Identical consensus sequence and conserved genomic polymorphism of hepatitis E virus during controlled interspecies transmission

Abstract

High-throughput sequencing of bile and feces from two pigs experimentally infected with human hepatitis E virus (HEV) of genotype 3f revealed the same full-length consensus sequence as in the human sample. Twenty-nine percent of polymorphic sites found in HEV from the human sample were conserved throughout the infection of the heterologous host. The interspecies transmission of HEV quasispecies is the result of a genomic negative-selection pressure on random mutations which can be deleterious to the viral population. HEV intrahost nucleotide diversity was found to be in the lower range of other human RNA viruses but correlated with values found for zoonotic viruses. HEV transmission between humans and pigs does not seem to be modulated by host-specific mutations, suggesting that adaptation is mainly regulated by ecological drivers.

Fig 1

Experimental infection of two pigs with human HEV. The HEV load of initial human fecal sample inoculated to pigs is plotted as a black square. Excretion of the virus in the feces of pigs is plotted as white squares for pig 1 and as gray squares for pig 2. The HEV load in the bile is plotted as white dots for pig 1 and as gray dots for pig 2. The presence of anti-HEV IgG in serum is indicated by black diamonds. Samples used in high-throughput sequencing are boxed in black. Times of inoculation, surgery, and euthanasia are indicated on the axis for days postinfection.

Fig 2

Coverage of the HEV genome by high-throughput sequencing. A schematic representation of the HEV genome is shown at the top of the figure. ORFs are drawn to scale, and the UTR, the hypervariable region (HVR), and the region coding for the RNA polymerase (RP) are highlighted. Numbers of reads are projected along the genomic position. Black line, bile samples pooled from the two pigs; plain gray line, feces sample pooled from the two pigs; dotted gray line, human sample.

Fig 3

Plot of the number of sequencing errors versus the number of nucleotides mapped over conserved genes of host species and bacteria from our HEV samples. The black line represents the linear regression resulting in an error rate of 0.28%.

Fig 4

SNPs along the HEV genome. A schematic representation of the HEV genome is aligned at the top of the figure (see the legend of Fig. 2). Bars indicate the percentage of validated SNPs along the HEV genome sequenced from the human sample (A), the feces of pigs (B), and the bile of pigs (C). Black arrows indicate the position of SNPs shared by the three samples.

Fig 5

Viral intrahost nucleotide diversity (π) of viruses. Values of π are displayed as percentages on a logarithmic number line for HEV alongside the West Nile virus (WNV), human immunodeficiency virus (HIV), and hepatitis C virus (HCV) (15, 33, 34).