The RNA genome of the hepatitis E virus (HEV) contains a hypervariable region (HVR) in ORF1 that tolerates small deletions with respect to infectivity. To further investigate the role of the HVR in HEV replication, we constructed a panel of mutants with overlapping deletions in the N-terminal, central, and C-terminal regions of the HVR by using a genotype 1 human HEV luciferase replicon and analyzed the effects of deletions on viral RNA replication in Huh7 cells. We found that the replication levels of the HVR deletion mutants were markedly reduced in Huh7 cells, suggesting a role of the HVR in viral replication efficiency. To further verify the results, we constructed HVR deletion mutants by using a genetically divergent, nonmammalian avian HEV, and similar effects on viral replication efficiency were observed when the avian HEV mutants were tested in LMH cells. Furthermore, the impact of complete HVR deletion on virus infectivity was tested in chickens, using an avian HEV mutant with a complete HVR deletion. Although the deletion mutant was still replication competent in LMH cells, the complete HVR deletion resulted in a loss of avian HEV infectivity in chickens. Since the HVR exhibits extensive variations in sequence and length among different HEV genotypes, we further examined the interchangeability of HVRs and demonstrated that HVR sequences are functionally exchangeable between HEV genotypes with regard to viral replication and infectivity in vitro, although genotype-specific HVR differences in replication efficiency were observed. The results showed that although the HVR tolerates small deletions with regard to infectivity, it may interact with viral and host factors to modulate the efficiency of HEV replication.Hepatitis E virus (HEV), the causative agent of hepatitis E, is classified in the genus Hepevirus of the family Hepeviridae (11,17). It is now known that hepatitis E is a zoonotic disease and that animal reservoirs exist for HEV (13, 26-29, 38, 40). The inefficient replication of HEV in cell cultures has hindered progress in understanding the biology of HEV. The problem has been overcome partially by either characterizing individually expressed proteins from expression vectors or transfecting cells and intrahepatically inoculating animals with capped RNA transcripts generated in vitro from infectious clones (16,17,32,33). More recently, efficient in vitro HEV replication systems have been reported (3,31,35,37), which may aid in future understanding of HEV replication.The 7.2-kb RNA genome of HEV contains three open reading frames (ORFs), namely, ORF1, ORF2, and ORF3, flanked by 5Ј-and 3Ј-nontranslated regions (2). The putative functional domains in the ORF1 protein include methyltransferase, protease, helicase, and RNA-dependent RNA polymerase (RdRp) domains (2). ORF2 encodes the major capsid protein, whereas ORF3 encodes a small multifunctional protein (2,6,18,30,39). The methyltransferase and guanylyltransferase activities in capping of the viral RNA (25), the role of RdRp in viral RNA synthesis...