Recombination analysis reveals a double recombination event in hepatitis E virus

Abstract

Recombination of Hepatitis E Virus (HEV) has rarely been reported. In the present study, phylogenetic and recombination analyses were performed on 134 complete HEV genomes. Three potentially significant recombination events, including both intra-genotype and one inter-genotype, were identified by recombination detection analysis. Recombination events I and II occurred intra-genotype and inter-genotype, respectively, among three isolates, including the lineage represented by CHN-XJ-SW13 (GU119961, swine isolate), E067-SIJ05C (AB369690, human isolate), and JJT-Kan (AB091394, human isolate), and lead to the recombinant swine isolate swCH31 (DQ450072). Recombination event III occurred between the lineage represented by the NA1 (M73218) and K52-87 (L25595), which resulted in the recombinant Xingjiang-1 (D11092). Our analyses proved that that recombination could occur between human and swine HEV strains, double recombination events existed in HEV, and recombination event could happen within ORF2 region of HEV. These results will provide valuable hints for future research on HEV diversity.

Figure 1

Phylogenetic tree for the 134 HEV genomes. The black shadow boxes indicated the two recombinants: DQ450072 and D11092. The green, blue, and red shadow boxes showed the parental isolates. The red line presented the recombination event.

Figure 2

Identification of recombination event I and II. (A) BOOTSCAN evidence for the recombination origin on the basis of pairwise distance, modeled with a window size 200, step size 20, and 100 Bootstrap replicates; (B) Neighbor joining tree (2,000 replicates, Kimura 2-parameter distance) constructed using the recombinant region (2021-2618 nt); (C) Neighbor joining tree constructed using the recombinant region (4754-5201 nt); (D) Neighbor joining tree constructed using the non-recombinant regions consisted of the rest of the genome. The green, blue, and red shadow boxes showed the parental isolates and the black boxes showed the daughter isolate.

Figure 3

Identification of recombination event III. (A)BOOTSCAN evidence for the recombination origin on the basis of pairwise distance, modeled with a window size 200, step size 20, and 100 Bootstrap replicates; (B)Neighbor joining tree constructed using the recombinant region (2592-2941nt); (C)Neighbor joining tree constructed using the non-recombinant regions consisted of the rest of the genome. The green and red shadow boxes showed the parental isolates and the black shadow boxes showed the daughter isolate.