococcosis (CE), no enough data in the literature about the exact status of the genotype in both animals and humans. Therefore, the present study aims to characterize the underlying genotypes that could be responsible for the transmission cycle and for the growing infectivity. Animal isolates were collected from 47 camels and 6 pigs. Human isolates are 31 CE cases including; 21 of hepatic cases, 5 of pulmonary cases and 5 multiple-organ affection cases. Hot-Start specific PCR followed by DNA sequencing for mitochondrial 12S rRNA gene, revealed G1 genotype in one (3.2%) of 31 human isolate only. G6 genotype was detected in all the 53 (100%) animal isolates and in 30 out of 31 (96.8%) human isolate. The Egyptian G6 strain nucleotide sequence revealed 100% homology with an Argentinean reference strain 99% homology with the Kenyan G6 strain. It was concluded that G6 genotype is the predominant genotype in Egypt.

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