Primary structure of open reading frame 2 and 3 of the hepatitis E virus isolated from Morocco

The nucleotide sequence from position 5,014 to 7,186 of the hepatitis E vir us (HEV) genome was determined using a set of 10 polymerase chain reaction (PCR) fragments amplified directly from a pool of fecal specimens obtained from patients with well-documented epidemic HEV infection in Morocco. This sequence contains the 3'-terminal region of open reading frame 1 (ORF1), fu ll length ORF2 and ORF3, and a portion of the 3'-noncoding region. The HEV Morocco nucleotide sequence was com pared with the corresponding sequences of 13 HEV strains. A region of ORF2 that overlaps with ORF3 was found to be the most conserved region of ORF2, whereas a protein segment encoded by th is region was found to be the most variable. Theoretical RNA secondary stru cture analysis predicted that this region may be folded into a strong secon dary structure that may constrain nucleotide sequence variability. In addit ion, the nucleotide sequence comparison revealed that the HEV Morocco seque nce is most homologous to the sequences of the HEV Asian strains compared w ith the HEV Mexico, swine, and US strains. Phylogenetic analysis performed on the entire ORF2 and ORF3 sequences and on a small fragment of ORF2 allow ed classification of the HEV Morocco strain together with a few other known African strains as a separate subtype within the Asian-African genotype. P ublished 1999 Wiley-Liss, Inc.