Hepatitis E virus (HEV) is an important but extremely understudied human pathogen, and the mechanisms of HEV replication and pathogenesis are largely unknown. We previously identified an attenuated genotype 3 HEV mutant (pSHEV-1) containing three unique amino acid mutations (F51L, T59A, and S390L) in the capsid protein. To determine the role of each of these mutations, we constructed three HEV single mutants (rF51L, rT59A, and rS390L) which were all found to be replication competent in Huh7 liver cells. To determine the pathogenicities of the mutants, we utilized the specific-pathogen-free (SPF) pig model for HEV and a unique inoculation procedure that bypasses the need for propagating infectious HEV in vitro. A total of 60 pigs were intrahepatically inoculated, via an ultrasound-guided technique, with in vitro-transcribed full-length capped RNA transcripts from the infectious clones of each single mutant, the pSHEV-1 triple mutant, wild-type pSHEV-3, or phosphate-buffered saline (PBS) buffer (n ؍ 10). The results showed that the F51L mutation partially contributed to virus attenuation, whereas the T59A and S390L mutations resulted in more drastic attenuation of HEV in pigs, as evidenced by a significantly lower incidence of viremia, a delayed appearance and shorter duration of fecal virus shedding and viremia, and lower viral loads in liver, bile, and intestinal content collected at three different necropsy times. The results indicate that the three mutations in the capsid protein collectively contribute to HEV attenuation. This study has important implications for developing a modified live-attenuated vaccine against HEV.Hepatitis E virus (HEV) is a major cause of enterically transmitted acute hepatitis in many developing countries in Asia, the Middle East, and Africa and in Mexico (2,13,[40][41][42]49), although the disease has also been reported in many industrialized countries, including the United States (53). HEV is transmitted primarily by the fecal-oral route through contaminated drinking water or food. The disease generally affects young adults and has a mortality rate of less than 1% in the general population, although a significantly higher rate of mortality, up to 30%, has been reported in infected pregnant women (47). HEV is a small nonenveloped virus, and its genome is a single-strand, positive-sense RNA molecule of approximately 7.2 kb in size. Currently, HEV is classified in the genus Hepevirus of the family Hepeviridae (9).The genomic RNA of HEV contains a short 5Ј noncoding region (NCR), three open reading frames (ORF1, -2, and -3), and a 3Ј NCR (22). A cap structure has been identified at the 5Ј end of the viral genome and is required for efficient virus replication in vivo (14). The ORF2 and ORF3 proteins are translated from a bicistronic subgenomic mRNA (18,25). ORF1 encodes a nonstructural protein with multiple functional domains, including methyltransferase, papain-like protease, helicase, and RNA-dependent RNA polymerase (RdRp) (29). It remains unclear whether the ORF1 polyprotein func...