Recombination analysis reveals a double recombination event in hepatitis E virus
© Wang et al; licensee BioMed Central Ltd. 2010
Received: 25 January 2010
Accepted: 14 June 2010
Published: 14 June 2010
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.
Hepatitis E virus (HEV), a member of the genus Hepevirus, is a non-enveloped virus with a positives-stranded RNA genome of approximately 7.2 kb in length (Reyes et al., 1990). HEV is believed to be transmitted by the faecal-oral route and its infection affects primarily young adults and is generally mild [1, 2]. The mortality rate of HEV infection is higher among women, and hepatitis E virus infection is highly prevalent among pregnant women [3, 4]. HEV and antibodies to HEV have been reportedly found in a wide variety of animals, especially swine [5–8]. A hypothesis has arisen that zoonosis is involved in the transmission of HEV.
The HEV genome has three partially overlapped open reading frames (ORFs). ORF1 is located at the 5'-terminus of the genome and encodes non-structural proteins. ORF2 is at the 3'-terminus of the HEV genome and encodes the viral capsid protein which has three glycosylation sites. ORF3 overlaps with either ORF1 or ORF2 . HEV isolates were divided into four distinct genotypes according to sequence and phylogenetic analyses. Genotype 1 was previously believed to only infect humans, but reportedly detected from a pig in Cambodia recently . Genotype 2 has only been identified in humans in Mexico and Africa (Nigeria, Chad). Genotype 3 is prevalent in swine herds and humans all over the world. Genotype 4 HEV is mainly distributed in China, Japan, India, Indonesia, and Vietnam. Genotype 4 HEV has a wide host range, being prevalent in humans, swine, and some other animals. These four types of virus are thought to comprise a single serotype .
Recombination is a relatively common phenomenon in positive-sense RNA viruses [11–13] and understanding recombination can be helpful in unravelling the evolution of pathogens and drug resistance. So far, two reports revealed the presence of HEV recombination. However, one of them was performed in 2005, when there were only about 30 HEV strains with full genome available in GenBank ; the other one was focused on the open reading frame structure analysis . In the present study, therefore, we analyze the available complete HEV genome sequences in GenBank in order to systematically investigate the presence of recombination among HEV strains.
The average P-value of three recombinant events analyzed by six recombination detection methods
3.59 × 10-12
5.56 × 10-24
1.31 × 10-39
8.31 × 10-18
7.55 × 10-10
1.52 × 10-17
4.18 × 10-19
1.25 × 10-25
1.26 × 10-45
1.67 × 10-16
3.77 × 10-18
5.69 × 10-16
6.73 × 10-10
1.78 × 10-6
6.57 × 10-10
5.76 × 10-6
4.31 × 10-5
1.47 × 10-4
Recombination within the capsid gene has been suggested for other positive-strand RNA virus such as norovirus [24, 25]. The recombination of the virus capsid gene may play a key role in virulence, allowing new recombinants to evade immune response and possible viral extinction. ORF2 of HEV encodes the capsid protein, which contains the antigenic regions and partial nucleotide sequence of ORF2 is predicted to be well suited for phylogenetic classification of HEV [26, 27]. In the present study, we detected that recombination event II occurred within the capsid gene of HEV (Fig 2A), and such mutations in the capsid gene will produce a protein which is better able to evade the host immune response, thereby allowing higher viral titer and greater overall fitness. Moreover, we should notice that recombination event II happened between human (E067-SIJ05C) and swine (CHN-XJ-SW13) HEV isolates. This suggested that recombination of HEV can occurred between viruses infecting different host species, which needs to be recorded, as they have serious implications for the future evolution of infectious agents.
In our study, Uigh179 (D11093) was revealed to be a potential recombinant (Additional file 1: Fig.S1), which is consistent with a previous report . However, the potential parental strains of this recombinant were different between the present study and previous study. Van's study didn't include the strain Xingjiang-1(D11092) which was indicated to be one of the most probable parental strains in the present study. The strain information of Uigh179 and Xingjiang-1 showed that the two strains were sequenced in the same lab in Nihon University School of Medicine in 1992. Therefore, it should be cared whether this recombination event non-naturally occurred by sequencing error and/or contamination in the lab. A genotype 3 HEV strains swJ13-1 (AB097811) was also found to be a potential recombinant in the present study (Additional file 2: Fig S2). It was isolated from a 4-month-old pig in 2002 in Japan . Our study suggested this recombination event occurred between HE-JA1 (AB097812) and swJB-H7 (AB481227). The potential recombinant swJ13-1 and its parental strain HE-JA1, which was isolated from a Japanese patient, were determined in the same lab and shared 99.0% sequence identity over the complete genome. The ORF2 and ORF3 of the two strains were even identical to each other . It is therefore tempting to speculate that this recombination event might happen non-naturally in the lab.
Taken together, we analyzed 134 non-redundant HEV complete genomes using detailed phylogenetic and recombination analytic methods and identified two recombinants (swCH31 and Xingjiang-1), and swCH31 was proved to be produced by double recombination events which occurred among three potential parental strains belonging to two different genotypes. Moreover, it should be noted that recombination could occur between human and swine HEV strains, double recombination events existed in HEV, and recombination event can happen within ORF2 region of HEV. Other two isolates (AB097811 and D11093) may be potential non-natural recombinants happened in the lab. The present study could reminder us that recombination also contribute to the genetic variety of HEV.
This work was supported by the Professional Research Foundation for Advanced Talents of Jiangsu University under Grant No.10JDG059 and Open Fund of State Key Laboratory of Veterinary Etiological Biology No. SKLVEB2010KFKT002.
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