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Announcement
15 September 2016

First Directly Sequenced Genome of Hepatitis E Virus from the Serum of a Patient from the United Kingdom

ABSTRACT

Hepatitis E virus (HEV) genotype 3 is endemic in the United Kingdom but the complete sequence of HEV, generated directly from a clinical sample, is lacking. We report a near full-length genome sequence of genotype 3 HEV from the serum of a patient with acute hepatitis.

GENOME ANNOUNCEMENT

Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis in the United Kingdom. The frequency of detection of acute HEV infection was reported to be 31-, 9-, and 12-times higher than that of hepatitis A, B, and C, respectively (1). About half of acute hepatitis E cases in England and Wales were reported to be autochthonous infections (25). At present, there is only one complete genome sequence of human HEV in GenBank from the United Kingdom, cell-adapted Kernow-C1 strain (6). A near full-length genome sequence of HEV was obtained from an anonymized residual serum sample from a patient with acute hepatitis from England, strain SLC-4.
RNA was extracted from 200-µl serum using the GenElute Mammalian Total RNA miniprep kit (Sigma Aldrich), and then treated with DNase (Roche). cDNA was synthesized using SuperScript III reverse transcriptase (Thermo Fisher). The viral genome was amplified in four segments using a nested PCR approach with a touchdown cycling protocol as previously described (7). Sequences at the extremity of the viral genome were determined by using 5′ and 3′ rapid amplification of cDNA ends (RACE) (Life Technologies). Sanger sequencing was performed using 16 primers covering the HEV genome (7). Overlapping sequences were assembled by the Vector NTI Express Designer software (Thermo Fisher Scientific).
A sequence of 7,229 bp in length with G+C content of 55% was generated from SLC-4. While 5′ RACE provided some sequences of the 5′ end of the HEV genome, due to the limited volume of clinical sample, we were unable to determine the 25 nucleotides of the 5′ untranslated region (UTR) and the first 18 nucleotides of open reading frame 1 (ORF-1). The genomic organization of SLC-4 was similar to those of other genotype 3 HEVs: ORF-1 (up to nucleotide [nt] 5,094), ORF-2 (nt 5,129 to 7,114), ORF-3 (nt 5,091 to 5,459), and 3′ UTR (nt 7,115 to 7,229). The nucleotide similarity of 90% and 86% was found between SLC-4 and sequences recovered from wild boars from Germany (FJ705359) and Mongolia (AB290312), respectively. The closest HEV genome (89%) recovered from a human was from a chronically infected kidney transplant recipient in southeastern France (KJ701409). Eighty-four percent homology was found between SLC-4 and Kernow-C1.
About 15% of pig meat consumed in the United Kingdom is imported (8), giving rise to the possibility of an enormous genomic diversity among locally prevalent strains. Homology between SLC-4 and other human and pig strains shows the extent of their genetic relatedness. However, due to the lack of genomic data, we are unable to examine the genetic relatedness of SLC-4 and strains prevalent in the United Kingdom. British epidemiological studies, quoted above, are based on sequencing data from a 304-nt segment of ORF-2 (2, 3), providing only a limited amount of information about the magnitude and nature of genomic diversity among HEV strains circulating in the United Kingdom. A comprehensive genetic analysis of HEV strains from the United Kingdom human and animal reservoirs is critical to gain a better knowledge of the diversity and epidemiology of this virus.

Accession number(s).

The sequence is available in GenBank under accession no. KX462160.

ACKNOWLEDGMENTS

We thank William Griffiths and Kate Rolfe for the provision and archiving of clinical samples, respectively.

REFERENCES

1.
Harvala H, Wong V, Simmonds P, Johannessen I, Ramalingam S. 2014. Acute viral hepatitis—should the current screening strategy be modified? J Clin Virol 59:184–187.
2.
Ijaz S, Said B, Boxall E, Smit E, Morgan D, Tedder RS. 2014. Indigenous hepatitis E in England and Wales from 2003 to 2012: evidence of an emerging novel phylotype of viruses. J Infect Dis 209:1212–1218.
3.
Ijaz S, Arnold E, Banks M, Bendall RP, Cramp ME, Cunningham R, Dalton HR, Harrison TJ, Hill SF, Macfarlane L, Meigh RE, Shafi S, Sheppard MJ, Smithson J, Wilson MP, Teo CG. 2005. Non-travel-associated hepatitis E in England and Wales: demographic, clinical, and molecular epidemiological characteristics. J Infect Dis 192:1166–1172.
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Said B, Ijaz S, Chand MA, Kafatos G, Tedder R, Morgan D. 2014. Hepatitis E virus in England and Wales: indigenous infection is associated with the consumption of processed pork products. Epidemiol Infect 142:1467–1475.
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Banks M, Heath GS, Grierson SS, King DP, Gresham A, Girones R, Widen F, Harrison TJ. 2004. Evidence for the presence of hepatitis E virus in pigs in the United Kingdom. Vet Rec 154:223–227.
6.
Shukla P, Nguyen HT, Torian U, Engle RE, Faulk K, Dalton HR, Bendall RP, Keane FE, Purcell RH, Emerson SU. 2011. Cross-species infections of cultured cells by hepatitis E virus and discovery of an infectious virus-host recombinant. Proc Natl Acad Sci U S A 108:2438–2443.
7.
Debing Y, Gisa A, Dallmeier K, Pischke S, Bremer B, Manns M, Wedemeyer H, Suneetha PV, Neyts J. 2014. A mutation in the hepatitis E virus RNA polymerase promotes its replication and associates with ribavirin treatment failure in organ transplant recipients. Gastroenterology 147:1008–1011.
8.
Agriculture and Horticulture Development Board (AHDB). 2016. AHDB, Warwickshire, United Kingdom. www.ahdb.org.uk.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 4Number 527 October 2016
eLocator: e00931-16
PubMed: 27634993

History

Received: 12 July 2016
Accepted: 22 July 2016
Published online: 15 September 2016

Contributors

Authors

Sarah L. Caddy
Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
Ian Goodfellow
Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
Public Health England, Cambridge, United Kingdom

Notes

Address correspondence to Hamid Jalal, [email protected].

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